Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005083.1 Hibiscus syriacus cultivar Beakdansim tig00011417_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: 344126
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:187 original size:31 final size:32
Alignment explanation
Indices: 126--188 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
116 CTGTTAATAA
126 CTAAGTAGTTTAGATATCATATGACTCTTATCT
1 CTAAGTAGTTTAGATATCATA-GACTCTTATCT
159 CTAAGTAGTTTAGATATTC-TA-ACTCTTATC
1 CTAAGTAGTTTAGATA-TCATAGACTCTTATC
189 ACTTAATAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 9 0.31
33 18 0.62
34 2 0.07
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (32 bp):
CTAAGTAGTTTAGATATCATAGACTCTTATCT
Found at i:6664 original size:13 final size:13
Alignment explanation
Indices: 6646--6670 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6636 GACTTATAGC
6646 ATAAGAACTTACG
1 ATAAGAACTTACG
6659 ATAAGAACTTAC
1 ATAAGAACTTAC
6671 TTTATGCACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (13 bp):
ATAAGAACTTACG
Found at i:7668 original size:14 final size:14
Alignment explanation
Indices: 7624--7670 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
7614 ACGAGTCAGG
*
7624 CGGGTTGGGTCAGA
1 CGGGTTGGGTCAAA
* *
7638 CAGGTTGGGTCATA
1 CGGGTTGGGTCAAA
*
7652 CGGGTTAGGTCAAA
1 CGGGTTGGGTCAAA
7666 CGGGT
1 CGGGT
7671 CAAGTTGACC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.19, C:0.15, G:0.43, T:0.23
Consensus pattern (14 bp):
CGGGTTGGGTCAAA
Found at i:12896 original size:2 final size:2
Alignment explanation
Indices: 12889--12960 Score: 135
Period size: 2 Copynumber: 35.5 Consensus size: 2
12879 GGTTTATACG
12889 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12931 AT AT AT AT AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
12961 AAAAATCAAT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 67 0.97
3 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14324 original size:24 final size:24
Alignment explanation
Indices: 14271--14324 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
14261 ACGACTCAGC
* *
14271 TGGACTAGTTCGGTCTGATTTAGA
1 TGGACTAGTTAGGTCTAATTTAGA
* *
14295 TAGACTAGTTAGGTTTAATTTA-A
1 TGGACTAGTTAGGTCTAATTTAGA
14318 TTGGACT
1 -TGGACT
14325 TATTTGGCCT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (24 bp):
TGGACTAGTTAGGTCTAATTTAGA
Found at i:20393 original size:16 final size:16
Alignment explanation
Indices: 20372--20404 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20362 TCTCGGCTCA
20372 ACCTCATTGTTCACGT
1 ACCTCATTGTTCACGT
20388 ACCTCATTGTTCACGT
1 ACCTCATTGTTCACGT
20404 A
1 A
20405 GATCTAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.36
Consensus pattern (16 bp):
ACCTCATTGTTCACGT
Found at i:22268 original size:11 final size:12
Alignment explanation
Indices: 22239--22274 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
22229 AATAAGGAAG
22239 AAGAAAAGAAAA
1 AAGAAAAGAAAA
22251 AAGAAAAGAAAA
1 AAGAAAAGAAAA
22263 AA-AAAAGAAAA
1 AAGAAAAGAAAA
22274 A
1 A
22275 GGATGTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAGAAAAGAAAA
Found at i:22275 original size:17 final size:17
Alignment explanation
Indices: 22239--22273 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
22229 AATAAGGAAG
22239 AAGAAAAGAAAAAAGAA
1 AAGAAAAGAAAAAAGAA
22256 AAGAAAA-AAAAAAGAA
1 AAGAAAAGAAAAAAGAA
22272 AA
1 AA
22274 AGGATGTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAGAAAAGAAAAAAGAA
Found at i:29990 original size:2 final size:2
Alignment explanation
Indices: 29983--30013 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29973 CTTTTCAGAA
29983 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
30014 AACACAATCT
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:31971 original size:20 final size:19
Alignment explanation
Indices: 31948--31987 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
31938 AGTATATTAT
31948 TAATAAAAAAATATGAAAAA
1 TAATAAAAAAATAT-AAAAA
* *
31968 TAATTAAAATATATAAAAA
1 TAATAAAAAAATATAAAAA
31987 T
1 T
31988 TTAAAATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (19 bp):
TAATAAAAAAATATAAAAA
Found at i:32963 original size:10 final size:10
Alignment explanation
Indices: 32948--32987 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
32938 TTTATCACAC
32948 CAAATTCTCT
1 CAAATTCTCT
32958 CAAATTCTCT
1 CAAATTCTCT
* *
32968 TAACTTCTCT
1 CAAATTCTCT
*
32978 CAAATACTCT
1 CAAATTCTCT
32988 TATAATCTCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:32977 original size:20 final size:20
Alignment explanation
Indices: 32952--32989 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
32942 TCACACCAAA
*
32952 TTCTCTCAAATTCTCTTAAC
1 TTCTCTCAAATACTCTTAAC
32972 TTCTCTCAAATACTCTTA
1 TTCTCTCAAATACTCTTA
32990 TAATCTCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (20 bp):
TTCTCTCAAATACTCTTAAC
Found at i:33045 original size:25 final size:26
Alignment explanation
Indices: 33007--33071 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 26
32997 TTCTAAGGTA
*
33007 TATTTTATTATATTTTTAATATTTT-G
1 TATTTAATT-TATTTTTAATATTTTAG
*
33033 TATTTAATTTA--TTTAATATTTTACT
1 TATTTAATTTATTTTTAATATTTTA-G
33058 TATTTAATTT-TTTT
1 TATTTAATTTATTTT
33072 GCAGATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
23 11 0.33
25 12 0.36
26 10 0.30
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (26 bp):
TATTTAATTTATTTTTAATATTTTAG
Found at i:35103 original size:3 final size:3
Alignment explanation
Indices: 35095--35133 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
35085 ACCTACTCAG
* * *
35095 GAC GAC GAC GAT GAC GAC GAC GAA GAC AAC GAC GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
35134 AGCTAGGAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.38, C:0.28, G:0.31, T:0.03
Consensus pattern (3 bp):
GAC
Found at i:40748 original size:30 final size:29
Alignment explanation
Indices: 40689--40748 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
40679 AGTTGAAGGA
* *
40689 CGAACTTGAACTTATAAAATTTTAGGGAG
1 CGAACTTGAACTAATAAAATTTAAGGGAG
*
40718 CGAACTTGAACTAATAAAGTTATAAGGGAG
1 CGAACTTGAACTAATAAAATT-TAAGGGAG
40748 C
1 C
40749 AAAAACATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.27
Consensus pattern (29 bp):
CGAACTTGAACTAATAAAATTTAAGGGAG
Found at i:41961 original size:2 final size:2
