Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008154.1 Hibiscus syriacus cultivar Beakdansim tig00110720_pilon, whole genome shotgun sequence
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: 185899
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
File 1 of 2
Found at i:10418 original size:19 final size:19
Alignment explanation
Indices: 10396--10432 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10386 CCAGAATAAT
*
10396 GACCGGTAGCGTGAATAGC
1 GACCGGTAGCATGAATAGC
*
10415 GACCGGTGGCATGAATAG
1 GACCGGTAGCATGAATAG
10433 TAACTGATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.19, G:0.38, T:0.16
Consensus pattern (19 bp):
GACCGGTAGCATGAATAGC
Found at i:11077 original size:19 final size:18
Alignment explanation
Indices: 11027--11078 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
11017 TAGTACTTAA
11027 AATAAAATAAT-ATAATG
1 AATAAAATAATAATAATG
11044 AATAGAAAAACTAATAATAATG
1 AAT---AAAA-TAATAATAATG
11066 ACATAAAATAATA
1 A-ATAAAATAATA
11079 CCATTATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
17 3 0.10
19 5 0.17
20 8 0.28
21 4 0.14
22 7 0.24
23 2 0.07
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (18 bp):
AATAAAATAATAATAATG
Found at i:12107 original size:45 final size:45
Alignment explanation
Indices: 12047--12141 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 45
12037 TAATTATATC
* * * *
12047 TCTTTATATTGAAAGAATAAATTTTTTTGTTGTACATTATTTGTT
1 TCTTTAGATTGAAAGAATAAATTTGTGTGTTGTACATTATTTATT
* * *
12092 TCTTTAGATTTAAAGATTATATTTGTGTGTTGTACATTATTTATT
1 TCTTTAGATTGAAAGAATAAATTTGTGTGTTGTACATTATTTATT
12137 TCTTT
1 TCTTT
12142 TTATGCTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57
Consensus pattern (45 bp):
TCTTTAGATTGAAAGAATAAATTTGTGTGTTGTACATTATTTATT
Found at i:12921 original size:14 final size:16
Alignment explanation
Indices: 12904--12936 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12894 CATACATGCA
12904 TTTGCA-TTCT-CATT
1 TTTGCATTTCTGCATT
12918 TTTGCATTTCTGCATT
1 TTTGCATTTCTGCATT
12934 TTT
1 TTT
12937 TATATTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 4 0.24
16 7 0.41
ACGTcount: A:0.12, C:0.18, G:0.09, T:0.61
Consensus pattern (16 bp):
TTTGCATTTCTGCATT
Found at i:12979 original size:20 final size:20
Alignment explanation
Indices: 12956--13086 Score: 72
Period size: 20 Copynumber: 6.5 Consensus size: 20
12946 TTTACATTCA
12956 CATCTTTGCATTTGCATTTG
1 CATCTTTGCATTTGCATTTG
* * * *
12976 CATCTTTACGTTTGTATTTA
1 CATCTTTGCATTTGCATTTG
* **
12996 CAT-TTT-CATTTTACATTCA
1 CATCTTTGCA-TTTGCATTTG
*
13015 CATCTTTGCATTTGCATTCG
1 CATCTTTGCATTTGCATTTG
* * * *
13035 TATCTTTACGTTTGTATTT-
1 CATCTTTGCATTTGCATTTG
* *
13054 -ATATTTTCATTTTTTGCATTTG
1 CATCTTTGCA---TTTGCATTTG
13076 CATCTTTGCAT
1 CATCTTTGCAT
13087 AGTTATATTT
Statistics
Matches: 82, Mismatches: 21, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
18 7 0.09
19 13 0.16
20 45 0.55
21 10 0.12
23 7 0.09
ACGTcount: A:0.18, C:0.18, G:0.10, T:0.54
Consensus pattern (20 bp):
CATCTTTGCATTTGCATTTG
Found at i:12994 original size:26 final size:25
Alignment explanation
Indices: 12960--13009 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
12950 CATTCACATC
*
12960 TTTGCATTTGCATTTGCATCTTTACG
1 TTTGCATTTACATTTGCAT-TTTACG
* *
12986 TTTGTATTTACATTTTCATTTTAC
1 TTTGCATTTACATTTGCATTTTAC
13010 ATTCACATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.56
Consensus pattern (25 bp):
TTTGCATTTACATTTGCATTTTACG
Found at i:13012 original size:59 final size:59
Alignment explanation
Indices: 12941--13066 Score: 225
Period size: 59 Copynumber: 2.1 Consensus size: 59
12931 ATTTTTTATA
*
12941 TTCATTTTACATTCACATCTTTGCATTTGCATTTGCATCTTTACGTTTGTATTTACATT
1 TTCATTTTACATTCACATCTTTGCATTTGCATTCGCATCTTTACGTTTGTATTTACATT
* *
13000 TTCATTTTACATTCACATCTTTGCATTTGCATTCGTATCTTTACGTTTGTATTTATATT
1 TTCATTTTACATTCACATCTTTGCATTTGCATTCGCATCTTTACGTTTGTATTTACATT
13059 TTCATTTT
1 TTCATTTT
13067 TTGCATTTGC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.20, C:0.17, G:0.08, T:0.55
Consensus pattern (59 bp):
TTCATTTTACATTCACATCTTTGCATTTGCATTCGCATCTTTACGTTTGTATTTACATT
Found at i:21091 original size:117 final size:117
Alignment explanation
Indices: 20871--21092 Score: 256
Period size: 117 Copynumber: 1.9 Consensus size: 117
20861 CTTTCAAATC
* * *
20871 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATTCTTCTTCAAGATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAAATTT
* * *
20936 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATACATTTACGTTTCTAAAAGAAGTTTGTTTAATTT
* * * *
20988 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGACAA-CTCTAACTCCTT-TCTCAAAA
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGA-AAGCTCTAAATCCTTCT-TCAAAA
* *
21050 TTTCATTTTGATTTTCTAAATATAGTTTGAC-TTTC-AAAAGAAG
63 TTTCATTTTGATTTTCAAAATACA-TTT-ACGTTTCTAAAAGAAG
21093 ATTATTTTTA
Statistics
Matches: 88, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
116 2 0.02
117 76 0.86
118 9 0.10
119 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.48
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAAATTT
CATTTTGATTTTCAAAATACATTTACGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:25829 original size:61 final size:62
Alignment explanation
Indices: 25736--25973 Score: 263
Period size: 61 Copynumber: 3.9 Consensus size: 62
25726 GAATCAATTT
* *
25736 TTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCC-GTAGAGTCAATCC
1 TTGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTCCTGACTCC-CCAGTAGAGTCAATCC
* ** * *
25798 TTGACTT-CTCTTGAAGAGAAGTCAACATTTATTATTTTTTACTCCTCAGTAGAGTCAATCC
1 TTGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTCCTGACTCCCCAGTAGAGTCAATCC
* * *
25859 TTGAC-T-CTCGTGAAGA-AAGTCAACCTTTATTATTCCTGACTCCCCAGTTGAGTCAAAT-T
1 TTGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTCCTGACTCCCCAGTAGAGTC-AATCC
* * * * * * *
25918 TTAACTTCCTCATTAAGAGAGGCCAACATTTGTTATTCCTGACTCCCCGGTAGAGT
1 TTGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTCCTGACTCCCCAGTAGAGT
25974 AGTGAAGCAA
Statistics
Matches: 149, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
59 36 0.24
60 15 0.10
61 60 0.40
62 38 0.26
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.35
Consensus pattern (62 bp):
TTGACTTCCTCGTGAAGAGAAGTCAACATTTATTATTCCTGACTCCCCAGTAGAGTCAATCC
Found at i:25971 original size:121 final size:121
Alignment explanation
Indices: 25744--25973 Score: 288
Period size: 121 Copynumber: 1.9 Consensus size: 121
25734 TTTTGACTTC
* *
25744 CTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCCGTAGAGTCAATCCTTGACTTCTCT
1 CTCGTGAAGAGAAGTCAACCTTTATTATTCCTGACTCCTCCGTAGAGTCAATCCTTAACTTCTCT
* ** * *
25809 TGAAGAGAAGTCAACATTTATTATTTTTTACTCCTCAGTAGAGTCAATCCTTGACT
66 TGAAGAGAAGCCAACATTTATTATTCCTGACTCCCCAGTAGAGTCAATCCTTGACT
* *
25865 CTCGTGAAGA-AAGTCAACCTTTATTATTCCTGACTCC-CCAGTTGAGTCAAAT-TTTAACTTCC
1 CTCGTGAAGAGAAGTCAACCTTTATTATTCCTGACTCCTCC-GTAGAGTC-AATCCTTAACTT-C
* * *
25927 TCATT-AAGAGAGGCCAACATTTGTTATTCCTGACTCCCCGGTAGAGT
63 TC-TTGAAGAGAAGCCAACATTTATTATTCCTGACTCCCCAGTAGAGT
25974 AGTGAAGCAA
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
119 2 0.02
120 39 0.42
121 50 0.54
122 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (121 bp):
CTCGTGAAGAGAAGTCAACCTTTATTATTCCTGACTCCTCCGTAGAGTCAATCCTTAACTTCTCT
TGAAGAGAAGCCAACATTTATTATTCCTGACTCCCCAGTAGAGTCAATCCTTGACT
Found at i:26016 original size:36 final size:36
Alignment explanation
Indices: 25960--26444 Score: 751
Period size: 36 Copynumber: 13.5 Consensus size: 36
25950 TTATTCCTGA
* * *
25960 CTCCCCGGTAGAGTAGTGAAGCAAAGCCATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
* * *
25996 CTCCACGAAAGAGTGGTGAAGCAAAACAATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
*
26032 CTCCATGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
* *
26068 CTCCACGAAAAAGTAGTGAAGCAAAGC-ATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
*
26103 CGCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
* * *
26139 CTCTACAGAAGAGTAGTGAAGCAAAGCAATCTTAAC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
* * **
26175 CTCCATGGAAGAGTAATGAAGTGAAGCAATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
*
26211 CTCCACGGAAGAGTAGTGAAGCAAAGCCATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
26247 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
26283 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
26319 CTCCACGGAAGAGTAGTGAAGCAAAG-ACATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCA-ATCTTAGC
*
26355 CTCCACGGAAGAGTAGTGAAGCAAATTC-ATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAA-GCAATCTTAGC
*
26391 CTCCACGGAAGAGTAGTGAAGCAAAGCTATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
26427 CTCCACGGAAGAGTAGTG
1 CTCCACGGAAGAGTAGTG
26445 GAACGAATTT
Statistics
Matches: 409, Mismatches: 35, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
35 34 0.08
36 375 0.92
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.18
Consensus pattern (36 bp):
CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
Found at i:35838 original size:29 final size:28
Alignment explanation
Indices: 35806--35882 Score: 77
