Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 12 of 150
Found at i:3380672 original size:17 final size:18
Alignment explanation
Indices: 3380652--3380685 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3380642 ACATTTTTAA
3380652 TATATATTTTT-AAAATC
1 TATATATTTTTCAAAATC
*
3380669 TATATTTTTTTCAAAAT
1 TATATATTTTTCAAAAT
3380686 TTATCAATCA
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:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATTTTTCAAAATC
Found at i:3380819 original size:9 final size:9
Alignment explanation
Indices: 3380800--3381236 Score: 410
Period size: 9 Copynumber: 48.0 Consensus size: 9
3380790 CTTATATATA
*
3380800 AACTTGCAT
1 AACTTACAT
*
3380809 AACTTATAT
1 AACTTACAT
*
3380818 AAATTACAT
1 AACTTACAT
3380827 AACTTACAT
1 AACTTACAT
* *
3380836 AAATTAAAT
1 AACTTACAT
3380845 AACTTACAT
1 AACTTACAT
3380854 AACTTACAT
1 AACTTACAT
3380863 AACTTACAT
1 AACTTACAT
* *
3380872 AAATTAAAT
1 AACTTACAT
3380881 AACTTACAT
1 AACTTACAT
3380890 AACTTACAT
1 AACTTACAT
* *
3380899 AAATTAAAT
1 AACTTACAT
*
3380908 AGCTTACAT
1 AACTTACAT
3380917 AACTTACAT
1 AACTTACAT
*
3380926 AACTTAAAT
1 AACTTACAT
3380935 AACTTACAT
1 AACTTACAT
3380944 AACTTACAT
1 AACTTACAT
*
3380953 AACTTAAAT
1 AACTTACAT
3380962 AACTTACAT
1 AACTTACAT
3380971 AACTTACAT
1 AACTTACAT
*
3380980 AACTTAAAT
1 AACTTACAT
3380989 AACTTACAT
1 AACTTACAT
3380998 AA--TACAT
1 AACTTACAT
*
3381005 AACTTTCCTAACT
1 AAC-TTAC--A-T
*
3381018 AACTTAAAT
1 AACTTACAT
3381027 AACTTACAT
1 AACTTACAT
3381036 AA--TACAT
1 AACTTACAT
*
3381043 AACCTT-CCT
1 AA-CTTACAT
*
3381052 AACTTAAATT
1 AACTTACA-T
*
3381062 ATTTATTTACAT
1 A---ACTTACAT
3381074 AA--TACAT
1 AACTTACAT
3381081 AACTTACAT
1 AACTTACAT
* *
3381090 AATTTTTTC-T
1 AA--CTTACAT
3381100 AAATTGCTTACAT
1 -AA---CTTACAT
* *
3381113 AAATTATAT
1 AACTTACAT
3381122 AACTTACAT
1 AACTTACAT
*
3381131 ATCTTACAT
1 AACTTACAT
3381140 AACTTACAT
1 AACTTACAT
* *
3381149 AAATTAAAT
1 AACTTACAT
3381158 AACTTACAT
1 AACTTACAT
3381167 AACTTACAT
1 AACTTACAT
3381176 AACTTACAT
1 AACTTACAT
3381185 AACTTACAT
1 AACTTACAT
*
3381194 AAATTACAT
1 AACTTACAT
3381203 AACTTACAT
1 AACTTACAT
3381212 AA--TACAT
1 AACTTACAT
*
3381219 AACCTT-CCT
1 AA-CTTACAT
3381228 AACTTACAT
1 AACTTACAT
3381237 TATTGTTTAA
Statistics
Matches: 350, Mismatches: 53, Indels: 50
0.77 0.12 0.11
Matches are distributed among these distances:
7 28 0.08
8 6 0.02
9 282 0.81
10 8 0.02
11 5 0.01
12 11 0.03
13 10 0.03
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.36
Consensus pattern (9 bp):
AACTTACAT
Found at i:3381030 original size:38 final size:39
Alignment explanation
Indices: 3380979--3381085 Score: 155
Period size: 38 Copynumber: 2.8 Consensus size: 39
3380969 ATAACTTACA
3380979 TAACTTAAATAACTTACATAATACATAACTTTCCTAAC-
1 TAACTTAAATAACTTACATAATACATAACTTTCCTAACT
*
3381017 TAACTTAAATAACTTACATAATACATAACCTTCCTAACT
1 TAACTTAAATAACTTACATAATACATAACTTTCCTAACT
* * * *
3381056 TAAATT-ATTTATTTACATAATACATAACTT
1 TAACTTAAATAACTTACATAATACATAACTT
3381086 ACATAATTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
38 57 0.92
39 5 0.08
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (39 bp):
TAACTTAAATAACTTACATAATACATAACTTTCCTAACT
Found at i:3383383 original size:21 final size:21
Alignment explanation
Indices: 3383357--3383422 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
3383347 CAACTTAAAA
* *
3383357 CAGAGGCGGCAGCGAGGGAAG
1 CAGAGGCGACAGCGAGAGAAG
*
3383378 CAGAGGCTACAGCGAGAGAAG
1 CAGAGGCGACAGCGAGAGAAG
* * * *
3383399 CAAAAGCCACAACGAGAGAAG
1 CAGAGGCGACAGCGAGAGAAG
3383420 CAG
1 CAG
3383423 CGAGAGAAGC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.39, C:0.21, G:0.38, T:0.02
Consensus pattern (21 bp):
CAGAGGCGACAGCGAGAGAAG
Found at i:3383903 original size:43 final size:43
Alignment explanation
Indices: 3383856--3383948 Score: 125
Period size: 43 Copynumber: 2.2 Consensus size: 43
3383846 ATCATATAGT
* *
3383856 GGCGTTTGTGAAAT-AAGCGCAGCGAAAGAACACTACTTTTCGC
1 GGCGTTTGT-AAATGAAGCGCAGCGAAAAAACACTACTTTTAGC
* * *
3383899 GGCGTTTGTAAATGAAGCGCCGCTAAAAAACATTACTTTTAGC
1 GGCGTTTGTAAATGAAGCGCAGCGAAAAAACACTACTTTTAGC
3383942 GGCGTTT
1 GGCGTTT
3383949 TTTACCAAGC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 4 0.09
43 40 0.91
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (43 bp):
GGCGTTTGTAAATGAAGCGCAGCGAAAAAACACTACTTTTAGC
Found at i:3383973 original size:42 final size:42
Alignment explanation
Indices: 3383870--3384078 Score: 213
Period size: 42 Copynumber: 4.9 Consensus size: 42
3383860 TTTGTGAAAT
* * * * ** **
3383870 AAGCGCAGCGAAAGAACACTACTTTTCGCGGCGTTTGTAAATG
1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTT-TTTACC
*
3383913 AAGCGCCGCTAAAAAACATTACTTTTAGCGGCGTTTTTTACC
1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACC
* *
3383955 AAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTTTTCCC
1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACC
* * * *
3383997 AAGCACCGCTAAAGAACATGA-TCATTAGCGGCGTTTTTTTCC
1 AAGCGCCGCTAAAGAACATTACT-TTTAGCGGCGTTTTTTACC
* * * *
3384039 TAAGTGCTGCTAAAGAACATAACCTTTAGCGGCGTTTTTT
1 -AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTT
3384079 TCTGTAAGCG
Statistics
Matches: 140, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
41 1 0.01
42 76 0.54
43 63 0.45
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTACC
Found at i:3383989 original size:85 final size:85
Alignment explanation
Indices: 3383869--3384076 Score: 213
Period size: 85 Copynumber: 2.4 Consensus size: 85
3383859 GTTTGTGAAA
* * * * ** * *
3383869 TAAGCGCAGCGAAAGAACACTACTTTTCGCGGCGTTTGTAAATGAAGCGCCGCTAAAAAACATTA
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTT-TAAACCAAGCACCGCTAAAAAACATGA
*
3383934 -CTTTTAGCGGCGTTTTTTACC
65 TC-ATTAGCGGCGTTTTTTACC
* *** *
3383955 -AAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTTTTCCCAAGCACCGCTAAAGAACATGAT
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTAAACCAAGCACCGCTAAAAAACATGAT
*
3384019 CATTAGCGGCGTTTTTTTCC
66 CATTAGCGGCGTTTTTTACC
* * * *
3384039 TAAGTGCTGCTAAAGAACATAACCTTTAGCGGCGTTTT
1 TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTT
3384077 TTTCTGTAAG
Statistics
Matches: 100, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
84 36 0.36
85 64 0.64
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (85 bp):
TAAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTAAACCAAGCACCGCTAAAAAACATGAT
CATTAGCGGCGTTTTTTACC
Found at i:3388240 original size:40 final size:40
Alignment explanation
Indices: 3388171--3388258 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
3388161 ATTCTGTGGC
* * * *
3388171 TGGCCGTGTGTGAGACACGGCCGTATGACTGTCGTAAGTG
1 TGGCCGTGTGTGAGACACGACCATATGACTGTCATAAGTA
* * * *
3388211 TGGCCGTTTGTGAGACACGATCATGTGACTGTCATAGGTA
1 TGGCCGTGTGTGAGACACGACCATATGACTGTCATAAGTA
3388251 TGGCCGTG
1 TGGCCGTG
3388259 CACGACACAC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.18, C:0.19, G:0.35, T:0.27
Consensus pattern (40 bp):
TGGCCGTGTGTGAGACACGACCATATGACTGTCATAAGTA
Found at i:3406153 original size:14 final size:14
Alignment explanation
Indices: 3406134--3406162 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3406124 TACATTACTC
3406134 ATGTACTGCATAAA
1 ATGTACTGCATAAA
3406148 ATGTACTGCATAAA
1 ATGTACTGCATAAA
3406162 A
1 A
3406163 AATTCTGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (14 bp):
ATGTACTGCATAAA
Found at i:3407349 original size:12 final size:12
Alignment explanation
Indices: 3407325--3407360 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
3407315 AAATTAAAAC
3407325 AAAA-ATTTT-A
1 AAAATATTTTAA
3407335 AAAATATTTTAA
1 AAAATATTTTAA
3407347 AAAATATTTTAA
1 AAAATATTTTAA
3407359 AA
1 AA
3407361 TTAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 4 0.17
11 5 0.21
12 15 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AAAATATTTTAA
Found at i:3407384 original size:41 final size:40
Alignment explanation
Indices: 3407307--3407456 Score: 155
Period size: 39 Copynumber: 3.7 Consensus size: 40
3407297 ACCAAAAATT
* *
3407307 TATTTTAAAAATTAAAACAAAAATTTTAAAA-ATATTTTAAAAAA
1 TATTTT-AAAATT-AAA-AAAAA-TTAAAAATGTATTTT-AAAAA
3407351 TATTTTAAAATTAAAAAAAATTAAAAATGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAATGTATTTTAAAAA
* * * *
3407391 -A-TTTAAAATTTAAAAAATTTAAAAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAAATT-AAAAATGTATTTTAAAAA
*
3407430 TATTTTAAAATT-AAAAAAATAAAAAAT
1 TATTTTAAAATTAAAAAAAATTAAAAAT
3407457 AATAAAAATA
Statistics
Matches: 93, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
38 17 0.18
39 22 0.24
40 19 0.20
41 20 0.22
42 3 0.03
43 6 0.06
44 6 0.06
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAAATTAAAAATGTATTTTAAAAA
Found at i:3407394 original size:10 final size:9
Alignment explanation
Indices: 3407325--3407416 Score: 62
Period size: 9 Copynumber: 9.7 Consensus size: 9
3407315 AAATTAAAAC
*
3407325 AAAAATTTT
1 AAAAAATTT
3407334 AAAAATATTTT
1 AAAAA-A-TTT
3407345 AAAAAATATT
1 AAAAAAT-TT
** *
3407355 TTAAAATTA
1 AAAAAATTT
*
3407364 AAAAAAATT
1 AAAAAATTT
3407373 AAAAATGTATTTT
1 AAAAA---A-TTT
3407386 AAAAAATTT
1 AAAAAATTT
3407395 --AAAATTT
1 AAAAAATTT
3407402 AAAAAATTT
1 AAAAAATTT
3407411 AAAAAA
1 AAAAAA
3407417 AGTATTTTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
7 7 0.11
9 33 0.51
10 9 0.14
11 8 0.12
12 1 0.02
13 7 0.11
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (9 bp):
AAAAAATTT
Found at i:3407404 original size:16 final size:16
Alignment explanation
Indices: 3407383--3407414 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3407373 AAAAATGTAT
3407383 TTTAAAAAATTTAAAA
1 TTTAAAAAATTTAAAA
3407399 TTTAAAAAATTTAAAA
1 TTTAAAAAATTTAAAA
3407415 AAAGTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTTAAAAAATTTAAAA
Found at i:3407428 original size:11 final size:11
Alignment explanation
Indices: 3407414--3407439 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3407404 AAAATTTAAA