Alignment explanation
Indices: 41954--41979 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41944 CAAGGCCTCG
41954 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
41980 TGCTATGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43757 original size:70 final size:70
Alignment explanation
Indices: 43644--43781 Score: 267
Period size: 70 Copynumber: 2.0 Consensus size: 70
43634 GGCAGTGCAG
43644 ACATGTTCAAAACGTGTTATTAGTAGTGGTAGTTGTTATGGAGGCCAAGGAAGTTATGGTGGTGG
1 ACATGTTCAAAACGTGTTATTAGTAGTGGTAGTTGTTATGGAGGCCAAGGAAGTTATGGTGGTGG
43709 TAATA
66 TAATA
*
43714 ACATGTTCAAAACGTGTTATTGGTAGTGGTAGTTGTTATGGAGGCCAAGGAAGTTATGGTGGTGG
1 ACATGTTCAAAACGTGTTATTAGTAGTGGTAGTTGTTATGGAGGCCAAGGAAGTTATGGTGGTGG
43779 TAA
66 TAA
43782 AAACTATGGC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.28, C:0.07, G:0.33, T:0.33
Consensus pattern (70 bp):
ACATGTTCAAAACGTGTTATTAGTAGTGGTAGTTGTTATGGAGGCCAAGGAAGTTATGGTGGTGG
TAATA
Found at i:44767 original size:43 final size:41
Alignment explanation
Indices: 44716--45058 Score: 237
Period size: 43 Copynumber: 7.9 Consensus size: 41
44706 TAATTTTAGT
44716 TTTTTATCTTTATAATTGAGGTCCCTAATTTTTATAATC-CTAC
1 TTTTTA-CTTTATAATTGAGGTCCCTAATTTTT-TAATCTC-AC
*
44759 TTTTTATCTTTATAATTGAGG-CCTTAATTTTTTGCAATCTC-C
1 TTTTTA-CTTTATAATTGAGGTCCCTAATTTTTT--AATCTCAC
* * *
44801 TTTTTTTTTTAAATTTATAATTGATGAT-CCTAAGTTTTCTAATCTCAC
1 -----TTTTT-ACTTTATAATTGA-GGTCCCTAA-TTTTTTAATCTCAC
* * * ** * *
44849 TTTGTACGTTTATAATTGAGCT-CTTGGTTTTATTTTAATATCAA
1 TTTTTAC-TTTATAATTGAGGTCCCT--AATT-TTTTAATCTCAC
* ** * *
44893 TTTTTGCCTTTATAATTGAGACCCCTAATTTTTCAATCTCAT
1 TTTTT-ACTTTATAATTGAGGTCCCTAATTTTTTAATCTCAC
* *
44935 TTTTTACTTATATAATTTAGGCCCCTAATTTTTTCAATCTCAC
1 TTTTTACTT-TATAATTGAGGTCCCTAATTTTTT-AATCTCAC
* * *
44978 TTTTTACTTTTAAAATTGAGGTCTCTATTTTTTTAATCTCAC
1 TTTTTAC-TTTATAATTGAGGTCCCTAATTTTTTAATCTCAC
*
45020 TTTTTACCTTTATAATTGAGGTCTCTAATTTTTTTAATC
1 TTTTTA-CTTTATAATTGAGGTCCCTAA-TTTTTTAATC
45059 ATAATTGAGG
Statistics
Matches: 240, Mismatches: 36, Indels: 48
0.74 0.11 0.15
Matches are distributed among these distances:
41 4 0.02
42 83 0.35
43 88 0.37
44 28 0.12
45 3 0.01
47 22 0.09
48 7 0.03
49 5 0.02
ACGTcount: A:0.24, C:0.15, G:0.08, T:0.52
Consensus pattern (41 bp):
TTTTTACTTTATAATTGAGGTCCCTAATTTTTTAATCTCAC
Found at i:45091 original size:30 final size:28
Alignment explanation
Indices: 45031--45091 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 28
45021 TTTTACCTTT
*
45031 ATAATTGAGGTCTCTAATTTTTTTAATC
1 ATAATTGAGGTCTCTAATTTTTTCAATC
45059 ATAATTGAGGTCTCTAATTTCTTGTCAATC
1 ATAATTGAGGTCTCTAATTT-TT-TCAATC
45089 ATA
1 ATA
45092 CTTTTTGCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 20 0.67
29 2 0.07
30 8 0.27
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (28 bp):
ATAATTGAGGTCTCTAATTTTTTCAATC
Found at i:47209 original size:27 final size:26
Alignment explanation
Indices: 47155--47214 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
47145 CAATTTTGAA
*
47155 TTTAATTATATGGATTATATTTATAT
1 TTTAATTATATAGATTATATTTATAT
47181 TTATAATTATATAG-TT-TATTATATGAT
1 TT-TAATTATATAGATTATATT-TAT-AT
47208 TTTAATT
1 TTTAATT
47215 TTAGGATGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 4 0.13
26 12 0.40
27 14 0.47
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (26 bp):
TTTAATTATATAGATTATATTTATAT
Found at i:49882 original size:2 final size:2
Alignment explanation
Indices: 49877--49901 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49867 ATTTTTTTAT
49877 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
49902 TAGATTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52129 original size:16 final size:16
Alignment explanation
Indices: 52107--52143 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
52097 ATCTTAAATG
52107 ATTCTTGAAACATCAA
1 ATTCTTGAAACATCAA
*
52123 TTTCTTGAAACATCAA
1 ATTCTTGAAACATCAA
52139 ATTCT
1 ATTCT
52144 AATGTAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTCTTGAAACATCAA
Found at i:55270 original size:37 final size:36
Alignment explanation
Indices: 55226--55503 Score: 228
Period size: 35 Copynumber: 7.4 Consensus size: 36
55216 TATATATATA
*
55226 TATATATATATGTTTTCAAAAATTATTTTTCAAAACC
1 TATATATATATGTTTTCAAAAATTGTTTTTCAAAA-C
55263 ATAATATATATATGTTTTC-AAAATTGTTTTTCAAAAC
1 -T-ATATATATATGTTTTCAAAAATTGTTTTTCAAAAC
* *
55300 TTTATAGTATATATGTTTTTAAAAAATGTTTTTCAAAACC
1 --TATA-TATATATGTTTTCAAAAATTGTTTTTCAAAA-C
*
55340 ATATAATATATAT-TTTTTAAAAA-TGTTTTTCAAAAC
1 -TAT-ATATATATGTTTTCAAAAATTGTTTTTCAAAAC
* * *
55376 TATATAATATACGTTTTCCAAAAAAAAGTGTTTTTCGAAAC
1 TATAT-ATATATGTTTT-C---AAAAATTGTTTTTCAAAAC
* *
55417 TATATAATATACGTTTTCAAAAA-CGTGTTTTCAAAAC
1 TATAT-ATATATGTTTTCAAAAATTGT-TTTTCAAAAC
** **
55454 TATA-ATATATGTTTT-TTAAATCATATTTTCAAAAC
1 TATATATATATGTTTTCAAAAATTGT-TTTTCAAAAC
*
55489 CATATA-ATATGTTTT
1 TATATATATATGTTTT
55504 TAAACCGATT
Statistics
Matches: 208, Mismatches: 16, Indels: 35
0.80 0.06 0.14
Matches are distributed among these distances:
34 5 0.02
35 42 0.20
36 8 0.04
37 34 0.16
38 40 0.19
39 42 0.20
40 8 0.04
41 29 0.14
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (36 bp):
TATATATATATGTTTTCAAAAATTGTTTTTCAAAAC
Found at i:55279 original size:39 final size:38
Alignment explanation
Indices: 55225--55498 Score: 237
Period size: 39 Copynumber: 7.3 Consensus size: 38
55215 ATATATATAT
*
55225 ATATATATATATGTTTTCAAAAATTATTTTTCAAAACC
1 ATATATATATATGTTTTCAAAAATTGTTTTTCAAAACC
*
55263 ATAATATATATATGTTTTC-AAAATTGTTTTTCAAAACT
1 AT-ATATATATATGTTTTCAAAAATTGTTTTTCAAAACC
* * *
55301 TTATAGTATATATGTTTTTAAAAAATGTTTTTCAAAACC
1 ATATA-TATATATGTTTTCAAAAATTGTTTTTCAAAACC
* *
55340 ATATAATATATAT-TTTTTAAAAA-TGTTTTTCAAAACT
1 ATAT-ATATATATGTTTTCAAAAATTGTTTTTCAAAACC
* * * *
55377 ATATA-ATATACGTTTTCCAAAAAAAAGTGTTTTTCGAAACT
1 ATATATATATATGTTTT-C---AAAAATTGTTTTTCAAAACC
* *
55418 ATATA-ATATACGTTTTCAAAAA-CGTGTTTTCAAAA-C
1 ATATATATATATGTTTTCAAAAATTGT-TTTTCAAAACC
** **
55454 -TATA-ATATATGTTTT-TTAAATCATATTTTCAAAACC
1 ATATATATATATGTTTTCAAAAATTGT-TTTTCAAAACC
55490 ATATA-ATAT
1 ATATATATAT
55499 GTTTTTAAAC
Statistics
Matches: 203, Mismatches: 19, Indels: 29
0.81 0.08 0.12
Matches are distributed among these distances:
34 3 0.01
35 30 0.15
36 8 0.04
37 41 0.20
38 42 0.21
39 43 0.21
40 7 0.03
41 29 0.14
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.44