Period size: 26 Copynumber: 2.8 Consensus size: 28
35796 AATATCACCA
* *
35806 TTTTAAAAATATTTACTAAAATATCATTTT
1 TTTTAAAAA-A-TTACGAAAATAGCATTTT
*
35836 TTTTCAAAAATTACGAAAATAGCA--TT
1 TTTTAAAAAATTACGAAAATAGCATTTT
* *
35862 TTTAAAAAAATTACAAAAATA
1 TTTTAAAAAATTACGAAAATA
35883 ACACCCTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 20 0.49
28 12 0.29
29 1 0.02
30 8 0.20
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.39
Consensus pattern (28 bp):
TTTTAAAAAATTACGAAAATAGCATTTT
Found at i:35902 original size:29 final size:29
Alignment explanation
Indices: 35742--35945 Score: 139
Period size: 29 Copynumber: 7.1 Consensus size: 29
35732 ACACATTTAT
* * *
35742 CACCTTTTTAAAAAAAATTCACAAAAATAG
1 CACCATTTTAAAAATAATT-ACAAAAATAC
* *
35772 CACCATTTTAAAAAATAATTAC-CAAATAT
1 CACCATTTT-AAAAATAATTACAAAAATAC
* * *
35801 CACCATTTTAAAAATATTTACTAAAATAT
1 CACCATTTTAAAAATAATTACAAAAATAC
*** ** * *
35830 CATTTTTTTTCAAA-AATTACGAAAATAG
1 CACCATTTTAAAAATAATTACAAAAATAC
* *
35858 CA--TTTTTAAAAA-AATTACAAAAATAA
1 CACCATTTTAAAAATAATTACAAAAATAC
* * * *
35884 CACCCTTTTCAAAATAATTACCAGAATAC
1 CACCATTTTAAAAATAATTACAAAAATAC
* * *
35913 CACCAGTTTCAAAATAATTACCAAAATAC
1 CACCATTTTAAAAATAATTACAAAAATAC
35942 CACC
1 CACC
35946 CGATCAACGG
Statistics
Matches: 143, Mismatches: 26, Indels: 11
0.79 0.14 0.06
Matches are distributed among these distances:
26 22 0.15
28 32 0.22
29 70 0.49
30 10 0.07
31 9 0.06
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.30
Consensus pattern (29 bp):
CACCATTTTAAAAATAATTACAAAAATAC
Found at i:36020 original size:20 final size:20
Alignment explanation
Indices: 35997--36034 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35987 TAGGGTCGAG
*
35997 CCGGGTCGAAACCGGTCAAA
1 CCGGGTCAAAACCGGTCAAA
*
36017 CCGGTTCAAAACCGGTCA
1 CCGGGTCAAAACCGGTCA
36035 TTTTGACCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.26, T:0.13
Consensus pattern (20 bp):
CCGGGTCAAAACCGGTCAAA
Found at i:43058 original size:29 final size:29
Alignment explanation
Indices: 43026--43208 Score: 125
Period size: 29 Copynumber: 6.3 Consensus size: 29
43016 TAAATTTTTT
43026 TTACAAAAATAGCACCATTTTAAAAATAA
1 TTACAAAAATAGCACCATTTTAAAAATAA
* * *
43055 TTACCAAAATATCACCATTTTAAAAATAT
1 TTACAAAAATAGCACCATTTTAAAAATAA
* * ** **
43084 TTACTAAAATATCACTTTTTTTTCAAA-AA
1 TTACAAAAATAGCAC-CATTTTAAAAATAA
** *** *
43113 TTATGAAAATAGCATTTTTTTAAAAACAA
1 TTACAAAAATAGCACCATTTTAAAAATAA
* * * *
43142 ATACAAAAATAACACCCTTTTCAAAATAA
1 TTACAAAAATAGCACCATTTTAAAAATAA
* * * * *
43171 TTACCAGAATACCACCAGTTTCAAAATAA
1 TTACAAAAATAGCACCATTTTAAAAATAA
43200 TTATCAAAA
1 TTA-CAAAA
43209 TACCACCCGG
Statistics
Matches: 119, Mismatches: 32, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
28 9 0.08
29 100 0.84
30 10 0.08
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.32
Consensus pattern (29 bp):
TTACAAAAATAGCACCATTTTAAAAATAA
Found at i:43210 original size:29 final size:29
Alignment explanation
Indices: 43160--43215 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
43150 ATAACACCCT
*
43160 TTTCAAAATAATTACCAGAATACCACCAG
1 TTTCAAAATAATTACCAAAATACCACCAG
*
43189 TTTCAAAATAATTATCAAAATACCACC
1 TTTCAAAATAATTACCAAAATACCACC
43216 CGGTCAACGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.46, C:0.23, G:0.04, T:0.27
Consensus pattern (29 bp):
TTTCAAAATAATTACCAAAATACCACCAG
Found at i:44387 original size:18 final size:18
Alignment explanation
Indices: 44344--44394 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
44334 TTTTAGACTT
* *
44344 CATCTTAACTTAAATTCA
1 CATCTTAAATTAAATTAA
*
44362 CATTTTAAATTAAATTAA
1 CATCTTAAATTAAATTAA
*
44380 TATCTTAACATTAAA
1 CATCTTAA-ATTAAA
44395 AATATATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 21 0.78
19 6 0.22
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (18 bp):
CATCTTAAATTAAATTAA
Found at i:44472 original size:25 final size:25
Alignment explanation
Indices: 44390--44498 Score: 103
Period size: 25 Copynumber: 4.2 Consensus size: 25
44380 TATCTTAACA
* *
44390 TTAAAAATATATATTTTATTTTTTTATC
1 TTAAAAA-ATATATTTTA--GTCTTATC
* * *
44418 TTAAATAAATTTTATTCTTA-TTTTAAC
1 TTAAA-AAA-TATATT-TTAGTCTTATC
*
44445 TTAAAATATATATTTTAGTCTTATC
1 TTAAAAAATATATTTTAGTCTTATC
44470 TTAAAAAATATATTTTAGTCTTATC
1 TTAAAAAATATATTTTAGTCTTATC
44495 TTAA
1 TTAA
44499 CTTAAAATAT
Statistics
Matches: 70, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
24 3 0.04
25 38 0.54
26 2 0.03
27 11 0.16
28 6 0.09
29 7 0.10
30 3 0.04
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (25 bp):
TTAAAAAATATATTTTAGTCTTATC
Found at i:44485 original size:55 final size:55
Alignment explanation
Indices: 44420--44615 Score: 163
Period size: 55 Copynumber: 3.8 Consensus size: 55
44410 TTTTTATCTT
*
44420 AAATAAATTTTATTCTTATTTTAACTTAAAATATATATTTTAGTCTTATCTTAAA
1 AAATATATTTTATTCTTATTTTAACTTAAAATATATATTTTAGTCTTATCTTAAA
* * *
44475 AAATATATTTTAGTCTTATCTTAACTTAAAATATA-A-TTTATTCTTA-CTTTAACA
1 AAATATATTTTATTCTTATTTTAACTTAAAATATATATTTTAGTCTTATC-TTAA-A
* * *
44529 TAAATATA---TATT-TT-TATT---TT--AATATATATTTTAGTTTTAT-TT-AC
1 -AAATATATTTTATTCTTATTTTAACTTAAAATATATATTTTAGTCTTATCTTAAA
*
44573 AAATGCATATTTTATTCTTATTTTAATTTAAAA-ATATATTTTA
1 AAAT--ATATTTTATTCTTATTTTAACTTAAAATATATATTTTA
44616 TTTTTTTCTT
Statistics
Matches: 113, Mismatches: 10, Indels: 37
0.71 0.06 0.23
Matches are distributed among these distances:
43 4 0.04
45 10 0.09
46 3 0.03
47 10 0.09
48 4 0.04
49 2 0.02
50 6 0.05
51 2 0.02
52 4 0.04
53 15 0.13
54 12 0.11
55 41 0.36
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (55 bp):
AAATATATTTTATTCTTATTTTAACTTAAAATATATATTTTAGTCTTATCTTAAA
Found at i:44602 original size:31 final size:28
Alignment explanation
Indices: 44555--44638 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 28
44545 TTTTAATATA
*
44555 TATTTTAGTTTT-ATTTACAAATGCATATTT
1 TATTTTA-TTTTAATTTAAAAAT--ATATTT
44585 TATTCTTATTTTAATTTAAAAATATATTT
1 TATT-TTATTTTAATTTAAAAATATATTT
* *
44614 TATTTTTTTCTTAATTTTAAAATAT
1 TATTTTATT-TTAATTTAAAAATAT
44639 TATAAGAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
28 4 0.08
29 24 0.50
30 8 0.17
31 12 0.25
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (28 bp):
TATTTTATTTTAATTTAAAAATATATTT
Found at i:44740 original size:43 final size:43
Alignment explanation
Indices: 44690--44802 Score: 217
Period size: 43 Copynumber: 2.6 Consensus size: 43
44680 AAATTATATT
44690 TTTAAGTTAAATTAAAATTAAGATAAAAATAAAATATATTTTA
1 TTTAAGTTAAATTAAAATTAAGATAAAAATAAAATATATTTTA
44733 TTTAAGTTAAATTAAAATTAAGATAAAAATAAAATATATTTTA
1 TTTAAGTTAAATTAAAATTAAGATAAAAATAAAATATATTTTA
*
44776 TTTAAGTTAAATTAAAGTTAAGATAAA
1 TTTAAGTTAAATTAAAATTAAGATAAA
44803 TTGAAATATA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (43 bp):
TTTAAGTTAAATTAAAATTAAGATAAAAATAAAATATATTTTA
Found at i:44846 original size:18 final size:18
Alignment explanation
Indices: 44817--44868 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
44807 AATATATATT
44817 TTTAATTTTAATATGTTAA
1 TTTAA-TTTAATATGTTAA
44836 TTTAATTTAATATGTTAA
1 TTTAATTTAATATGTTAA
* *
44854 TTTAAGTTAAAATGT
1 TTTAATTTAATATGT
44869 AGTATAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 26 0.84
19 5 0.16
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (18 bp):
TTTAATTTAATATGTTAA
Found at i:44943 original size:24 final size:24
Alignment explanation
Indices: 44911--44967 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
44901 GGATTGTGGG
* *
44911 ATTCTCATGGGATGAGAATCTCAC
1 ATTCCCATGGGATGAGAATCCCAC
44935 ATTCCCATGGGATGAGAATCCCAC
1 ATTCCCATGGGATGAGAATCCCAC
44959 ATTCCCATG
1 ATTCCCATG
44968 TTTGGTTGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (24 bp):
ATTCCCATGGGATGAGAATCCCAC
Found at i:45546 original size:20 final size:20
Alignment explanation
Indices: 45510--45547 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
45500 ATCCTATTCC
**
45510 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
45530 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
45548 ATGAACAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:46010 original size:32 final size:32
Alignment explanation
Indices: 45968--46035 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
45958 GTGACTAAAA
* *
45968 TTTATATATGATTTTGAAATTCTTTTTGAAAT
1 TTTATATATGATTTTGAAATTCTTTTGGAAAG
*
46000 TTTATGTATGATTTTGAAATTCTTTTGGAAAG
1 TTTATATATGATTTTGAAATTCTTTTGGAAAG
46032 TTTA
1 TTTA
46036 AGTACTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.54
Consensus pattern (32 bp):
TTTATATATGATTTTGAAATTCTTTTGGAAAG
Found at i:48959 original size:3 final size:3
Alignment explanation
Indices: 48951--49008 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
48941 TGATTTGAAG
48951 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
48999 TAA TAA TAA T
1 TAA TAA TAA T
49009 TGCCTTCCCC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:49634 original size:26 final size:22
Alignment explanation
Indices: 49597--49650 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
49587 TTTAACAAAC
*
49597 TGAATACATAAGTGAGGTACTA
1 TGAATACATAAGTAAGGTACTA
49619 TGAATACATAAGTAAGGTACTA
1 TGAATACATAAGTAAGGTACTA