3407414 AAAAGTATTTT
1 AAAAGTATTTT
3407425 AAAAGTATTTT
1 AAAAGTATTTT
3407436 AAAA
1 AAAA
3407440 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:3409134 original size:16 final size:15
Alignment explanation
Indices: 3409088--3409131 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
3409078 CTATAAATTA
3409088 AATCTTTGTATTTTT
1 AATCTTTGTATTTTT
*
3409103 -AT-TTAGTCATTTTT
1 AATCTTTGT-ATTTTT
3409117 AATCTTTGTATTTTT
1 AATCTTTGTATTTTT
3409132 TAAAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
13 4 0.17
14 8 0.33
15 8 0.33
16 4 0.17
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.66
Consensus pattern (15 bp):
AATCTTTGTATTTTT
Found at i:3411433 original size:14 final size:15
Alignment explanation
Indices: 3411413--3411453 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
3411403 TTTGATTGCC
3411413 AGTAAAATATTTTC-
1 AGTAAAATATTTTCT
* *
3411427 CGTAAAATAATTTCT
1 AGTAAAATATTTTCT
3411442 AG-AAAATATTTT
1 AGTAAAATATTTT
3411454 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 21 0.95
15 1 0.05
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (15 bp):
AGTAAAATATTTTCT
Found at i:3411460 original size:34 final size:35
Alignment explanation
Indices: 3411422--3411488 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 35
3411412 CAGTAAAATA
3411422 TTTTCCGTAAAATAATTT-CT-AGAAAATATTTTAC
1 TTTTCCGTAAAATAATTTACTGA-AAAATATTTTAC
* *
3411456 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGAAAAATATTTT
3411489 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 16 0.55
35 12 0.41
36 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGAAAAATATTTTAC
Found at i:3422270 original size:98 final size:98
Alignment explanation
Indices: 3422125--3422319 Score: 363
Period size: 98 Copynumber: 2.0 Consensus size: 98
3422115 CAATAAAACT
*
3422125 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
*
3422190 TTTAGAATCCCAAACTCGGAATATTTCCTTTAC
66 TTTAAAATCCCAAACTCGGAATATTTCCTTTAC
*
3422223 TTTAAAAGAACATCCACTTATCCAATATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
3422288 TTTAAAATCCCAAACTCGGAATATTTCCTTTA
66 TTTAAAATCCCAAACTCGGAATATTTCCTTTA
3422320 TTATTTTTTA
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
TTTAAAATCCCAAACTCGGAATATTTCCTTTAC
Found at i:3424968 original size:44 final size:44
Alignment explanation
Indices: 3424836--3425433 Score: 291
Period size: 44 Copynumber: 13.8 Consensus size: 44
3424826 GACTTGCTTA
* * *
3424836 TTTAGTCTGCTCCATTGCAACTTCAGGGAGATAAGACTA--GA-
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGAC
** * ** **
3424877 TGCAATCTGCT-CTCTGCAACTTCAAAGAGATAAGATCTGA--GGT
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T-ATCGAC
* *
3424920 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGAC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGAC
* * * *
3424964 TTTAATCTGCTCCTCTGTAACTTCAGGGAGATAAGACTT-GCCATC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTATCGA-C
* * * * *
3425009 TTCAGTCTGC-CTCACTGCAACTTTA-GGAGGATAAGACTT-GCTTAC
1 TTTAATCTGCTC-CACTGCAACTTCAGGGA-GATAAGA-TTATC-GAC
* *
3425054 -TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA--GA-
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGAC
*** * * *
3425094 TGCGATCTGCT-CTCTGCAACTTCAGAGAGAT-A-A-TATCTGAGGT
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATC-GA--C
* * * *
3425137 TTTAATCCGCTCCAATGCAACTTCAGGGAGATAGGATTATCGGC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGAC
* * *
3425181 TTTAATCTGCTCCTCTGTAACTTCAGGGAGATAAGACTTGTC-ATC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTATCGA-C
* * * * * *
3425226 TTCAGTTTGCCCCACTGCAACTTCA-GGAGGATAAGACTT-GCTTAC
1 TTTAATCTGCTCCACTGCAACTTCAGGGA-GATAAGA-TTATC-GAC
* * **
3425271 -TTAGTCTGCTCCACTGCAACTTCAGAGAGATAAGGCTA--GA-
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGAC
*** * * * * **
3425311 TGCGATCTGCT-CTCTGCAAATTTAGAGAGATAAGATCTGA--GGT
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T-ATCGAC
* * *
3425354 TTTAATCCGCTCCAATGCAACTTCAGGGAGATAGGATTATCGAC
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGAC
*
3425398 TTTAATCTACTCCACTGCAACTTCA-GGAGGATAAGA
1 TTTAATCTGCTCCACTGCAACTTCAGGGA-GATAAGA
3425434 CTTGCCATCT
Statistics
Matches: 420, Mismatches: 97, Indels: 77
0.71 0.16 0.13
Matches are distributed among these distances:
37 2 0.00
38 1 0.00
39 1 0.00
40 60 0.14
41 24 0.06
42 6 0.01
43 29 0.07
44 214 0.51
45 75 0.18
46 4 0.01
47 4 0.01
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (44 bp):
TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGAC
Found at i:3425012 original size:217 final size:217
Alignment explanation
Indices: 3424771--3425445 Score: 1129
Period size: 217 Copynumber: 3.1 Consensus size: 217
3424761 ACTACTGCTT
** *
3424771 AGGGAGATAAGA-TCTGAAATCTTCAGTCTGCCTCACTACAACTTCAGGAGGATAAGACTTGCTT
1 AGGGAGATAAGACT-TGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTT
* * *
3424835 ATTTAGTCTGCTCCATTGCAACTTCAGGGAGATAAGACTAGATGCAATCTGCTCTCTGCAACTTC
65 ACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTC
* *
3424900 AAAGAGATAAGATCTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGACT
130 AGAGAGATAAGATCTGAGGTTTTAATCCGCTCCAATGCAACTTCAGGGAGATAGGATTATCGACT
3424965 TTAATCTGCTCCTCTGTAACTTC
195 TTAATCTGCTCCTCTGTAACTTC
*
3424988 AGGGAGATAAGACTTGCCATCTTCAGTCTGCCTCACTGCAACTTTAGGAGGATAAGACTTGCTTA
1 AGGGAGATAAGACTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTA
3425053 CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCA
66 CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCA
* *
3425118 GAGAGATAATATCTGAGGTTTTAATCCGCTCCAATGCAACTTCAGGGAGATAGGATTATCGGCTT
131 GAGAGATAAGATCTGAGGTTTTAATCCGCTCCAATGCAACTTCAGGGAGATAGGATTATCGACTT
3425183 TAATCTGCTCCTCTGTAACTTC
196 TAATCTGCTCCTCTGTAACTTC
* * *
3425205 AGGGAGATAAGACTTGTCATCTTCAGTTTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTA
1 AGGGAGATAAGACTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTA
* * * *
3425270 CTTAGTCTGCTCCACTGCAACTTCAGAGAGATAAGGCTAGATGCGATCTGCTCTCTGCAAATTTA
66 CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCA
3425335 GAGAGATAAGATCTGAGGTTTTAATCCGCTCCAATGCAACTTCAGGGAGATAGGATTATCGACTT
131 GAGAGATAAGATCTGAGGTTTTAATCCGCTCCAATGCAACTTCAGGGAGATAGGATTATCGACTT
* * *
3425400 TAATCTACTCCACTGCAACTTC
196 TAATCTGCTCCTCTGTAACTTC
3425422 A-GGAGGATAAGACTTGCCATCTTC
1 AGGGA-GATAAGACTTGCCATCTTC
3425446 GATTTGCTCC
Statistics
Matches: 431, Mismatches: 25, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
216 3 0.01
217 427 0.99
218 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (217 bp):
AGGGAGATAAGACTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTA
CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCA
GAGAGATAAGATCTGAGGTTTTAATCCGCTCCAATGCAACTTCAGGGAGATAGGATTATCGACTT
TAATCTGCTCCTCTGTAACTTC
Found at i:3425042 original size:45 final size:44
Alignment explanation
Indices: 3424753--3425304 Score: 300
Period size: 44 Copynumber: 12.7 Consensus size: 44
3424743 TCATCTTCGA
* ** *
3424753 TCTGCTCCACTACTGCTT-AGGGAGATAAGA-TCTG-AAATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT-TGCATA-CTT-AG
* * *
3424797 TCTGC-CTCACTACAACTTCA-GGAGGATAAGACTTGCTTATTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCATACTTAG
* * * *
3424841 TCTGCTCCATTGCAACTTCAGGGAGATAAGACTAG-ATGC--AA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATACTTAG
* ** * *
3424882 TCTGCT-CTCTGCAACTTCAAAGAGATAAGA-TCTG-AGGT-TTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT-TGCA--TACTTAG
* * *
3424925 TCCGCTCCACTGCAACTTCAGGGAGATAGGA-TT--ATCGACTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCAT--AC-TTAG
* *
3424969 TCTGCTCCTCTGTAACTTCAGGGAGATAAGACTTGCCAT-CTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CATACTT-AG
* *
3425014 TCTGC-CTCACTGCAACTTTA-GGAGGATAAGACTTGCTTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCATACTTAG
* * *
3425058 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG-ATGC-GA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATACTTAG
* * * * *
3425099 TCTGCT-CTCTGCAACTTCAGAGAGATAATA-TCTG-AGGT-TTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT-TGCA--TACTTAG
* * * * *
3425142 TCCGCTCCAATGCAACTTCAGGGAGATAGGA-TT--ATCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCAT--AC-TTAG
* *
3425186 TCTGCTCCTCTGTAACTTCAGGGAGATAAGACTTGTCAT-CTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CATACTT-AG
* * *
3425231 TTTGCCCCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTTAG
1 TCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCATACTTAG
*
3425275 TCTGCTCCACTGCAACTTCAGAGAGATAAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAG
3425305 GCTAGATGCG
Statistics
Matches: 398, Mismatches: 65, Indels: 90
0.72 0.12 0.16
Matches are distributed among these distances:
39 2 0.01
40 47 0.12
41 13 0.03
42 6 0.02
43 18 0.05
44 217 0.55
45 89 0.22
46 2 0.01
48 4 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATACTTAG
Found at i:3426672 original size:6 final size:6
Alignment explanation
Indices: 3426661--3426688 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3426651 CTCCATTTTA
3426661 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
3426689 ATCACTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:3430795 original size:13 final size:13
Alignment explanation
Indices: 3430777--3430807 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3430767 AAAAGCGATA
3430777 ATATATTTTAAAT
1 ATATATTTTAAAT
3430790 ATATATTTTAAAT
1 ATATATTTTAAAT
3430803 A-ATAT
1 ATATAT
3430808 CAACTTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATATTTTAAAT
Found at i:3437198 original size:12 final size:12
Alignment explanation
Indices: 3437181--3437205 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3437171 GGTGTTCATT
3437181 CGGTTAACCGAC
1 CGGTTAACCGAC
3437193 CGGTTAACCGAC
1 CGGTTAACCGAC
3437205 C
1 C
3437206 CGAAATTACT
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:3437379 original size:9 final size:9