Consensus pattern (38 bp):
ATATATATATATGTTTTCAAAAATTGTTTTTCAAAACC
Found at i:55427 original size:76 final size:74
Alignment explanation
Indices: 55224--55457 Score: 238
Period size: 77 Copynumber: 3.1 Consensus size: 74
55214 AATATATATA
* * * * * *
55224 TATATATATATATGTTTTCAAAAATTATTTTTCAAAACCATAATATATATATGTTTTCAAAATTG
1 TATATAGATATACGTTTTAAAAAAATGTTTTTCAAAACCAT-ATATATATAT-TTTTCAAAAATG
55289 TTTTTCAAAAC
64 TTTTTCAAAAC
* * * *
55300 TTTATAGTATATATGTTTTTAAAAAATGTTTTTCAAAACCATATAATATATATTTTTTAAAAATG
1 TATATAG-ATATACGTTTTAAAAAAATGTTTTTCAAAACCATAT-ATATATATTTTTCAAAAATG
55365 TTTTTCAAAAC
64 TTTTTCAAAAC
* * *
55376 TATATA-ATATACGTTTTCCAAAAAAAAGTGTTTTTCGAAACTATATA-ATATACGTTTTCAAAA
1 TATATAGATATACGTTTT---AAAAAAA-TGTTTTTCAAAACCATATATATATA-TTTTTCAAAA
*
55439 ACGTGTTTTCAAAAC
61 ATGT-TTTTCAAAAC
55454 TATA
1 TATA
55458 ATATATGTTT
Statistics
Matches: 135, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
74 10 0.07
76 38 0.28
77 57 0.42
78 30 0.22
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (74 bp):
TATATAGATATACGTTTTAAAAAAATGTTTTTCAAAACCATATATATATATTTTTCAAAAATGTT
TTTCAAAAC
Found at i:63540 original size:24 final size:24
Alignment explanation
Indices: 63513--63563 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
63503 ATTGTCTGAA
*
63513 ACTTTCGTTATGCTTATTCTCCAT
1 ACTTTCGTTATGATTATTCTCCAT
*
63537 ACTTTCGTTATGATTCTTCTCCAT
1 ACTTTCGTTATGATTATTCTCCAT
63561 ACT
1 ACT
63564 CTCCTGGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.25, G:0.08, T:0.49
Consensus pattern (24 bp):
ACTTTCGTTATGATTATTCTCCAT
Found at i:67144 original size:42 final size:42
Alignment explanation
Indices: 67085--67182 Score: 196
Period size: 42 Copynumber: 2.3 Consensus size: 42
67075 TAAGCTCTTT
67085 CTGGAACCCACTTGCATGCACCAAAATTGCCAGACCAAAAAC
1 CTGGAACCCACTTGCATGCACCAAAATTGCCAGACCAAAAAC
67127 CTGGAACCCACTTGCATGCACCAAAATTGCCAGACCAAAAAC
1 CTGGAACCCACTTGCATGCACCAAAATTGCCAGACCAAAAAC
67169 CTGGAACCCACTTG
1 CTGGAACCCACTTG
67183 AAGAGAACAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.36, C:0.34, G:0.15, T:0.15
Consensus pattern (42 bp):
CTGGAACCCACTTGCATGCACCAAAATTGCCAGACCAAAAAC
Found at i:68651 original size:85 final size:85
Alignment explanation
Indices: 68536--68696 Score: 236
Period size: 85 Copynumber: 1.9 Consensus size: 85
68526 TGTAAGTCGT
* * * *
68536 ACAAATGTGTGTCATCTTCATTTATTACGGGGGCTTCAATGACACGCAAT-A-TAAGTCATACAT
1 ACAAATGTGTGTCATCTTCATTTATAACGGGGGCATAAATGACACGCAATGAGT-A-TCATAAAT
*
68599 GCGTGTCATAAATTTATGACAC
64 GCGCGTCATAAATTTATGACAC
*
68621 ACAAATGTGTGTCATCTTCATTTATAACGGGGGCATAAATGACGCGCAATGAGTATCATAAATGC
1 ACAAATGTGTGTCATCTTCATTTATAACGGGGGCATAAATGACACGCAATGAGTATCATAAATGC
68686 GCGTCATAAAT
66 GCGTCATAAAT
68697 GCTTGTCATA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
85 65 0.96
86 2 0.03
87 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (85 bp):
ACAAATGTGTGTCATCTTCATTTATAACGGGGGCATAAATGACACGCAATGAGTATCATAAATGC
GCGTCATAAATTTATGACAC
Found at i:68692 original size:13 final size:13
Alignment explanation
Indices: 68676--68719 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
68666 GCAATGAGTA
*
68676 TCATAAATGCGCG
1 TCATAAATGCGTG
*
68689 TCATAAATGCTTG
1 TCATAAATGCGTG
*
68702 TCATAAATACGTG
1 TCATAAATGCGTG
68715 TCATA
1 TCATA
68720 GATTTATAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TCATAAATGCGTG
Found at i:69183 original size:10 final size:10
Alignment explanation
Indices: 69165--69194 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
69155 GTGAATGTAA
69165 AGAAAAAAAG
1 AGAAAAAAAG
69175 AGGAAAAAAAG
1 A-GAAAAAAAG
69186 AGAAAAAAA
1 AGAAAAAAA
69195 ATAACAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAG
Found at i:73694 original size:16 final size:16
Alignment explanation
Indices: 73658--73688 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
73648 TTGTACCTGA
*
73658 AAATAAAAACTGAAAT
1 AAATAAAAACTAAAAT
73674 AAATAAAAACTAAAA
1 AAATAAAAACTAAAA
73689 GTAATATGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.16
Consensus pattern (16 bp):
AAATAAAAACTAAAAT
Found at i:73835 original size:39 final size:38
Alignment explanation
Indices: 73730--73838 Score: 114
Period size: 38 Copynumber: 2.8 Consensus size: 38
73720 AGGTTTCCAA
* *
73730 AAAAATCATTTTT-AAAACTATATATTACATATGATTTC
1 AAAAATTATTTTTCAAAACTATATA-TATATATGATTTC
* * * *
73768 AAAAATTA-TTTTCGAAATTATCTAATATATATGTTTTC
1 AAAAATTATTTTTCAAAACTATAT-ATATATATGATTTC
*
73806 AAAAATTATTTTTCAAAACCATAATATATATAT
1 AAAAATTATTTTTCAAAACTAT-ATATATATAT
73839 ATATATATAT
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
37 4 0.07
38 33 0.58
39 19 0.33
40 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (38 bp):
AAAAATTATTTTTCAAAACTATATATATATATGATTTC
Found at i:73836 original size:2 final size:2
Alignment explanation
Indices: 73829--73862 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
73819 CAAAACCATA
73829 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
73863 TCAAAAATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73905 original size:39 final size:37
Alignment explanation
Indices: 73846--74046 Score: 237
Period size: 39 Copynumber: 5.3 Consensus size: 37
73836 TATATATATA
* *
73846 TATATATATATATATATTCAAAAATTGTTTTTCAAAAC
1 TATATATATATATGTTTTCAAAAA-TGTTTTTCAAAAC
*
73884 CATAATATATATATGTTTTCAAAAAATGTTTTTCAAAAC
1 TAT-ATATATATATGTTTTC-AAAAATGTTTTTCAAAAC
*
73923 CATATAATATATATGTTTTCAAAAATGTTTTTCAAAAC
1 TATAT-ATATATATGTTTTCAAAAATGTTTTTCAAAAC
* * *
73961 TATATA-ATATATGTTTTAAAAAAAATTGTTTTTCGAAAT
1 TATATATATATATGTTTT--CAAAAA-TGTTTTTCAAAAC
*
74000 TATATA-ATATACGTTTTCAAAAATGTGTTTTCAAAAC
1 TATATATATATATGTTTTCAAAAATGT-TTTTCAAAAC
74037 TATA-ATATAT
1 TATATATATAT
74047 GCTTTTTAAA
Statistics
Matches: 144, Mismatches: 11, Indels: 17
0.84 0.06 0.10
Matches are distributed among these distances:
36 15 0.10
37 22 0.15
38 31 0.22
39 71 0.49
40 5 0.03
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (37 bp):
TATATATATATATGTTTTCAAAAATGTTTTTCAAAAC
Found at i:73985 original size:77 final size:74
Alignment explanation
Indices: 73845--74077 Score: 244
Period size: 75 Copynumber: 3.1 Consensus size: 74
73835 ATATATATAT
* * *
73845 ATATATATATATATATATTCAAAAATTGTTTTTCAAAACCATAATATATATATGTTTTCAAAAAA
1 ATATA-ATATATATGTTTTCAAAAA-TGTTTTTCAAAA-CAT-ATA-ATATATGTTTTAAAAAAA
73910 TGTTTTTCAAAACC
