Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 12 of 211
Found at i:3345042 original size:13 final size:13
Alignment explanation
Indices: 3345026--3345051 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3345016 TTATAACTTG
3345026 AATTTAATATTTA
1 AATTTAATATTTA
3345039 AATTTAATATTTA
1 AATTTAATATTTA
3345052 TTTTTCAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTAATATTTA
Found at i:3346807 original size:15 final size:16
Alignment explanation
Indices: 3346787--3346823 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3346777 GATTTTTCCC
*
3346787 TAAAAA-AATCAAATA
1 TAAAAATAATAAAATA
3346802 TAAAAATAATAAAATA
1 TAAAAATAATAAAATA
3346818 TAAAAA
1 TAAAAA
3346824 GCATCAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (16 bp):
TAAAAATAATAAAATA
Found at i:3355186 original size:17 final size:17
Alignment explanation
Indices: 3355161--3355195 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3355151 TCACTGGCAA
3355161 ATTAAATTTTAACAACT
1 ATTAAATTTTAACAACT
* *
3355178 ATTAGATTTTAGCAACT
1 ATTAAATTTTAACAACT
3355195 A
1 A
3355196 AGAGTACGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (17 bp):
ATTAAATTTTAACAACT
Found at i:3356165 original size:51 final size:51
Alignment explanation
Indices: 3356109--3356205 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
3356099 GTTGTTGCTT
* *
3356109 TGGTTAAGATACTTAGTAGTTTGTTTTAATTTTTGAAGATTTTATGGCTAG
1 TGGTTAAGATACTTAGTAATTTGTTTTAATTATTGAAGATTTTATGGCTAG
* * *
3356160 TGGTTAAGTTACTTATTAATTTGTTTTAGTTATTGAAGATTTTATG
1 TGGTTAAGATACTTAGTAATTTGTTTTAATTATTGAAGATTTTATG
3356206 TCTCAATACT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.26, C:0.03, G:0.20, T:0.52
Consensus pattern (51 bp):
TGGTTAAGATACTTAGTAATTTGTTTTAATTATTGAAGATTTTATGGCTAG
Found at i:3356836 original size:13 final size:13
Alignment explanation
Indices: 3356818--3356842 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3356808 AATATTGCCT
3356818 TTATTATTATTTG
1 TTATTATTATTTG
3356831 TTATTATTATTT
1 TTATTATTATTT
3356843 TTTAGAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTATTATTATTTG
Found at i:3357670 original size:18 final size:16
Alignment explanation
Indices: 3357647--3357682 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
3357637 ATAGGGTTTT
3357647 TAAAAGTATATTATAAAA
1 TAAAAGT-TATTA-AAAA
3357665 TAAAAGTTATTAAAAA
1 TAAAAGTTATTAAAAA
3357681 TA
1 TA
3357683 TATTATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
TAAAAGTTATTAAAAA
Found at i:3357769 original size:39 final size:38
Alignment explanation
Indices: 3357723--3357798 Score: 98
Period size: 39 Copynumber: 2.0 Consensus size: 38
3357713 CATCACAAAG
* * *
3357723 TTAAAATAATAATGTATGATAATAATAAAATAAAATAAT
1 TTAAAATAATAATGCATAATAA-AATAAAAAAAAATAAT
* *
3357762 TTAAAATAATAGTGCATAATAAAGTAAAAAAAAATAA
1 TTAAAATAATAATGCATAATAAAATAAAAAAAAATAA
3357799 GTAACTGAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
38 13 0.41
39 19 0.59
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.29
Consensus pattern (38 bp):
TTAAAATAATAATGCATAATAAAATAAAAAAAAATAAT
Found at i:3357863 original size:23 final size:23
Alignment explanation
Indices: 3357837--3357881 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3357827 ATAATGTCAA
3357837 TAATAATAATAATAA-TAATAAAT
1 TAATAATAA-AATAATTAATAAAT
* *
3357860 TAATATTAAACTAATTAATAAA
1 TAATAATAAAATAATTAATAAA
3357882 ACAATGGGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
TAATAATAAAATAATTAATAAAT
Found at i:3358822 original size:11 final size:11
Alignment explanation
Indices: 3358802--3358868 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
3358792 CAAAAATTAA
3358802 AAAAAGTATTTT
1 AAAAA-TATTTT
3358814 AAAAATATTTT
1 AAAAATATTTT
3358825 --AAA-A-TTT
1 AAAAATATTTT
* *
3358832 AAAAA-AATTA
1 AAAAATATTTT
3358842 AAAAAGTATTTT
1 AAAAA-TATTTT
*
3358854 AAAAAAATTTT
1 AAAAATATTTT
3358865 AAAA
1 AAAA
3358869 TTAAAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
7 3 0.07
8 1 0.02
9 7 0.15
10 7 0.15
11 15 0.33
12 13 0.28
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:3358842 original size:9 final size:9
Alignment explanation
Indices: 3358825--3358886 Score: 54
Period size: 9 Copynumber: 6.6 Consensus size: 9
3358815 AAAATATTTT
*
3358825 AAAATTTAA
1 AAAAATTAA
3358834 AAAAATTAA
1 AAAAATTAA
3358843 AAAAGTATTTTAA
1 AAAA--A--TTAA
*
3358856 AAAAATT-T
1 AAAAATTAA
*
3358864 TAAAATTAA
1 AAAAATTAA
3358873 AAAAATTAA
1 AAAAATTAA
3358882 AAAAA
1 AAAAA
3358887 AGTATTTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
8 6 0.14
9 27 0.63
11 2 0.05
13 8 0.19
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAAATTAA
Found at i:3358859 original size:41 final size:40
Alignment explanation
Indices: 3358775--3358924 Score: 214
Period size: 41 Copynumber: 3.6 Consensus size: 40
3358765 ACCAAAAATT
3358775 TATTTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATTAAAAAAAGTATTTTAAAAA
3358819 TATTTTAAAATTTAAAAAAATT-AAAAAAGTATTTTAAAAA
1 TATTTTAAAA-TTAAAAAAATTAAAAAAAGTATTTTAAAAA
* *
3358859 AATTTTAAAATTAAAAAAATTAAAAAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAATT-AAAAAAAGTATTTTAAAAA
3358900 TATTTTAAAATTAAAAAAA-TAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAA
3358925 TATTTATTAT
Statistics
Matches: 100, Mismatches: 3, Indels: 11
0.88 0.03 0.10
Matches are distributed among these distances:
39 16 0.16
40 28 0.28
41 42 0.42
42 2 0.02
43 4 0.04
44 8 0.08
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:3358885 original size:17 final size:17
Alignment explanation
Indices: 3358852--3358885 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3358842 AAAAAGTATT
**
3358852 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTAAAAAA
3358869 TTAAAAAAATTAAAAAA
1 TTAAAAAAATTAAAAAA
3358886 AAGTATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TTAAAAAAATTAAAAAA
Found at i:3358894 original size:30 final size:29
Alignment explanation
Indices: 3358835--3358898 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
3358825 AAAATTTAAA
**
3358835 AAAATTAAAAAAGTATTTTAAAAAAATTTT
1 AAAATTAAAAAAG-ATTAAAAAAAAATTTT
3358865 AAAATTAAAAAA-ATTAAAAAAAAGTATTTT
1 AAAATTAAAAAAGATTAAAAAAAA--ATTTT
3358895 AAAA
1 AAAA
3358899 GTATTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 9 0.30
30 21 0.70
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (29 bp):
AAAATTAAAAAAGATTAAAAAAAAATTTT
Found at i:3358898 original size:11 final size:11
Alignment explanation
Indices: 3358884--3358909 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3358874 AAAATTAAAA
3358884 AAAAGTATTTT
1 AAAAGTATTTT
3358895 AAAAGTATTTT
1 AAAAGTATTTT
3358906 AAAA
1 AAAA
3358910 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:3371753 original size:19 final size:19
Alignment explanation
Indices: 3371729--3371879 Score: 212
Period size: 19 Copynumber: 7.8 Consensus size: 19
3371719 AATTTTTGAG
3371729 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
3371748 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
3371767 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
3371788 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
** *
3371807 GATATATAATTTTAGATAT
1 GATATGCAATCTTAGATAT
*
3371826 GATATGCAATCTTAGAGAT
1 GATATGCAATCTTAGATAT
**
3371845 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3371864 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
3371880 ATATATGATT
Statistics
Matches: 114, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
19 97 0.85
21 17 0.15
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:3371774 original size:40 final size:38
Alignment explanation
Indices: 3371736--3371879 Score: 234
Period size: 38 Copynumber: 3.7 Consensus size: 38
3371726 GAGGATATGC
**
3371736 AATCTTAGATATGATATGCAATCCAAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
3371774 GCAATCTTAGATATGATATGCAATCTTAGATATGATATAT
1 --AATCTTAGATATGATATGCAATCTTAGATATGATATAT
* *
3371814 AATTTTAGATATGATATGCAATCTTAGAGATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
3371852 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
3371880 ATATATGATT
Statistics
Matches: 99, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
38 63 0.64
40 36 0.36
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.37
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATGATATAT
Found at i:3373316 original size:98 final size:98
Alignment explanation
Indices: 3373196--3373392 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
3373186 TTAAAAATAA
* * *
3373196 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTAATTTC
3373261 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
3373294 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTAATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTAATTTC
*
3373359 TTAAATCTTGGATGAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
3373392 T
1 T
3373393 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTAATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:3373556 original size:94 final size:94
Alignment explanation
Indices: 3373395--3373584 Score: 380
Period size: 94 Copynumber: 2.0 Consensus size: 94
3373385 TTTAAAGTTT
3373395 TATTGTACAAGTATTTTGGCCCAATTCATTTTGGGGAAAATTAGAATGCTGTGCCCTAACGCATT
1 TATTGTACAAGTATTTTGGCCCAATTCATTTTGGGGAAAATTAGAATGCTGTGCCCTAACGCATT
3373460 GGGTGTGGTATCTTCTTTCTCTGAAATAA
66 GGGTGTGGTATCTTCTTTCTCTGAAATAA
3373489 TATTGTACAAGTATTTTGGCCCAATTCATTTTGGGGAAAATTAGAATGCTGTGCCCTAACGCATT
1 TATTGTACAAGTATTTTGGCCCAATTCATTTTGGGGAAAATTAGAATGCTGTGCCCTAACGCATT
3373554 GGGTGTGGTATCTTCTTTCTCTGAAATAA
66 GGGTGTGGTATCTTCTTTCTCTGAAATAA
3373583 TA
1 TA
3373585 AGGGTCTTAA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 96 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (94 bp):
TATTGTACAAGTATTTTGGCCCAATTCATTTTGGGGAAAATTAGAATGCTGTGCCCTAACGCATT
GGGTGTGGTATCTTCTTTCTCTGAAATAA
Found at i:3377602 original size:20 final size:20
Alignment explanation
Indices: 3377566--3377621 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
3377556 AAAATATTTC
*
3377566 AAAA-AAAAAGAGGAAAAAG-
1 AAAAGAAAAAG-GAAAAAAGT