49641 TGAATACATA
1 TGAATACATA
49651 TGCTTACAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (22 bp):
TGAATACATAAGTAAGGTACTA
Found at i:50035 original size:32 final size:32
Alignment explanation
Indices: 49980--50041 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
49970 ATTGGCTCTT
* *
49980 TGTGCATTATCTGAATGCCATACTAACTCTGA
1 TGTGCATTATCAGAATGCAATACTAACTCTGA
* *
50012 TGTGCATTATCAGAATGTAATACTGACTCT
1 TGTGCATTATCAGAATGCAATACTAACTCT
50042 ATTGTGACTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTGCATTATCAGAATGCAATACTAACTCTGA
Found at i:52112 original size:21 final size:21
Alignment explanation
Indices: 52086--52134 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
52076 GGGCCCTGTA
* *
52086 TCGAGACCAACACTTCCATTC
1 TCGAGACAAACACTTCCAGTC
*
52107 TCGAGACAAACACTTCTAGTC
1 TCGAGACAAACACTTCCAGTC
52128 TCGAGAC
1 TCGAGAC
52135 TGAATGGGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.33, G:0.14, T:0.22
Consensus pattern (21 bp):
TCGAGACAAACACTTCCAGTC
Found at i:56188 original size:19 final size:17
Alignment explanation
Indices: 56164--56210 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
56154 GGACCCTTAA
*
56164 TGCATCGGTGCACTAAGAG
1 TGCATCGATGCA-TAA-AG
56183 TGCATCGATGCATAAAG
1 TGCATCGATGCATAAAG
56200 TGCATTCGATG
1 TGCA-TCGATG
56211 TTTCAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.23
18 9 0.35
19 11 0.42
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (17 bp):
TGCATCGATGCATAAAG
Found at i:56249 original size:45 final size:46
Alignment explanation
Indices: 56180--56286 Score: 157
Period size: 46 Copynumber: 2.3 Consensus size: 46
56170 GGTGCACTAA
*
56180 GAGTGCATCGATGCATAAAGTGCATTCGATG-TTTCA-AACAAGCCC
1 GAGTGCATCGATGCATAAAGTGCATTCGATGTTTTCATAA-AAACCC
*
56225 GAGTGCATCGATGCATCAAA-TGCATTCGATGTTTTCATAAAAACCT
1 GAGTGCATCGATGCAT-AAAGTGCATTCGATGTTTTCATAAAAACCC
56271 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
56287 GGTATGTGCA
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
45 27 0.47
46 28 0.49
47 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (46 bp):
GAGTGCATCGATGCATAAAGTGCATTCGATGTTTTCATAAAAACCC
Found at i:63228 original size:117 final size:117
Alignment explanation
Indices: 63008--63228 Score: 268
Period size: 117 Copynumber: 1.9 Consensus size: 117
62998 CTTTCAAATC
* *
63008 AAAATTTTCTTTTTCAATACTTTTAAATTTCATTTTTGAAAGCTCTAAATCATTCTTCAAGATTT
1 AAAAATTTCTTTTTCAATACTTTTAAATTTCATTTTTGAAAGCTCTAAATCATTCTTCAACATTT
* * *
63073 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTAATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
* * * * *
63125 AAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTC-TTTTCTCAACAT
1 AAAAATTTCTTTTTCAATACTTTT-AAATTTCATTTTTGAAAGCTCTAAATCATTCT-TCAACAT
* * **
63188 TTCATTTTAATTTTCCAAGTCTGTTTTAGCTTT-TAAAAGAA
64 TTCATTTTAATTTTCAAAATCCATTTTAG-TTTCTAAAAGAA
63229 TATCATTTTT
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
116 8 0.09
117 76 0.87
118 3 0.03
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.49
Consensus pattern (117 bp):
AAAAATTTCTTTTTCAATACTTTTAAATTTCATTTTTGAAAGCTCTAAATCATTCTTCAACATTT
CATTTTAATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:64564 original size:19 final size:19
Alignment explanation
Indices: 64540--64584 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
64530 GGACCCTTAC
64540 TGCATCGGTGCACTAAGAG
1 TGCATCGGTGCACTAAGAG
64559 TGCATCGGTGCACTAAGAG
1 TGCATCGGTGCACTAAGAG
64578 TGCATCG
1 TGCATCG
64585 ATGTATAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.22
Consensus pattern (19 bp):
TGCATCGGTGCACTAAGAG
Found at i:64598 original size:17 final size:19
Alignment explanation
Indices: 64540--64599 Score: 79
Period size: 19 Copynumber: 3.3 Consensus size: 19
64530 GGACCCTTAC
*
64540 TGCATCGGTGCACTAAGAG
1 TGCATCGATGCACTAAGAG
*
64559 TGCATCGGTGCACTAAGAG
1 TGCATCGATGCACTAAGAG
*
64578 TGCATCGATGTA-TAA-AG
1 TGCATCGATGCACTAAGAG
64595 TGCAT
1 TGCAT
64600 TCGACGTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.18
18 3 0.08
19 29 0.74
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.25
Consensus pattern (19 bp):
TGCATCGATGCACTAAGAG
Found at i:65032 original size:27 final size:27
Alignment explanation
Indices: 64990--65057 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
64980 TTGTAGGAAT
64990 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
65015 TATAGAGATATGATTTGTTATCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
65042 TATAGAGATATGATTT
1 TATAGAGATATGATTT
65058 TGTAAATAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 7 0.17
27 33 0.82
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:68798 original size:27 final size:27
Alignment explanation
Indices: 68756--68823 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
68746 GTGTAGGAAT
68756 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
68781 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
68808 TATAGAGATATGATTT
1 TATAGAGATATGATTT
68824 TATAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:79357 original size:19 final size:20
Alignment explanation
Indices: 79335--79376 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
79325 TTAAACTGAT
*
79335 TTAAATAATTTAATAAA-TA
1 TTAAATAATTTAAAAAATTA
*
79354 TTAAATATTTTAAAAAATTA
1 TTAAATAATTTAAAAAATTA
79374 TTA
1 TTA
79377 TTAAATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAATAATTTAAAAAATTA
Found at i:79842 original size:16 final size:18
Alignment explanation
Indices: 79806--79843 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
79796 TCAAAGATTC
*
79806 AAATTATATAACTAGAAA
1 AAATTATATAAATAGAAA
79824 AAATTAT-TAAATA-AAA
1 AAATTATATAAATAGAAA
79840 AAAT
1 AAAT
79844 AAAAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 5 0.26
18 7 0.37
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AAATTATATAAATAGAAA
Found at i:81388 original size:4 final size:4
Alignment explanation
Indices: 81379--81405 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
81369 CAATGCATGT
81379 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
81406 GTTGAACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:92426 original size:3 final size:3
Alignment explanation
Indices: 92418--92445 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
92408 ACAAATGCAA
92418 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
92446 GTTGTTGTTG
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:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:95843 original size:20 final size:20
Alignment explanation
Indices: 95807--95854 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
95797 TCAAAATCAT
* *
95807 TTTTCAAAATTTCATTTTTC
1 TTTTCAAAATTCCATTTTGC
95827 TTTTCAAAA-TCCAATTTTGC
1 TTTTCAAAATTCC-ATTTTGC
95847 -TTTCAAAA
1 TTTTCAAAA
95855 AAAAGCCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTGC
Found at i:98885 original size:13 final size:13
Alignment explanation
Indices: 98869--98965 Score: 67
Period size: 13 Copynumber: 7.2 Consensus size: 13
98859 AAATTAAATG
98869 AATATAATAATTA
1 AATATAATAATTA
*
98882 AATATAATAATATT
1 AATATAATAAT-TA
98896 AAT-TAATAATATTA
1 AATATAAT-A-ATTA
*
98910 AATAT--TAAATA
1 AATATAATAATTA
98921 TAATA-AATAATTAA
1 -AATATAATAATT-A
98935 AATATAATAATATATA
1 AATATAAT-A-AT-TA
*
98951 AATATAGTAATTA
1 AATATAATAATTA
98964 AA
1 AA
98966 ATAGATATTT
Statistics
Matches: 67, Mismatches: 5, Indels: 24
0.70 0.05 0.25
Matches are distributed among these distances:
11 3 0.04
12 5 0.07
13 28 0.42
14 15 0.22
15 5 0.07
16 10 0.15
17 1 0.01
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (13 bp):
AATATAATAATTA
Found at i:98893 original size:16 final size:16
Alignment explanation
Indices: 98872--98961 Score: 76
Period size: 16 Copynumber: 5.3 Consensus size: 16
98862 TTAAATGAAT
98872 ATAATAATTAAATATA
1 ATAATAATTAAATATA
*
98888 ATAAT-ATTAATTAATA
1 ATAATAATTAAAT-ATA
*
98904 ATATTAAATATTAAATATA
1 ATA--ATA-ATTAAATATA
98923 ATAAATAATTAAAATATA
1 AT-AATAATT-AAATATA
98941 ATAAT-ATATAAATATA
1 ATAATAAT-TAAATATA
*
98957 GTAAT
1 ATAAT
98962 TAAAATAGAT
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
15 6 0.10
16 24 0.39
17 7 0.11
18 12 0.20
19 5 0.08
20 7 0.11
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (16 bp):
ATAATAATTAAATATA
Found at i:98902 original size:26 final size:26
Alignment explanation
Indices: 98873--98965 Score: 91
Period size: 26 Copynumber: 3.4 Consensus size: 26
98863 TAAATGAATA
98873 TAATAATTAAATATAATAATATTAAT
1 TAATAATTAAATATAATAATATTAAT
*
98899 TAATAATATTAAATATTA-AATA-TAAT
1 TAAT-A-ATTAAATATAATAATATTAAT
*
98925 AAATAATTAAAATATAATAATATATAAAT
1 TAATAATT-AAATATAATAATAT-T-AAT
*
98954 ATAGTAATTAAA
1 -TAATAATTAAA
98966 ATAGATATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
24 3 0.06
25 8 0.15
26 15 0.28
27 5 0.09
28 11 0.20
29 6 0.11
30 6 0.11
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (26 bp):
TAATAATTAAATATAATAATATTAAT
Found at i:98918 original size:35 final size:34
Alignment explanation
Indices: 98869--98961 Score: 113
Period size: 34 Copynumber: 2.8 Consensus size: 34
98859 AAATTAAATG
98869 AATATAAT-A-ATTAAATATAATAATATTAATTAA