61 TGTTTTTCAAAACC
73924 ATATAATATATATGTTTTCAAAAATGTTTTTCAAAACTATATAATATATGTTTTAAAAAAAATTG
1 ATATAATATATATGTTTTCAAAAATGTTTTTCAAAAC-ATATAATATATGTTTT-AAAAAAA-TG
* **
73989 TTTTTCGAAATT
63 TTTTTCAAAACC
* *
74001 ATAT-A-ATATACGTTTTCAAAAATGTGTTTTCAAAAC-TATAATATATGCTTTT---TAAATCG
1 ATATAATATATATGTTTTCAAAAATGT-TTTTCAAAACATATAATATATG-TTTTAAAAAAAT-G
74060 TATTTTCAAAACC
63 T-TTTTCAAAACC
74073 ATATA
1 ATATA
74078 GTATGTTTTT
Statistics
Matches: 135, Mismatches: 11, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
70 1 0.01
71 5 0.04
72 12 0.09
74 11 0.08
75 34 0.25
76 21 0.16
77 29 0.21
78 17 0.13
79 5 0.04
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (74 bp):
ATATAATATATATGTTTTCAAAAATGTTTTTCAAAACATATAATATATGTTTTAAAAAAATGTTT
TTCAAAACC
Found at i:74066 original size:35 final size:34
Alignment explanation
Indices: 74027--74120 Score: 102
Period size: 35 Copynumber: 2.7 Consensus size: 34
74017 CAAAAATGTG
74027 TTTTCAAAACTATAATATATGCTTTTTAAATCGTA
1 TTTTCAAAACTATAATATATGCTTTTTAAATC-TA
* *
74062 TTTTCAAAACCAT-ATAGTATG-TTTTTAAATCTT
1 TTTTCAAAACTATAATA-TATGCTTTTTAAATCTA
* *
74095 TTTTTAAAATTATATATTATATGCTT
1 TTTTCAAAACTATA-A-TATATGCTT
74121 AGAAAACATT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
33 11 0.22
34 13 0.27
35 21 0.43
36 4 0.08
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (34 bp):
TTTTCAAAACTATAATATATGCTTTTTAAATCTA
Found at i:75893 original size:16 final size:16
Alignment explanation
Indices: 75874--75933 Score: 56
Period size: 16 Copynumber: 4.0 Consensus size: 16
75864 AATATTACTG
75874 CTAATTAAAAGTAATA
1 CTAATTAAAAGTAATA
*
75890 CTAA-T-AAAGT-TTA
1 CTAATTAAAAGTAATA
*
75903 AT-ATTAAAAGTAATA
1 CTAATTAAAAGTAATA
* *
75918 CTAATAAAAATTAATA
1 CTAATTAAAAGTAATA
75934 ATTAAAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
12 1 0.03
13 4 0.12
14 10 0.29
15 4 0.12
16 15 0.44
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
CTAATTAAAAGTAATA
Found at i:75908 original size:28 final size:29
Alignment explanation
Indices: 75875--75940 Score: 107
Period size: 28 Copynumber: 2.3 Consensus size: 29
75865 ATATTACTGC
**
75875 TAATTAAAAGTAATACTAATAAAGTTTAA
1 TAATTAAAAGTAATACTAATAAAAATTAA
75904 T-ATTAAAAGTAATACTAATAAAAATTAA
1 TAATTAAAAGTAATACTAATAAAAATTAA
75932 TAATTAAAA
1 TAATTAAAA
75941 TAAAATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 26 0.76
29 8 0.24
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (29 bp):
TAATTAAAAGTAATACTAATAAAAATTAA
Found at i:75942 original size:19 final size:19
Alignment explanation
Indices: 75920--75957 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
75910 AAGTAATACT
75920 AATAAAA-ATTAATAATTAA
1 AATAAAATATTAA-AATTAA
75939 AATAAAATATTAAAATTAA
1 AATAAAATATTAAAATTAA
75958 TGTTAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAAAATATTAAAATTAA
Found at i:81677 original size:20 final size:20
Alignment explanation
Indices: 81652--81689 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
81642 ATTCTACGCA
* *
81652 GGGGTTTCGAAACCTTTAAG
1 GGGGTTTCAAAACATTTAAG
81672 GGGGTTTCAAAACATTTA
1 GGGGTTTCAAAACATTTA
81690 GGAAGTTTTG
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:0.13, G:0.26, T:0.32
Consensus pattern (20 bp):
GGGGTTTCAAAACATTTAAG
Found at i:84296 original size:21 final size:22
Alignment explanation
Indices: 84272--84312 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
84262 ACATATGATG
84272 TAAAATAA-AATATTTACAACA
1 TAAAATAACAATATTTACAACA
*
84293 TAAAATAACATTATTTACAA
1 TAAAATAACAATATTTACAA
84313 TATATGCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAAATAACAATATTTACAACA
Found at i:84548 original size:29 final size:28
Alignment explanation
Indices: 84447--84600 Score: 82
Period size: 30 Copynumber: 5.4 Consensus size: 28
84437 AAAACCTAAA
84447 GACTAAAATAG-AAAAATTAGGAAT-TTAGG
1 GACTAAAATAGCAAAAA--A-GAATCTTAGG
* ** * *
84476 GACTAAAACAATAAAAATAGAATACTAAAG
1 GACTAAAATAGCAAAAA-AGAAT-CTTAGG
* * *
84506 AACCAAAATA--AAAAATGAATCTTAGG
1 GACTAAAATAGCAAAAAAGAATCTTAGG
*
84532 GACTAAAATAGCAAAAACAGAAGCTTAGAG
1 GACTAAAATAGCAAAAA-AGAATCTTAG-G
* * * * * *
84562 GAATAAACTCGTAAAATAGAATCTTGGG
1 GACTAAAATAGCAAAAAAGAATCTTAGG
84590 GACTAAAATAG
1 GACTAAAATAG
84601 AAGAAACTTA
Statistics
Matches: 94, Mismatches: 24, Indels: 15
0.71 0.18 0.11
Matches are distributed among these distances:
26 12 0.13
27 4 0.04
28 23 0.24
29 27 0.29
30 28 0.30
ACGTcount: A:0.54, C:0.10, G:0.17, T:0.19
Consensus pattern (28 bp):
GACTAAAATAGCAAAAAAGAATCTTAGG
Found at i:86187 original size:3 final size:3
Alignment explanation
Indices: 86179--86235 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
86169 ACATGTAAAT
* *
86179 TAA TAA TAA TAA TAC TAA TCA TAA T-A TAAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
*
86224 TAA TAT TAA TAA
1 TAA TAA TAA TAA
86236 AATCAAATAG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.91
4 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:86700 original size:28 final size:28
Alignment explanation
Indices: 86659--86767 Score: 80
Period size: 28 Copynumber: 3.8 Consensus size: 28
86649 AGGGATTATG
* *
86659 GTTTCAAGATAAACTGACTCAAAGATAA
1 GTTTCAAAAGAAACTGACTCAAAGATAA
* * **
86687 GTTTCAAAAGAAACAGACACAAAGATTT
1 GTTTCAAAAGAAACTGACTCAAAGATAA
*
86715 GTTTCAAGAA-AAAC-AACTCAAAGATAA
1 GTTTCAA-AAGAAACTGACTCAAAGATAA
*
86742 TGTGTTTCAAAAGCAACT-ACCTCAAA
1 ---GTTTCAAAAGAAACTGA-CTCAAA
86768 AGAGACAAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
27 9 0.14
28 33 0.52
29 4 0.06
30 11 0.17
31 6 0.10
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.23
Consensus pattern (28 bp):
GTTTCAAAAGAAACTGACTCAAAGATAA
Found at i:86927 original size:32 final size:33
Alignment explanation
Indices: 86876--86971 Score: 86
Period size: 38 Copynumber: 2.8 Consensus size: 33
86866 AAGATTGGCT
* *
86876 TTTCGAGAGAAACAAACTCAAAGATGTT-TTTG
1 TTTCAAGAAAAACAAACTCAAAGATGTTGTTTG
* *
86908 TTTCAAGAAAAACATACTCAATGATTTTGTTTGTTTCG
1 TTTCAAGAAAAACAAACTCAAAGA---TG-TTGTTT-G
**
86946 TTTCAAGGGAAACAAACTCAAAGATG
1 TTTCAAGAAAAACAAACTCAAAGATG
86972 GTAAATTTTG
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
32 20 0.40
35 4 0.08
36 2 0.04
37 3 0.06
38 21 0.42
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (33 bp):
TTTCAAGAAAAACAAACTCAAAGATGTTGTTTG
Found at i:87100 original size:63 final size:64
Alignment explanation