3377585 AAAAGGAAAAAGGAAAAAAGT
1 AAAA-GAAAAAGGAAAAAAGT
*
3377606 AAAAGAAAAAGTAAAA
1 AAAAGAAAAAGGAAAA
3377622 GGAGAGGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.12
20 18 0.56
21 10 0.31
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.04
Consensus pattern (20 bp):
AAAAGAAAAAGGAAAAAAGT
Found at i:3377614 original size:12 final size:12
Alignment explanation
Indices: 3377580--3377622 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
3377570 AAAAAGAGGA
* *
3377580 AAAAGAAAAGGA
1 AAAAGAAAAAGT
3377592 AAAAGGAAAAAAGT
1 AAAA-G-AAAAAGT
3377606 AAAAGAAAAAGT
1 AAAAGAAAAAGT
3377618 AAAAG
1 AAAAG
3377623 GAGAGGCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 16 0.59
13 2 0.07
14 9 0.33
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (12 bp):
AAAAGAAAAAGT
Found at i:3379071 original size:132 final size:132
Alignment explanation
Indices: 3378829--3379445 Score: 1058
Period size: 132 Copynumber: 4.7 Consensus size: 132
3378819 AACAGATCAG
* *
3378829 TGAAAATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATC-AACGACGGCGAATCTTATC
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAA-GACAGCGAATCTTATC
*
3378893 TTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAA
65 TTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAA
3378958 GGT
130 GGT
* *
3378961 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACAGCGAATCTTATCT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGAATCTTATCT
3379026 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
3379091 GT
131 GT
* *
3379093 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATAT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGAATCTTATCT
* *
3379158 TTCCAAGATAGTGGGAAGCAGATTTAAGCCATCAAGCCTTGTCTCCCTGAGCAGCCGCGGAGAAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
3379223 GT
131 GT
* *
3379225 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAACAAATCTTATCT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGAATCTTATCT
* *
3379290 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTTTCCCTGAGCAGCAGCGGAGTAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
3379355 GT
131 GT
* * *
3379357 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC-GACAAATCATATC
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAG-CGAATCTTATC
3379421 TTTCCAAGATAGTGGGAAGCAGATT
65 TTTCCAAGATAGTGGGAAGCAGATT
3379446 AAAGTCGACA
Statistics
Matches: 461, Mismatches: 22, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
132 459 1.00
133 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (132 bp):
TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGAATCTTATCT
TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAG
GT
Found at i:3379153 original size:44 final size:44
Alignment explanation
Indices: 3378841--3379407 Score: 134
Period size: 44 Copynumber: 12.9 Consensus size: 44
3378831 AAAATTGTAG
* * *
3378841 ATCTTATCTCCCTAAACAGTAGTGGAGCAGA-TCAACGACGGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAA-GACCGCGA
* * * *
3378885 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACCGCGA
* * * * * * ** *
3378928 AGCCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAGATTG-TA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCGCGA
* * *
3378972 GATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACAGCGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCGCGA
* * * *
3379017 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACCGCGA
* * * * * * * * ** *
3379060 AGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAAATTG-TA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCGCGA
* *
3379104 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCGCGA
* * * *
3379149 ATCTTATATTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCATC-A
1 ATCTTAT-CTCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACC-GCGA
* * * ** * * * * ** *
3379192 AGCCTTGTCTCCCTGAGCAGCCGCGGAGAAGGTTGAAAATTG-TA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCGCGA
* ** *
3379236 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAACAA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCGCGA
* * * *
3379281 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACCGCGA
* * * * * * * * ** *
3379324 AGCCTTGTTTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTG-TA
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCGCGA
*
3379368 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC
3379408 GACAAATCAT
Statistics
Matches: 355, Mismatches: 126, Indels: 84
0.63 0.22 0.15
Matches are distributed among these distances:
42 16 0.05
43 39 0.11
44 259 0.73
45 34 0.10
46 7 0.02
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCGCGA
Found at i:3379558 original size:84 final size:83
Alignment explanation
Indices: 3379460--3379838 Score: 327
Period size: 84 Copynumber: 4.4 Consensus size: 83
3379450 TCGACAATCC
* *
3379460 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCATAGATCTTATCCCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCA-AGATCTTATCCCTCTGAAGTTACAGAG
*
3379525 AGCAAATCGCATCTAGTCT
65 AGCAGATCGCATCTAGTCT
* * * * * *
3379544 TATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGTAAACAAG-TCTTATCCTTCTAAAGTTACAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCAAGATCTTATCCCTCTGAAGTTACAGA
* * *
3379608 GAGGCAGA-CTGAAGATGGCAAATCT
64 GA-GCAGATC-G--CAT--CTAGTCT
* * *
3379633 TATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAATTACAGATCTTATCTCTCTGAAGTTACAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCA-AGATCTTATCCCTCTGAAGTTACAGAG
3379698 AGCAGATCGCATCTAGTCT
65 AGCAGATCGCATCTAGTCT
* * * *
3379717 TATCTCCCTGAAGTTACGGTGGA-CAAGACTAAGTAAGCAAG-TCTTAT-CCTCCTGAAGTTACA
1 TATCTCCCTGAAGTTGCAGTGGAGC-AGATTAA--AATCAAGATCTTATCCCT-CTGAAGTTACA
* * * * *
3379779 GTGAGGCAGATTGAAGATGGCAAATCT
62 GAGA-GCAGATCG--CAT--CTAGTCT
*
3379806 TATCTTCCTGAAGTTGCAGTGGAGCAGATTAAA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
3379839 GCCGACAATC
Statistics
Matches: 234, Mismatches: 40, Indels: 39
0.75 0.13 0.12
Matches are distributed among these distances:
83 3 0.01
84 102 0.44
85 16 0.07
86 9 0.04
87 8 0.03
88 8 0.03
89 87 0.37
90 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (83 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCAAGATCTTATCCCTCTGAAGTTACAGAGA
GCAGATCGCATCTAGTCT
Found at i:3379654 original size:89 final size:88
Alignment explanation
Indices: 3379541--3380263 Score: 361
Period size: 89 Copynumber: 8.3 Consensus size: 88
3379531 TCGCATCTAG
* *
3379541 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTTATCCTTCTAAAGTTACA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTTATCCTTCTGAAGTTACA
3379606 GTGAGGCAGACTGAAGATGGCAAA
66 GTGAGGCAGA-TGAAGATGGCAAA
* *
3379630 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAA--AATTAC-AGATCTTAT-CTCTCTGAAGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA--ACAAG-TCTTATCCT-TCTGAAGT
* * * *
3379691 TACAGAGA-GCAGATCG--CAT--CTAG
62 TACAGTGAGGCAGAT-GAAGATGGCAAA
* * * *
3379714 TCTTATCTCCCTGAAGTTACGGTGGA-CAAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGC-AGACTAAGTAAACAAGTCTTATCCTTCTGAAGTTAC
3379778 AGTGAGGCAGATTGAAGATGGCAAA
65 AGTGAGGCAGA-TGAAGATGGCAAA
* * *** * * * *
3379803 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAA-TCCTAT-CTCCCTAAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAACAAGTCTTATCCT-TCTGAAGTTA
* * * * *
3379866 CAGTG-GAGCGGATTAAAATTAG-AGA
64 CAGTGAG-GCAGATGAAGA-TGGCAAA
* * * * * * * *
3379891 TCTTATCTCTCTGAAGTTACAG-AGAGCAGA-T-CG-CATCTAA-TCTTAT-CTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAAC-AAGTCTTATCCT-TCTGAAGTTA
* * * * *
3379950 CGGTG-GACA-AGGCTAAG-TAAGCAAG
64 CAGTGAGGCAGATG--AAGAT-GGCAAA
* ** *
3379975 TCTTATC-CTCCTGAAGTTACAGT-GAGGCAGACTGAAG-ATGGCAAATCTTAT-CTTCCTGAAG
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AACAAGTCTTATCCTT-CTGAAG
* * *
3380036 TTGCAGTG-GAGCAGATTAA-A-GCCGATAA
61 TTACAGTGAG-GCAGATGAAGATGGC-A-AA
* * * * * *
3380064 TCCTATCTTCCTGAAGTTGCAGTAGAGCGGATTAA--AATCACAGATCTTAT-CTCTCTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACA-AG-TCTTATCCT-TCTGAAGTT
* * * * *
3380126 GCAGAGA-GCAGATCG--CAT--CTAG
63 ACAGTGAGGCAGAT-GAAGATGGCAAA
* * * *
3380148 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGGAAGCAAGTCTTATCCTCCTGAAGTTACA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTTATCCTTCTGAAGTTACA
3380213 GTGAGGCAGACTGAAGATGGCAAA
66 GTGAGGCAGA-TGAAGATGGCAAA
3380237 TCTTATCTCCCTGAAGTTGCAGTGGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG
3380264 TATATTGAAG
Statistics
Matches: 487, Mismatches: 89, Indels: 116
0.70 0.13 0.17
Matches are distributed among these distances:
82 2 0.00
83 7 0.01
84 150 0.31
85 25 0.05
86 15 0.03
87 24 0.05
88 65 0.13
89 187 0.38
90 11 0.02
91 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTTATCCTTCTGAAGTTACA
GTGAGGCAGATGAAGATGGCAAA
Found at i:3379665 original size:173 final size:173
Alignment explanation
Indices: 3379455--3379838 Score: 617
Period size: 173 Copynumber: 2.2 Consensus size: 173
3379445 TAAAGTCGAC
* * * * *
3379455 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCATAGATCTTATCCCTCTGAAGTTG
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCCCTCTGAAGTTA
*
3379520 CAGAGAGCAAATCGCATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAGC-AGACTAAGTAAACAA
66 CAGAGAGCAAATCGCATCTAGTCTTATCTCCCTAAAGTTACAGTGGA-CAAGACTAAGTAAACAA
*
3379584 GTCTTATCCTTCTAAAGTTACAGTGAGGCAGACTGAAGATGGCA
130 GTCTTATCCTCCTAAAGTTACAGTGAGGCAGACTGAAGATGGCA
* *
3379628 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAATTACAGATCTTATCTCTCTGAAGTTA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCCCTCTGAAGTTA
* * * *
3379693 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTACGGTGGACAAGACTAAGTAAGCAAG
66 CAGAGAGCAAATCGCATCTAGTCTTATCTCCCTAAAGTTACAGTGGACAAGACTAAGTAAACAAG
* *
3379758 TCTTATCCTCCTGAAGTTACAGTGAGGCAGATTGAAGATGGCA
131 TCTTATCCTCCTAAAGTTACAGTGAGGCAGACTGAAGATGGCA
3379801 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAA
3379839 GCCGACAATC
Statistics