Alignment explanation
Indices: 3437365--3437450 Score: 118
Period size: 9 Copynumber: 9.4 Consensus size: 9
3437355 TTTGGTTAAA
3437365 AATTACCCG
1 AATTACCCG
3437374 AATTACCCG
1 AATTACCCG
3437383 AATTACCCG
1 AATTACCCG
3437392 AATTACCCG
1 AATTACCCG
*
3437401 AATTAACCG
1 AATTACCCG
*
3437410 AATTAACCG
1 AATTACCCG
**
3437419 AATTACCATA
1 AATTACC-CG
*
3437429 AAATACCCG
1 AATTACCCG
3437438 AATTACCCG
1 AATTACCCG
3437447 AATT
1 AATT
3437451 TTTTTATTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
9 62 0.91
10 6 0.09
ACGTcount: A:0.40, C:0.28, G:0.09, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:3442871 original size:28 final size:28
Alignment explanation
Indices: 3442828--3442894 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 28
3442818 GCTAGAAGTG
*
3442828 TTTTATAAAAAA-CAA-CTCATTCCCGTAA
1 TTTT-TAAAAAATCAACCT-ATTCCAGTAA
*
3442856 TTTTTAAAAAATCAACCTATTTCAGTAA
1 TTTTTAAAAAATCAACCTATTCCAGTAA
3442884 -TTTTAAAAAAT
1 TTTTTAAAAAAT
3442895 AATTTTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 18 0.51
28 15 0.43
29 2 0.06
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.37
Consensus pattern (28 bp):
TTTTTAAAAAATCAACCTATTCCAGTAA
Found at i:3444445 original size:96 final size:98
Alignment explanation
Indices: 3444280--3444569 Score: 388
Period size: 103 Copynumber: 2.9 Consensus size: 98
3444270 TGGATTCAGC
* * * *
3444280 ACTTAGCAACCCCTTTCACATTCAAAGATATGGTGGAATCAGCACTTAGCAACCACCAATCATTC
1 ACTTAGCAACCCCCTTCACATTTAAAGATATGGTGGAATCAGCACTTAGCAACCACCAATGAATC
3444345 GGGGAAATCAGCACTTAGCAACCCCTT-GGGG-G
66 GGGG-AATCAGCACTTAGCAACCCCTTGGGGGAG
*
3444377 -CTTAGCAACCCCCTTCACATTTAAAGATATGGTGGAATCAGCACTTAGCAACCACTAATGAATC
1 ACTTAGCAACCCCCTTCACATTTAAAGATATGGTGGAATCAGCACTTAGCAACCACCAATGAATC
3444441 GGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAG
66 GGGGAATCAGCACTTAGCAACCCCTTGGGGG----AG
* * * * * * *
3444478 CACTTAGCAACCCCCTTTATATTTAAAGATACGATGGGATCAGCACTTAGCAACCACCAAAGAGT
1 -ACTTAGCAACCCCCTTCACATTTAAAGATATGGTGGAATCAGCACTTAGCAACCACCAATGAAT
*
3444543 CAGGGAATCAGCACTTAGCAACCCCTT
65 CGGGGAATCAGCACTTAGCAACCCCTT
3444570 CATATTCAAT
Statistics
Matches: 171, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
95 22 0.13
96 67 0.39
101 1 0.01
103 81 0.47
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (98 bp):
ACTTAGCAACCCCCTTCACATTTAAAGATATGGTGGAATCAGCACTTAGCAACCACCAATGAATC
GGGGAATCAGCACTTAGCAACCCCTTGGGGGAG
Found at i:3444452 original size:33 final size:27
Alignment explanation
Indices: 3444410--3444489 Score: 97
Period size: 27 Copynumber: 2.7 Consensus size: 27
3444400 AAGATATGGT
3444410 GGAATCAGCACTTAGCAACCACTAATGAATCGG
1 GGAATCAGCACTTAGCAACCACT--TG----GG
*
3444443 GGAATCAGCACTTAGCAACCCCTTGGG
1 GGAATCAGCACTTAGCAACCACTTGGG
3444470 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
3444490 CCCTTTATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
27 22 0.48
31 2 0.04
33 22 0.48
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.17
Consensus pattern (27 bp):
GGAATCAGCACTTAGCAACCACTTGGG
Found at i:3447383 original size:11 final size:11
Alignment explanation
Indices: 3447367--3447392 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3447357 TACATTTAAT
3447367 TAAAGATAAAA
1 TAAAGATAAAA
3447378 TAAAGATAAAA
1 TAAAGATAAAA
3447389 TAAA
1 TAAA
3447393 ATCCTAAAAA
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:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (11 bp):
TAAAGATAAAA
Found at i:3449103 original size:24 final size:23
Alignment explanation
Indices: 3449037--3449103 Score: 57
Period size: 24 Copynumber: 2.8 Consensus size: 23
3449027 TATTAATATC
*
3449037 CAAATAAGTAATAAATAATAAAATA
1 CAAATAA-TAA-AAATAAAAAAATA
* *
3449062 -AAATAA-AGTAAAGAAAAAAATAA
1 CAAATAATA-AAAATAAAAAAAT-A
3449085 CAAATAATAAAAATAAAAA
1 CAAATAATAAAAATAAAAA
3449104 TTGGGTTGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 9
0.70 0.11 0.19
Matches are distributed among these distances:
22 11 0.33
23 1 0.03
24 20 0.61
25 1 0.03
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (23 bp):
CAAATAATAAAAATAAAAAAATA
Found at i:3463758 original size:3 final size:3
Alignment explanation
Indices: 3463750--3463777 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3463740 TGCGAAATGT
3463750 GGA GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA G
3463778 TAACCTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:3471467 original size:19 final size:17
Alignment explanation
Indices: 3471445--3471479 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
3471435 TAAAATTCAA
3471445 TAATAAATTAATTATTTTT
1 TAATAAA-T-ATTATTTTT
3471464 TAATAAATATTATTTT
1 TAATAAATATTATTTT
3471480 AACCAATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TAATAAATATTATTTTT
Found at i:3471839 original size:7 final size:7
Alignment explanation
Indices: 3471827--3471856 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3471817 TATATATACA
3471827 CATATCT
1 CATATCT
3471834 CATATCT
1 CATATCT
3471841 CATATCT
1 CATATCT
*
3471848 CACATCT
1 CATATCT
3471855 CA
1 CA
3471857 CATTGCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (7 bp):
CATATCT
Found at i:3476203 original size:11 final size:10
Alignment explanation
Indices: 3476176--3476201 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3476166 CTTTAATTTG
3476176 ATTTTTATTA
1 ATTTTTATTA
3476186 ATTTTTATTA
1 ATTTTTATTA
3476196 ATTTTT
1 ATTTTT
3476202 TAAACACTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
ATTTTTATTA
Found at i:3477213 original size:108 final size:108
Alignment explanation
Indices: 3476950--3477379 Score: 650
Period size: 108 Copynumber: 3.9 Consensus size: 108
3476940 AAAATTCAAG
* * *
3476950 AGGATATTAAGCAATTTGG-CTAAACGTGAAATCGAAACCCAGCACCTTAGGGCACGTTTCTCGA
1 AGGATATTAAGCAATTTGGTC-AAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
* * *
3477014 ATTTTCAAACGTAAAATATTGCCTTATTTTTAAAAAGTTTTTTGAAA
65 ATTTCCAAACGCAAAATATTGCCTTA-TTTTGAAAA--TTTTTGAAA
* * *
3477061 AGGATATTTAGCTATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCAAA
1 AGGATATTAAGCAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
*
3477126 TTTCCAAACGTAAAATATTGCCTTATTTTGAAAATTTTTGAAA
66 TTTCCAAACGCAAAATATTGCCTTATTTTGAAAATTTTTGAAA
**
3477169 AGGATATTAAGTC-ATTTGGTGGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
1 AGGATATTAAG-CAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
*
3477233 ATTTCCAAACGCAAAATATTGCGTTATTTTGAAAATTTTTGAAA
65 ATTTCCAAACGCAAAATATTGCCTTATTTTGAAAATTTTTGAAA
*
3477277 AGGATATTAAGTC-ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
1 AGGATATTAAG-CAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
3477341 ATTTCCAAACGCAAAATATTGCCTTATTTTGAAATATTT
65 ATTTCCAAACGCAAAATATTGCCTTATTTTGAAA-ATTT
3477380 CCCTTTTTAA
Statistics
Matches: 300, Mismatches: 16, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
108 205 0.68
109 5 0.02
110 8 0.03
111 81 0.27
112 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (108 bp):
AGGATATTAAGCAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
TTTCCAAACGCAAAATATTGCCTTATTTTGAAAATTTTTGAAA
Found at i:3478011 original size:30 final size:29
Alignment explanation
Indices: 3477977--3478044 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 29
3477967 TAAATTTGCT
*
3477977 AAAAACGGACTAAATCGAAATAAAAACAAA
1 AAAAACGGACGAAATCGAAATAAAAA-AAA
* * *
3478007 AAAAACTGGGCGAATTCGAAATAAAAAAAC
1 AAAAAC-GGACGAAATCGAAATAAAAAAAA
3478037 AAAAACGG
1 AAAAACGG
3478045 GATTAAATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 2 0.06
30 14 0.42
31 17 0.52
ACGTcount: A:0.62, C:0.13, G:0.15, T:0.10
Consensus pattern (29 bp):
AAAAACGGACGAAATCGAAATAAAAAAAA
Found at i:3481357 original size:31 final size:31
Alignment explanation
Indices: 3481286--3481353 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
3481276 TTTTTTTTAA
* *
3481286 AATATAATAATAAATAAGATTTAAATAATTT
1 AATATAATGATAAATAAGATTTAAATAAGTT
* *
3481317 AATATAATGATAAATGATATTTAAAT-AGTT
1 AATATAATGATAAATAAGATTTAAATAAGTT
3481347 AATATAA
1 AATATAA
3481354 ATGACGATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 10 0.30
31 23 0.70
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (31 bp):
AATATAATGATAAATAAGATTTAAATAAGTT
Found at i:3482381 original size:21 final size:22
Alignment explanation
Indices: 3482343--3482385 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3482333 AACTAATATA
3482343 TTAAAAATATTTCAATTATAAT
1 TTAAAAATATTTCAATTATAAT
3482365 TTAAAAAT-TTT-ATATTATAAT
1 TTAAAAATATTTCA-ATTATAAT
3482386 ATTTAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.05
21 11 0.55
22 8 0.40
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAAAAATATTTCAATTATAAT
Found at i:3482389 original size:23 final size:24
Alignment explanation
Indices: 3482336--3482392 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
3482326 AAAATAAAAC
3482336 TAATATATTAAAAATATTTCAATTA
1 TAATAT-TTAAAAATATTTCAATTA
3482361 T-A-ATTTAAAAAT-TTT-ATATTA
1 TAATATTTAAAAATATTTCA-ATTA
3482382 TAATATTTAAA
1 TAATATTTAAA
3482393 TTTTAATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 1 0.03
21 8 0.28
22 9 0.31
23 9 0.31
24 1 0.03
25 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATATTTAAAAATATTTCAATTA
Found at i:3487710 original size:39 final size:40
Alignment explanation
Indices: 3487648--3487728 Score: 146
Period size: 39 Copynumber: 2.0 Consensus size: 40
3487638 ACACTAAAGA
3487648 AAGAGAAATTTTTTTTCCAAATAAAAACAACATATTCAAT
1 AAGAGAAATTTTTTTTCCAAATAAAAACAACATATTCAAT
*
3487688 AAGAGAAA-TTTTTTTCCAAATAAAAACAATATATTCAAT
1 AAGAGAAATTTTTTTTCCAAATAAAAACAACATATTCAAT
3487727 AA
1 AA
3487729 TTGATTTAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 32 0.80
40 8 0.20
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (40 bp):
AAGAGAAATTTTTTTTCCAAATAAAAACAACATATTCAAT
Found at i:3489894 original size:15 final size:15
Alignment explanation