Indices: 86974--87109 Score: 166
Period size: 63 Copynumber: 2.1 Consensus size: 64
86964 CAAAGATGGT
* * * *
86974 AAATTTTGTTTCTAAAGAAATAGACTCAAAGATTTTTCTTAAAAGAAAATGTCTCAAAAGAGACA
1 AAATTTTGTTTCCAAAGAAACAGACTCAAAGA-TTTTCTCAAAAGAAAATGGCTCAAAAGAGACA
* * * * *
87039 AAATTTTGTTTCCAAAGAAACATATTCAATGA-TTTCTCAAAAGAAATTGGCTCAAGAGAGACA
1 AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTCTCAAAAGAAAATGGCTCAAAAGAGACA
*
87102 AAACTTTG
1 AAATTTTG
87110 ATTTTTAGAA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
63 34 0.56
65 27 0.44
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.30
Consensus pattern (64 bp):
AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTCTCAAAAGAAAATGGCTCAAAAGAGACA
Found at i:87813 original size:36 final size:36
Alignment explanation
Indices: 87768--87862 Score: 104
Period size: 36 Copynumber: 2.6 Consensus size: 36
87758 ATAATTTGGA
87768 AAATTGTCTCAAGTGAAACAACA-TTTGTTTTTAGAG
1 AAATTGTCTCAAGTGAAACAACAGTTTGTTTTT-GAG
** *
87804 AAATTGTCTCAAACGAGACAA-AGTTTGTTTTTGAG
1 AAATTGTCTCAAGTGAAACAACAGTTTGTTTTTGAG
**
87839 AAAACGATCTCAAGTGAAATCAAC
1 AAATTG-TCTCAAGTGAAA-CAAC
87863 TCTGTTTAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
35 8 0.17
36 36 0.77
37 3 0.06
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (36 bp):
AAATTGTCTCAAGTGAAACAACAGTTTGTTTTTGAG
Found at i:88185 original size:37 final size:35
Alignment explanation
Indices: 88108--88192 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 35
88098 ATGAGAAATG
*
88108 TCTCAAGCGAGAAAAAATTTGTTTTTAGAAAAGTTG
1 TCTCAAGCGAGAAAAAATTTGTTTTTAGAAAAG-TA
* *
88144 TCTCAAGCGAGACAAAGTTTGTTTTTTTAGAAAACG-A
1 TCTCAAGCGAGAAAAAATTTG--TTTTTAGAAAA-GTA
*
88181 TCTCAAGTGAGA
1 TCTCAAGCGAGA
88193 TCAACTTTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
36 19 0.45
37 11 0.26
38 11 0.26
39 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (35 bp):
TCTCAAGCGAGAAAAAATTTGTTTTTAGAAAAGTA
Found at i:88293 original size:36 final size:37
Alignment explanation
Indices: 88253--88349 Score: 148
Period size: 35 Copynumber: 2.7 Consensus size: 37
88243 AGGTCTCCAG
88253 CGAGACAAAATTTGTTTTTCAAGAA-ATTGTCTCAAA
1 CGAGACAAAATTTGTTTTTCAAGAAGATTGTCTCAAA
*
88289 CGAGACAAAATTTGTTTTT--AGAAGATTGTCTCAAG
1 CGAGACAAAATTTGTTTTTCAAGAAGATTGTCTCAAA
*
88324 CGAGACAAAATTTATTTTTCAA-AAGA
1 CGAGACAAAATTTGTTTTTCAAGAAGA
88350 AGTTGTCTAT
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
34 4 0.07
35 28 0.50
36 23 0.41
37 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (37 bp):
CGAGACAAAATTTGTTTTTCAAGAAGATTGTCTCAAA
Found at i:89025 original size:25 final size:22
Alignment explanation
Indices: 88995--89052 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 22
88985 TTCAAAAGTA
88995 TGAAAATATTAATTAAAAGAGTTT
1 TGAAAATATTAA-TAAAA-AGTTT
*
89019 TGAAAAATATTTAATCAAAAGTTT
1 TG-AAAATA-TTAATAAAAAGTTT
89043 TGAAAATATT
1 TGAAAATATT
89053 GCTCCTTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 2 0.06
23 6 0.19
24 9 0.29
25 10 0.32
26 4 0.13
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (22 bp):
TGAAAATATTAATAAAAAGTTT
Found at i:89052 original size:23 final size:24
Alignment explanation
Indices: 88985--89052 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 24
88975 TTATTGTATT
*
88985 TTCAAAAG-TATGAAAATA-TTAA
1 TTCAAAAGTTTTGAAAATATTTAA
*
89007 TTAAAAGAGTTTTGAAAAATATTTAA
1 TTCAAA-AGTTTTG-AAAATATTTAA
89033 -TCAAAAGTTTTGAAAATATT
1 TTCAAAAGTTTTGAAAATATT
89053 GCTCCTTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 5 0.13
23 10 0.26
24 10 0.26
25 10 0.26
26 4 0.10
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.37
Consensus pattern (24 bp):
TTCAAAAGTTTTGAAAATATTTAA
Found at i:89963 original size:14 final size:13
Alignment explanation
Indices: 89921--90038 Score: 50
Period size: 13 Copynumber: 8.8 Consensus size: 13
89911 CTCTTTTTGT
*
89921 TCTTTGCTTTTTC
1 TCTTTGTTTTTTC
89934 T-TTTGTTCTTTT-
1 TCTTTGTT-TTTTC
89946 TCTTTGATTTTTTC
1 TCTTTG-TTTTTTC
* *
89960 TCTTTTTCTCTTTGTT
1 TCTTTGT-T-TTT-TC
89976 TCTTT-TTCTTTTC
1 TCTTTGTT-TTTTC
* *
89989 TTTTTTTTTACTTTAC
1 TCTTTGTTT--TTT-C
90005 TCTTTGTTTTATT-
1 TCTTTGTTTT-TTC
*
90018 T-GTTG-TTTTTC
1 TCTTTGTTTTTTC
90029 TCTTTGTTTT
1 TCTTTGTTTT
90039 GATTTGATCT
Statistics
Matches: 81, Mismatches: 9, Indels: 30
0.68 0.08 0.25
Matches are distributed among these distances:
10 2 0.02
11 4 0.05
12 12 0.15
13 24 0.30
14 16 0.20
15 9 0.11
16 14 0.17
ACGTcount: A:0.03, C:0.14, G:0.07, T:0.75
Consensus pattern (13 bp):
TCTTTGTTTTTTC
Found at i:89981 original size:16 final size:15
Alignment explanation
Indices: 89960--90002 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
89950 TGATTTTTTC
*
89960 TCTTTTTCTCTTTGTT
1 TCTTTTTCT-TTTCTT
89976 TCTTTTTCTTTTCTT
1 TCTTTTTCTTTTCTT
*
89991 TTTTTTTACTTT
1 TCTTTTT-CTTT
90003 ACTCTTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (15 bp):
TCTTTTTCTTTTCTT
Found at i:93976 original size:29 final size:29
Alignment explanation
Indices: 93944--94045 Score: 95
Period size: 27 Copynumber: 3.6 Consensus size: 29
93934 TAAACCTAAA
93944 GACTAAAATAGCAAAATTAGGAAT-TTAGG
1 GACTAAAATAGCAAAA-TAGGAATCTTAGG
** * *
93973 GACTAAAATATTAAAAATA-GAATACTAAAG
1 GACTAAAATA-GCAAAATAGGAAT-CTTAGG
* *
94003 GACCAAAATA--AAAAAAGGAATCTTAGG
1 GACTAAAATAGCAAAATAGGAATCTTAGG
94030 GACTAAAATAGCAAAA
1 GACTAAAATAGCAAAA
94046 ACAGAAGCTT
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
27 18 0.31
28 8 0.14
29 16 0.28
30 16 0.28
ACGTcount: A:0.56, C:0.09, G:0.16, T:0.20
Consensus pattern (29 bp):
GACTAAAATAGCAAAATAGGAATCTTAGG
Found at i:94046 original size:29 final size:29
Alignment explanation
Indices: 93944--94046 Score: 97
Period size: 29 Copynumber: 3.6 Consensus size: 29
93934 TAAACCTAAA
*
93944 GACTAAAATAGCAAAATTAGGAAT-TTAGG
1 GACTAAAATAGCAAAA-AAGGAATCTTAGG
** * *
93973 GACTAAAATATTAAAAATA-GAATACTAAAG
1 GACTAAAATAGCAAAAA-AGGAAT-CTTAGG
*
94003 GACCAAAATA--AAAAAAGGAATCTTAGG
1 GACTAAAATAGCAAAAAAGGAATCTTAGG
94030 GACTAAAATAGCAAAAA
1 GACTAAAATAGCAAAAA
94047 CAGAAGCTTA
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
27 14 0.24
28 13 0.22
29 20 0.34
30 12 0.20
ACGTcount: A:0.56, C:0.09, G:0.16, T:0.19
Consensus pattern (29 bp):
GACTAAAATAGCAAAAAAGGAATCTTAGG
Found at i:95682 original size:3 final size:3
Alignment explanation