1 AATATAATAATATTAAATATAATAATA-TAATTAA
*
98902 TAATATTA-AATATTAAATATAATAA-ATAATTAA
1 -AATATAATAATATTAAATATAATAATATAATTAA
*
98935 AATATAATAATATATAAATATAGTAAT
1 AATATAATAATAT-TAAATATAATAAT
98962 TAAAATAGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
32 6 0.12
33 12 0.24
34 19 0.37
35 14 0.27
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (34 bp):
AATATAATAATATTAAATATAATAATATAATTAA
Found at i:98923 original size:48 final size:41
Alignment explanation
Indices: 98870--98955 Score: 114
Period size: 35 Copynumber: 2.2 Consensus size: 41
98860 AATTAAATGA
98870 ATAT-AATAATTAAATATAAT-AAT-ATT--AAT-TAATAAT
1 ATATAAAT-ATTAAATATAATAAATAATTAAAATATAATAAT
98906 AT-TAAATATTAAATATAATAAATAATTAAAATATAATAAT
1 ATATAAATATTAAATATAATAAATAATTAAAATATAATAAT
98946 ATATAAATAT
1 ATATAAATAT
98956 AGTAATTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
35 13 0.30
36 8 0.19
37 3 0.07
39 3 0.07
40 9 0.21
41 7 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (41 bp):
ATATAAATATTAAATATAATAAATAATTAAAATATAATAAT
Found at i:98968 original size:48 final size:53
Alignment explanation
Indices: 98869--98968 Score: 122
Period size: 53 Copynumber: 2.0 Consensus size: 53
98859 AAATTAAATG
* * *
98869 AATATAATAATTAAATATAATAATATTAATTAATAATATTAAATATTAAATAT
1 AATATAATAATTAAATATAATAATATTAATAAATAATAGTAAATATAAAATAT
98922 AATA-AATAATTAAAATATAATAATA-T-ATAAAT-ATAGT-AAT-TAAAATA
1 AATATAATAATT-AAATATAATAATATTAATAAATAATAGTAAATATAAAATA
98969 GATATTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
48 6 0.14
49 3 0.07
50 4 0.09
51 5 0.12
52 8 0.19
53 17 0.40
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (53 bp):
AATATAATAATTAAATATAATAATATTAATAAATAATAGTAAATATAAAATAT
Found at i:101808 original size:29 final size:29
Alignment explanation
Indices: 101773--101830 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
101763 AGATATAGAT
101773 GATGAGATTTGTCTTATTTCTGATAGTGA
1 GATGAGATTTGTCTTATTTCTGATAGTGA
101802 GATGAGATTTGTCTTATTTCTGATAGTGA
1 GATGAGATTTGTCTTATTTCTGATAGTGA
101831 CATTGATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.45
Consensus pattern (29 bp):
GATGAGATTTGTCTTATTTCTGATAGTGA
Found at i:108141 original size:61 final size:60
Alignment explanation
Indices: 108045--108191 Score: 168
Period size: 61 Copynumber: 2.4 Consensus size: 60
108035 AAAATGGTCA
* * * * ** *
108045 TTAAACTTTTGAATATTTTAAATTCATCTACAAACTATGATTCTCATTCTAAATTAGTTC
1 TTAAACTTTTGAATATTTTAATTTCACCCACAAACTATAAACCTCATTCTAAATTAGTCC
* * *
108105 TTAAACTTTTTGAATATTCTAATTTCACCCATAAACTATAAACCTCTTTCTAAATTAGTCC
1 TTAAAC-TTTTGAATATTTTAATTTCACCCACAAACTATAAACCTCATTCTAAATTAGTCC
** *
108166 CCAAACTTTTGAAGATTTTAATTTCA
1 TTAAACTTTTGAATATTTTAATTTCA
108192 TCCTCAAATT
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
60 24 0.33
61 48 0.67
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.43
Consensus pattern (60 bp):
TTAAACTTTTGAATATTTTAATTTCACCCACAAACTATAAACCTCATTCTAAATTAGTCC
Found at i:111400 original size:18 final size:18
Alignment explanation
Indices: 111377--111436 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
111367 ACTACTATAC
111377 TATTTCCAAGTGATTTTG
1 TATTTCCAAGTGATTTTG
* * **
111395 TATTTCTTTAAGT--TATAC
1 TATTTC--CAAGTGATTTTG
111413 TATTTCCAAGTGATTTTG
1 TATTTCCAAGTGATTTTG
111431 TATTTC
1 TATTTC
111437 TTTAAGTTGT
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
16 4 0.13
18 22 0.73
20 4 0.13
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (18 bp):
TATTTCCAAGTGATTTTG
Found at i:111419 original size:36 final size:36
Alignment explanation
Indices: 111372--111444 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
111362 CCACAACTAC
111372 TATACTATTTCCAAGTGATTTTGTATTTCTTTAAGT
1 TATACTATTTCCAAGTGATTTTGTATTTCTTTAAGT
111408 TATACTATTTCCAAGTGATTTTGTATTTCTTTAAGT
1 TATACTATTTCCAAGTGATTTTGTATTTCTTTAAGT
111444 T
1 T
111445 GTATATAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.53
Consensus pattern (36 bp):
TATACTATTTCCAAGTGATTTTGTATTTCTTTAAGT
Found at i:113682 original size:18 final size:18
Alignment explanation
Indices: 113661--113795 Score: 96
Period size: 18 Copynumber: 7.5 Consensus size: 18
113651 CGTCAATAAT
*
113661 ATTATCATAATCTATATC
1 ATTATCATGATCTATATC
* *
113679 ATTATCCA-CATCAATATC
1 ATTAT-CATGATCTATATC
*
113697 ATTATCATGATCTCTATC
1 ATTATCATGATCTATATC
**
113715 -TCTATCAACAT-TAATATC
1 AT-TATCATGATCT-ATATC
*
113733 ATTATCATGATCTCTATC
1 ATTATCATGATCTATATC
* * * * *
113751 ACTATTATCATCGATTTC
1 ATTATCATGATCTATATC
*
113769 ATTATCATGATCTCTATC
1 ATTATCATGATCTATATC
*
113787 ACTATCATG
1 ATTATCATG
113796 TATTAATATT
Statistics
Matches: 87, Mismatches: 24, Indels: 12
0.71 0.20 0.10
Matches are distributed among these distances:
17 4 0.05
18 79 0.91
19 4 0.05
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (18 bp):
ATTATCATGATCTATATC
Found at i:113694 original size:36 final size:37
Alignment explanation
Indices: 113648--113793 Score: 167
Period size: 36 Copynumber: 4.1 Consensus size: 37
113638 CCATTATTAA
* * *
113648 CAACGTCAATAAT-ATTATCATAATCTATATCAT-TAT
1 CAACATCAAT-ATCATTATCATGATCTCTATCATCTAT
*
113684 CCACATCAATATCATTATCATGATCTCTATC-TCTAT
1 CAACATCAATATCATTATCATGATCTCTATCATCTAT
*
113720 CAACATTAATATCATTATCATGATCTCTATCA-CTAT
1 CAACATCAATATCATTATCATGATCTCTATCATCTAT
* * * *
113756 TATCATCGATTTCATTATCATGATCTCTATCA-CTAT
1 CAACATCAATATCATTATCATGATCTCTATCATCTAT
113792 CA
1 CA
113794 TGTATTAATA
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
35 3 0.03
36 92 0.97
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (37 bp):
CAACATCAATATCATTATCATGATCTCTATCATCTAT
Found at i:114070 original size:31 final size:31
Alignment explanation
Indices: 114033--114157 Score: 182
Period size: 31 Copynumber: 4.0 Consensus size: 31
114023 CCCGAAAGAC
*
114033 CAGTCCATA-GATCCCGAAGAATC-TAGGTAAT
1 CAGTCCATATG-TCCCGAAGAA-CATAGGTAAA
114064 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
114095 CAGTACATATGTCCCGAAGAACATAGGCAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
114126 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
114157 C
1 C
114158 CCTCGACCCT
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
30 1 0.01
31 84 0.98
32 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:115620 original size:20 final size:20
Alignment explanation
Indices: 115597--115648 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
115587 CCCTAACTGA
*
115597 GGTATATATACCCTGCCTAT
1 GGTATAAATACCCTGCCTAT
*
115617 GGTATAAATACCCTGTCTAT
1 GGTATAAATACCCTGCCTAT
*
115637 GGTATAGATACC
1 GGTATAAATACC
115649 ATGATAACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (20 bp):
GGTATAAATACCCTGCCTAT
Found at i:117965 original size:18 final size:18
Alignment explanation
Indices: 117944--118078 Score: 105
Period size: 18 Copynumber: 7.5 Consensus size: 18
117934 CGTCAATAAT
*
117944 ATTATCATAATCTCTATC
1 ATTATCATGATCTCTATC
* **
117962 ATTATCCA-CATCAATATC
1 ATTAT-CATGATCTCTATC
117980 ATTATCATGATCTCTATC
1 ATTATCATGATCTCTATC
** *
117998 -TCTATCAACAT-TAATATC
1 AT-TATCATGATCT-CTATC
118016 ATTATCATGATCTCTATC
1 ATTATCATGATCTCTATC
* * * **
118034 ACTATTATCATCGATATC
1 ATTATCATGATCTCTATC
118052 ATTATCATGATCTCTATC
1 ATTATCATGATCTCTATC
*
118070 ACTATCATG
1 ATTATCATG
118079 TATTAATATT
Statistics
Matches: 88, Mismatches: 23, Indels: 12
0.72 0.19 0.10
Matches are distributed among these distances:
17 4 0.05
18 80 0.91
19 4 0.05
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.41
Consensus pattern (18 bp):
ATTATCATGATCTCTATC
Found at i:117976 original size:36 final size:36
Alignment explanation
Indices: 117931--118076 Score: 195
Period size: 36 Copynumber: 4.1 Consensus size: 36
117921 CCATCATTAA
* * *
117931 CAACGTCAATAAT-ATTATCATAATCTCTATCATTAT
1 CAACATCAAT-ATCATTATCATGATCTCTATCACTAT
* *
117967 CCACATCAATATCATTATCATGATCTCTATCTCTAT
1 CAACATCAATATCATTATCATGATCTCTATCACTAT
*
118003 CAACATTAATATCATTATCATGATCTCTATCACTAT
1 CAACATCAATATCATTATCATGATCTCTATCACTAT
* * *
118039 TATCATCGATATCATTATCATGATCTCTATCACTAT
1 CAACATCAATATCATTATCATGATCTCTATCACTAT
118075 CA
1 CA
118077 TGTATTAATA
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
35 2 0.02
36 94 0.98
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.39
Consensus pattern (36 bp):
CAACATCAATATCATTATCATGATCTCTATCACTAT
Found at i:118354 original size:31 final size:31
Alignment explanation
Indices: 118316--118471 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
118306 CCCGAAGGAC
** *
118316 CAGTCCATA-GATCCCGAAGAATTTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
118347 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
118378 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
**
118409 CAGTCCATATGTCCCGAAGAACATAAATAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
118440 CAATCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
118471 C
1 C
118472 CCTCGACTCA
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:119927 original size:20 final size:20
Alignment explanation
Indices: 119904--119954 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
119894 CCCTAACTGA
119904 GGTATAGATACCCTACCTAT