Matches: 195, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
172 1 0.01
173 194 0.99
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (173 bp):
AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCCCTCTGAAGTTA
CAGAGAGCAAATCGCATCTAGTCTTATCTCCCTAAAGTTACAGTGGACAAGACTAAGTAAACAAG
TCTTATCCTCCTAAAGTTACAGTGAGGCAGACTGAAGATGGCA
Found at i:3379873 original size:217 final size:217
Alignment explanation
Indices: 3379628--3380263 Score: 1110
Period size: 217 Copynumber: 2.9 Consensus size: 217
3379618 GAAGATGGCA
* *
3379628 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAATTACAGATCTTATCTCTCTGAAGTTA
1 AATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAATTACAGATCTTATCTCTCTGAAGTTA
*
3379693 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTACGGTGGACAAGACTAAGTAAGCAAG
66 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCGGTGGACAAGACTAAGTAAGCAAG
*
3379758 TCTTATCCTCCTGAAGTTACAGTGAGGCAGATTGAAGATGGCAAATCTTATCTTCCTGAAGTTGC
131 TCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTTCCTGAAGTTGC
3379823 AGTGGAGCAGATTAAAGCCGAC
196 AGTGGAGCAGATTAAAGCCGAC
* * *
3379845 AATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATTAGAGATCTTATCTCTCTGAAGTTA
1 AATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAATTACAGATCTTATCTCTCTGAAGTTA
* *
3379910 CAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCGGTGGACAAGGCTAAGTAAGCAAG
66 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCGGTGGACAAGACTAAGTAAGCAAG
3379975 TCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTTCCTGAAGTTGC
131 TCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTTCCTGAAGTTGC
*
3380040 AGTGGAGCAGATTAAAGCCGAT
196 AGTGGAGCAGATTAAAGCCGAC
* * *
3380062 AATCCTATCTTCCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAATTACAGATCTTATCTCTCTGAAGTTA
* ** *
3380127 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGGAAGCAAG
66 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCGGTGGACAAGACTAAGTAAGCAAG
*
3380192 TCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGC
131 TCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTTCCTGAAGTTGC
3380257 AGTGGAG
196 AGTGGAG
3380264 TATATTGAAG
Statistics
Matches: 396, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
217 396 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (217 bp):
AATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAATTACAGATCTTATCTCTCTGAAGTTA
CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCGGTGGACAAGACTAAGTAAGCAAG
TCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCTTATCTTCCTGAAGTTGC
AGTGGAGCAGATTAAAGCCGAC
Found at i:3379948 original size:173 final size:173
Alignment explanation
Indices: 3379455--3379914 Score: 507
Period size: 173 Copynumber: 2.6 Consensus size: 173
3379445 TAAAGTCGAC
* * * * * *
3379455 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATC-ATAGATCTTATC-CCTCTGAAGT
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAA-CGACAGATCCTATCTCC-CTAAAGT
* * *** * * * *
3379518 TGCAGAGAGCAAATCGCATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAGC-AGACTAAGTAAAC
64 TACAGAGAGCAGATAAAATCTAGTCTTATCTCCCTGAAGTTACAGAGGA-CAAGACTAAGTAAGC
* *
3379582 AAGTCTTATCCTTCTAAAGTTACAGTGAGGCAGACTGAAGATGGCA
128 AAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCA
** * * *
3379628 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAATTACAGATCTTATCTCTCTGAAGTTA
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAACGACAGATCCTATCTCCCTAAAGTTA
*** * *
3379693 CAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTACGGTGGACAAGACTAAGTAAGCAAG
66 CAGAGAGCAGATAAAATCTAGTCTTATCTCCCTGAAGTTACAGAGGACAAGACTAAGTAAGCAAG
*
3379758 TCTTATCCTCCTGAAGTTACAGTGAGGCAGATTGAAGATGGCA
131 TCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCA
*
3379801 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACA-ATCCTATCTCCCTAAAGTT
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAA-ACGACAGATCCTATCTCCCTAAAGTT
* * * *
3379865 GCAGTGGAGCGGATTAAAAT-TAGAGATCTTATCTCTCTGAAGTTACAGAG
65 ACAG-AGAGCAGA-TAAAATCT--AG-TCTTATCTCCCTGAAGTTACAGAG
3379915 AGCAGATCGC
Statistics
Matches: 248, Mismatches: 30, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
172 1 0.00
173 210 0.85
174 11 0.04
175 3 0.01
176 2 0.01
177 21 0.08
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (173 bp):
AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAACGACAGATCCTATCTCCCTAAAGTTA
CAGAGAGCAGATAAAATCTAGTCTTATCTCCCTGAAGTTACAGAGGACAAGACTAAGTAAGCAAG
TCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCA
Found at i:3380163 original size:390 final size:388
Alignment explanation
Indices: 3379438--3380263 Score: 1026
Period size: 390 Copynumber: 2.1 Consensus size: 388
3379428 GATAGTGGGA
* *
3379438 AGCAGATTAAAGTCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCATAGATC
1 AGCAGATTAAAGACGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGAGATC
* *
3379503 TTATCCCTCTGAAGTTGCAGAGAGCAAATCGCATCTAGTCTTATCTCCCTAAAGTTGCAGTGGAG
66 TTATCCCTCTGAAGTTACAGAGAGCAAATCGCATCTAATCTTATCTCCCTAAAGTTGCAGTGGAG
*
3379568 CAGACTAAGTAAACAAGTCTTATCCTTCTAAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCT
131 CAGACTAAGTAAACAAGTCTTATCCTCCTAAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCT
** *
3379633 TATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAATTACAGATCTTATCTCTCTGAAGTTACAGAG
196 TATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAACGACAGATCCTATCTCTCTGAAGTTACAGAG
*** * * *
3379698 AGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTACGGTGGACAAGACTAAGTAAGCAAGTCTTA
261 AGCAGATAAAATCCAGTCTTATCTCCCTGAAGTTACAGAGGACAAGACTAAGTAAGCAAGTCTTA
* * * *
3379763 TCCTCCTGAAGTTACAGT-GAGGCAGATTGAA-GATGGCAAATCTTATCTTCCTGAAGTTGCAGT
326 TCCTCCTGAAGTTACAGTGGA-GCAGACT-AAGGA-AGCAAATCTTATCCTCCTGAAGTTACAGT
3379826 GG
388 -G
* * *
3379828 AGCAGATTAAAGCCGACAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATTAGAGATC
1 AGCAGATTAAAGACGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGAGATC
* * * *
3379893 TTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCGGTGGA-
66 TTATCCCTCTGAAGTTACAGAGAGCAAATCGCATCTAATCTTATCTCCCTAAAGTTGCAGTGGAG
* * *
3379957 CAAGGCTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATC
131 C-AGACTAAGTAAACAAGTCTTATCCTCCTAAAGTTACAGTGAGGCAGACTGAAGATGGCAAATC
* * *
3380022 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATA-ATCCTATCT-TCCTGAAGTTGCA
195 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAA-ACGACAGATCCTATCTCT-CTGAAGTTACA
* * * * * *
3380085 GTAGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGA-GAGC-AGA-T-CG-CATC
258 G-AGAGCAGA-TAAAATC-CAG-TCTTATCTCCCTGAAGTTACAGAGGA-CAAGACTAAGTAAGC
* * * *
3380145 TAGTCTTAT-CTCCCTGAAGTTGCAGTGGAGTAGACTAAGGAAGCAAGTCTTATCCTCCTGAAGT
318 AAGTCTTATCCT-CCTGAAGTTACAGTGGAGCAGACTAAGGAAGCAAATCTTATCCTCCTGAAGT
3380209 TACAGTG
382 TACAGTG
* * * * *
3380216 AGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAG
1 A-GCAGATTAAAGACGAC-AATCCTATCTCCCTGAAGTTGCAGTGGAG
3380264 TATATTGAAG
Statistics
Matches: 376, Mismatches: 47, Indels: 26
0.84 0.10 0.06
Matches are distributed among these distances:
388 2 0.01
389 42 0.11
390 288 0.77
391 12 0.03
392 5 0.01
393 7 0.02
394 20 0.05
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (388 bp):
AGCAGATTAAAGACGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGAGATC
TTATCCCTCTGAAGTTACAGAGAGCAAATCGCATCTAATCTTATCTCCCTAAAGTTGCAGTGGAG
CAGACTAAGTAAACAAGTCTTATCCTCCTAAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCT
TATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAACGACAGATCCTATCTCTCTGAAGTTACAGAG
AGCAGATAAAATCCAGTCTTATCTCCCTGAAGTTACAGAGGACAAGACTAAGTAAGCAAGTCTTA
TCCTCCTGAAGTTACAGTGGAGCAGACTAAGGAAGCAAATCTTATCCTCCTGAAGTTACAGTG
Found at i:3380204 original size:128 final size:129
Alignment explanation
Indices: 3380020--3380258 Score: 286
Period size: 128 Copynumber: 1.9 Consensus size: 129
3380010 AGATGGCAAA
* * ** * *
3380020 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAGATAATCCTATCCTCCTGAAGTTACA
* * * *
3380085 GT-AGAGCGGA-TTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
66 GTGAG-GCAGACTGAAAATCACAAATCTTATCTCCCTGAAGTTGCAGAGAGCAGATCGCATCTAG
* * * *
3380148 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGGAAGCA-AGTCTTATCCTCCTGAAGTTAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAG-ATAATCCTATCCTCCTGAAGTTAC
* **
3380212 AGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAG
65 AGTGAGGCAGACTGAAAATCACAAATCTTATCTCCCTGAAGTTGCAG
3380259 TGGAGTATAT
Statistics
Matches: 91, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
128 59 0.65
129 32 0.35
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (129 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAGATAATCCTATCCTCCTGAAGTTACA
GTGAGGCAGACTGAAAATCACAAATCTTATCTCCCTGAAGTTGCAGAGAGCAGATCGCATCTAG
Found at i:3380273 original size:45 final size:44
Alignment explanation
Indices: 3379541--3380265 Score: 236
Period size: 44 Copynumber: 16.7 Consensus size: 44
3379531 TCGCATCTAG
* * * *
3379541 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACT-AAGTAAACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAG-AAGCAAA
* * * * *
3379585 TCTTATC-CTTCTAAAGTTACAGT-GAGGCAGACTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GTAGACTGAAGA-AGCAAA
* * * * *
3379630 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGA-TTAA-AATTACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAA--GCAAA
* * * * * * * * *
3379674 TCTTATCTCTCTGAAGTTACAG-AGAGCAGA-T--CGCATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAGCAAA
* * ** *
3379714 TCTTATCTCCCTGAAGTTACGGTGGACAAGACT-AAGTAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAG-AAGCAAA
* * * *
3379758 TCTTATC-CTCCTGAAGTTACAGT-GAGGCAGATTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GTAGACTGAAGA-AGCAAA
* * * * **
3379803 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCG-ACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAGCA-AA
* * ** * * *
3379847 TCCTATCTCCCTAAAGTTGCAGTGGAGCGGA-TTAAAATTAG-AGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGA--AGCAAA
* * * * * * * *