Indices: 95674--95724 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
95664 ATATGTACAT
* * * *
95674 TAA TAA TAA TAA TAC CAA TCA TAA T-A TAAA TAA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
95719 TAA TAA
1 TAA TAA
95725 AATCAAATAG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 34 0.89
4 2 0.05
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:98552 original size:3 final size:3
Alignment explanation
Indices: 98544--98568 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
98534 TTTGCCCATC
98544 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
98569 GGGTAAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:98976 original size:16 final size:16
Alignment explanation
Indices: 98957--99023 Score: 53
Period size: 16 Copynumber: 4.2 Consensus size: 16
98947 CAATATACGA
98957 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
98973 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
** * **
98989 ATTTAGATATATAAAT
1 ATAAAAATATATTTAT
* *
99005 AAAAAAATATATTCAT
1 ATAAAAATATATTTAT
99021 ATA
1 ATA
99024 TTAATGTATG
Statistics
Matches: 36, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:99065 original size:17 final size:19
Alignment explanation
Indices: 99032--99066 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
99022 TATTAATGTA
99032 TGAATCATTTATATTTTTT
1 TGAATCATTTATATTTTTT
99051 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
99067 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.66
Consensus pattern (19 bp):
TGAATCATTTATATTTTTT
Found at i:99727 original size:130 final size:130
Alignment explanation
Indices: 99523--99770 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
99513 AATTTTCTTC
* *
99523 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
99588 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
99653 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
99718 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
99771 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:100211 original size:35 final size:35
Alignment explanation
Indices: 100161--100236 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
100151 AATTGAATTT
* *
100161 AATTGAATTATTTTGGAATTTAGGGTTTAGAATAA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATAA
* *
100196 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATAA
100231 AATTGA
1 AATTGA
100237 GGACTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATAA
Found at i:100465 original size:3 final size:3
Alignment explanation
Indices: 100459--100551 Score: 186
Period size: 3 Copynumber: 31.0 Consensus size: 3
100449 TACTTTACCC
100459 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
100507 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
100552 CAGGCCTGAA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:102870 original size:18 final size:19
Alignment explanation
Indices: 102841--102878 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
102831 TTAGGAAAAA
102841 TTATTATATTTTTTAATAT
1 TTATTATATTTTTTAATAT
102860 TTATT-TATTTTTTAATAT
1 TTATTATATTTTTTAATAT
102878 T
1 T
102879 AAAGAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATTATATTTTTTAATAT
Found at i:103519 original size:39 final size:39
Alignment explanation
Indices: 103475--103576 Score: 145
Period size: 39 Copynumber: 2.6 Consensus size: 39
103465 TAAATAATGT
103475 AATGCTATCACTTATTCCATTCAATCAATCAAATTGTGA
1 AATGCTATCACTTATTCCATTCAATCAATCAAATTGTGA
* *
103514 AATGCTATCACTTATTTCATTCAATCAATCAAATTGTGT
1 AATGCTATCACTTATTCCATTCAATCAATCAAATTGTGA
*
103553 AATACCTATCAC--ACTTCCATTCAA
1 AAT-GCTATCACTTA-TTCCATTCAA
103577 CGAATAACTA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
38 1 0.02
39 49 0.86
40 7 0.12
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.36
Consensus pattern (39 bp):
AATGCTATCACTTATTCCATTCAATCAATCAAATTGTGA
Found at i:107961 original size:3 final size:3
Alignment explanation
Indices: 107953--108002 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
107943 AATTTATTAG
*
107953 TAA TAA TAA TAA TAA TAA T-A TAGA TAA TAA -AA TAC TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
107996 TTAA TAA
1 -TAA TAA
108003 AGTTTTTTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 6 0.15
3 28 0.70
4 6 0.15
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:107991 original size:20 final size:19
Alignment explanation
Indices: 107953--108003 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 19
107943 AATTTATTAG
107953 TAATAATAATAATAATAATA
1 TAATAATAA-AATAATAATA
*
107973 TAGATAATAAAATACTAATA
1 TA-ATAATAAAATAATAATA
107993 TAATTAATAAA
1 TAA-TAATAAA
108004 GTTTTTTTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.04
20 20 0.71
21 7 0.25
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
TAATAATAAAATAATAATA
Found at i:108419 original size:135 final size:134
Alignment explanation
Indices: 108220--108846 Score: 746
Period size: 129 Copynumber: 4.7 Consensus size: 134
108210 TGAGAATATC
* * * * *
108220 TAGTCAAGAGATGACACTGCTCATACGTGATGAAGAGTTCTTGACCATCTTTAGGAAGGGTGATA
1 TAGTC-AGTGATGACACTACTCATACGTGATGAAGAGTTCTTGGCCATCTTTAAGAAGGATGATA
* * * * * *
108285 ACTTGGTTCCTACGCGATGAAGATTG-CTGGTTATCAAAGGTTGACATAACTCCTACATAATGAG
65 ACTCGGTTCCTACGCGATGAGGA-CGACTGGTTATCAAAGGTTGACACAACTCCTACGTGATGAG
108349 GAAATT
129 GAAATT
* **
108355 TAGTCGAGTGATAACACTACTCATACGTGATGAAGAGTTCTTGGCCATCTTTAAGAATAATGATA
1 TAGTC-AGTGATGACACTACTCATACGTGATGAAGAGTTCTTGGCCATCTTTAAGAAGGATGATA
108420 ACTCGGTTCCTATC-CGATGAGGACGACTGGTTATCAAAGGTT-ACACAACTCCTACGTGATGAG
65 ACTCGGTTCCTA-CGCGATGAGGACGACTGGTTATCAAAGGTTGACACAACTCCTACGTGATGAG
108483 GAAATT
129 GAAATT
* * *
108489 TAGTCGAGTGATGACATTACTCATACATGATGAAGAGTTCTTGGCCATTTTTAAGAAGGATGATA
1 TAGTC-AGTGATGACACTACTCATACGTGATGAAGAGTTCTTGGCCATCTTTAAGAAGGATGATA
* * *
108554 ACTCGGTTCCTACGGGATGAGGACGACTGGTTATCTAAGGTTGACACAACTCCTACGTGTTGAGG
65 ACTCGGTTCCTACGCGATGAGGACGACTGGTTATCAAAGGTTGACACAACTCCTACGTGATGAGG
* *
108619 AGATC
130 AAATT
* ** *
108624 AAGTCAGGTGATGACACGGCTCATACGTGATGAAGAGTTC-TGGTCATC--T-A-AAGG-TGATA
1 TAGTCA-GTGATGACACTACTCATACGTGATGAAGAGTTCTTGGCCATCTTTAAGAAGGATGATA
* * * * *
108683 ACACGGTTCCTACGTGATCAGGACGACTGGTTATTAAAGGTTGACATAACTCCTACGTGATGAGG
65 ACTCGGTTCCTACGCGATGAGGACGACTGGTTATCAAAGGTTGACACAACTCCTACGTGATGAGG
*
108748 AGA-T
130 AAATT
* *