1 GGTATAGATACCCTACCTAT
***
119924 GGTATAGATACCCTGTTTAT
1 GGTATAGATACCCTACCTAT
119944 GGTATAGATAC
1 GGTATAGATAC
119955 TCTGATAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (20 bp):
GGTATAGATACCCTACCTAT
Found at i:122245 original size:18 final size:18
Alignment explanation
Indices: 122224--122358 Score: 114
Period size: 18 Copynumber: 7.5 Consensus size: 18
122214 TGTCAATTAT
*
122224 ATTATCATAATCTCTATC
1 ATTATCATGATCTCTATC
* **
122242 ATTATCCA-CATCAATATC
1 ATTAT-CATGATCTCTATC
122260 ATTATCATGATCTCTATC
1 ATTATCATGATCTCTATC
** *
122278 -TCTATCAACAT-TAATATC
1 AT-TATCATGATCT-CTATC
122296 ATTATCATGATCTCTATC
1 ATTATCATGATCTCTATC
* * **
122314 ATTATTATCATCGATATC
1 ATTATCATGATCTCTATC
122332 ATTATCATGATCTCTATC
1 ATTATCATGATCTCTATC
*
122350 ACTATCATG
1 ATTATCATG
122359 TATTAATATT
Statistics
Matches: 90, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
17 4 0.04
18 82 0.91
19 4 0.04
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (18 bp):
ATTATCATGATCTCTATC
Found at i:122256 original size:36 final size:36
Alignment explanation
Indices: 122216--122356 Score: 187
Period size: 36 Copynumber: 3.9 Consensus size: 36
122206 ATTAACAATG
* *
122216 TCAATTAT-ATTATCATAATCTCTATCATTATCCACA
1 TCAA-TATCATTATCATGATCTCTATCATTATCAACA
122252 TCAATATCATTATCATGATCTCTATC-TCTATCAACA
1 TCAATATCATTATCATGATCTCTATCAT-TATCAACA
* * *
122288 TTAATATCATTATCATGATCTCTATCATTATTATCA
1 TCAATATCATTATCATGATCTCTATCATTATCAACA
* *
122324 TCGATATCATTATCATGATCTCTATCACTATCA
1 TCAATATCATTATCATGATCTCTATCATTATCA
122357 TGTATTAATA
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
35 4 0.04
36 88 0.95
37 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (36 bp):
TCAATATCATTATCATGATCTCTATCATTATCAACA
Found at i:122634 original size:31 final size:31
Alignment explanation
Indices: 122596--122782 Score: 277
Period size: 31 Copynumber: 6.0 Consensus size: 31
122586 CTCGAAGGAC
* ** *
122596 CAGTCCATA-GATCCTGAAGAATTTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
122627 CAGTCCATATGTCCAGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
122658 CAGTCCATATATCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
122689 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
122720 CAGTCCATATGTCCCGAAGAACATAGGTTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
122751 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
122782 C
1 C
122783 CCTCGACCCT
Statistics
Matches: 143, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
31 142 0.99
32 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:124226 original size:20 final size:20
Alignment explanation
Indices: 124203--124257 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
124193 CCCTAACTGA
*
124203 GGTATGGATACCCTGCCTAT
1 GGTATAGATACCCTGCCTAT
**
124223 GGTATAGATACCCTATCTAT
1 GGTATAGATACCCTGCCTAT
124243 GGTATAGATACCCTG
1 GGTATAGATACCCTG
124258 ATAACATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (20 bp):
GGTATAGATACCCTGCCTAT
Found at i:126889 original size:19 final size:20
Alignment explanation
Indices: 126834--126889 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
126824 AACCAATAAT
126834 AATAAACATAAAAT-AATTGG
1 AATAAA-ATAAAATAAATTGG
*
126854 ATTAAAA-AAAATGAAATT-G
1 AATAAAATAAAAT-AAATTGG
126873 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
126890 GAAGGTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 5 0.16
19 12 0.39
20 14 0.45
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (20 bp):
AATAAAATAAAATAAATTGG
Found at i:127006 original size:21 final size:20
Alignment explanation
Indices: 126980--127107 Score: 68
Period size: 21 Copynumber: 6.2 Consensus size: 20
126970 GAAACTAAAA
126980 ATATAATGAAAATAATAA-AT
1 ATATAAT-AAAATAATAATAT
127000 AGTATAAATAAAATAATAATAT
1 A-TAT-AATAAAATAATAATAT
*
127022 ATATATATATAAATATAAAATGTAT
1 ATATA-ATA-AAATA-ATAA--TAT
* *
127047 GTATAATATAATAA-AATACT
1 ATATAATAAAATAATAATA-T
* * *
127067 AAATAGTAATAATAATAATAA
1 ATATAATAA-AATAATAATAT
*
127088 ATA-AATGAAA-AATAA-AT
1 ATATAATAAAATAATAATAT
127105 ATA
1 ATA
127108 CATATAATAT
Statistics
Matches: 85, Mismatches: 12, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
17 4 0.05
18 5 0.06
19 4 0.05
20 11 0.13
21 28 0.33
22 16 0.19
23 7 0.08
24 3 0.04
25 7 0.08
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (20 bp):
ATATAATAAAATAATAATAT
Found at i:127008 original size:27 final size:27
Alignment explanation
Indices: 126978--127039 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
126968 AAGAAACTAA
126978 AAATATAATGAA-AATA-ATAAATAGTAT
1 AAATATAAT-AATAATATATAAATA-TAT
* *
127005 AAATAAAATAATAATATATATATATAT
1 AAATATAATAATAATATATAAATATAT
127032 AAATATAA
1 AAATATAA
127040 AATGTATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 2 0.07
27 22 0.73
28 6 0.20
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (27 bp):
AAATATAATAATAATATATAAATATAT
Found at i:127163 original size:29 final size:28
Alignment explanation
Indices: 126994--127177 Score: 82
Period size: 30 Copynumber: 6.3 Consensus size: 28
126984 AATGAAAATA
126994 ATAAATAGTATAAATAAAATAA-TAATATAT
1 ATAAATA-TA-AAATAAAATAAGTAATA-AT
* *
127024 ATATATATAAATATAAAAT--GT-AT-GT
1 ATAAATATAAA-ATAAAATAAGTAATAAT
127049 ATAATATAATAAAATACTAAAT-AGTAATAAT
1 ATAA-AT-ATAAAATA--AAATAAGTAATAAT
* *
127080 A-ATAATAAATAAATGAAAAATAAAT-ATACAT
1 ATA-AATATA-AAAT--AAAATAAGTAATA-AT
*
127111 AT-AATATTAACTAAAAAAAT-AGTAATAAT
1 ATAAATA-TAA--AATAAAATAAGTAATAAT
*
127140 ATAAATATAAAATAAAATGAAGTAAGAAT
1 ATAAATATAAAATAAAAT-AAGTAATAAT
*
127169 ATATATATA
1 ATAAATATA
127178 TATATATATA
Statistics
Matches: 119, Mismatches: 12, Indels: 47
0.67 0.07 0.26
Matches are distributed among these distances:
25 4 0.03
26 5 0.04
27 14 0.12
28 7 0.06
29 38 0.32
30 39 0.33
31 9 0.08
32 3 0.03
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (28 bp):
ATAAATATAAAATAAAATAAGTAATAAT
Found at i:127174 original size:2 final size:2
Alignment explanation
Indices: 127167--127199 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
127157 TGAAGTAAGA
127167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
127200 GGAAAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:127222 original size:15 final size:15
Alignment explanation
Indices: 127202--127231 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
127192 TATATATAGG
127202 AAAAAATATAGTAAA
1 AAAAAATATAGTAAA
127217 AAAAAATATAGTAAA
1 AAAAAATATAGTAAA
127232 TAAGTAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (15 bp):
AAAAAATATAGTAAA
Found at i:127321 original size:10 final size:9
Alignment explanation
Indices: 127308--127345 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
127298 AAAATGAAAA
127308 AAATTATAAT
1 AAATTA-AAT
127318 AAA-TAAAT
1 AAATTAAAT
127326 AAATTAAAT
1 AAATTAAAT
127335 ATAATTAAAT
1 A-AATTAAAT
127345 A
1 A
127346 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 6 0.23
9 8 0.31
10 12 0.46
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AAATTAAAT
Found at i:127855 original size:37 final size:37
Alignment explanation
Indices: 127762--127862 Score: 130
Period size: 37 Copynumber: 2.7 Consensus size: 37
127752 ATGCTTGTGG
* ** ** *
127762 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATCTTTAGGAGTTTGAATCCTAACAAAACTCT
* *
127799 ATCCTATTTTTAGGAGTTTGAATCCTAACAAAATTCT
1 ATCCTATCTTTAGGAGTTTGAATCCTAACAAAACTCT
127836 ATCCTATCTTTAGGAGTTTGAATCCTA
1 ATCCTATCTTTAGGAGTTTGAATCCTA
127863 GTAGGACGAA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (37 bp):
ATCCTATCTTTAGGAGTTTGAATCCTAACAAAACTCT
Found at i:128934 original size:106 final size:106
Alignment explanation
Indices: 128616--130096 Score: 2120
Period size: 106 Copynumber: 14.0 Consensus size: 106
128606 GCATTGTTCC
* * * ** * *
128616 GAGTCTAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
* * * *
128680 ACCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
128722 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
128781 TCAGCCG-CCCTTTCGTCGTGAAGTTGAGA-TTGTGTTGTCTTG
66 CCAGCGGTCCC-TTCGTCGTGAAGTTGA-ACTTGCGTTGTC-TG
* * *
128823 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTATGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
128887 CCAGCGGTCCCTTCGTTGTGAAGCTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
128928 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
128993 CCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
129034 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
129099 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
129140 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAGTTTTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
129205 TCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
129246 GAGTTCAATATCTTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * **
129311 CTAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCCA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
129352 GAGTCCAATATCCTTCGTTTTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
129417 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