Indices: 3489874--3489904 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3489864 TATGAATGTC
3489874 ACAATAACAAATACA
1 ACAATAACAAATACA
*
3489889 ACAATAATAAATACA
1 ACAATAACAAATACA
3489904 A
1 A
3489905 TAATGGCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (15 bp):
ACAATAACAAATACA
Found at i:3490068 original size:18 final size:18
Alignment explanation
Indices: 3490040--3490091 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
3490030 TATGTAAATG
* *
3490040 AAAATACAAATAAATAAA
1 AAAATAAAAATAAACAAA
*
3490058 CAAATAAAAATAAACAAA
1 AAAATAAAAATAAACAAA
3490076 AAATATAAAGAATAAA
1 AAA-ATAAA-AATAAA
3490092 AAGTACATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 17 0.61
19 5 0.18
20 6 0.21
ACGTcount: A:0.77, C:0.06, G:0.02, T:0.15
Consensus pattern (18 bp):
AAAATAAAAATAAACAAA
Found at i:3490070 original size:14 final size:14
Alignment explanation
Indices: 3490051--3490093 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
3490041 AAATACAAAT
3490051 AAATAAACAAATAA
1 AAATAAACAAATAA
3490065 AAATAAACAAA-AA
1 AAATAAACAAATAA
* *
3490078 ATATAAA-GAATAA
1 AAATAAACAAATAA
3490091 AAA
1 AAA
3490094 GTACATGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 2 0.08
13 12 0.48
14 11 0.44
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (14 bp):
AAATAAACAAATAA
Found at i:3490150 original size:13 final size:13
Alignment explanation
Indices: 3490134--3490175 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 13
3490124 AATACACATG
3490134 AATTTATATATAA
1 AATTTATATATAA
*
3490147 AATTTAGATTATAAA
1 AATTTATA-TAT-AA
3490162 AATTTATATA-AA
1 AATTTATATATAA
3490174 AA
1 AA
3490176 AATACATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 4 0.16
13 7 0.28
14 5 0.20
15 9 0.36
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
AATTTATATATAA
Found at i:3490459 original size:19 final size:18
Alignment explanation
Indices: 3490423--3490461 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3490413 AATATCAGTT
* *
3490423 TAAAAAAAATTATGTACA
1 TAAAAAAAATAATATACA
3490441 TAAAAAAAATAAATATACA
1 TAAAAAAAAT-AATATACA
3490460 TA
1 TA
3490462 TATATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (18 bp):
TAAAAAAAATAATATACA
Found at i:3497972 original size:12 final size:12
Alignment explanation
Indices: 3497957--3497990 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
3497947 AATATTTCAT
3497957 AAAAAAAGGAAA
1 AAAAAAAGGAAA
3497969 AAAAAAA-GAAA
1 AAAAAAAGGAAA
3497980 AAGAAAAAGGA
1 AA-AAAAAGGA
3497991 GAGGTCAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 6 0.30
12 12 0.60
13 2 0.10
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAAAGGAAA
Found at i:3498885 original size:44 final size:45
Alignment explanation
Indices: 3498835--3499057 Score: 181
Period size: 44 Copynumber: 4.9 Consensus size: 45
3498825 CATTATGGAG
*
3498835 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGCCA-CT
1 AATCTTATCTCCCTGAAGTTGTAGTGAAGCAGATTGAAGCCAGCT
* *
3498879 AATCTTATAC-CCCTGAAGTTGTAGTG--GGATGAATTGAAGTCATCCTAGCA
1 AATCTTAT-CTCCCTGAAGTTGTAGTGAAGCA-G-ATTGAAG----CC-AGCT
* *
3498929 AATCTTATCTCCCTGAAGATGTAGTGGAGCA-AGTTGAAGCCA-CT
1 AATCTTATCTCCCTGAAGTTGTAGTGAAGCAGA-TTGAAGCCAGCT
* * * ** *
3498973 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCG
1 AATCTTATCTCCCTGAAGTTGTAGTGAAGCAGATTGAAGCCAGCT
* **
3499018 AATCTTATTTCCCTGAAGTTACAGTGGAA-CAGATTGAAGC
1 AATCTTATCTCCCTGAAGTTGTAGT-GAAGCAGATTGAAGC
3499058 TATAAATAAC
Statistics
Matches: 144, Mismatches: 19, Indels: 31
0.74 0.10 0.16
Matches are distributed among these distances:
42 2 0.01
43 1 0.01
44 66 0.46
45 34 0.24
46 4 0.03
48 2 0.01
49 3 0.02
50 30 0.21
52 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (45 bp):
AATCTTATCTCCCTGAAGTTGTAGTGAAGCAGATTGAAGCCAGCT
Found at i:3498943 original size:50 final size:49
Alignment explanation
Indices: 3498795--3499037 Score: 166
Period size: 44 Copynumber: 5.2 Consensus size: 49
3498785 AATCCTATAC
* * * *
3498795 CCCTAAAGTTGCAGTGGGATG-AATTGAAGTCATTATGGAGAATCTTATCT
1 CCCTGAAGTTGTAGTGGGATGCAATTGAAGTCACTA-GCA-AATCTTATCT
* * *
3498845 CCCTGAAGTTGCAGT--GAAGCAGATTGAAG-C-C-A-CTAATCTTATAC-
1 CCCTGAAGTTGTAGTGGGATGCA-ATTGAAGTCACTAGCAAATCTTAT-CT
3498889 CCCTGAAGTTGTAGTGGGATG-AATTGAAGTCATCCTAGCAAATCTTATCT
1 CCCTGAAGTTGTAGTGGGATGCAATTGAAGTCA--CTAGCAAATCTTATCT
* *
3498939 CCCTGAAGATGTAGT-GGA-GCAAGTTGAAGCCACTAG----TCTTATCT
1 CCCTGAAGTTGTAGTGGGATGCAA-TTGAAGTCACTAGCAAATCTTATCT
* * *
3498983 CCCTGAAGTTGTAGT-GGA-GCAGACTGAAG--A-TAGCGAATCTTATTT
1 CCCTGAAGTTGTAGTGGGATGCA-ATTGAAGTCACTAGCAAATCTTATCT
3499028 CCCTGAAGTT
1 CCCTGAAGTT
3499038 ACAGTGGAAC
Statistics
Matches: 161, Mismatches: 13, Indels: 43
0.74 0.06 0.20
Matches are distributed among these distances:
41 3 0.02
42 1 0.01
44 62 0.39
45 21 0.13
46 3 0.02
47 1 0.01
48 9 0.06
49 9 0.06
50 52 0.32
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (49 bp):
CCCTGAAGTTGTAGTGGGATGCAATTGAAGTCACTAGCAAATCTTATCT
Found at i:3498966 original size:94 final size:94
Alignment explanation
Indices: 3498775--3498999 Score: 296
Period size: 94 Copynumber: 2.4 Consensus size: 94
3498765 AACAGGTCAG
* * * * * *
3498775 TGAAACCACAAATCCTATACCCCTAAAGTTGCAGTGGGATGAATTGAAGTCATTATGGAGAATCT
1 TGAAGCCACTAATCTTATACCCCTGAAGTTGTAGTGGGATGAATTGAAGTCATTATGCAGAATCT
*
3498840 TATCTCCCTGAAGTTGCAGTGAAGCAGAT
66 TATCTCCCTGAAGATGCAGTGAAGCAGAT
3498869 TGAAGCCACTAATCTTATACCCCTGAAGTTGTAGTGGGATGAATTGAAGTCATCCTA-GCA-AAT
1 TGAAGCCACTAATCTTATACCCCTGAAGTTGTAGTGGGATGAATTGAAGTCAT--TATGCAGAAT
* *
3498932 CTTATCTCCCTGAAGATGTAGTGGAGCA-AGT
64 CTTATCTCCCTGAAGATGCAGTGAAGCAGA-T
*
3498963 TGAAGCCACTAGTCTTAT-CTCCCTGAAGTTGTAGTGG
1 TGAAGCCACTAATCTTATAC-CCCTGAAGTTGTAGTGG
3499000 AGCAGACTGA
Statistics
Matches: 117, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
93 2 0.02
94 111 0.95
95 2 0.02
96 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (94 bp):
TGAAGCCACTAATCTTATACCCCTGAAGTTGTAGTGGGATGAATTGAAGTCATTATGCAGAATCT
TATCTCCCTGAAGATGCAGTGAAGCAGAT
Found at i:3499523 original size:363 final size:366
Alignment explanation
Indices: 3498924--3499603 Score: 889
Period size: 363 Copynumber: 1.9 Consensus size: 366
3498914 GAAGTCATCC
* ** * * *
3498924 TAGCAAATCTTATCTCCCTGAAGATGTAGTGGAGCAAGTTGAAGCCACTAGTCTTATCTCCCTGA
1 TAGCAAACCTTATCTCCCTGAAGATACAGTGGAGCAAGTTGAAGACACAAGTCTCATCTCCCTGA
* * *
3498989 AGTTGTAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTACAGTGGAACAGATTG
66 AGTTATAGTGAAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTACAGTGGAACAAATTG
* * * * *
3499054 AAGCTATAAATAACAGATCTTATCTCTCTGAAGTTGCAATAGTGTAGATCATATAAAACTTTATC
131 AAGCTATAAATAACAAATCTTATCTCTCTAAAGTTGCAATAGAGCAGATCATATAAAACCTTATC
** * * *
3499119 TTTCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCAATCTTATATCCCTAAAGTTATAGTGGAGC
196 TCCCTAAAGTTGCAATGGAGCAGGTTGAAGATACAAATCTTATATCCCTAAAGTTATAGTGGAGC
* ** *
3499184 ATATTG-A-A-GCTATTAATCCTATCTCACTGAAGTTGCAGTGGAGCGGATTAAAACGATAAATC
261 AGATTGAAGAGGCTACAAATCCTATCTCACTGAAGTTGCAGTGGAGCAGATTAAAACGATAAATC
3499246 CTTTACCTCTAAGGCTGCAGTAGGTCGGATTAAATCTATCA
326 CTTTACCTCTAAGGCTGCAGTAGGTCGGATTAAATCTATCA
* * * * **
3499287 TAGCAAACCTTATCTCCTTGAAGTTACAGTGGAGCAGGTTGAAGATACAAGTCTCATCTCTGTGA
1 TAGCAAACCTTATCTCCCTGAAGATACAGTGGAGCAAGTTGAAGACACAAGTCTCATCTCCCTGA
* * * *
3499352 AGTTATAGTGAAGCAGATTGAAGATAGCGAATCTTATTTTCTTGAAGTTATAGTGGAACAAATTG
66 AGTTATAGTGAAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTACAGTGGAACAAATTG
* * *
3499417 AAGCTGTAAATAACAAATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCATATCAAACCTTATC
131 AAGCTATAAATAACAAATCTTATCTCTCTAAAGTTGCAATAGAGCAGATCATATAAAACCTTATC
* * * * * * * * * *
3499482 TCCCTAAAGTTGCAATGGAGTAGGTTGGAGTTGCAAATCTTATCTTCTTGAAGTTGTAGTGGGGC
196 TCCCTAAAGTTGCAATGGAGCAGGTTGAAGATACAAATCTTATATCCCTAAAGTTATAGTGGAGC
* *
3499547 AGATTGAAGACGGGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
261 AGATTGAAGA--GGCTACAAATCCTATCTCACTGAAGTTGCAGTGGAGCAGATTAAA
3499604 GCCGCAAACC
Statistics
Matches: 264, Mismatches: 48, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
363 223 0.84
364 1 0.00
365 1 0.00
368 39 0.15
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (366 bp):
TAGCAAACCTTATCTCCCTGAAGATACAGTGGAGCAAGTTGAAGACACAAGTCTCATCTCCCTGA
AGTTATAGTGAAGCAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTACAGTGGAACAAATTG
AAGCTATAAATAACAAATCTTATCTCTCTAAAGTTGCAATAGAGCAGATCATATAAAACCTTATC
TCCCTAAAGTTGCAATGGAGCAGGTTGAAGATACAAATCTTATATCCCTAAAGTTATAGTGGAGC
AGATTGAAGAGGCTACAAATCCTATCTCACTGAAGTTGCAGTGGAGCAGATTAAAACGATAAATC
CTTTACCTCTAAGGCTGCAGTAGGTCGGATTAAATCTATCA
Found at i:3499632 original size:44 final size:44
Alignment explanation
Indices: 3499430--3499641 Score: 162
Period size: 44 Copynumber: 4.8 Consensus size: 44
3499420 CTGTAAATAA
* * *
3499430 CAAATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCATA--T-
1 CAAATCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTAAAGCTG
* * * * * ** *
3499471 CAAACCTTATCTCCCTAAAGTTGCAATGGAGTAGGTTGGAGTTG
1 CAAATCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTAAAGCTG
* * * *
3499515 CAAATCTTATCT-TCTTGAAGTTGTAGTGGGGCAGATTGAAGACGGGCTA
1 CAAATCTTATCTCTC-TAAAGTTGCAGTGGAGCAGATT-AA-A---GCTG
* * *
3499564 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCG
1 CAAATCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTAAAGCTG
* *
3499608 CAAACCTTATCTCTCTAAAGTTGCAGTAGAGCAG
1 CAAATCTTATCTCTCTAAAGTTGCAGTGGAGCAG
3499642 GTTACAAATT
Statistics
Matches: 131, Mismatches: 30, Indels: 17
0.74 0.17 0.10
Matches are distributed among these distances:
41 31 0.24
43 2 0.02
44 59 0.45
46 1 0.01
47 1 0.01
48 2 0.02
49 34 0.26
50 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (44 bp):
CAAATCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTAAAGCTG
Found at i:3499738 original size:41 final size:41
Alignment explanation
Indices: 3499681--3499778 Score: 162
Period size: 41 Copynumber: 2.4 Consensus size: 41
3499671 ATTACAGATA
* *
3499681 TTATCTCTCTGAAGTTGTAGTAGAGCAGATCATATCAAACC