3379891 TCTTATCTCTCTGAAGTTACAG-AGAGCAGA-T--CGCATCTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAGCAAA
* ** * *
3379931 TCTTATCTCCCTGAAGTTGCGGTGGACAAGGCT-AAGTAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAG-AAGCAAA
* * *
3379975 TCTTATC-CTCCTGAAGTTACAGT-GAGGCAGACTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GTAGACTGAAGA-AGCAAA
* * * * **
3380020 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCG-ATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAGCA-AA
* * * ** * *
3380064 TCCTATCTTCCTGAAGTTGCAGTAGAGCGGA-TTAA-AATCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAGCA-A-A
* * * * * * * *
3380108 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T--CGCATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAGCAAA
*
3380148 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACT-AAGGAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAA-GAAGCAAA
* * *
3380192 TCTTATC-CTCCTGAAGTTACAGT-GAGGCAGACTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GTAGACTGAAGA-AGCAAA
3380237 TCTTATCTCCCTGAAGTTGCAGTGGAGTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTA
3380266 TATTGAAGCA
Statistics
Matches: 516, Mismatches: 118, Indels: 93
0.71 0.16 0.13
Matches are distributed among these distances:
39 1 0.00
40 62 0.12
41 16 0.03
42 7 0.01
43 48 0.09
44 241 0.47
45 132 0.26
46 9 0.02
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAGCAAA
Found at i:3380501 original size:19 final size:19
Alignment explanation
Indices: 3380477--3380627 Score: 203
Period size: 19 Copynumber: 7.8 Consensus size: 19
3380467 AATTTTTGAG
*
3380477 GATATGCAATTTTAGATAT
1 GATATGCAATCTTAGATAT
**
3380496 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
3380515 GATAGATGCAATCTTAGATAT
1 GAT--ATGCAATCTTAGATAT
*
3380536 GATATGCAATCTTAGAGAT
1 GATATGCAATCTTAGATAT
**
3380555 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
3380574 GATATGCAATCTTAGAGAT
1 GATATGCAATCTTAGATAT
**
3380593 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3380612 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
3380628 ATATATGATT
Statistics
Matches: 113, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
19 96 0.85
21 17 0.15
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:3380575 original size:38 final size:38
Alignment explanation
Indices: 3380488--3380627 Score: 226
Period size: 38 Copynumber: 3.6 Consensus size: 38
3380478 ATATGCAATT
** * *
3380488 TTAGATATGATATGCAATCCAAGATATGATAGATGCAATC
1 TTAGATATGATATGCAATCTTAGAGATGATATAT--AATC
3380528 TTAGATATGATATGCAATCTTAGAGATGATATATAATC
1 TTAGATATGATATGCAATCTTAGAGATGATATATAATC
3380566 TTAGATATGATATGCAATCTTAGAGATGATATATAATC
1 TTAGATATGATATGCAATCTTAGAGATGATATATAATC
3380604 TTAGATATGATATGCAATCTTAGA
1 TTAGATATGATATGCAATCTTAGA
3380628 ATATATGATT
Statistics
Matches: 96, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
38 66 0.69
40 30 0.31
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (38 bp):
TTAGATATGATATGCAATCTTAGAGATGATATATAATC
Found at i:3382063 original size:98 final size:98
Alignment explanation
Indices: 3381945--3382141 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
3381935 TTAAAAATAA
* * *
3381945 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCTTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
3382010 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
3382043 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
3382108 TTAAATCTTGGATGAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
3382141 T
1 T
3382142 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:3392254 original size:5 final size:5
Alignment explanation
Indices: 3392240--3392275 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
3392230 AATTATTAAG
3392240 TATA- TATAT TATAT TATAT TATAT TATAT TATAT TA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA
3392276 CAATAAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:3392309 original size:21 final size:21
Alignment explanation
Indices: 3392277--3392318 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3392267 ATTATATTAC
* *
3392277 AATAAAACAAAATAAATAAAG
1 AATAAAACAAAAGAAAGAAAG
3392298 AATAAATA-AAAAGAAAGAAAG
1 AATAAA-ACAAAAGAAAGAAAG
3392319 GTACTTAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (21 bp):
AATAAAACAAAAGAAAGAAAG
Found at i:3393640 original size:45 final size:45
Alignment explanation
Indices: 3393581--3393690 Score: 115
Period size: 45 Copynumber: 2.6 Consensus size: 45
3393571 TTTGGTTCGC
* *
3393581 TGTATTGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
* * ***
3393626 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
3393670 TG--A---AATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
3393691 TAATGGAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
39 15 0.27
42 1 0.02
44 18 0.33
45 21 0.38
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (45 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
Found at i:3393857 original size:18 final size:17
Alignment explanation
Indices: 3393836--3393870 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3393826 TTATTATTAA
*
3393836 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3393854 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3393871 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3394003 original size:16 final size:16
Alignment explanation
Indices: 3393984--3394014 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3393974 TTTAAACATA
*
3393984 ATAATTATAATATATT
1 ATAATTAAAATATATT
3394000 ATAATTAAAATATAT
1 ATAATTAAAATATAT
3394015 AATTTAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:3394037 original size:157 final size:157
Alignment explanation
Indices: 3393724--3394039 Score: 537
Period size: 159 Copynumber: 2.0 Consensus size: 157
3393714 AGAATACCCG
* *
3393724 TAGCATAAATTTGTTTTGGTAAATGGTTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAT
1 TAGCAGAAATTTGTTTTGGTAAATGGTTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAA
* * *
3393789 TATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAAT
66 TATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAAAT
3393854 ATATAATTTAATAAAATTCTTAATAAT
131 ATATAATTTAATAAAATTCTTAATAAT
**
3393881 TAGCAGAAATTTGTTTTGGTAAATTATTTTATTGTTATTGTTATTTAAATTTTAATAAGATTATT
1 TAGCAGAAATTTGTTTTGGTAAA-T-GGTTATTGTTATTGTTATTTAAATTTTAATAAGATTATT
3393946 AATATCAATAATAAATAATTTAATCATATTTAAACATAATAATTA-T-AATATATTATAATTAAA
64 AATATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAA
3394009 ATATATAATTTAATAAAATTCTTAATAAT
129 ATATATAATTTAATAAAATTCTTAATAAT
3394038 TA
1 TA
3394040 ATATTCTTAT
Statistics
Matches: 150, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
157 69 0.46
158 2 0.01
159 79 0.53
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TAGCAGAAATTTGTTTTGGTAAATGGTTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAA
TATCAATAATAAATAATTTAATCATATTTAAACATAATAATTATTAAATATATTATAATTAAAAT
ATATAATTTAATAAAATTCTTAATAAT
Found at i:3394141 original size:14 final size:15
Alignment explanation
Indices: 3394092--3394143 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
3394082 GTAAAATATA
3394092 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
3394107 TATTAAATATATTAT
1 AATTAAATATATTAT
3394122 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
3394135 AATTTAATA
1 AATTAAATA
3394144 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:3394260 original size:14 final size:15
Alignment explanation
Indices: 3394211--3394262 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
3394201 GTAAAATATA
3394211 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
3394226 TATTAAATATATTAT
1 AATTAAATATATTAT
3394241 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
3394254 AATTTAATA
1 AATTAAATA
3394263 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:3394333 original size:119 final size:120
Alignment explanation
Indices: 3393978--3394325 Score: 648
Period size: 119 Copynumber: 2.9 Consensus size: 120
3393968 ATCATATTTA
*
3393978 AACATAATAATTA-T-AATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
3394041 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
3394096 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTCA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
3394161 TATTCTTATATGAATTTAC-CAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
3394215 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
3394280 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAA
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAA
3394326 TGAAAATTTG
Statistics
Matches: 223, Mismatches: 4, Indels: 4
0.97 0.02 0.02
Matches are distributed among these distances:
118 12 0.05
119 119 0.53
120 92 0.41
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:3394465 original size:24 final size:25
Alignment explanation
Indices: 3394419--3394466 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
3394409 TATGAATTTG
3394419 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
3394445 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
3394467 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:3394543 original size:91 final size:91
Alignment explanation
Indices: 3394394--3394601 Score: 260
Period size: 91 Copynumber: 2.3 Consensus size: 91
3394384 GAATTATAAC
* * * * * * *
3394394 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAATAATTATTACATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATAATTATTAAATATAATTTAAT-AG
* *
3394459 TAATAT-TAAATTTCATAAACTTCTTGA
65 TAATATAT-AATTTCATAAAATTCTTAA
3394486 TAATAAATTTTCTTATATGAATTTATACAA-TTAAAATAATTAA-TATTAAATATAATTTAATAG
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAA-TAATTATTAAATATAATTTAATAG
*
3394549 TGATATATAATTTCATAAAATTCTTAA
65 TAATATATAATTTCATAAAATTCTTAA
*
3394576 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
3394602 CTAAAATCAA
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
90 27 0.26
91 47 0.46
92 28 0.27
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATAATTATTAAATATAATTTAATAGT
AATATATAATTTCATAAAATTCTTAA