129458 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGCCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
129523 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
129564 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
129629 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
129670 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
129735 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
129776 GAGTCCAATATCCTTCGCCGTGAAGTTAAAATTGGCTCTGAAATTGGAAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
129841 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTATATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
129882 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
129947 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
129988 GAGTCCAATATCCTTGGCTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTG-TTGTTGTCAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
130052 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
130093 GAGT
1 GAGT
130097 GGCACGATAT
Statistics
Matches: 1247, Mismatches: 115, Indels: 27
0.90 0.08 0.02
Matches are distributed among these distances:
99 3 0.00
100 75 0.06
101 6 0.00
102 4 0.00
104 3 0.00
105 55 0.04
106 1097 0.88
107 4 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:130889 original size:22 final size:22
Alignment explanation
Indices: 130864--130914 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
130854 TTTGGTCAAA
* *
130864 GGTTTGGCTTTTGATGCTCATT
1 GGTTTGACATTTGATGCTCATT
**
130886 GGTTTGACATTTGATGCTCAAA
1 GGTTTGACATTTGATGCTCATT
130908 GGTTTGA
1 GGTTTGA
130915 TGGGGTAGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.18, C:0.12, G:0.27, T:0.43
Consensus pattern (22 bp):
GGTTTGACATTTGATGCTCATT
Found at i:131542 original size:17 final size:15
Alignment explanation
Indices: 131516--131582 Score: 71
Period size: 16 Copynumber: 4.2 Consensus size: 15
131506 TTTTTGTCCC
*
131516 TTTTTCTTTTTGATT
1 TTTTTCTTTTTTATT
*
131531 TTTGTTCTTTTTTTTGT
1 TTT-TTCTTTTTTAT-T
*
131548 TTTCTTCTTTTTTGTT
1 TTT-TTCTTTTTTATT
131564 TCTTTTCTTTTTTATT
1 T-TTTTCTTTTTTATT
131580 TTT
1 TTT
131583 CCCTTTTTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
15 5 0.11
16 23 0.52
17 16 0.36
ACGTcount: A:0.03, C:0.09, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTTTCTTTTTTATT
Found at i:131552 original size:14 final size:14
Alignment explanation
Indices: 131517--131574 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 14
131507 TTTTGTCCCT
131517 TTTTCTTTTTGATTT-
1 TTTTCTTTTT--TTTG
131532 TTGTTCTTTTTTTTG
1 TT-TTCTTTTTTTTG
131547 TTTTCTTCTTTTTTG
1 TTTTCTT-TTTTTTG
131562 -TTTCTTTTCTTTT
1 TTTTCTTTT-TTTT
131575 TTATTTTTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.05
14 18 0.46
15 11 0.28
16 8 0.21
ACGTcount: A:0.02, C:0.10, G:0.07, T:0.81
Consensus pattern (14 bp):
TTTTCTTTTTTTTG
Found at i:131569 original size:19 final size:17
Alignment explanation
Indices: 131538--131583 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
131528 ATTTTTGTTC
*
131538 TTTTTTTTGTTTTCTTCT
1 TTTTTTTTCTTTTCTT-T
131556 TTTTTGTTTCTTTTCTTT
1 TTTTT-TTTCTTTTCTTT
131574 TTTATTTTTC
1 TTT-TTTTTC
131584 CCTTTTTGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.02, C:0.11, G:0.04, T:0.83
Consensus pattern (17 bp):
TTTTTTTTCTTTTCTTT
Found at i:135926 original size:19 final size:19
Alignment explanation
Indices: 135872--135926 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
135862 AACCAATAAT
135872 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
* *
135891 GATTAAA-AAAATGAAATTG
1 AATAAAATAAAAT-AAATTG
135910 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
135927 GAAGATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 5 0.17
18 1 0.03
19 18 0.62
20 5 0.17
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.25
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:136035 original size:21 final size:21
Alignment explanation
Indices: 136011--136077 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 21
136001 GCAAAGAAAC
136011 TAAAAATATAATGAAAATAAA
1 TAAAAATATAATGAAAATAAA
*
136032 TAAATAGTATAAAT-AAAAT-AA
1 TAAA-AATAT-AATGAAAATAAA
136053 TAAAATATATATATAGAAATATAAA
1 TAAAA-ATATA-AT-GAAA-ATAAA
136078 AATGTATGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
20 2 0.06
21 15 0.42
22 9 0.25
23 6 0.17
24 2 0.06
25 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (21 bp):
TAAAAATATAATGAAAATAAA
Found at i:136058 original size:22 final size:21
Alignment explanation
Indices: 136011--136145 Score: 77
Period size: 22 Copynumber: 6.4 Consensus size: 21
136001 GCAAAGAAAC
136011 TAAAA-ATAT-AATGAAAATAA
1 TAAAATATATAAAT-AAAATAA
136031 -ATAAATAGTATAAATAAAATAA
1 TA-AAATA-TATAAATAAAATAA
*
136053 TAAAATATATATATAGAAAT-A
1 TAAAATATATAAATA-AAATAA
* ** *
136074 TAAAAATGTATGTATAATATAA
1 T-AAAATATATAAATAAAATAA
* *
136096 TAAAATA-CTAAATAGTAATAA
1 TAAAATATATAAATA-AAATAA
* *
136117 TAATAATAAATAAATGAAA-AA
1 TAA-AATATATAAATAAAATAA
136138 T-AAATATA
1 TAAAATATA
136146 CATATAATAT
Statistics
Matches: 90, Mismatches: 14, Indels: 23
0.71 0.11 0.18
Matches are distributed among these distances:
19 6 0.07
20 8 0.09
21 28 0.31
22 39 0.43
23 9 0.10
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (21 bp):
TAAAATATATAAATAAAATAA
Found at i:136078 original size:21 final size:22
Alignment explanation
Indices: 136024--136191 Score: 68
Period size: 22 Copynumber: 7.6 Consensus size: 22
136014 AAATATAATG
136024 AAAATAA-ATAAATAGTATAAAT
1 AAAATAATA-AAATAGTATAAAT
*
136046 AAAATAATAAAATA-TATATAT
1 AAAATAATAAAATAGTATAAAT
**
136067 AGAAAT-ATAAAA-ATGTATGTAT
1 A-AAATAATAAAATA-GTATAAAT
* *
136089 AATATAATAAAATA--CTAAAT
1 AAAATAATAAAATAGTATAAAT
* *
136109 AGTAATAATAATAATA-AATAAAT
1 A-AAATAATAA-AATAGTATAAAT
* *
136132 GAAA-AATAAATATACATATAATAT
1 AAAATAATAAA-ATA-GTATAA-AT
* * *
136156 TAACTAAAAAAATAGTA-ATAAT
1 AAAATAATAAAATAGTATA-AAT
136178 AGAAAT-ATAAAATA
1 A-AAATAATAAAATA
136192 AAATGAAGTA
Statistics
Matches: 111, Mismatches: 19, Indels: 32
0.69 0.12 0.20
Matches are distributed among these distances:
20 6 0.05
21 31 0.28
22 45 0.41
23 17 0.15
24 7 0.06
25 5 0.05
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (22 bp):
AAAATAATAAAATAGTATAAAT
Found at i:136280 original size:2 final size:2
Alignment explanation
Indices: 136275--136305 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
136265 ATAAAAAATA
136275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
136306 ATAATAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:136365 original size:4 final size:4
Alignment explanation
Indices: 136356--136398 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
136346 AAAAAATTAT
* *
136356 AATA AATA AATA AATA AATA AATA AATA AA-A TATA ATTA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
136399 TATATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 2 0.06
4 32 0.94
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:136401 original size:12 final size:12
Alignment explanation
Indices: 136356--136429 Score: 73
Period size: 12 Copynumber: 6.4 Consensus size: 12
136346 AAAAAATTAT
*
136356 AATAAATAAATA
1 AATAAATATATA
*
136368 AATAAATAAATA
1 AATAAATATATA
136380 AATAAA-ATATA
1 AATAAATATATA
*
136391 ATTAAATATAT-
1 AATAAATATATA
*
136402 -ATATATATATA
1 AATAAATATATA
* *
136413 TATATATATATA
1 AATAAATATATA
136425 AATAA
1 AATAA
136430 TAAGGGCTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
10 8 0.15
11 9 0.17
12 36 0.68
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AATAAATATATA
Found at i:136403 original size:2 final size:2
Alignment explanation
Indices: 136396--136424 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
136386 ATATAATTAA
136396 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
136425 AATAATAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:138018 original size:20 final size:22
Alignment explanation
Indices: 137993--138032 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
137983 AGTCGTATAT
137993 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
138013 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
138033 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:138085 original size:21 final size:21
Alignment explanation
Indices: 138060--138102 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
138050 CCCAGAATAG
*
138060 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
138081 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
138102 A
1 A
138103 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:138164 original size:21 final size:21
Alignment explanation
Indices: 138138--138180 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
138128 CTGTTGAACA
138138 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
138159 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
138180 G
1 G
138181 ACATTCTGTT
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:0.14, C:0.28, G:0.44, T:0.14
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTG
Found at i:139705 original size:20 final size:22
Alignment explanation
Indices: 139680--139719 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