1 TTATCTCTCTGAAGTTGTAGTAGAGCAGATCAGAGCAAACC
3499722 TTATCTCTCTGAAGTTGTAGTAGAGCAGATCAGAGCAAACC
1 TTATCTCTCTGAAGTTGTAGTAGAGCAGATCAGAGCAAACC
3499763 TTATCTC-CTTGAAGTT
1 TTATCTCTC-TGAAGTT
3499779 ACAGTGGAGT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
40 1 0.02
41 53 0.98
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (41 bp):
TTATCTCTCTGAAGTTGTAGTAGAGCAGATCAGAGCAAACC
Found at i:3499920 original size:44 final size:42
Alignment explanation
Indices: 3499762--3499929 Score: 142
Period size: 44 Copynumber: 3.9 Consensus size: 42
3499752 CAGAGCAAAC
* * * *
3499762 CTTATCTCCTTGAAGTTACAGTGGAGTAGGTTGAATATACCAAT
1 CTTATCTCC-TAAAGTTACAGTGGAGCAGATTGAAAATA-CAAT
* **
3499806 CTTATCTCCCTAAAGTTGCAGTGGAGCTTATT-AAAATTACAAGT
1 CTTATCT-CCTAAAGTTACAGTGGAGCAGATTGAAAA-TACAA-T
*
3499850 CTTATCTCTCTAAAGTTACAGTGGAGCAGATTGAAGATAACTAAT
1 CTTATCTC-CTAAAGTTACAGTGGAGCAGATTGAAAAT-AC-AAT
* * * *
3499895 CCTATCTCCTGAAGTTGCAGTGGAGCGGATT-AAAA
1 CTTATCTCCTAAAGTTACAGTGGAGCAGATTGAAAA
3499930 CGATGAATCC
Statistics
Matches: 101, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
43 10 0.10
44 74 0.73
45 15 0.15
46 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (42 bp):
CTTATCTCCTAAAGTTACAGTGGAGCAGATTGAAAATACAAT
Found at i:3499954 original size:88 final size:88
Alignment explanation
Indices: 3499764--3499959 Score: 202
Period size: 88 Copynumber: 2.2 Consensus size: 88
3499754 GAGCAAACCT
* * * *
3499764 TATCTC-CTTGAAGTTACAGTGGAGTAGGTTGAATATACCAATCTTATCTCCCTAAAGTTGCAGT
1 TATCTCTC-TGAAGTTACAGTGGAGCAGATTGAAGATACCAATCCTATCTCCCTAAAGTTGCAGT
** ** *
3499828 GGAGCTTATTAAAATTACAAGTCT
65 GGAGCGGATTAAAACGACAAGTCC
* * *
3499852 TATCTCTCTAAAGTTACAGTGGAGCAGATTGAAGATAACTAATCCTATCT-CCTGAAGTTGCAGT
1 TATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGAT-ACCAATCCTATCTCCCTAAAGTTGCAGT
*
3499916 GGAGCGGATTAAAACGATGAA-TCC
65 GGAGCGGATTAAAACGA-CAAGTCC
*
3499940 TATAC-CTCTGAAGTTGCAGT
1 TAT-CTCTCTGAAGTTACAGT
3499960 AGGTTGGATT
Statistics
Matches: 89, Mismatches: 15, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
88 74 0.83
89 15 0.17
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (88 bp):
TATCTCTCTGAAGTTACAGTGGAGCAGATTGAAGATACCAATCCTATCTCCCTAAAGTTGCAGTG
GAGCGGATTAAAACGACAAGTCC
Found at i:3505001 original size:27 final size:27
Alignment explanation
Indices: 3504962--3505027 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
3504952 TGAAACTGAT
3504962 ATAAAATGACTGTTATGCCCCCATGTG
1 ATAAAATGACTGTTATGCCCCCATGTG
* * *
3504989 GTAAAATGACTGTTATGCCCCTATGTT
1 ATAAAATGACTGTTATGCCCCCATGTG
3505016 ATAAAATGACTG
1 ATAAAATGACTG
3505028 CATGCTCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (27 bp):
ATAAAATGACTGTTATGCCCCCATGTG
Found at i:3505340 original size:6 final size:6
Alignment explanation
Indices: 3505329--3505362 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
3505319 TAAGGCCCAC
*
3505329 ACTGAT ACTGAT ATTGAT ACTGAT ACTGAT ACTG
1 ACTGAT ACTGAT ACTGAT ACTGAT ACTGAT ACTG
3505363 TATTGGGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (6 bp):
ACTGAT
Found at i:3505348 original size:12 final size:12
Alignment explanation
Indices: 3505331--3505367 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
3505321 AGGCCCACAC
3505331 TGATACTGATAT
1 TGATACTGATAT
*
3505343 TGATACTGATAC
1 TGATACTGATAT
3505355 TGATACTG-TAT
1 TGATACTGATAT
3505366 TG
1 TG
3505368 GGCAAAGGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 4 0.17
12 19 0.83
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (12 bp):
TGATACTGATAT
Found at i:3515588 original size:21 final size:21
Alignment explanation
Indices: 3515557--3515598 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3515547 AAAATTATAA
3515557 TTATAAATTTTTATAACTTTTT
1 TTATAAATTTTTATAA-TTTTT
*
3515579 TTAT-AATTTTTGTAATTTTT
1 TTATAAATTTTTATAATTTTT
3515599 AATAGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 10 0.53
22 4 0.21
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATAAATTTTTATAATTTTT
Found at i:3515607 original size:19 final size:18
Alignment explanation
Indices: 3515575--3515615 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
3515565 TTTTATAACT
*
3515575 TTTTTTATAATTTTTGTAA
1 TTTTTAATAATTTTT-TAA
*
3515594 TTTTTAATAGTTTTTTAA
1 TTTTTAATAATTTTTTAA
3515612 TTTT
1 TTTT
3515616 AAAATGGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (18 bp):
TTTTTAATAATTTTTTAA
Found at i:3516751 original size:9 final size:9
Alignment explanation
Indices: 3516716--3516757 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
3516706 CCACATCAAG
3516716 AAATAATTTA
1 AAAT-ATTTA
3516726 AAAT-TTATA
1 AAATATT-TA
3516735 AAAGTATTTA
1 AAA-TATTTA
3516745 AAATATTTA
1 AAATATTTA
3516754 AAAT
1 AAAT
3516758 TAAAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 2 0.07
9 15 0.52
10 10 0.34
11 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (9 bp):
AAATATTTA
Found at i:3524064 original size:46 final size:46
Alignment explanation
Indices: 3523893--3524063 Score: 200
Period size: 46 Copynumber: 3.7 Consensus size: 46
3523883 AGTAAGTTAC
* * *
3523893 CTCTACTAACAGTTCGTGGGATCGAATGATAAAAGAACTCGATACGA
1 CTCTACTAACAGCTCGTGGGATCGAATGGTAAAA-AACTCGATACTA
* * * *
3523940 CTCTATTAACAGCTCGTGGAATTGAATGGTAAAAAACTCAATACTA
1 CTCTACTAACAGCTCGTGGGATCGAATGGTAAAAAACTCGATACTA
** * * *
3523986 CTCTACTAGTAGCTCGTGGGATCAAATGGTAAGAAACTCGATGCTA
1 CTCTACTAACAGCTCGTGGGATCGAATGGTAAAAAACTCGATACTA
*
3524032 CTCTACTAACCA-CTCGTGAGATCGAATGGTAA
1 CTCTACTAA-CAGCTCGTGGGATCGAATGGTAA
3524064 GTAGCTCGAC
Statistics
Matches: 103, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
46 73 0.71
47 30 0.29
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (46 bp):
CTCTACTAACAGCTCGTGGGATCGAATGGTAAAAAACTCGATACTA
Found at i:3536351 original size:39 final size:39
Alignment explanation
Indices: 3536308--3536394 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
3536298 GAACACTTAA
*
3536308 ACTTACCCCATGATACTTCTTGAAGTTATATAATTAACG
1 ACTTACCCCATGATACTTCTTGAAGTTATATAAATAACG
*
3536347 ACTTACCCCATGATACTTCTTGAAGTTATATAAATAATG
1 ACTTACCCCATGATACTTCTTGAAGTTATATAAATAACG
3536386 ACTTACCCC
1 ACTTACCCC
3536395 TCCTCCACAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.34
Consensus pattern (39 bp):
ACTTACCCCATGATACTTCTTGAAGTTATATAAATAACG
Found at i:3549428 original size:11 final size:11
Alignment explanation
Indices: 3549412--3549439 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3549402 TTACATTCGT
3549412 ATCATAAATCA
1 ATCATAAATCA
3549423 ATCATAAATCA
1 ATCATAAATCA
3549434 ATCATA
1 ATCATA
3549440 TTGTCCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.29
Consensus pattern (11 bp):
ATCATAAATCA
Found at i:3552917 original size:26 final size:27
Alignment explanation
Indices: 3552888--3552939 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
3552878 ACCAATGATC
*
3552888 CGGG-GAATCAGCACTTAGCAACCCCT
1 CGGGAGAATCAACACTTAGCAACCCCT
3552914 CGGGAGAATCAACACTTAGCAACCCC
1 CGGGAGAATCAACACTTAGCAACCCC
3552940 CTTCACATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.31, C:0.35, G:0.21, T:0.13
Consensus pattern (27 bp):
CGGGAGAATCAACACTTAGCAACCCCT
Found at i:3552978 original size:42 final size:42
Alignment explanation
Indices: 3552919--3553054 Score: 146
Period size: 42 Copynumber: 3.5 Consensus size: 42
3552909 CCCCTCGGGA
3552919 GAATCAACACTTAGCAACCCCCTTCACATTTAAGATACGGTG
1 GAATCAACACTTAGCAACCCCCTTCACATTTAAGATACGGTG
* * * *
3552961 GAATCAGCACTTTGCAA-CCAC--CA-A--TGAG-T-CGG-G
1 GAATCAACACTTAGCAACCCCCTTCACATTTAAGATACGGTG
* *
3552994 GAATCAACACTTAGCAACCCCTTTCACATTTAATATACGGTG
1 GAATCAACACTTAGCAACCCCCTTCACATTTAAGATACGGTG
*
3553036 GAATCAGCACTTAGCAACC
1 GAATCAACACTTAGCAACC
3553055 ACCAATGAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
33 16 0.22
34 5 0.07
35 1 0.01
36 5 0.07
37 1 0.01
38 1 0.01
39 4 0.05
40 1 0.01
41 6 0.08
42 34 0.46
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (42 bp):
GAATCAACACTTAGCAACCCCCTTCACATTTAAGATACGGTG
Found at i:3553090 original size:75 final size:75
Alignment explanation
Indices: 3552913--3553091 Score: 295
Period size: 75 Copynumber: 2.4 Consensus size: 75
3552903 TAGCAACCCC
* *
3552913 TCGGGAGAATCAACACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTTGCAA
1 TCGGG-GAATCAACACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAA
*
3552978 CCACCAATGAG
65 CCACCAATGAA
*
3552989 TCGGGGAATCAACACTTAGCAACCCCTTTCACATTTAATATACGGTGGAATCAGCACTTAGCAAC
1 TCGGGGAATCAACACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAAC
3553054 CACCAATGAA
66 CACCAATGAA
* *
3553064 TCGGGGAATCAGCACATAGCAACCCCTT
1 TCGGGGAATCAACACTTAGCAACCCCTT
3553092 GGGGGAATCA
Statistics
Matches: 97, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
75 92 0.95
76 5 0.05
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (75 bp):
TCGGGGAATCAACACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAAC
CACCAATGAA
Found at i:3555298 original size:25 final size:24
Alignment explanation
Indices: 3555270--3555365 Score: 93
Period size: 25 Copynumber: 3.9 Consensus size: 24
3555260 GAAACTCCGG
*
3555270 AGAGCCATTAATCAGTAAGCTCCTA
1 AGAGCCATT-ATCAGGAAGCTCCTA
* *
3555295 AGAGCCAGTTATCGGGAAGCTCCGA
1 AGAGCCA-TTATCAGGAAGCTCCTA
* *
3555320 AGAGCCAATTATTAGGAAGCTCATA
1 AGAGCC-ATTATCAGGAAGCTCCTA
* * *
3555345 AGAGTCATAATCGGGAAGCTC
1 AGAGCCATTATCAGGAAGCTC
3555366 GCAAGAACCA
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
24 12 0.21
25 43 0.74
26 3 0.05
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (24 bp):
AGAGCCATTATCAGGAAGCTCCTA
Found at i:3555324 original size:50 final size:49
Alignment explanation
Indices: 3555258--3555365 Score: 128
Period size: 50 Copynumber: 2.2 Consensus size: 49
3555248 AGCCAATATA
* * * * *
3555258 GGGAAACTCCGGAGAGCC-ATTAATCAGTAAGCTCCTAAGAGCCAGTTATC
1 GGGAAGCTCCGAAGAGCCAATT-ATCAGGAAGCTCATAAGAGCCA-TAATC
* *
3555308 GGGAAGCTCCGAAGAGCCAATTATTAGGAAGCTCATAAGAGTCATAATC