Found at i:3401024 original size:24 final size:24
Alignment explanation
Indices: 3400997--3401043 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3400987 ATTGAAATGG
3400997 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
3401021 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
3401044 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:3401041 original size:15 final size:15
Alignment explanation
Indices: 3401021--3401070 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
3401011 TGATGAATTT
3401021 ATTGAATTTATATTG
1 ATTGAATTTATATTG
3401036 ATTGAATTGGTATATATAG
1 ATTGAATT--TATAT-T-G
3401055 ATTGAA--TATATTG
1 ATTGAATTTATATTG
3401068 ATT
1 ATT
3401071 ATTTGAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 4 0.13
14 1 0.03
15 13 0.42
17 5 0.16
18 1 0.03
19 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:3401301 original size:40 final size:41
Alignment explanation
Indices: 3401206--3401307 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
3401196 ACTTCGAGTC
* * * * *
3401206 GATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTT
1 GATGAGGCACTGGGTGTCAAATTACTACTTCGAATTAATCT
*
3401247 GATGAGGCACTGGGTGTCAAATTATTACTTCGAATT-ATCT
1 GATGAGGCACTGGGTGTCAAATTACTACTTCGAATTAATCT
*
3401287 GATGAGGCACTGGGTGCCAAA
1 GATGAGGCACTGGGTGTCAAA
3401308 CTGGTGTGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 23 0.43
41 31 0.57
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32
Consensus pattern (41 bp):
GATGAGGCACTGGGTGTCAAATTACTACTTCGAATTAATCT
Found at i:3401792 original size:28 final size:27
Alignment explanation
Indices: 3401742--3401796 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
3401732 TACTTAACTT
* *
3401742 TTAAGTTTTAATATTATAATATATATA
1 TTAACTTTAAATATTATAATATATATA
3401769 TTAACTTTAAATATTTATAATATATATA
1 TTAACTTTAAATA-TTATAATATATATA
3401797 CTCTTATGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TTAACTTTAAATATTATAATATATATA
Found at i:3404648 original size:60 final size:60
Alignment explanation
Indices: 3404513--3404648 Score: 148
Period size: 60 Copynumber: 2.3 Consensus size: 60
3404503 CTAAATATAA
* * * * ** **
3404513 AAAAAATCAACAAATTTAGCACTCAATATTTACAAAATTTTTCATTTTAGTTTTAATTCT
1 AAAAAATCAAAAAATTTACCACTCAATATTTACAAAATCTATCATTTTAGTCCTAACACT
** *
3404573 AAAAGTTCAATAAATTTGACCA-TCAATATTTACAAAATCTATCATTTTAGTCCTAACACT
1 AAAAAATCAAAAAATTT-ACCACTCAATATTTACAAAATCTATCATTTTAGTCCTAACACT
*
3404633 AAAAAATAAAAAAATT
1 AAAAAATCAAAAAATT
3404649 ATAAAAAAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
60 58 0.95
61 3 0.05
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.36
Consensus pattern (60 bp):
AAAAAATCAAAAAATTTACCACTCAATATTTACAAAATCTATCATTTTAGTCCTAACACT
Found at i:3407565 original size:10 final size:10
Alignment explanation
Indices: 3407533--3407576 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
3407523 AAAATTTTAA
3407533 TAAATTATAAT
1 TAAATTAT-AT
3407544 TATAATTAATAT
1 TA-AATT-ATAT
3407556 TAAATTATAT
1 TAAATTATAT
*
3407566 TATATTATAT
1 TAAATTATAT
3407576 T
1 T
3407577 TTAATATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 14 0.47
11 6 0.20
12 8 0.27
13 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TAAATTATAT
Found at i:3410041 original size:11 final size:11
Alignment explanation
Indices: 3410025--3410055 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3410015 ATACCCATAC
3410025 CCCATACCTTG
1 CCCATACCTTG
*
3410036 CCCATACCTTT
1 CCCATACCTTG
3410047 CCCATACCT
1 CCCATACCT
3410056 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:3410626 original size:18 final size:18
Alignment explanation
Indices: 3410599--3410691 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
3410589 TACGACCGTT
3410599 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
3410617 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
3410635 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
3410653 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
3410671 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
3410689 TAC
1 TAC
3410692 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:3414748 original size:11 final size:11
Alignment explanation
Indices: 3414732--3414762 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3414722 TATACCCATA
3414732 CCCATACCTTG
1 CCCATACCTTG
*
3414743 CCCATACCTTT
1 CCCATACCTTG
3414754 CCCATACCT
1 CCCATACCT
3414763 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:3418497 original size:19 final size:20
Alignment explanation
Indices: 3418473--3418511 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3418463 ATATTTTATA
3418473 TTAAAA-TTTAATAATTTTT
1 TTAAAATTTTAATAATTTTT
*
3418492 TTAAAATTTTATTAATTTTT
1 TTAAAATTTTAATAATTTTT
3418512 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAAAATTTTAATAATTTTT
Found at i:3418501 original size:11 final size:12
Alignment explanation
Indices: 3418479--3418529 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
3418469 TATATTAAAA
3418479 TTTAATAATTTT
1 TTTAATAATTTT
3418491 TTTAA-AATTTT
1 TTTAATAATTTT
* **
3418502 ATTAATTTTTATT
1 TTTAATAATT-TT
*
3418515 TTTTATAATTTT
1 TTTAATAATTTT
3418527 TTT
1 TTT
3418530 GCCACATGCC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
11 10 0.33
12 12 0.40
13 8 0.27
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTAATAATTTT
Found at i:3420967 original size:56 final size:56
Alignment explanation
Indices: 3420900--3421011 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
3420890 TATAAATTTC
* *
3420900 ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCGTGTGTCAATTCAAA
1 ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCATATGTCAATTCAAA
3420956 ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCATATGTCAATTCAAA
1 ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCATATGTCAATTCAAA
3421012 CATTACATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.25, C:0.36, G:0.04, T:0.36
Consensus pattern (56 bp):
ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCATATGTCAATTCAAA
Found at i:3434915 original size:27 final size:27
Alignment explanation
Indices: 3434865--3434943 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
3434855 TTGGGGTCTT
* **
3434865 CCTCATCTTCTTCCTCAGTTGAAGAC-
1 CCTCTTCTTCTTCCTCAGAAGAAGACA
*
3434891 CCTTCTTCTTCTTCCTCAGAAGAAGTCA
1 CC-TCTTCTTCTTCCTCAGAAGAAGACA
* * *
3434919 CCTCTTCATCTTCTTCAGAGGAAGA
1 CCTCTTCTTCTTCCTCAGAAGAAGA
3434944 AGCGGCTGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
26 2 0.05
27 39 0.91
28 2 0.05
ACGTcount: A:0.22, C:0.32, G:0.13, T:0.34
Consensus pattern (27 bp):
CCTCTTCTTCTTCCTCAGAAGAAGACA
Found at i:3435442 original size:9 final size:9
Alignment explanation
Indices: 3435428--3435494 Score: 89
Period size: 9 Copynumber: 7.4 Consensus size: 9
3435418 TTTGGTTAAA
3435428 AATTAACCG
1 AATTAACCG
*
3435437 AATTAACCT
1 AATTAACCG
*
3435446 AATTACCCG
1 AATTAACCG
3435455 AATTAACCG
1 AATTAACCG
*
3435464 AATTAACCA
1 AATTAACCG
*
3435473 AATTACCCG
1 AATTAACCG
*
3435482 AATTAACCA
1 AATTAACCG
3435491 AATT
1 AATT
3435495 GAATCACTAC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:3435466 original size:27 final size:27
Alignment explanation
Indices: 3435428--3435494 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
3435418 TTTGGTTAAA
*
3435428 AATTAACCGAATTAACCTAATTACCCG
1 AATTAACCGAATTAACCAAATTACCCG
3435455 AATTAACCGAATTAACCAAATTACCCG
1 AATTAACCGAATTAACCAAATTACCCG
*
3435482 AATTAACCAAATT
1 AATTAACCGAATT
3435495 GAATCACTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.25
Consensus pattern (27 bp):
AATTAACCGAATTAACCAAATTACCCG
Found at i:3435629 original size:18 final size:18
Alignment explanation
Indices: 3435589--3435632 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
3435579 AATTTTTATG
**
3435589 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
3435607 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
3435625 CTTGGGTT
1 ATTGGGTT
3435633 TAGATTGGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:3436169 original size:10 final size:9
Alignment explanation
Indices: 3436144--3436356 Score: 65
Period size: 9 Copynumber: 22.2 Consensus size: 9
3436134 ATGATTAAAA
*
3436144 ATAAAAATCA
1 ATAAAAAT-T
*
3436154 ATAAAAGTT
1 ATAAAAATT
3436163 ATAAAAATT
1 ATAAAAATT
**
3436172 ATTAAATTTT
1 A-TAAAAATT
3436182 AATAAAAAATT
1 -AT-AAAAATT
3436193 ATAAAAA-T
1 ATAAAAATT
3436201 ATTAAAAATT
1 A-TAAAAATT
* *
3436211 AGAAAAGTT
1 ATAAAAATT
* *
3436220 TTAAAATTAT
1 ATAAAAAT-T
3436230 ATAAAAATT
1 ATAAAAATT
* *
3436239 GTAAAAAATG
1 AT-AAAAATT
3436249 AT-AAAATAT
1 ATAAAAAT-T
*
3436258 ATAGAAATAT
1 ATAAAAAT-T
*
3436268 AGGAAAAAATT
1 A--TAAAAATT
*
3436279 TTAAAATATT
1 ATAAAA-ATT
* *
3436289 AT-AAAGTC
1 ATAAAAATT
3436297 ATAAGAAAATT
1 AT-A-AAAATT
*
3436308 ATAAAAAAT
1 ATAAAAATT
* *
3436317 GTAAAGAAAT
1 ATAAA-AATT
3436327 AT-AAAATT
1 ATAAAAATT
*
3436335 CGTAAAAAATT
1 -AT-AAAAATT
*
3436346 ATAAACATT
1 ATAAAAATT
3436355 AT
1 AT
3436357 CGTACTAAAA
Statistics
Matches: 149, Mismatches: 35, Indels: 39
0.67 0.16 0.17
Matches are distributed among these distances:
8 13 0.09
9 62 0.42
10 50 0.34
11 19 0.13
12 5 0.03
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:3436277 original size:40 final size:38
Alignment explanation
Indices: 3436222--3436346 Score: 96
Period size: 40 Copynumber: 3.2 Consensus size: 38
3436212 GAAAAGTTTT
*
3436222 AAAATTATATAAAAATTGTAAAAAATGATAAAAT-ATATAG
1 AAAATTAGA-AAAAATTGTAAAAAAT-ATAAAATCATA-AG
* * *
3436262 -AAATATAGGAAAAAATTTTAAAATATTATAAAGTCATAAG
1 AAAAT-TA-GAAAAAATTGTAAAA-AATATAAAATCATAAG
* *
3436302 AAAATTATAAAAAA-TGTAAAGAAATATAAAATTCGTAA-
1 AAAATTAGAAAAAATTGTAAA-AAATATAAAA-TCATAAG
3436340 AAAATTA
1 AAAATTA
3436347 TAAACATTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
38 19 0.28
39 16 0.23
40 24 0.35
41 10 0.14
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.29
Consensus pattern (38 bp):
AAAATTAGAAAAAATTGTAAAAAATATAAAATCATAAG
Found at i:3436392 original size:11 final size:10
Alignment explanation
Indices: 3436373--3436408 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