139670 AGTCGTATAT
139680 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
139700 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
139720 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:139771 original size:21 final size:21
Alignment explanation
Indices: 139747--139789 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
139737 CCCAGAATAG
*
139747 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
139768 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
139789 A
1 A
139790 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:139850 original size:21 final size:21
Alignment explanation
Indices: 139825--139866 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
139815 CTGTTGAACA
139825 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
139846 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
139867 ACATTCTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.29, G:0.43, T:0.14
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:139925 original size:21 final size:21
Alignment explanation
Indices: 139900--139978 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
139890 AAAACCTGTA
139900 GGGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
139921 GGGGGTATCTGTA--CCC---
1 GGGGGTATCTGTACCCCCTGG
139937 -GGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
* *
139957 GGGGGAATCTATACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
139978 G
1 G
139979 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 32 0.64
ACGTcount: A:0.13, C:0.28, G:0.37, T:0.23
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:139941 original size:36 final size:36
Alignment explanation
Indices: 139901--139972 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
139891 AAACCTGTAG
* *
139901 GGGGTATCTGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
139937 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
139973 CCTGGGCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.14, C:0.28, G:0.35, T:0.24
Consensus pattern (36 bp):
GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
Found at i:139942 original size:15 final size:15
Alignment explanation
Indices: 139922--139951 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
139912 ACCCCCTGGG
139922 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
139937 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
139952 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:140100 original size:29 final size:31
Alignment explanation
Indices: 140068--140127 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
140058 AAACTTTGAA
140068 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
140097 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
140128 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:143245 original size:20 final size:22
Alignment explanation
Indices: 143220--143259 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
143210 AGTCGTATAT
143220 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
143240 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
143260 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:143311 original size:21 final size:21
Alignment explanation
Indices: 143287--143329 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
143277 CCCAGAATAG
*
143287 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
143308 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
143329 A
1 A
143330 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:143391 original size:20 final size:22
Alignment explanation
Indices: 143365--143405 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
143355 CTGTTGAACA
143365 GGGGG-GAATCGGTACCCCCCT
1 GGGGGAGAATCGGTACCCCCCT
143386 GGGGGAGAATCGGTACCCCC
1 GGGGGAGAATCGGTACCCCC
143406 TGGACATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.17, C:0.32, G:0.39, T:0.12
Consensus pattern (22 bp):
GGGGGAGAATCGGTACCCCCCT
Found at i:143467 original size:20 final size:20
Alignment explanation
Indices: 143442--143519 Score: 94
Period size: 20 Copynumber: 4.1 Consensus size: 20
143432 AAAACATGCA
143442 GGGGGTATCTGTACCCCCTG
1 GGGGGTATCTGTACCCCCTG
143462 GGGGGTATCTGTA---CCT-
1 GGGGGTATCTGTACCCCCTG
143478 -GGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCT-G
* *
143498 GGGGGAATCTATACCCCCTG
1 GGGGGTATCTGTACCCCCTG
143518 GG
1 GG
143520 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
18 3 0.06
20 16 0.32
21 16 0.32
ACGTcount: A:0.13, C:0.27, G:0.36, T:0.24
Consensus pattern (20 bp):
GGGGGTATCTGTACCCCCTG
Found at i:143483 original size:15 final size:15
Alignment explanation
Indices: 143463--143491 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
143453 TACCCCCTGG
143463 GGGGTATCTGTACCT
1 GGGGTATCTGTACCT
143478 GGGGTATCTGTACC
1 GGGGTATCTGTACC
143492 CCCTGGGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.34, T:0.31
Consensus pattern (15 bp):
GGGGTATCTGTACCT
Found at i:143641 original size:29 final size:32
Alignment explanation
Indices: 143609--143669 Score: 92
Period size: 29 Copynumber: 2.0 Consensus size: 32
143599 AAACTTTGAA
143609 TAAACTCAATT-AAGTCC-AAAAA-CATTTTG
1 TAAACTCAATTCAAGTCCAAAAAACCATTTTG
*
143638 TAAATTCAATTCAAGTCCAAAAAACCATTTTG
1 TAAACTCAATTCAAGTCCAAAAAACCATTTTG
143670 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 10 0.36
30 6 0.21
31 5 0.18
32 7 0.25
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (32 bp):
TAAACTCAATTCAAGTCCAAAAAACCATTTTG
Found at i:145139 original size:61 final size:60
Alignment explanation
Indices: 145043--145189 Score: 168
Period size: 61 Copynumber: 2.4 Consensus size: 60
145033 AAAATGGTCA
* * * * ** *
145043 TTAAACTTTTGAATATTTTAAATTCATCTACAAACTATGATTCTCATTCTAAATTAGTTC
1 TTAAACTTTTGAATATTTTAATTTCACCCACAAACTATAAACCTCATTCTAAATTAGTCC
* * *
145103 TTAAACTTTTTGAATATTCTAATTTCACCCATAAACTATAAACCTCTTTCTAAATTAGTCC
1 TTAAAC-TTTTGAATATTTTAATTTCACCCACAAACTATAAACCTCATTCTAAATTAGTCC
** *
145164 CCAAACTTTTGAAGATTTTAATTTCA
1 TTAAACTTTTGAATATTTTAATTTCA
145190 TCCTCAAAGT
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
60 24 0.33
61 48 0.67
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.43
Consensus pattern (60 bp):
TTAAACTTTTGAATATTTTAATTTCACCCACAAACTATAAACCTCATTCTAAATTAGTCC
Found at i:145441 original size:60 final size:60
Alignment explanation
Indices: 145320--145447 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 60
145310 GTATATACAT
* * * * * *
145320 ATAGTTTGGGATGAAATTGGAATTTTCAAAAAGTTTGAGGATTAATTTAATATAATAGTC
1 ATAGTTTGGGATGAAATTGAAAATATCAAAAAGTTTAAGGACTAATTTAAAATAATAGTC
* * *
145380 ATAGTTTAGGGATGAAATT-AAAATATCTAAAAGTTTAAGGACTAATTTAAAATGATGGTC
1 ATAGTTT-GGGATGAAATTGAAAATATCAAAAAGTTTAAGGACTAATTTAAAATAATAGTC
*
145440 ATACTTTG
1 ATAGTTTG
145448 AGAATATATG
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
59 1 0.02
60 45 0.79
61 11 0.19
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.37
Consensus pattern (60 bp):
ATAGTTTGGGATGAAATTGAAAATATCAAAAAGTTTAAGGACTAATTTAAAATAATAGTC
Found at i:148825 original size:61 final size:60
Alignment explanation
Indices: 148729--148875 Score: 168
Period size: 61 Copynumber: 2.4 Consensus size: 60
148719 AAAATGGTCA
* * * * ** *
148729 TTAAACTTTTGAATATTTTAAATTCATCTACAAACTATGATTCTCATTCTAAATTAGTTC
1 TTAAACTTTTGAATATTTTAATTTCACCCACAAACTATAAACCTCATTCTAAATTAGTCC
* * *
148789 TTAAACTTTTTGAATATTCTAATTTCACCCATAAACTATAAACCTCTTTCTAAATTAGTCC
1 TTAAAC-TTTTGAATATTTTAATTTCACCCACAAACTATAAACCTCATTCTAAATTAGTCC
** *
148850 CCAAACTTTTGAAGATTTTAATTTCA
1 TTAAACTTTTGAATATTTTAATTTCA
148876 TCCTCAAATT
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
60 24 0.33
61 48 0.67
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.43
Consensus pattern (60 bp):
TTAAACTTTTGAATATTTTAATTTCACCCACAAACTATAAACCTCATTCTAAATTAGTCC
Found at i:152625 original size:2 final size:2
Alignment explanation
Indices: 152620--152660 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
152610 AAAAGATTGA
152620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
152661 TTTAATGGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:154019 original size:11 final size:12
Alignment explanation
Indices: 153989--154021 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
153979 AGCTCAAGAC
153989 TCAAACTCAATT
1 TCAAACTCAATT
*
154001 TTAAACTCAA-T
1 TCAAACTCAATT
154012 TCAAACTCAA
1 TCAAACTCAA
154022 CTGATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (12 bp):
TCAAACTCAATT
Found at i:154188 original size:12 final size:12
Alignment explanation
Indices: 154171--154204 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
154161 GTATCGCAAA
154171 TTCGCGTTGCAT
1 TTCGCGTTGCAT
154183 TTCGCGTTGCAT
1 TTCGCGTTGCAT
154195 TTCGCGTTGC
1 TTCGCGTTGC
154205 GATAGTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.06, C:0.26, G:0.26, T:0.41
Consensus pattern (12 bp):
TTCGCGTTGCAT
Found at i:154244 original size:21 final size:21
Alignment explanation
Indices: 154220--154352 Score: 116
Period size: 21 Copynumber: 6.4 Consensus size: 21
154210 TTGAAAATCG
154220 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