1 GGGAAGCTCCGAAGAGCCAATTATCAGGAAGCTCATAAGAGCCATAATC
3555357 GGGAAGCTC
1 GGGAAGCTC
3555366 GCAAGAACCA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
49 13 0.26
50 34 0.68
51 3 0.06
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.19
Consensus pattern (49 bp):
GGGAAGCTCCGAAGAGCCAATTATCAGGAAGCTCATAAGAGCCATAATC
Found at i:3559007 original size:36 final size:36
Alignment explanation
Indices: 3558960--3559241 Score: 268
Period size: 36 Copynumber: 7.8 Consensus size: 36
3558950 GCCAGCAGAA
* * * * *
3558960 CGGCCAGACCCTGCACCATTGCTTGCGCCAACAGGC
1 CGGCCAGACCCAGTACCATTGCTAGCACCACCAGGC
* * * *
3558996 CGGCCAGACCCTGCACCATTGCTAGCAGCACCAGCC
1 CGGCCAGACCCAGTACCATTGCTAGCACCACCAGGC
* * *
3559032 CGGCCAGGA-CCAGAACCACTGTTAGCACCACCAGGC
1 CGGCCA-GACCCAGTACCATTGCTAGCACCACCAGGC
* * *
3559068 CGACCAGGCCCAGTACCATTGCTTA-CACCACCAGGT
1 CGGCCAGACCCAGTACCATTGC-TAGCACCACCAGGC
* * *
3559104 CGGCTAGGCCCGGTACCATTGCTAGCACCACCAGGC
1 CGGCCAGACCCAGTACCATTGCTAGCACCACCAGGC
*
3559140 CGGCCAGGCCCCA-TACCATTGCTAGCACCACCAGGC
1 CGGCCA-GACCCAGTACCATTGCTAGCACCACCAGGC
* *
3559176 CGGCCAGGCCCCA-TACCATTGCTAACACCACCAGGC
1 CGGCCA-GACCCAGTACCATTGCTAGCACCACCAGGC
* * *
3559212 CGGCCTGGCCCCA-TACCATTGCTAACACCA
1 CGGCC-AGACCCAGTACCATTGCTAGCACCA
3559242 TGCTGCTTTC
Statistics
Matches: 214, Mismatches: 26, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
35 3 0.01
36 203 0.95
37 8 0.04
ACGTcount: A:0.23, C:0.42, G:0.22, T:0.13
Consensus pattern (36 bp):
CGGCCAGACCCAGTACCATTGCTAGCACCACCAGGC
Found at i:3559086 original size:72 final size:72
Alignment explanation
Indices: 3558960--3559241 Score: 309
Period size: 72 Copynumber: 3.9 Consensus size: 72
3558950 GCCAGCAGAA
* * * * * * * *** *
3558960 CGGCCAGACCCTGCACCATTGCTTGCGCCAACAGGCCGGCCAGACCCTGCACCATTGCTAGCAGC
1 CGGCCAGGCCCAGTACCATTGCTAGCACCACCAGGCCGGCCAGGCCCCATACCATTGCTAGCACC
*
3559025 ACCAGCC
66 ACCAGGC
* * * * *
3559032 CGGCCAGGACCAGAACCACTGTTAGCACCACCAGGCCGACCAGG-CCCAGTACCATTGCTTA-CA
1 CGGCCAGGCCCAGTACCATTGCTAGCACCACCAGGCCGGCCAGGCCCCA-TACCATTGC-TAGCA
*
3559095 CCACCAGGT
64 CCACCAGGC
* *
3559104 CGGCTAGGCCCGGTACCATTGCTAGCACCACCAGGCCGGCCAGGCCCCATACCATTGCTAGCACC
1 CGGCCAGGCCCAGTACCATTGCTAGCACCACCAGGCCGGCCAGGCCCCATACCATTGCTAGCACC
3559169 ACCAGGC
66 ACCAGGC
* * *
3559176 CGGCCAGGCCCCA-TACCATTGCTAACACCACCAGGCCGGCCTGGCCCCATACCATTGCTAACAC
1 CGGCCAGG-CCCAGTACCATTGCTAGCACCACCAGGCCGGCCAGGCCCCATACCATTGCTAGCAC
3559240 CA
65 CA
3559242 TGCTGCTTTC
Statistics
Matches: 175, Mismatches: 30, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
71 4 0.02
72 162 0.93
73 9 0.05
ACGTcount: A:0.23, C:0.42, G:0.22, T:0.13
Consensus pattern (72 bp):
CGGCCAGGCCCAGTACCATTGCTAGCACCACCAGGCCGGCCAGGCCCCATACCATTGCTAGCACC
ACCAGGC
Found at i:3559166 original size:108 final size:108
Alignment explanation
Indices: 3558974--3559241 Score: 317
Period size: 108 Copynumber: 2.5 Consensus size: 108
3558964 CAGACCCTGC
* * * * * * * *
3558974 ACCATTGCTTGCGCCAACAGGCCGGCCAGACCCTGCACCATTGCTAGCAGCACCAGCCCGGCCAG
1 ACCATTGCTTACACCACCAGGCCGGCTAGGCCCCGTACCATTGCTAGCACCACCAGCCCGGCCAG
*
3559039 GACCAGAACCACTGTTAGCACCACCAGGCCGACCAGG-CCCAGT
66 GACCAGAACCACTGCTAGCACCACCAGGCCGACCAGGCCCCA-T
* * *
3559082 ACCATTGCTTACACCACCAGGTCGGCTAGGCCCGGTACCATTGCTAGCACCACCAGGCCGGCCAG
1 ACCATTGCTTACACCACCAGGCCGGCTAGGCCCCGTACCATTGCTAGCACCACCAGCCCGGCCAG
* * * *
3559147 GCCCCA-TACCATTGCTAGCACCACCAGGCCGGCCAGGCCCCAT
66 G-ACCAGAACCACTGCTAGCACCACCAGGCCGACCAGGCCCCAT
* * *
3559190 ACCATTGCTAACACCACCAGGCCGGCCT-GGCCCCATACCATTGCTAACACCA
1 ACCATTGCTTACACCACCAGGCCGG-CTAGGCCCCGTACCATTGCTAGCACCA
3559242 TGCTGCTTTC
Statistics
Matches: 137, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
108 128 0.93
109 9 0.07
ACGTcount: A:0.24, C:0.41, G:0.22, T:0.13
Consensus pattern (108 bp):
ACCATTGCTTACACCACCAGGCCGGCTAGGCCCCGTACCATTGCTAGCACCACCAGCCCGGCCAG
GACCAGAACCACTGCTAGCACCACCAGGCCGACCAGGCCCCAT
Found at i:3562704 original size:10 final size:9
Alignment explanation
Indices: 3562652--3562709 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
3562642 TAGAATTTTT
3562652 TTATAAAAA
1 TTATAAAAA
3562661 TTAT-AAAA
1 TTATAAAAA
*
3562669 TATATAGAAA
1 T-TATAAAAA
*
3562679 -TAT-AAAT
1 TTATAAAAA
3562686 TTCATAAAAAA
1 TT-AT-AAAAA
3562697 TTATAAAAA
1 TTATAAAAA
3562706 TTAT
1 TTAT
3562710 TATACCAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
7 2 0.05
8 9 0.23
9 18 0.46
10 5 0.13
11 5 0.13
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (9 bp):
TTATAAAAA
Found at i:3562757 original size:10 final size:9
Alignment explanation
Indices: 3562736--3562776 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
3562726 TTTTATAATT
*
3562736 TTTTTATAA
1 TTTTTATTA
3562745 TTTTTATTGA
1 TTTTTATT-A
3562755 TTTTTATT-
1 TTTTTATTA
3562763 TTTTTATTA
1 TTTTTATTA
3562772 TTTTT
1 TTTTT
3562777 CATCACATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 8 0.28
9 12 0.41
10 9 0.31
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (9 bp):
TTTTTATTA
Found at i:3562872 original size:29 final size:29
Alignment explanation
Indices: 3562841--3562906 Score: 123
Period size: 29 Copynumber: 2.2 Consensus size: 29
3562831 GGTCGTTAAA
3562841 TTTTTATTGATTTTTATAAAATTTTATAAT
1 TTTTTA-TGATTTTTATAAAATTTTATAAT
3562871 TTTTTATGATTTTTATAAAATTTTATAAT
1 TTTTTATGATTTTTATAAAATTTTATAAT
3562900 TTTTTAT
1 TTTTTAT
3562907 TTTTACTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 30 0.83
30 6 0.17
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (29 bp):
TTTTTATGATTTTTATAAAATTTTATAAT
Found at i:3562883 original size:9 final size:9
Alignment explanation
Indices: 3562839--3562923 Score: 68
Period size: 10 Copynumber: 9.2 Consensus size: 9
3562829 GAGGTCGTTA
3562839 AATTTTTATT
1 AATTTTTA-T
*
3562849 GATTTTTAT
1 AATTTTTAT
*
3562858 AAAATTTTAT
1 -AATTTTTAT
3562868 AATTTTTTAT
1 AA-TTTTTAT
*
3562878 GATTTTTAT
1 AATTTTTAT
*
3562887 AAAATTTTAT
1 -AATTTTTAT
3562897 AATTTTT-T
1 AATTTTTAT
3562905 -ATTTTTACT
1 AATTTTTA-T
3562914 -ATTTTTAT
1 AATTTTTAT
3562922 AA
1 AA
3562924 AAAAATTCTA
Statistics
Matches: 61, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
7 6 0.10
8 2 0.03
9 25 0.41
10 28 0.46
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (9 bp):
AATTTTTAT
Found at i:3562904 original size:10 final size:10
Alignment explanation
Indices: 3562837--3562906 Score: 70
Period size: 10 Copynumber: 7.1 Consensus size: 10
3562827 TAGAGGTCGT
3562837 TAAATTTTTA
1 TAAATTTTTA
**
3562847 TTGATTTTTA
1 TAAATTTTTA
*
3562857 TAAAATTTTA
1 TAAATTTTTA
*
3562867 TAATTTTTTA
1 TAAATTTTTA
*
3562877 T-GATTTTTA
1 TAAATTTTTA
*
3562886 TAAAATTTTA
1 TAAATTTTTA
*
3562896 TAATTTTTTA
1 TAAATTTTTA
3562906 T
1 T
3562907 TTTTACTATT
Statistics
Matches: 46, Mismatches: 13, Indels: 2
0.75 0.21 0.03
Matches are distributed among these distances:
9 7 0.15
10 39 0.85
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (10 bp):
TAAATTTTTA
Found at i:3568641 original size:14 final size:14
Alignment explanation
Indices: 3568603--3568645 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
3568593 CAAAATGTAC
3568603 AATATAATTAAA-T
1 AATATAATTAAATT
3568616 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
3568631 AA-ATAATTTAATT
1 AATATAATTAAATT
3568644 AA
1 AA
3568646 CTGATTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:3570445 original size:14 final size:15
Alignment explanation
Indices: 3570414--3570446 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3570404 GGATTTTATA
*
3570414 TTTTATATTGTTTTG
1 TTTTATATTGTCTTG
3570429 TTTTATATT-TCTTG
1 TTTTATATTGTCTTG
3570443 TTTT
1 TTTT
3570447 GAATCTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.76
Consensus pattern (15 bp):
TTTTATATTGTCTTG
Found at i:3572456 original size:13 final size:13
Alignment explanation
Indices: 3572419--3572469 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
3572409 TTCTTCATTA
3572419 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
*
3572432 C-TGTGAAAAAGTG
1 CTTTTG-AAAAGTG
* *
3572445 TTTTTGAGAAGTG
1 CTTTTGAAAAGTG
3572458 CTTTTGAAAAGT
1 CTTTTGAAAAGT
3572470 TTGGTTTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
12 3 0.10
13 24 0.80
14 3 0.10
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.37
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:3578765 original size:6 final size:6
Alignment explanation
Indices: 3578754--3578779 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3578744 TTTATTTTAT
3578754 AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
3578780 CGGACTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:3582793 original size:18 final size:18
Alignment explanation
Indices: 3582770--3582822 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
3582760 AATATATTTT
3582770 TTATTTTTAATTTTAAAA
1 TTATTTTTAATTTTAAAA
*
3582788 TTATTTTTTATTTTTAAAA
1 TTA-TTTTTAATTTTAAAA
*
3582807 TAATTTTTAATGTTTA
1 TTATTTTTAAT-TTTA
3582823 TTTTAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 10 0.33
19 20 0.67
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTATTTTTAATTTTAAAA
Found at i:3589477 original size:14 final size:16
Alignment explanation
Indices: 3589446--3589477 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3589436 TAAACACCAT
3589446 TAAAAATATTAGAAAA
1 TAAAAATATTAGAAAA
3589462 TAAAAAT-TTA-AAAA
1 TAAAAATATTAGAAAA
3589476 TA
1 TA
3589478 TAATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 3 0.19
16 7 0.44
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (16 bp):
TAAAAATATTAGAAAA
Found at i:3589512 original size:14 final size:16
Alignment explanation
Indices: 3589473--3589512 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
3589463 AAAAATTTAA
*
3589473 AAATATAATATATAAT
1 AAATTTAATATATAAT
3589489 AAATTT-ATATA-AAT
1 AAATTTAATATATAAT
3589503 -AATTTAATAT
1 AAATTTAATAT
3589513 TAAAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 5 0.23
14 7 0.32
15 5 0.23
16 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATTTAATATATAAT
Found at i:3600807 original size:2 final size:2
Alignment explanation
Indices: 3600795--3600827 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3600785 TAAAGTTAAG
3600795 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3600828 GGAGGAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3600855 original size:17 final size:17
Alignment explanation
Indices: 3600833--3600875 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3600823 ATATAGGAGG
3600833 AAAT-AGTGATACAATGA
1 AAATAAGTGATA-AATGA
3600850 AAATAGAGTGATAAATGA
1 AAATA-AGTGATAAATGA
*
3600868 AATTAAGT
1 AAATAAGT
3600876 AAAATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 7 0.30
18 9 0.39
19 7 0.30
ACGTcount: A:0.53, C:0.02, G:0.19, T:0.26
Consensus pattern (17 bp):
AAATAAGTGATAAATGA
Found at i:3601242 original size:14 final size:14
Alignment explanation
Indices: 3601223--3601262 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3601213 TTGATTAGCA
3601223 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
3601237 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
3601251 GGAAAATGTTTT
1 GTAAAATGTTTT
3601263 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:3601275 original size:34 final size:35
Alignment explanation
Indices: 3601231--3601297 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
3601221 CAGTAAAATG
* *
3601231 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
3601265 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
3601298 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:3601284 original size:20 final size:20
Alignment explanation
Indices: 3601246--3601285 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3601236 CGTAAAATGA
**
3601246 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
3601266 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
3601286 GGAAAATATT
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:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:3604251 original size:22 final size:22
Alignment explanation
Indices: 3604226--3604271 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
3604216 GATCATAGTT
3604226 AATACAATACTTCAATTGGTGC
1 AATACAATACTTCAATTGGTGC
3604248 AATACAATACTTCAATTGGTGC
1 AATACAATACTTCAATTGGTGC
3604270 AA
1 AA
3604272 GAGTTTGTTA
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:0.39, C:0.17, G:0.13, T:0.30
Consensus pattern (22 bp):
AATACAATACTTCAATTGGTGC
Found at i:3604496 original size:71 final size:71
Alignment explanation
Indices: 3604344--3604496 Score: 170
Period size: 71 Copynumber: 2.1 Consensus size: 71
3604334 GTTTTAAATT
* *
3604344 ATAATATGTTTCATGTATTAAAGTTACCATGACTTAAAATATCTTTCATGTATTGTTATATATTG
1 ATAATATGTTT--T-TA-TAAAGTTACCATGACTTAAAATATATTTCATGTATTGTTATAAATTG
* *
3604409 ATCATAGTTA
62 ACCATACTTA
3604419 ATAATATGTTTTTATAAAGTTACCATGACTTAAAATATATTGATCATG-ATT-TTATAAAGTT-A
1 ATAATATGTTTTTATAAAGTTACCATGACTTAAAATATATT--TCATGTATTGTTATAAA-TTGA
3604481 CCATGACTTA
63 CCAT-ACTTA
3604491 A-AATAT
1 ATAATAT
3604497 ATTGCCCAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
71 41 0.59
72 12 0.17
73 6 0.09
75 11 0.16
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (71 bp):
ATAATATGTTTTTATAAAGTTACCATGACTTAAAATATATTTCATGTATTGTTATAAATTGACCA
TACTTA
Found at i:3604497 original size:23 final size:23
Alignment explanation
Indices: 3604431--3604497 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 23
3604421 AATATGTTTT
3604431 TATAAAGTTACCATGACTTAAAA
1 TATAAAGTTACCATGACTTAAAA
* *
3604454 TAT--A-TTGATCATGA-TT---T
1 TATAAAGTT-ACCATGACTTAAAA
3604471 TATAAAGTTACCATGACTTAAAA
1 TATAAAGTTACCATGACTTAAAA
3604494 TATA
1 TATA
3604498 TTGCCCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 16
0.62 0.08 0.31
Matches are distributed among these distances:
17 3 0.09
19 7 0.22
20 8 0.25
21 7 0.22
23 7 0.22
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.37
Consensus pattern (23 bp):
TATAAAGTTACCATGACTTAAAA
Found at i:3607588 original size:15 final size:14
Alignment explanation
Indices: 3607568--3607608 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
3607558 ATGTAAATGT
*
3607568 TTATAAATAGATAGA
1 TTATAAATAAATA-A
3607583 TTATAAATTAAATAA
1 TTATAAA-TAAATAA
3607598 TTATAAATAAA
1 TTATAAATAAA
3607609 CGATGATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 15 0.62
16 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (14 bp):
TTATAAATAAATAA
Found at i:3615767 original size:7 final size:7
Alignment explanation
Indices: 3615726--3615750 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3615716 AAATTTAGTT
3615726 TTTTATA
1 TTTTATA
3615733 TTTTATA
1 TTTTATA
3615740 TTTTATA
1 TTTTATA
3615747 TTTT
1 TTTT
3615751 TAGAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTATA
Found at i:3619675 original size:3 final size:3
Alignment explanation
Indices: 3619667--3619692 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3619657 CATGGCTTTC
3619667 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
3619693 TTTCTGGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:3620876 original size:20 final size:20
Alignment explanation
Indices: 3620853--3620909 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 20
3620843 AATATATTTT
3620853 TTTAAAAATATAATATTAAA
1 TTTAAAAATATAATATTAAA
3620873 TTT--AAATAT-AT-TT---
1 TTTAAAAATATAATATTAAA
*
3620886 TTTGAAAATATAATATTAAA
1 TTTAAAAATATAATATTAAA
3620906 TTTA
1 TTTA
3620910 TTATTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
13 3 0.10
15 6 0.21
16 4 0.14
17 4 0.14
18 6 0.21
20 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
TTTAAAAATATAATATTAAA
Found at i:3620907 original size:33 final size:34
Alignment explanation
Indices: 3620841--3620909 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 34
3620831 TAAATAAGAA
3620841 TAAATATATTTTTTTAAAAATATAATATTAAATT
1 TAAATATATTTTTTTAAAAATATAATATTAAATT
*
3620875 TAAATATA-TTTTTTGAAAATATAATATTAAATT
1 TAAATATATTTTTTTAAAAATATAATATTAAATT
3620908 TA
1 TA
3620910 TTATTTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 26 0.76
34 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (34 bp):
TAAATATATTTTTTTAAAAATATAATATTAAATT
Found at i:3620934 original size:6 final size:6
Alignment explanation
Indices: 3620925--3620950 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3620915 TTATTTTTAT
3620925 TTAATA TTAATA TTAATA TTAATA TT
1 TTAATA TTAATA TTAATA TTAATA TT
3620951 TATTATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTAATA
Found at i:3620961 original size:12 final size:12
Alignment explanation
Indices: 3620907--3620963 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
3620897 AATATTAAAT
3620907 TTATTAT-TTTA
1 TTATTATATTTA
3620918 TT-TT-TATTTA
1 TTATTATATTTA
*
3620928 ATATTA-ATATTA
1 TTATTATAT-TTA
*
3620940 ATATTAATATTTA
1 TTATT-ATATTTA
3620953 TTATTATATTT
1 TTATTATATTT
3620964 TTTTGAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
9 1 0.03
10 7 0.18
11 6 0.16
12 14 0.37
13 8 0.21
14 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTATTATATTTA
Found at i:3620976 original size:22 final size:23
Alignment explanation
Indices: 3620951--3620999 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
3620941 TATTAATATT
*
3620951 TATTAT-TATATTTTTTTGAAA-A
1 TATTATATATATTTCTTT-AAATA
3620973 TATT-TATATATTTCTTTAAATA
1 TATTATATATATTTCTTTAAATA
3620995 TATTA
1 TATTA
3621000 GAATTAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TATTATATATATTTCTTTAAATA
Found at i:3623139 original size:21 final size:22
Alignment explanation
Indices: 3623112--3623160 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3623102 CCATGTTATA
3623112 TTTTAT-AAAAATAATAT-ATT
1 TTTTATAAAAAATAATATAATT
*
3623132 TATTTATAAAAAATATTATAATT
1 T-TTTATAAAAAATAATATAATT
3623155 TTTTAT
1 TTTTAT
3623161 CATAACTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 5 0.20
22 15 0.60
23 4 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTATAAAAAATAATATAATT
Found at i:3629399 original size:21 final size:21
Alignment explanation
Indices: 3629348--3629399 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
3629338 TTCACTATTT
* * *
3629348 CTAATCTCACTGCTATGGTAT
1 CTAATCTCACCGCTATAGTAA
*
3629369 CCAATCTCACCGCTATAGTAA
1 CTAATCTCACCGCTATAGTAA
*
3629390 CTAATATCAC
1 CTAATCTCAC
3629400 AGCCATCGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.31
Consensus pattern (21 bp):
CTAATCTCACCGCTATAGTAA
Found at i:3638591 original size:16 final size:16
Alignment explanation
Indices: 3638547--3638593 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
3638537 CAATAAACAG
3638547 AACAAAAAAGAAAAATA
1 AACAAAAAA-AAAAATA
* *
3638564 AACCAAACAAAAAATA
1 AACAAAAAAAAAAATA
*
3638580 AGCAAAAAAAAAAA
1 AACAAAAAAAAAAA
3638594 CACGGAAGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.81, C:0.11, G:0.04, T:0.04
Consensus pattern (16 bp):
AACAAAAAAAAAAATA
Found at i:3638592 original size:15 final size:16
Alignment explanation
Indices: 3638551--3638592 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
3638541 AAACAGAACA
3638551 AAAAAGAAAAATAAACC
1 AAAAA-AAAAATAAACC
* *
3638568 AAACAAAAAAT-AAGC
1 AAAAAAAAAATAAACC
3638583 AAAAAAAAAA
1 AAAAAAAAAA
3638593 ACACGGAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 12 0.55
16 6 0.27
17 4 0.18
ACGTcount: A:0.81, C:0.10, G:0.05, T:0.05
Consensus pattern (16 bp):
AAAAAAAAAATAAACC
Found at i:3654813 original size:17 final size:17
Alignment explanation
Indices: 3654793--3654853 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
3654783 TTTTAAAATA
3654793 TTTTTAAAATACTTTTT
1 TTTTTAAAATACTTTTT
* * *
3654810 TTTTAAAAAT-GTTTTA
1 TTTTTAAAATACTTTTT
3654826 TTTTTAAAATACTTTTT
1 TTTTTAAAATACTTTTT
*
3654843 TATTTTTAAAT
1 T-TTTTAAAAT
3654854 TTTTTTTGGT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
16 13 0.37
17 14 0.40
18 8 0.23
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (17 bp):
TTTTTAAAATACTTTTT