3436363 AAAAGAAGCA
3436373 TTTTATAATT
1 TTTTATAATT
3436383 TTTCTATAA-T
1 TTT-TATAATT
3436393 TTTTATAATT
1 TTTTATAATT
3436403 TTTTAT
1 TTTTAT
3436409 TTTTTCTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 5 0.21
10 14 0.58
11 5 0.21
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATAATT
Found at i:3436550 original size:19 final size:19
Alignment explanation
Indices: 3436526--3436603 Score: 83
Period size: 18 Copynumber: 4.3 Consensus size: 19
3436516 ATTAAATGAC
3436526 ATTTTTTATGCA-TTTTATA
1 ATTTTTTAT-CATTTTTATA
3436545 ATTTTTTATCATTTTTATA
1 ATTTTTTATCATTTTTATA
**
3436564 AAATTTTAT-ATTTTTAT-
1 ATTTTTTATCATTTTTATA
* *
3436581 ATTTTTTCTAATTTTTAT-
1 ATTTTTTATCATTTTTATA
3436599 ATTTT
1 ATTTT
3436604 ACATTTTTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.12
18 23 0.44
19 23 0.44
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (19 bp):
ATTTTTTATCATTTTTATA
Found at i:3436551 original size:10 final size:10
Alignment explanation
Indices: 3436538--3436596 Score: 54
Period size: 10 Copynumber: 6.3 Consensus size: 10
3436528 TTTTTATGCA
3436538 TTTTATAATT
1 TTTTATAATT
*
3436548 TTTTATCA-T
1 TTTTATAATT
**
3436557 TTTTATAAAA
1 TTTTATAATT
3436567 TTTTAT-A-T
1 TTTTATAATT
3436575 TTTTAT-ATT
1 TTTTATAATT
*
3436584 TTTTCTAATT
1 TTTTATAATT
3436594 TTT
1 TTT
3436597 ATATTTTACA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
8 7 0.17
9 15 0.37
10 19 0.46
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATAATT
Found at i:3436578 original size:8 final size:8
Alignment explanation
Indices: 3436547--3436613 Score: 55
Period size: 9 Copynumber: 7.9 Consensus size: 8
3436537 ATTTTATAAT
3436547 TTTTTATCA
1 TTTTTAT-A
3436556 TTTTTATAAA
1 TTTTTAT--A
*
3436566 ATTTTATA
1 TTTTTATA
3436574 TTTTTATA
1 TTTTTATA
*
3436582 TTTTTTCTAA
1 -TTTTTAT-A
3436592 TTTTTATA
1 TTTTTATA
*
3436600 -TTTTACA
1 TTTTTATA
3436607 TTTTTAT
1 TTTTTAT
3436614 TAAAATTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
7 6 0.13
8 14 0.30
9 19 0.40
10 8 0.17
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (8 bp):
TTTTTATA
Found at i:3436584 original size:26 final size:26
Alignment explanation
Indices: 3436537--3436660 Score: 101
Period size: 25 Copynumber: 4.6 Consensus size: 26
3436527 TTTTTTATGC
3436537 ATTTTATAATTTTTTATCATTTTTATAAA
1 ATTTTAT-A-TTTTTAT-ATTTTTATAAA
**
3436566 ATTTTATATTTTTATATTTTT-TCTA
1 ATTTTATATTTTTATATTTTTATAAA
*
3436591 ATTTT-TATATTTTACATTTTTATTAAA
1 ATTTTATAT-TTTTATATTTTTA-TAAA
* * **
3436618 ATTTAATATTTTTTATAACTTTTATTTA
1 ATTTTATA-TTTTTAT-ATTTTTATAAA
3436646 ATTTTAT-TTTTTATA
1 ATTTTATATTTTTATA
3436661 AATTTTTTGC
Statistics
Matches: 78, Mismatches: 11, Indels: 16
0.74 0.10 0.15
Matches are distributed among these distances:
24 3 0.04
25 19 0.24
26 13 0.17
27 13 0.17
28 16 0.21
29 14 0.18
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (26 bp):
ATTTTATATTTTTATATTTTTATAAA
Found at i:3436654 original size:52 final size:51
Alignment explanation
Indices: 3436548--3436659 Score: 138
Period size: 52 Copynumber: 2.1 Consensus size: 51
3436538 TTTTATAATT
*
3436548 TTTTATCATTTTTATAAAATTTTATATTTTTATATTTTTTCTAATTTTTATA
1 TTTTATCATTTTTATAAAATTTAATATTTTTATATTTTTTCTAA-TTTTATA
*
3436600 TTTTA-CATTTTTATTAAAATTTAATATTTTTTATAACTTTTATT-TAATTTTATT
1 TTTTATCATTTTTA-TAAAATTTAATA-TTTTTAT-A-TTTT-TTCTAATTTTATA
3436654 TTTTAT
1 TTTTAT
3436660 AAATTTTTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
51 8 0.15
52 16 0.31
53 7 0.13
54 12 0.23
55 7 0.13
56 2 0.04
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (51 bp):
TTTTATCATTTTTATAAAATTTAATATTTTTATATTTTTTCTAATTTTATA
Found at i:3436661 original size:26 final size:27
Alignment explanation
Indices: 3436545--3436667 Score: 105
Period size: 26 Copynumber: 4.6 Consensus size: 27
3436535 GCATTTTATA
*
3436545 ATTTTTTATCATTTTTA-TAAAATTTT
1 ATTTTTTATAATTTTTATTAAAATTTT
*
3436571 ATATTTTTAT-ATTTTT-TCT-AATTTTT
1 AT-TTTTTATAATTTTTAT-TAAAATTTT
* *
3436597 ATATTTTA-CATTTTTATTAAAATTTAAT
1 ATTTTTTATAATTTTTATTAAAATTT--T
* *
3436625 ATTTTTTATAACTTTTATT-TAATTTT
1 ATTTTTTATAATTTTTATTAAAATTTT
3436651 ATTTTTTATAAATTTTT
1 ATTTTTTAT-AATTTTT
3436668 TGCCACATGG
Statistics
Matches: 79, Mismatches: 8, Indels: 19
0.75 0.08 0.18
Matches are distributed among these distances:
25 12 0.15
26 32 0.41
27 14 0.18
28 13 0.16
29 8 0.10
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (27 bp):
ATTTTTTATAATTTTTATTAAAATTTT
Found at i:3436936 original size:91 final size:90
Alignment explanation
Indices: 3436766--3437036 Score: 274
Period size: 89 Copynumber: 3.0 Consensus size: 90
3436756 TAATAGCCAA
* * * * * *
3436766 AGGGCCTTTTTGATGCA-TTTGACAGTTCAAGTACCTAATTGAGTG-AAAAACAAAATCAAGGGC
1 AGGGTCTTTTTTATGCATTTTGAAAGTTCAAGTACCTAATTAAGTGCAAAAAAAAAAGCAAGGGC
*
3436829 TTAATTATTTTATTTTTTTGAAAAGTTTG
66 TTAATTA--CTATTTTTTT--AAAGTTTG
*
3436858 A-GG-CTTTTTTATGCATTTTGAAAGTTCAAGTACCTAATTAAGTGCAAAAAAAAAAGCAATGGC
1 AGGGTCTTTTTTATGCATTTTGAAAGTTCAAGTACCTAATTAAGTGCAAAAAAAAAAGCAAGGGC
*
3436921 TTAATTGCT-TTTTTTTAAAGTTTG
66 TTAATTACTATTTTTTTAAAGTTTG
* * * **
3436945 AGGGTTTTTTTTATGCATTTTAAAAGTTTAAGTA-CTCAATTGAA-TGCAAAAAAAAAAG-TTGG
1 AGGGTCTTTTTTATGCATTTTGAAAGTTCAAGTACCT-AATT-AAGTGCAAAAAAAAAAGCAAGG
*
3437007 AGCTTAATTACT-TTTTTTT-AATTTTG
64 -GCTTAATTACTATTTTTTTAAAGTTTG
3437033 AGGG
1 AGGG
3437037 CATTTTACAT
Statistics
Matches: 156, Mismatches: 16, Indels: 18
0.82 0.08 0.09
Matches are distributed among these distances:
87 9 0.06
88 15 0.10
89 68 0.44
90 14 0.09
91 28 0.18
92 22 0.14
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (90 bp):
AGGGTCTTTTTTATGCATTTTGAAAGTTCAAGTACCTAATTAAGTGCAAAAAAAAAAGCAAGGGC
TTAATTACTATTTTTTTAAAGTTTG
Found at i:3447696 original size:90 final size:90
Alignment explanation
Indices: 3447599--3447767 Score: 225
Period size: 90 Copynumber: 1.9 Consensus size: 90
3447589 ATTTAGTGGC
* * * *
3447599 TCATCCTATAAATTCAGT-AGGTTTATCAAGTCTGTCTCAATAGGACCACCCAAACTCT-AGGCT
1 TCATCCTATAAATTCAGTGA-ATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTCTGA-GCA
*
3447662 GTGAACTCATTAAGAGCTTCTGGTAGT
64 ATGAACTCATTAAGAGCTTCTGGTAGT
** * *
3447689 TCATCCTATAAATTTGGTGAATTCATCAAGTCCGTCTTAGTAGGACCACCCAAACTCTGAGCAAT
1 TCATCCTATAAATTCAGTGAATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTCTGAGCAAT
3447754 GAACTCATTAAGAG
66 GAACTCATTAAGAG
3447768 TAACAAACTC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
90 66 0.97
91 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (90 bp):
TCATCCTATAAATTCAGTGAATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTCTGAGCAAT
GAACTCATTAAGAGCTTCTGGTAGT
Found at i:3472104 original size:6 final size:6
Alignment explanation
Indices: 3472093--3472125 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
3472083 TTACACTATG
3472093 CTTTTT CTTTTT C-TTTT C-TTTT CTTTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT
3472126 ATATCATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
CTTTTT
Found at i:3472116 original size:16 final size:16
Alignment explanation
Indices: 3472095--3472125 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3472085 ACACTATGCT
3472095 TTTTCTTTTTCTTTTC
1 TTTTCTTTTTCTTTTC
3472111 TTTTCTTTTTCTTTT
1 TTTTCTTTTTCTTTT
3472126 ATATCATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTC
Found at i:3477513 original size:17 final size:18
Alignment explanation
Indices: 3477493--3477526 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3477483 CAAAATTTAT
*
3477493 ATTTTTTTAAA-AAAATA
1 ATTTTTTAAAATAAAATA
3477510 ATTTTTTAAAATAAAAT
1 ATTTTTTAAAATAAAAT
3477527 TCTAAATAAT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTTTTAAAATAAAATA
Found at i:3477560 original size:18 final size:18
Alignment explanation
Indices: 3477537--3477575 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3477527 TCTAAATAAT
3477537 ATATAAAGAAAATT-AAAA
1 ATATAAA-AAAATTCAAAA
3477555 ATATAAAAAAATTCAAAA
1 ATATAAAAAAATTCAAAA
3477573 ATA
1 ATA
3477576 ATATTTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (18 bp):
ATATAAAAAAATTCAAAA
Found at i:3477819 original size:5 final size:5
Alignment explanation
Indices: 3477777--3477817 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
3477767 AAACAATTTC
* * *
3477777 ATTCG ATTCA ATTCA ATTCG ATTCG ATTCG ATTCG ACTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
3477818 CTTGAATTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (5 bp):
ATTCG
Found at i:3483257 original size:3 final size:3
Alignment explanation
Indices: 3483249--3483275 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3483239 TCCTCTCAAA
3483249 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
3483276 TCAATTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3488122 original size:23 final size:21
Alignment explanation
Indices: 3488069--3488116 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
3488059 TAAACTCGAA
3488069 AAATA-AAAATATTAAATTTCT
1 AAATATAAAA-ATTAAATTTCT
3488090 AAATATAAAAATTAAATTT-T
1 AAATATAAAAATTAAATTTCT
3488110 AAATATA
1 AAATATA
3488117 CGAAAACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.31
21 14 0.54
22 4 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATATAAAAATTAAATTTCT
Found at i:3488638 original size:23 final size:22
Alignment explanation
Indices: 3488604--3488649 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 22
3488594 TTTATGAAAT
3488604 GGACGTGGTTGTCAATGCAGAA
1 GGACGTGGTTGTCAATGCAGAA
3488626 GGACGTAGGTTGTCAATGCAGAA
1 GGACGT-GGTTGTCAATGCAGAA
3488649 G
1 G
3488650 TTATAGGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.28, C:0.13, G:0.37, T:0.22
Consensus pattern (22 bp):
GGACGTGGTTGTCAATGCAGAA
Found at i:3497922 original size:6 final size:6
Alignment explanation
Indices: 3497913--3497958 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
3497903 CACCGATCTT
* *
3497913 CCCTTT CCCTTT CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCT
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCT
3497959 ATCCTTGACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
CCCTTC
Found at i:3500960 original size:25 final size:26