*
154241 CGTTGCGATAATCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * * *
154262 CGTTGTGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
154280 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
* * *
154303 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
154321 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
154344 CGTTGCGAT
1 CGTTGCGAT
154353 TTTCCATTTC
Statistics
Matches: 87, Mismatches: 15, Indels: 20
0.71 0.12 0.16
Matches are distributed among these distances:
18 4 0.05
19 8 0.09
20 17 0.20
21 46 0.53
22 8 0.09
23 4 0.05
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.38
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:154328 original size:20 final size:20
Alignment explanation
Indices: 154262--154372 Score: 68
Period size: 20 Copynumber: 5.5 Consensus size: 20
154252 TCTACAGTGT
*
154262 CGTTGTGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* * *
154282 CGTTGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTCCATTTCG
154302 TCGTTGCGATTTTCCATTTCG
1 -CGTTGCGATTTTCCATTTCG
* * *
154323 CGTTGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTCCATTTCG
*
154343 TCGTTGCGATTTTCCATTTCA
1 -CGTTGCGATTTTCCATTTCG
154364 CGTTGCGAT
1 CGTTGCGAT
154373 AGTTGAAAAT
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
19 8 0.12
20 30 0.45
21 21 0.31
22 8 0.12
ACGTcount: A:0.14, C:0.22, G:0.23, T:0.41
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:154348 original size:62 final size:59
Alignment explanation
Indices: 154282--154526 Score: 170
Period size: 62 Copynumber: 4.2 Consensus size: 59
154272 TTCCATTTCG
*
154282 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
1 CGTTGCGAT-GT-TACA-TGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTGTACAGTGT
* * * * ** ** *
154344 CGTTGCGATTTTCCATTTCACGTTGCGATAGTTGAAAATCGCGTTGCGATAGTGTACACTGT
1 CGTTGCGATGTTACATGT--CGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTGTACAGTGT
* * *
154406 CATTGC---G----A--TCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCG-
1 CGTTGCGATGTTACATGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTGT-ACAGT-GT
* * *
154456 CGTTGCGATAGTGTACAGTGTCATTGCGATTTTCCATCTCGCATTGCGATAGTGTACAGTGT
1 CGTTGCGAT-GT-TACA-TGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTGTACAGTGT
154518 CGTTGCGAT
1 CGTTGCGAT
154527 TTTCCATTTC
Statistics
Matches: 139, Mismatches: 25, Indels: 38
0.69 0.12 0.19
Matches are distributed among these distances:
49 1 0.01
50 26 0.19
51 10 0.07
53 1 0.01
54 1 0.01
55 1 0.01
59 3 0.02
60 3 0.02
61 11 0.08
62 81 0.58
63 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (59 bp):
CGTTGCGATGTTACATGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTGTACAGTGT
Found at i:154389 original size:82 final size:82
Alignment explanation
Indices: 154192--154485 Score: 296
Period size: 71 Copynumber: 3.7 Consensus size: 82
154182 TTTCGCGTTG
154192 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTGTCGTTGCGATAATCTAC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATA-TCTACAGTGTCGTTGCGATAATCTAC
*
154257 AGTGTCGTTGTGATTTTC
65 AGTGTCGTTGCGATTTTC
* * * * * *
154275 CATTTCGCGTTGCGATAGTCT-ACAGT-GTCGTTGCGAT-TTTCCA-TTTCGCGTTGCGATAGTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATATCTACAGTGT--CGTTGCGATAATC
154336 TACAGTGTCGTTGCGATTTTC
62 TACAGTGTCGTTGCGATTTTC
* * * *
154357 CATTTCACGTTGCGATAGTTGAAAATCGCGTTGCGATAGTGTACACTGTCATTGCG---------
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATA-TCTACAGTGTCGTTGCGATAATCTAC
154413 A---TCGTTGCGATTTTC
65 AGTGTCGTTGCGATTTTC
* *
154428 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTGTACAGTGTCATTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATA-TCTACAGTGTCGTTGCGAT
154486 TTTCCATCTC
Statistics
Matches: 184, Mismatches: 16, Indels: 32
0.79 0.07 0.14
Matches are distributed among these distances:
71 68 0.37
74 1 0.01
80 2 0.01
81 5 0.03
82 63 0.34
83 38 0.21
84 5 0.03
85 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (82 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATATCTACAGTGTCGTTGCGATAATCTACA
GTGTCGTTGCGATTTTC
Found at i:154393 original size:41 final size:41
Alignment explanation
Indices: 154241--154375 Score: 243
Period size: 41 Copynumber: 3.3 Consensus size: 41
154231 TCTACAGTGT
* *
154241 CGTTGCGATAATCTACAGTGTCGTTGTGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
154282 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
*
154323 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCA
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
154364 CGTTGCGATAGT
1 CGTTGCGATAGT
154376 TGAAAATCGC
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 91 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
Found at i:154482 original size:21 final size:21
Alignment explanation
Indices: 154458--154526 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
154448 GAAAATCGCG
154458 TTGCGATAGTGTACAGTGTCA
1 TTGCGATAGTGTACAGTGTCA
* * *
154479 TTGCGAT--TTTCCA-TCTCGCA
1 TTGCGATAGTGTACAGTGT--CA
*
154499 TTGCGATAGTGTACAGTGTCG
1 TTGCGATAGTGTACAGTGTCA
154520 TTGCGAT
1 TTGCGAT
154527 TTTCCATTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
18 2 0.06
19 4 0.11
20 9 0.25
21 15 0.42
22 4 0.11
23 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (21 bp):
TTGCGATAGTGTACAGTGTCA
Found at i:154503 original size:41 final size:41
Alignment explanation
Indices: 154453--154573 Score: 206
Period size: 41 Copynumber: 3.0 Consensus size: 41
154443 TAGTTGAAAA
*
154453 TCGCGTTGCGATAGTGTACAGTGTCATTGCGATTTTCCATC
1 TCGCGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATC
* *
154494 TCGCATTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATC
*
154535 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCA
1 TCGCGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCA
154574 AATTCGTCGC
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 75 1.00
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (41 bp):
TCGCGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATC
Found at i:154687 original size:6 final size:6
Alignment explanation
Indices: 154676--154717 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
154666 GACACGTACT
154676 ACCACG ACCACG ACCACG ACCACG ACC-CG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
154718 GACGGCGGCG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:155203 original size:5 final size:5
Alignment explanation
Indices: 155193--155219 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
155183 CCGCCGCCGC
155193 CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CG
155220 GGTCGTGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.37
Consensus pattern (5 bp):
CGTCT
Found at i:155231 original size:6 final size:6
Alignment explanation
Indices: 155220--155259 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
155210 TCTCGTCTCG
155220 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
155260 ATACGTGTCT
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:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:155356 original size:20 final size:20
Alignment explanation
Indices: 155331--155403 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
155321 ACTGTAGACT
155331 ATCGCAACGCGAAATAAAAA
1 ATCGCAACGCGAAATAAAAA
** * **
155351 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATAAAAA
*
155372 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATAAAAA
*
155392 ATCGCAATGCGA
1 ATCGCAACGCGA
155404 TTTTCAACTA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATAAAAA
Found at i:155356 original size:41 final size:41
Alignment explanation
Indices: 155310--155427 Score: 130
Period size: 41 Copynumber: 2.9 Consensus size: 41
155300 AGAGAAAATT
*
155310 ATCGCAACGATACTGT-AGACTATCGCAACGCGAAATAAAAA
1 ATCGCAACGAGACTGTCA-ACTATCGCAACGCGAAATAAAAA
* * * *
155351 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATAGAAA
1 ATCGCAACGAGACTGTCAACTATCGCAACGCGAAATAAAAA
* * * * *
155392 ATCGCAATGCGATTTTCAACTATCACAACGCGAAAT
1 ATCGCAACGAGACTGTCAACTATCGCAACGCGAAAT
155428 GCAGCGCGAA
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 68 0.99
42 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGACTGTCAACTATCGCAACGCGAAATAAAAA
Found at i:155377 original size:21 final size:21
Alignment explanation
Indices: 155351--155424 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
155341 GAAATAAAAA
155351 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
155372 ATCGCAACGCGAAATAGAA-A
1 ATCGCAACGCGATTTTCAACT
*
155392 ATCGCAATGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
155413 ATCACAACGCGA
1 ATCGCAACGCGA
155425 AATGCAGCGC
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 14 0.36
21 25 0.64
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:158047 original size:14 final size:14
Alignment explanation
Indices: 158028--158057 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
158018 TATAATTATC
*
158028 AATAATGTATTTTT
1 AATAATGTAATTTT
158042 AATAATGTAATTTT
1 AATAATGTAATTTT
158056 AA
1 AA
158058 AAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Done.