108752 CAGGTCAGGTGATGACACGACTCATACGTGATGAAGAGTTC-TGGCCATC--T-A-AAGG-TGAT
1 TA-GTCA-GTGATGACACTACTCATACGTGATGAAGAGTTCTTGGCCATCTTTAAGAAGGATGAT
* *
108811 AACACGGTTCCTACGTGATGAGGACGACTGGTTATC
64 AACTCGGTTCCTACGCGATGAGGACGACTGGTTATC
108847 TGGGGTAAAA
Statistics
Matches: 440, Mismatches: 46, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
128 1 0.00
129 154 0.35
130 4 0.01
131 1 0.00
132 1 0.00
133 1 0.00
134 129 0.29
135 148 0.34
136 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (134 bp):
TAGTCAGTGATGACACTACTCATACGTGATGAAGAGTTCTTGGCCATCTTTAAGAAGGATGATAA
CTCGGTTCCTACGCGATGAGGACGACTGGTTATCAAAGGTTGACACAACTCCTACGTGATGAGGA
AATT
Found at i:108697 original size:46 final size:46
Alignment explanation
Indices: 108629--108831 Score: 156
Period size: 46 Copynumber: 4.6 Consensus size: 46
108619 AGATCAAGTC
* *
108629 AGGTGATGACACGGCTCATACGTGATGAAGAGTTCTGGTCATCTAA
1 AGGTGATAACACGGCTCCTACGTGATGAAGAGTTCTGGTCATCTAA
* * * * *
108675 AGGTGATAACACGGTTCCTACGTGATCAGGACG-ACTGGTTAT-TAA
1 AGGTGATAACACGGCTCCTACGTGATGAAGA-GTTCTGGTCATCTAA
* *** * * *
108720 AGGT--TGACATAACTCCTACGTGATGAGGAGATCAGG---TC---
1 AGGTGATAACACGGCTCCTACGTGATGAAGAGTTCTGGTCATCTAA
* * * *
108758 AGGTGATGACACGACTCATACGTGATGAAGAGTTCTGGCCATCTAA
1 AGGTGATAACACGGCTCCTACGTGATGAAGAGTTCTGGTCATCTAA
*
108804 AGGTGATAACACGGTTCCTACGTGATGA
1 AGGTGATAACACGGCTCCTACGTGATGA
108832 GGACGACTGG
Statistics
Matches: 121, Mismatches: 25, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
38 4 0.03
40 27 0.22
42 1 0.01
43 24 0.20
45 7 0.06
46 57 0.47
47 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (46 bp):
AGGTGATAACACGGCTCCTACGTGATGAAGAGTTCTGGTCATCTAA
Found at i:109918 original size:8 final size:9
Alignment explanation
Indices: 109900--109925 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
109890 CCCTTCATTA
109900 TTTCTTTTT
1 TTTCTTTTT
109909 TTTCTTTTT
1 TTTCTTTTT
109918 TTTCTTTT
1 TTTCTTTT
109926 CTTCTTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:123228 original size:21 final size:21
Alignment explanation
Indices: 123204--123244 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
123194 ACGTTTTCAC
*
123204 CTTTCACTTTCTATCTTTTTA
1 CTTTCACTTTCTATCATTTTA
*
123225 CTTTTACTTTCTATCATTTT
1 CTTTCACTTTCTATCATTTT
123245 CTTCTCCCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (21 bp):
CTTTCACTTTCTATCATTTTA
Found at i:134435 original size:14 final size:14
Alignment explanation
Indices: 134408--134454 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
134398 GTAATACTAT
134408 TAATA-ATA-ATAA
1 TAATATATATATAA
134420 TAATATATATATAA
1 TAATATATATATAA
*
134434 TAAAATACTATATAA
1 TAATATA-TATATAA
134449 TTAATA
1 -TAATA
134455 ACGTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 5 0.17
13 3 0.10
14 10 0.34
15 7 0.24
16 4 0.14
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATATATATATAA
Found at i:134435 original size:17 final size:17
Alignment explanation
Indices: 134413--134447 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
134403 ACTATTAATA
134413 ATAATAATAATA-TATAT
1 ATAATAA-AATACTATAT
134430 ATAATAAAATACTATAT
1 ATAATAAAATACTATAT
134447 A
1 A
134448 ATTAATAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAATAAAATACTATAT
Found at i:134886 original size:135 final size:135
Alignment explanation
Indices: 134656--135295 Score: 549
Period size: 135 Copynumber: 4.8 Consensus size: 135
134646 GGGTGACAAG
* * * * * *
134656 ACTCCTATATAGTGA-GAATATCTAGTCAAGAGATGACACTGCTCATACGTGAGGAAGAGTTCTT
1 ACTCCTACATAATGAGGAA-ATTTAGTCAAGTGATGACACTACTCATACGTGATGAAGAGTTCTT
* * * * *
134720 GACCATATTTAGGAAGGATGATAACTTGGTTCCTACGCGATGAAGATTG-TTAGTTAACAAAGGT
65 GGCCATATTTAAGAAGGATGATAACTCGGTTCCTACGCGATGAAGA-CGACTAGTTAACAAAGGT
* *
134784 TGACATA
129 TAACACA
* * *
134791 ACTCCTACATAATGAGGAAATTTAGTCAAGTGATAAAACTACTCATATGTGATGAAGAGTTCTTG
1 ACTCCTACATAATGAGGAAATTTAGTCAAGTGATGACACTACTCATACGTGATGAAGAGTTCTTG
* ** * * *
134856 GCCATCTTTAAGAATAATGATAACTCGGTTCCTACGCGATGAGGACGACTGGTTATCAAAGGTTA
66 GCCATATTTAAGAAGGATGATAACTCGGTTCCTACGCGATGAAGACGACTAGTTAACAAAGGTTA
134921 ACACA
131 ACACA
* * * * *
134926 ACTCCTACGTGATGAGGAAATTTAGTCGAGTGATGACATTACTCATACATGATGAAGAGTTCTTG
1 ACTCCTACATAATGAGGAAATTTAGTCAAGTGATGACACTACTCATACGTGATGAAGAGTTCTTG
* * * * * *
134991 GCCATTTTTAAGAAGGATGATAACTCGGTTCCTACGCGATGAGGACGACTGGTTATCTAAGGTTG
66 GCCATATTTAAGAAGGATGATAACTCGGTTCCTACGCGATGAAGACGACTAGTTAACAAAGGTTA
135056 ACACA
131 ACACA
* * * * ** * * *
135061 ACTCCTACGTATTAAGGAGATCAAGTC-AGATGATGGCACGACTCATATGTGATGAAGAGTTC-T
1 ACTCCTACATAATGAGGAAATTTAGTCAAG-TGATGACACTACTCATACGTGATGAAGAGTTCTT
* * ** * * * **
135124 GGTCATA--T-A-AAGG-TGATAACACGGTTCCTACATGATGAGGATGACTGGTTATTAAAGGTT
65 GGCCATATTTAAGAAGGATGATAACTCGGTTCCTACGCGATGAAGACGACTAGTTAACAAAGGTT
*
135184 GACACA
130 AACACA
* * * * * * *
135190 ACTCCTACGTGATGAGGAGA-TCAGGTCAGGTGATGACA-TGGCTCATACGTGATGAAGAGTT-A
1 ACTCCTACATAATGAGGAAATTTA-GTCAAGTGATGACACT-ACTCATACGTGATGAAGAGTTCT
* * * *
135252 TGGCC--ATCT-A-AAGG-TGATAACACGGTTCCTACGTGATGAGGACG
64 TGGCCATATTTAAGAAGGATGATAACTCGGTTCCTACGCGATGAAGACG
135296 GTTGGTTATC
Statistics
Matches: 429, Mismatches: 67, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
127 1 0.00
128 1 0.00
129 131 0.31
130 5 0.01
131 1 0.00
132 1 0.00
134 9 0.02
135 277 0.65
136 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (135 bp):
ACTCCTACATAATGAGGAAATTTAGTCAAGTGATGACACTACTCATACGTGATGAAGAGTTCTTG
GCCATATTTAAGAAGGATGATAACTCGGTTCCTACGCGATGAAGACGACTAGTTAACAAAGGTTA
ACACA
Found at i:136383 original size:11 final size:11
Alignment explanation
Indices: 136355--136387 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
136345 TAAACCCTTC
136355 TTTATTTC-TT
1 TTTATTTCTTT
136365 TTTATTTCTTT
1 TTTATTTCTTT
*
136376 TTTTTTTCTTT
1 TTTATTTCTTT
136387 T
1 T
136388 CTTCTTCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTATTTCTTT
Found at i:147190 original size:16 final size:15
Alignment explanation
Indices: 147155--147192 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
147145 AAAATTGTCT
147155 TTTTAAG-AAAACAA
1 TTTTAAGAAAAACAA
*
147169 TTTTAAGAAAAATCAG
1 TTTTAAGAAAAA-CAA
147185 TTTTAAGA
1 TTTTAAGA
147193 CCAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (15 bp):
TTTTAAGAAAAACAA
Found at i:149692 original size:20 final size:20
Alignment explanation