Alignment explanation
Indices: 3500932--3500980 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
3500922 CAAATTCCAA
3500932 AAAAGTAAATCATTTTT-AGAAAAGT
1 AAAAGTAAATCATTTTTCAGAAAAGT
3500957 AAAAGTAAATCATTTTTCAGAAAA
1 AAAAGTAAATCATTTTTCAGAAAA
3500981 CATTTTACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.31
Consensus pattern (26 bp):
AAAAGTAAATCATTTTTCAGAAAAGT
Found at i:3509828 original size:37 final size:39
Alignment explanation
Indices: 3509787--3509883 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 39
3509777 AGATTTATTC
**
3509787 GATGAGGCACTAGGTGCCAA-TT-TACTTCGGTTTAACT
1 GATGAGGCACTAGGTGCCAATTTATACTTCGAATTAACT
* * *
3509824 GATGAGGCACTGGGTGTCAATTTACTACTTCGAATTATCT
1 GATGAGGCACTAGGTGCCAATTTA-TACTTCGAATTAACT
3509864 GATGAGGCACTAGGTGCCAA
1 GATGAGGCACTAGGTGCCAA
3509884 ATTGGTGTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
37 18 0.36
38 2 0.04
40 30 0.60
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (39 bp):
GATGAGGCACTAGGTGCCAATTTATACTTCGAATTAACT
Found at i:3518804 original size:27 final size:27
Alignment explanation
Indices: 3518766--3518820 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
3518756 ACAATTAGAG
3518766 TTAGTTTTTCTTCCTCTGCTTGTCATA
1 TTAGTTTTTCTTCCTCTGCTTGTCATA
3518793 TTAGTTTTTCTTCCTCTGCTTGTCATA
1 TTAGTTTTTCTTCCTCTGCTTGTCATA
3518820 T
1 T
3518821 CTGGGGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.11, C:0.22, G:0.11, T:0.56
Consensus pattern (27 bp):
TTAGTTTTTCTTCCTCTGCTTGTCATA
Found at i:3525222 original size:20 final size:21
Alignment explanation
Indices: 3525197--3525246 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
3525187 TGACTCGAAT
3525197 GTATCGATACCCTTAACAA-A
1 GTATCGATACCCTTAACAACA
* *
3525217 GTATCGATACCTTTCACAACA
1 GTATCGATACCCTTAACAACA
3525238 GTATCGATA
1 GTATCGATA
3525247 TCATGCCCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (21 bp):
GTATCGATACCCTTAACAACA
Found at i:3529048 original size:20 final size:19
Alignment explanation
Indices: 3529019--3529056 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3529009 ATATATCTTG
*
3529019 ATATTTTTTAGTTAAAATT
1 ATATTTTTTAATTAAAATT
3529038 ATATATTTTTAATTAAAAT
1 ATAT-TTTTTAATTAAAAT
3529057 AATAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
ATATTTTTTAATTAAAATT
Found at i:3529066 original size:21 final size:20
Alignment explanation
Indices: 3529023--3529062 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3529013 ATCTTGATAT
* * *
3529023 TTTTTAGTTAAAATTATATA
1 TTTTTAATTAAAATAATAAA
3529043 TTTTTAATTAAAATAATAAA
1 TTTTTAATTAAAATAATAAA
3529063 ATTTACAAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTTTAATTAAAATAATAAA
Found at i:3538143 original size:15 final size:15
Alignment explanation
Indices: 3538119--3538151 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3538109 AACATTGGGG
3538119 TAAT-ATTAAATATA
1 TAATAATTAAATATA
3538133 TAATAATTAAATATA
1 TAATAATTAAATATA
3538148 -AATA
1 TAATA
3538152 CAATGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATAATTAAATATA
Found at i:3545075 original size:38 final size:38
Alignment explanation
Indices: 3545033--3545110 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
3545023 TGATCAAAGC
3545033 AAATTCAATCTTTAAAATCTTTATTGAAATATAGCTTA
1 AAATTCAATCTTTAAAATCTTTATTGAAATATAGCTTA
3545071 AAATTCAATCTTTAAAATCTTTATTGAAATATAGCTTA
1 AAATTCAATCTTTAAAATCTTTATTGAAATATAGCTTA
3545109 AA
1 AA
3545111 CTATACGATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (38 bp):
AAATTCAATCTTTAAAATCTTTATTGAAATATAGCTTA
Found at i:3546897 original size:24 final size:24
Alignment explanation
Indices: 3546870--3546915 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
3546860 ACATATTAAG
*
3546870 TTAAAGTTATTTTTGTTTTGTGTT
1 TTAAAGTTATTTTTGTCTTGTGTT
** *
3546894 TTAATTTTTTTTTTGTCTTGTG
1 TTAAAGTTATTTTTGTCTTGTG
3546916 ATCTAATGCC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.13, C:0.02, G:0.15, T:0.70
Consensus pattern (24 bp):
TTAAAGTTATTTTTGTCTTGTGTT
Found at i:3550181 original size:21 final size:21
Alignment explanation
Indices: 3550143--3550182 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3550133 TAATCTGTCC
*
3550143 ATTAAAGCTTATGTTGCTAAA
1 ATTAAAGATTATGTTGCTAAA
3550164 ATTAAAGATT-TGTGTGCTA
1 ATTAAAGATTATGT-TGCTA
3550183 TGTTAGATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.40
Consensus pattern (21 bp):
ATTAAAGATTATGTTGCTAAA
Found at i:3554733 original size:33 final size:29
Alignment explanation
Indices: 3554695--3554766 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 29
3554685 CTATAAGTGT
3554695 CGAATGCACATATTCACTTATACCCACCTATGC
1 CGAATGCACATA-T-A--TATACCCACCTATGC
*
3554728 CGAATGCATACATATATATATCCACCTATGC
1 CGAATGC--ACATATATATACCCACCTATGC
3554759 CGAATGCA
1 CGAATGCA
3554767 TACATAAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
29 1 0.03
31 21 0.58
33 8 0.22
34 1 0.03
35 5 0.14
ACGTcount: A:0.33, C:0.29, G:0.11, T:0.26
Consensus pattern (29 bp):
CGAATGCACATATATATACCCACCTATGC
Found at i:3554756 original size:31 final size:31
Alignment explanation
Indices: 3554713--3554772 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
3554703 CATATTCACT
3554713 TATACCCACCTATGCCGAATGCATACATATA
1 TATACCCACCTATGCCGAATGCATACATATA
*
3554744 TATATCCACCTATGCCGAATGCATACATA
1 TATACCCACCTATGCCGAATGCATACATA
3554773 AACACACTTA
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:0.35, C:0.28, G:0.10, T:0.27
Consensus pattern (31 bp):
TATACCCACCTATGCCGAATGCATACATATA
Found at i:3555027 original size:41 final size:42
Alignment explanation
Indices: 3554977--3555158 Score: 212
Period size: 41 Copynumber: 4.4 Consensus size: 42
3554967 TGGCACGTCA
* * * *
3554977 CCTGATAGGCTTATAGTCC-AATTCTGTTCATCGGCACTTAG
1 CCTGCTAGGCGTATAGTCCTAATTCAGTTCACCGGCACTTAG
* *
3555018 CCTGCTAGGCCTATAG-CCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCGTATAGTCCTAATTCAGTTCACCGGCACTTAG
* * *
3555059 CCTGCTAGGCTTGTAG-CCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCGTATAGTCCTAATTCAGTTCACCGGCACTTAG
* *
3555100 CCTG-TTGGACGTATAGTCC-AATTCAATTCACCGGCACTTAG
1 CCTGCTAGG-CGTATAGTCCTAATTCAGTTCACCGGCACTTAG
*
3555141 CCTGCTAGACGTATAGTC
1 CCTGCTAGGCGTATAGTC
3555159 TGAACAGTTT
Statistics
Matches: 123, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
40 5 0.04
41 114 0.93
42 4 0.03
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (42 bp):
CCTGCTAGGCGTATAGTCCTAATTCAGTTCACCGGCACTTAG
Found at i:3555171 original size:41 final size:41
Alignment explanation
Indices: 3555002--3555176 Score: 183
Period size: 41 Copynumber: 4.3 Consensus size: 41
3554992 GTCCAATTCT
* * * *
3555002 GTTCATCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCA
1 GTTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATACA
* * * *
3555043 GTTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCA
1 GTTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATACA
* * * *
3555084 GTTCACCGGCACTTAGCCTGTTGGACGTATAGTCC-AATTCA
1 GTTCACCGGCACTTAGCCTGCTAGACGTATAG-CCTGATACA
* *
3555125 ATTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGA-ACA
1 GTTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATACA
*
3555165 GTTTCACTGGCA
1 G-TTCACCGGCA
3555177 ATAAATCCAA
Statistics
Matches: 114, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
40 3 0.03
41 109 0.96
42 2 0.02
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (41 bp):
GTTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATACA
Found at i:3555171 original size:82 final size:82
Alignment explanation
Indices: 3555002--3555176 Score: 203
Period size: 82 Copynumber: 2.1 Consensus size: 82
3554992 GTCCAATTCT
* * *
3555002 GTTCATCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAG
1 GTTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTAATTCAATTCACCGGCACTTAGCCTGCTAG
* * * *
3555067 GCTTGTAGCCTGATTCA
66 ACGTATAGCCTGATACA
* *
3555084 GTTCACCGGCACTTAGCCTG-TTGGACGTATAGTCC-AATTCAATTCACCGGCACTTAGCCTGCT
1 GTTCACCGGCACTTAGCCTGCTAGG-CCTATAG-CCTAATTCAATTCACCGGCACTTAGCCTGCT
*
3555147 AGACGTATAGTCTGA-ACA
64 AGACGTATAGCCTGATACA
*
3555165 GTTTCACTGGCA
1 G-TTCACCGGCA
3555177 ATAAATCCAA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
81 6 0.08
82 71 0.90
83 2 0.03
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (82 bp):
GTTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTAATTCAATTCACCGGCACTTAGCCTGCTAG
ACGTATAGCCTGATACA
Found at i:3563662 original size:6 final size:6
Alignment explanation
Indices: 3563651--3563690 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
3563641 TAATGGTGTG
3563651 CATATA CATATA CATATA CATATA CATATA CATATA CATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATA
3563691 GAGAGTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
CATATA
Found at i:3567191 original size:6 final size:6
Alignment explanation
Indices: 3567176--3567204 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3567166 AAATAGGCTA
3567176 ATAA-C ATAATC ATAATC ATAATC ATAATC
1 ATAATC ATAATC ATAATC ATAATC ATAATC
3567205 TTTAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (6 bp):
ATAATC
Found at i:3567689 original size:13 final size:13
Alignment explanation
Indices: 3567671--3567698 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3567661 TTAATAAATT
3567671 CATTTTTATTACA
1 CATTTTTATTACA
3567684 CATTTTTATTACA
1 CATTTTTATTACA
3567697 CA
1 CA
3567699 ATCAGTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (13 bp):
CATTTTTATTACA
Found at i:3571847 original size:19 final size:19
Alignment explanation
Indices: 3571815--3571852 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3571805 ATATAATTAA
* *
3571815 ATAAATTATTAAAAAAATC
1 ATAAAATATAAAAAAAATC
3571834 ATAAAATATAAAAAAAATC
1 ATAAAATATAAAAAAAATC
3571853 TAGTTCAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
ATAAAATATAAAAAAAATC
Found at i:3573542 original size:42 final size:44
Alignment explanation
Indices: 3573465--3573552 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 44
3573455 TTACATCTTG
* * *
3573465 AAAGAGATGAATTGATTATTATAAGAATCGGGTGAGCAG-TTAT