Found at i:3654860 original size:19 final size:19
Alignment explanation
Indices: 3654791--3654852 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
3654781 TATTTTAAAA
3654791 TATTTTTAAAATAC--TTT
1 TATTTTTAAAATACTTTTT
*
3654808 T-TTTTTAAAA-A-TGTTT
1 TATTTTTAAAATACTTTTT
3654824 TATTTTTAAAATACTTTTT
1 TATTTTTAAAATACTTTTT
3654843 TATTTTTAAA
1 TATTTTTAAA
3654853 TTTTTTTTGG
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
15 1 0.03
16 13 0.33
17 10 0.26
18 1 0.03
19 14 0.36
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (19 bp):
TATTTTTAAAATACTTTTT
Found at i:3660619 original size:90 final size:90
Alignment explanation
Indices: 3660386--3660690 Score: 400
Period size: 90 Copynumber: 3.4 Consensus size: 90
3660376 CTAAAAACAA
* * *
3660386 CAGATCTTATTTTCCTGTATTGGCAGCGAAATAGATCGAAGATAGCAAGTATTGTCTTCCTGTAT
1 CAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCTGTAT
* ** * *
3660451 TGGTAGCAAAGTAGATTGAAGATAA
66 TGGCAGTGAAGTAGACTGAAGATAG
*
3660476 CATATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCTGTAT
1 CAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCTGTAT
3660541 TGGCAGTGAAGTAGACTGAAGATAG
66 TGGCAGTGAAGTAGACTGAAGATAG
* *
3660566 CAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCATA-TCTTGTCTCCCT-AA
1 CAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCA-AGTCTTGTCTTCCTGTA
*** * * *
3660629 ACAGCAGTGGAGTAG-GTCGAAGATTG
65 TTGGCAGTGAAGTAGACT-GAAGATAG
* *
3660655 TAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
1 CAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGAT
3660691 TGGAGATTGG
Statistics
Matches: 193, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
88 1 0.01
89 53 0.27
90 138 0.72
91 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (90 bp):
CAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCTGTAT
TGGCAGTGAAGTAGACTGAAGATAG
Found at i:3660699 original size:7 final size:7
Alignment explanation
Indices: 3660687--3660718 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
3660677 GCAGCGAAGT
3660687 AGATTGG
1 AGATTGG
3660694 AGATTGG
1 AGATTGG
3660701 AGATTGG
1 AGATTGG
*
3660708 AGATTGC
1 AGATTGG
3660715 AGAT
1 AGAT
3660719 CTTGTCTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.31, C:0.03, G:0.38, T:0.28
Consensus pattern (7 bp):
AGATTGG
Found at i:3660699 original size:45 final size:45
Alignment explanation
Indices: 3660386--3660690 Score: 348
Period size: 45 Copynumber: 6.8 Consensus size: 45
3660376 CTAAAAACAA
* * *
3660386 CAGATCTTATTTTCCTGTATTGGCAGCGAAATAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAG
* * * * *
3660431 CA-AGTATTGTCTTCCTGTATTGGTAGCAAAGTAGATTGAAGATAA
1 CAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAG
* *
3660476 CATATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAG
*
3660521 CA-AGTCTTGTCTTCCTGTATTGGCAGTGAAGTAGA-CTGAAGATAG
1 CAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAGATAG
*
3660566 CAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAG
* * * *** * * * *
3660611 CATATCTTGTCTCCCT-AAACAGCAGTGGAGTAGGTCGAAGATTG
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAG
*
3660655 TAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
1 CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
3660691 TGGAGATTGG
Statistics
Matches: 214, Mismatches: 39, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
44 36 0.17
45 175 0.82
46 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (45 bp):
CAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAG
Found at i:3660801 original size:45 final size:45
Alignment explanation
Indices: 3660737--3660825 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
3660727 CCTGTACTGA
3660737 TAGTGAAGCGGATAAAAAAAAACTA-ATCCTATCTCCCTGAAGTTG
1 TAGTGAAGCGGATAAAAAAAAA-TAGATCCTATCTCCCTGAAGTTG
* * * * *
3660782 TAGTGGAGCGGATTAAAAAACATAGATCTTATCTCTCTGAAGTT
1 TAGTGAAGCGGATAAAAAAAAATAGATCCTATCTCCCTGAAGTT
3660826 ACATTAGAGC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 2 0.05
45 36 0.95
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (45 bp):
TAGTGAAGCGGATAAAAAAAAATAGATCCTATCTCCCTGAAGTTG
Found at i:3663092 original size:106 final size:106
Alignment explanation
Indices: 3662868--3663093 Score: 344
Period size: 106 Copynumber: 2.1 Consensus size: 106
3662858 TACAAAAATG
*
3662868 AAAATTTCAAAGTAAGACAATATTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAACGTGCTGG
1 AAAATTTCAAAGTAAGACAATATTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAACGTGCTGG
* * * *
3662933 GTTTCGATTTCTCGTTTGACCAAATAGCTAAATATCCTTTT
66 GTTCCGATTTCTCGTTCGACCAAATAGCCAAATATCCTCTT
** * * *
3662974 AAGGTTTCAAAGTAAGGCAATATTTTGCGTTTGGAAATTCGGGAAAACATGCCCTAACGTGCTGG
1 AAAATTTCAAAGTAAGACAATATTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAACGTGCTGG
*
3663039 GTTCCGATTTCTTGTTCGACCAAATAGCCAAATATCCTCTT
66 GTTCCGATTTCTCGTTCGACCAAATAGCCAAATATCCTCTT
*
3663080 AAAATTTTAAAGTA
1 AAAATTTCAAAGTA
3663094 TGGGTTGTGG
Statistics
Matches: 106, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (106 bp):
AAAATTTCAAAGTAAGACAATATTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAACGTGCTGG
GTTCCGATTTCTCGTTCGACCAAATAGCCAAATATCCTCTT
Found at i:3668803 original size:20 final size:21
Alignment explanation
Indices: 3668764--3668803 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3668754 AGAAGTTTAA
*
3668764 AATGAAAATTTTTAATAGTTG
1 AATGAAAATTTGTAATAGTTG
*
3668785 AATGATAATTTGT-ATAGTT
1 AATGAAAATTTGTAATAGTT
3668804 TATCTTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (21 bp):
AATGAAAATTTGTAATAGTTG
Found at i:3672330 original size:30 final size:32
Alignment explanation
Indices: 3672285--3672345 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
3672275 AGATAGTATA
3672285 AAAAGTCAAATG-TTTTGCACT-TTATTTTTG
1 AAAAGTCAAATGTTTTTGCACTGTTATTTTTG
3672315 AAAA-TCAAATTGTTTTTGCACTGTTATTTTT
1 AAAAGTCAAA-TGTTTTTGCACTGTTATTTTT
3672346 ACCCTTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 5 0.18
30 6 0.21
31 9 0.32
32 8 0.29
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.49
Consensus pattern (32 bp):
AAAAGTCAAATGTTTTTGCACTGTTATTTTTG
Found at i:3675184 original size:33 final size:33
Alignment explanation
Indices: 3675142--3675205 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
3675132 GAGCTATGGC
* *
3675142 CATCTGGCGGACGAGAGGATGGCAAGTTGTGGA
1 CATCAGGCGGACAAGAGGATGGCAAGTTGTGGA
*
3675175 CATCAGGCGGACAAGGGGATGGCAAGTTGTG
1 CATCAGGCGGACAAGAGGATGGCAAGTTGTG
3675206 TAGATTTCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.25, C:0.16, G:0.42, T:0.17
Consensus pattern (33 bp):
CATCAGGCGGACAAGAGGATGGCAAGTTGTGGA
Found at i:3679993 original size:21 final size:21
Alignment explanation
Indices: 3679969--3680011 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3679959 GTGTAAACAT
3679969 ATTATTTCCTTTGAAGTTTAA
1 ATTATTTCCTTTGAAGTTTAA
3679990 ATTATTTCCTTTGAAGTTTAA
1 ATTATTTCCTTTGAAGTTTAA
3680011 A
1 A
3680012 ATAGTTCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.51
Consensus pattern (21 bp):
ATTATTTCCTTTGAAGTTTAA
Found at i:3681062 original size:3 final size:3
Alignment explanation
Indices: 3681054--3681118 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
3681044 AAAATTTTAA
3681054 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3681102 AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AA
3681119 ATGAGATATA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3683782 original size:39 final size:39
Alignment explanation
Indices: 3683728--3683806 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
3683718 TGATATTGAT
3683728 GTTAATTTTTTTGGGTATACTGATAGTAATTATGCAGGG
1 GTTAATTTTTTTGGGTATACTGATAGTAATTATGCAGGG
*
3683767 GTTAATTTTTTTGGGTATATTGATAGTAATTATGCAGGG
1 GTTAATTTTTTTGGGTATACTGATAGTAATTATGCAGGG
3683806 G
1 G
3683807 ATATTGATGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.25, C:0.04, G:0.27, T:0.44
Consensus pattern (39 bp):
GTTAATTTTTTTGGGTATACTGATAGTAATTATGCAGGG
Found at i:3690508 original size:17 final size:18
Alignment explanation
Indices: 3690486--3690519 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3690476 AAAACGAAAA
3690486 TTAAAA-AAATTAATTTT
1 TTAAAACAAATTAATTTT
3690503 TTAAAACAAATTAATTT
1 TTAAAACAAATTAATTT
3690520 ACTTAATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAAACAAATTAATTTT
Found at i:3696516 original size:19 final size:19
Alignment explanation
Indices: 3696492--3696529 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3696482 ATTAAATGAA
*
3696492 AGAAAAACATAGATAAAAG
1 AGAAAAACACAGATAAAAG
3696511 AGAAAAACACAGATAAAAG
1 AGAAAAACACAGATAAAAG
3696530 CAACAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (19 bp):
AGAAAAACACAGATAAAAG
Found at i:3700973 original size:13 final size:13
Alignment explanation
Indices: 3700957--3700996 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
3700947 TTTAAACCAA
3700957 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
3700970 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
3700983 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
3700996 A
1 A
3700997 ATGAAGAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:3708137 original size:60 final size:60
Alignment explanation
Indices: 3708063--3708231 Score: 257
Period size: 60 Copynumber: 2.8 Consensus size: 60
3708053 CTCCTTGAGT
3708063 CCACAACCACTGCTATTCACCATGCTTCCACAACCTCCGCCGCACCCACCACAGCCAGAG
1 CCACAACCACTGCTATTCACCATGCTTCCACAACCTCCGCCGCACCCACCACAGCCAGAG
* * *
3708123 CCACAGCCACTGCTATTCACCATGCTTCCGCAACCTCCGCCACACCCACCACAGCCAGAG
1 CCACAACCACTGCTATTCACCATGCTTCCACAACCTCCGCCGCACCCACCACAGCCAGAG
** * * * *
3708183 CCACAACTGCCGCTATTCACTATGCTTCCACAACCACCCCCGCACCCAC
1 CCACAACCACTGCTATTCACCATGCTTCCACAACCTCCGCCGCACCCAC
3708232 TACCGCAACC
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 97 1.00
ACGTcount: A:0.25, C:0.49, G:0.11, T:0.14
Consensus pattern (60 bp):
CCACAACCACTGCTATTCACCATGCTTCCACAACCTCCGCCGCACCCACCACAGCCAGAG
Done.