1 AAAGAGATGAAGTGATTATTACAAGAATCGAGTGAGCAGTTTAT
* * *
3573508 AAAGAGAT-AAGTGATTGTTACAAGTATCGAGTGAGTAGTTTAT
1 AAAGAGATGAAGTGATTATTACAAGAATCGAGTGAGCAGTTTAT
3573551 AA
1 AA
3573553 GGAGTAGTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 24 0.63
43 14 0.37
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.31
Consensus pattern (44 bp):
AAAGAGATGAAGTGATTATTACAAGAATCGAGTGAGCAGTTTAT
Found at i:3575923 original size:17 final size:17
Alignment explanation
Indices: 3575901--3575935 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3575891 ATTCTTAGTC
*
3575901 CTATTATTAGTGCATGT
1 CTATTATTAGTCCATGT
3575918 CTATTATTAGTCCATGT
1 CTATTATTAGTCCATGT
3575935 C
1 C
3575936 ATTGAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (17 bp):
CTATTATTAGTCCATGT
Found at i:3587808 original size:27 final size:27
Alignment explanation
Indices: 3587778--3587840 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
3587768 GGTAATCGAA
*
3587778 AGGCGGCACCAAAGGTGCCTTTC-CGAT
1 AGGCGGCACCAAAGGTACCTTTCTC-AT
* *
3587805 AGGCGGCACCGATGGTACCTTTCTCAT
1 AGGCGGCACCAAAGGTACCTTTCTCAT
*
3587832 AGGTGGCAC
1 AGGCGGCAC
3587841 AAGACTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.21, C:0.29, G:0.30, T:0.21
Consensus pattern (27 bp):
AGGCGGCACCAAAGGTACCTTTCTCAT
Found at i:3588354 original size:27 final size:27
Alignment explanation
Indices: 3588311--3588373 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
3588301 TTTTAGTCTT
3588311 GTGCCGCCTATGAGAAAGGCACCATCG
1 GTGCCGCCTATGAGAAAGGCACCATCG
* *
3588338 GTGCCGCCTATCG-GAAAGGCACCTTTG
1 GTGCCGCCTAT-GAGAAAGGCACCATCG
3588365 GTGCCGCCT
1 GTGCCGCCT
3588374 TTCCATTACC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.19, C:0.32, G:0.30, T:0.19
Consensus pattern (27 bp):
GTGCCGCCTATGAGAAAGGCACCATCG
Found at i:3592957 original size:22 final size:22
Alignment explanation
Indices: 3592929--3592974 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
3592919 GTGAGAGTCG
3592929 ATAAGCTCTGATACCATATGAA
1 ATAAGCTCTGATACCATATGAA
3592951 ATAAGCTCTGATACCATATGAA
1 ATAAGCTCTGATACCATATGAA
3592973 AT
1 AT
3592975 CAAGGGAGGA
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:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (22 bp):
ATAAGCTCTGATACCATATGAA
Found at i:3598616 original size:24 final size:26
Alignment explanation
Indices: 3598591--3598641 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
3598581 CTAAAATGTT
*
3598591 ATTTTTTTTATTTACGAAAATATTATA
1 ATTTTTTTTATTTACCAAAATA-TATA
3598618 ATTTTTTTTATTTACCAAAATATA
1 ATTTTTTTTATTTACCAAAATATA
3598642 CCAAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (26 bp):
ATTTTTTTTATTTACCAAAATATATA
Found at i:3598743 original size:27 final size:26
Alignment explanation
Indices: 3598705--3598778 Score: 94
Period size: 27 Copynumber: 2.8 Consensus size: 26
3598695 ATCACATTGG
3598705 AAGGTGCCAAAGTGATTGGCGGCACCA
1 AAGGTGCCAAAGTGATTGGCGG-ACCA
*
3598732 AAGGTGCCAAAGTGATTGGTCTGACCA
1 AAGGTGCCAAAGTGATTGG-CGGACCA
* * *
3598759 AAAGTGCTAAAGAGATTGGC
1 AAGGTGCCAAAGTGATTGGC
3598779 CTGACCGGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 1 0.02
27 39 0.93
28 2 0.05
ACGTcount: A:0.32, C:0.18, G:0.31, T:0.19
Consensus pattern (26 bp):
AAGGTGCCAAAGTGATTGGCGGACCA
Found at i:3599480 original size:19 final size:19
Alignment explanation
Indices: 3599456--3599518 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
3599446 TCTAATTAAG
3599456 TAATAACTCTATTTTACTT
1 TAATAACTCTATTTTACTT
* * ** ***
3599475 TAATAAGTTTATTAAAAAG
1 TAATAACTCTATTTTACTT
3599494 TAATAACTCTATTTTACTT
1 TAATAACTCTATTTTACTT
3599513 TAATAA
1 TAATAA
3599519 ACTATTGCTT
Statistics
Matches: 30, Mismatches: 14, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (19 bp):
TAATAACTCTATTTTACTT
Found at i:3601858 original size:21 final size:22
Alignment explanation
Indices: 3601808--3601859 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
3601798 ATCAAATTTA
*
3601808 ACTAAAAAATAAAAATTAAATTG
1 ACTAAAATATAAAAATTAAA-TG
* *
3601831 ACAAAAATATAAATATTAAA-G
1 ACTAAAATATAAAAATTAAATG
3601852 ACTAAAAT
1 ACTAAAAT
3601860 TTGACATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
23 17 0.68
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (22 bp):
ACTAAAATATAAAAATTAAATG
Found at i:3608445 original size:12 final size:13
Alignment explanation
Indices: 3608428--3608459 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3608418 CTAAAACCGC
3608428 TTTTATTTTAT-T
1 TTTTATTTTATAT
3608440 TTTTA-TTTATAT
1 TTTTATTTTATAT
3608452 TTTTATTT
1 TTTTATTT
3608460 GCTGATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTATTTTATAT
Found at i:3608918 original size:12 final size:12
Alignment explanation
Indices: 3608901--3608925 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3608891 AGATAATAAT
3608901 AAAAAAAAGAAA
1 AAAAAAAAGAAA
3608913 AAAAAAAAGAAA
1 AAAAAAAAGAAA
3608925 A
1 A
3608926 CCCATTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:3624551 original size:38 final size:38
Alignment explanation
Indices: 3624499--3624572 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
3624489 GTAGTTGAAA
* *
3624499 ATGTTAATGAGTGACTGATTTGTAACTTTTCGATAATG
1 ATGTTAATGAGTGACAGATTTGTAACTTTTCAATAATG
*
3624537 ATGTTAAT-AGGTGACAGATTTGTCACTTTTCAATAA
1 ATGTTAATGA-GTGACAGATTTGTAACTTTTCAATAA
3624573 CATTAGTGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 31 0.97
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (38 bp):
ATGTTAATGAGTGACAGATTTGTAACTTTTCAATAATG
Found at i:3629969 original size:42 final size:43
Alignment explanation
Indices: 3629904--3629993 Score: 137
Period size: 43 Copynumber: 2.1 Consensus size: 43
3629894 AGAATCCACC
* *
3629904 TTGAGAACTTAGTGGAAATTTCC-TTTTCTATTAAAATGATTT
1 TTGAAAACTTAGTGGAAAATTCCTTTTTCTATTAAAATGATTT
* *
3629946 TTGAAAACTTGGTGTAAAATTCCTTTTTCTATTAAAATGATTT
1 TTGAAAACTTAGTGGAAAATTCCTTTTTCTATTAAAATGATTT
3629989 TTGAA
1 TTGAA
3629994 CTAATTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 19 0.44
43 24 0.56
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (43 bp):
TTGAAAACTTAGTGGAAAATTCCTTTTTCTATTAAAATGATTT
Found at i:3633175 original size:5 final size:5
Alignment explanation
Indices: 3633165--3633189 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3633155 TGTTGGGCAT
3633165 ATTAA ATTAA ATTAA ATTAA ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA
3633190 TAATTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTAA
Found at i:3634458 original size:9 final size:9
Alignment explanation
Indices: 3634446--3634521 Score: 54
Period size: 9 Copynumber: 8.4 Consensus size: 9
3634436 TTTATTTTTT
3634446 AAAATTATA
1 AAAATTATA
3634455 AAAATT-TA
1 AAAATTATA
*
3634463 AAAAATATAA
1 AAAATTAT-A
*
3634473 AAATATTTTTA
1 AAA-A-TTATA
3634484 AAAATT-T-
1 AAAATTATA
3634491 AAAATT-T-
1 AAAATTATA
3634498 AAAATTATTAA
1 AAAATTA-T-A
3634509 AAAATTATA
1 AAAATTATA
3634518 AAAA
1 AAAA
3634522 CAAAAATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
7 13 0.23
8 8 0.14
9 15 0.27
10 6 0.11
11 12 0.21
12 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAATTATA
Found at i:3635670 original size:12 final size:12
Alignment explanation
Indices: 3635650--3635693 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
3635640 ACACCTCTTA
*
3635650 TGTTTAAATTGC
1 TGTTCAAATTGC
3635662 TGTTCAAATTGC
1 TGTTCAAATTGC
3635674 TGTTCAAATTGC
1 TGTTCAAATTGC
3635686 TGTTCAAA
1 TGTTCAAA
3635694 CTGGCACTCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (12 bp):
TGTTCAAATTGC
Found at i:3639696 original size:15 final size:15
Alignment explanation
Indices: 3639654--3639701 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
3639644 GCATATATAT
3639654 ATTTGAAATAAATACTA
1 ATTTGAAATAAA-A-TA
**
3639671 A-TTGATTTAAAATA
1 ATTTGAAATAAAATA
3639685 ATTTGAAATAAAATA
1 ATTTGAAATAAAATA
3639700 AT
1 AT
3639702 GTATATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 3 0.12
15 14 0.54
16 8 0.31
17 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (15 bp):
ATTTGAAATAAAATA
Found at i:3641841 original size:7 final size:7
Alignment explanation
Indices: 3641824--3641873 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
3641814 TAGTGCCTAT
3641824 GGTTTATG
1 GGTTTA-G
3641832 GGTTTAG
1 GGTTTAG
3641839 GGTTTTAG
1 GG-TTTAG
3641847 GGTTTAG
1 GGTTTAG
*
3641854 TGTTTAG
1 GGTTTAG
**
3641861 AATTTAG
1 GGTTTAG
3641868 GGTTTA
1 GGTTTA
3641874 AGATTTAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
7 23 0.64
8 13 0.36
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (7 bp):
GGTTTAG
Found at i:3641887 original size:21 final size:22
Alignment explanation
Indices: 3641841--3641887 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
3641831 GGGTTTAGGG
*
3641841 TTTTAGGGTTTAGTGTTTAGAA
1 TTTTAGGGTTTAGTATTTAGAA
3641863 -TTTAGGGTTTAAG-ATTTA-AA
1 TTTTAGGGTTT-AGTATTTAGAA
3641883 TTTTA
1 TTTTA
3641888 ATATTTTGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 2 0.09
21 18 0.82
22 2 0.09
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (22 bp):
TTTTAGGGTTTAGTATTTAGAA
Found at i:3642805 original size:18 final size:18
Alignment explanation
Indices: 3642779--3642833 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
3642769 TGTATTCCAT
*
3642779 TTTTTCTTCTCATTATTA
1 TTTTACTTCTCATTATTA
* *
3642797 TTTTGCTTCTCATCATTA
1 TTTTACTTCTCATTATTA
* *
3642815 TTATACTTCTTATTATTA
1 TTTTACTTCTCATTATTA
3642833 T
1 T
3642834 AGTAGAGAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.20, C:0.16, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTACTTCTCATTATTA
Found at i:3648089 original size:14 final size:14
Alignment explanation
Indices: 3648070--3648116 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
3648060 ACCGGCACCT
3648070 ACAACAAATCAA-AC
1 ACAACAAA-CAACAC
*
3648084 ACAACACACAACAC
1 ACAACAAACAACAC
* *
3648098 ACAACAAGCAACAA
1 ACAACAAACAACAC
3648112 ACAAC
1 ACAAC
3648117 CAAAAAGGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 3 0.11
14 25 0.89
ACGTcount: A:0.62, C:0.34, G:0.02, T:0.02
Consensus pattern (14 bp):
ACAACAAACAACAC
Done.