Indices: 149664--149704 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
149654 TAATATTAAT
149664 AATAATAATATAGA-TAATAA
1 AATAATAATATA-ATTAATAA
*
149684 AATACTAATATAATTAATAA
1 AATAATAATATAATTAATAA
149704 A
1 A
149705 GTTTTTTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
AATAATAATATAATTAATAA
Found at i:159523 original size:17 final size:17
Alignment explanation
Indices: 159501--159533 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
159491 ATTCAGAGTT
159501 AGTTTAATAAATGAACC
1 AGTTTAATAAATGAACC
*
159518 AGTTTAATTAATGAAC
1 AGTTTAATAAATGAAC
159534 TAACTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.33
Consensus pattern (17 bp):
AGTTTAATAAATGAACC
Found at i:162335 original size:16 final size:16
Alignment explanation
Indices: 162295--162335 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
162285 GTTTCTTTTA
*
162295 TCCACTC-TCTCATTT
1 TCCACTCTTTTCATTT
*
162310 T-CATTCTTTTCATTT
1 TCCACTCTTTTCATTT
162325 TCCACTCTTTT
1 TCCACTCTTTT
162336 TATTCCATGC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 4 0.19
15 9 0.43
16 8 0.38
ACGTcount: A:0.12, C:0.32, G:0.00, T:0.56
Consensus pattern (16 bp):
TCCACTCTTTTCATTT
Found at i:163422 original size:20 final size:21
Alignment explanation
Indices: 163380--163425 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
163370 ATCAAAACAT
163380 TATCGGTACCCTATAGAGGGG
1 TATCGGTACCCTATAGAGGGG
163401 TATCGGTACCCTATAG-GGGG
1 TATCGGTACCCTATAGAGGGG
163421 TATCG
1 TATCG
163426 ATACTATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.26
Consensus pattern (21 bp):
TATCGGTACCCTATAGAGGGG
Found at i:165680 original size:2 final size:2
Alignment explanation
Indices: 165673--165706 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
165663 TTTGGAAATA
165673 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
165707 TATTTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:166161 original size:22 final size:22
Alignment explanation
Indices: 166134--166211 Score: 90
Period size: 21 Copynumber: 3.5 Consensus size: 22
166124 ACCATCAGGG
166134 GGTATCGATACC-ATTCAAAGA
1 GGTATCGATACCTATTCAAAGA
166155 TGGTATCGATACCTATTGC--AGA
1 -GGTATCGATACCTATT-CAAAGA
*
166177 GGTATCGATACCTATTCAAAGGG
1 GGTATCGATACCTATTCAAA-GA
*
166200 GGTATTGATACC
1 GGTATCGATACC
166212 GGTCTTAGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
20 1 0.02
21 16 0.33
22 16 0.33
23 15 0.31
24 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (22 bp):
GGTATCGATACCTATTCAAAGA
Found at i:166225 original size:44 final size:43
Alignment explanation
Indices: 166112--166236 Score: 116
Period size: 44 Copynumber: 2.9 Consensus size: 43
166102 AGACCCCGTG
166112 GAGGGTATC-AGTACC-A-TCAGGGGGTATCGATACC-ATTCAAA
1 GAGGGTATCGA-TACCTATTCA-GGGGTATCGATACCTATTCAAA
* *
166153 GATGGTATCGATACCTATTGCAGAGGTATCGATACCTATTCAAA
1 GAGGGTATCGATACCTATT-CAGGGGTATCGATACCTATTCAAA
* * *
166197 GGGGGTATTGATACCGGTCTT-AGGGGTATCGATACTCTAT
1 GAGGGTATCGATACC--TATTCAGGGGTATCGATAC-CTAT
166237 GCACAAAAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
41 12 0.17
42 2 0.03
43 14 0.20
44 34 0.49
45 4 0.06
46 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (43 bp):
GAGGGTATCGATACCTATTCAGGGGTATCGATACCTATTCAAA
Found at i:172005 original size:20 final size:19
Alignment explanation
Indices: 171980--172053 Score: 78
Period size: 19 Copynumber: 3.7 Consensus size: 19
171970 ATATGCCTTA
*
171980 GGGTATCGGTACCTCCTGAG
1 GGGTATCGGTACCTCATG-G
172000 GGGTATCGGTACCATTGCATGG
1 GGGTATCGGTACC--T-CATGG
*
172022 GGGTATCGATACCT-ATGGG
1 GGGTATCGGTACCTCAT-GG
172041 GGGTATCGGTACC
1 GGGTATCGGTACC
172054 ATCCGAGCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
18 2 0.04
19 14 0.30
20 14 0.30
22 14 0.30
23 3 0.06
ACGTcount: A:0.18, C:0.20, G:0.36, T:0.26
Consensus pattern (19 bp):
GGGTATCGGTACCTCATGG
Found at i:174791 original size:17 final size:17
Alignment explanation
Indices: 174769--174840 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 17
174759 ATTTAAGAGT
174769 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
174786 TAGTTTGATGAATGAGC
1 TAGTTTAATAAATGAAC
* * *
174803 TAGGTTAATTAATTAAC
1 TAGTTTAATAAATGAAC
* * *
174820 TAACTTTATTCAATGAAC
1 T-AGTTTAATAAATGAAC
174838 TAG
1 TAG
174841 ATTCTTTAAA
Statistics
Matches: 40, Mismatches: 14, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
17 28 0.70
18 12 0.30
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:176067 original size:16 final size:16
Alignment explanation
Indices: 176027--176067 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
176017 GTTTCTTTTA
*
176027 TCCACTC-TCTCATTT
1 TCCACTCTTTTCATTT
*
176042 T-CATTCTTTTCATTT
1 TCCACTCTTTTCATTT
176057 TCCACTCTTTT
1 TCCACTCTTTT
176068 TCTTACATGC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 4 0.19
15 9 0.43
16 8 0.38
ACGTcount: A:0.12, C:0.32, G:0.00, T:0.56
Consensus pattern (16 bp):
TCCACTCTTTTCATTT
Found at i:183765 original size:20 final size:21
Alignment explanation
Indices: 183735--183779 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
183725 ATAAAAAATA
183735 TTTTTATTTTAAA-ATTGTTGT
1 TTTTTATTTTAAATA-TGTTGT
*
183756 TTTTTA-TTTAATTATGTTGT
1 TTTTTATTTTAAATATGTTGT
183776 TTTT
1 TTTT
183780 AATGAAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (21 bp):
TTTTTATTTTAAATATGTTGT
Found at i:185417 original size:13 final size:13
Alignment explanation
Indices: 185399--185423 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
185389 TTACCATTAC
185399 ATATTGTTTATGA
1 ATATTGTTTATGA
185412 ATATTGTTTATG
1 ATATTGTTTATG
185424 GACTAATGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (13 bp):
ATATTGTTTATGA
Found at i:188423 original size:17 final size:17
Alignment explanation
Indices: 188401--188472 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
188391 AATTAAGAGT
188401 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
188418 TAGTTTGATGAATGAGC
1 TAGTTTAATAAATGAAC
*
188435 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* * *
188452 TAACTTTATTCAATGAAC
1 T-AGTTTAATAAATGAAC
188470 TAG
1 TAG
188473 ATGCTTTAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
17 30 0.68
18 14 0.32
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:189909 original size:2 final size:2
Alignment explanation
Indices: 189902--189931 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
189892 AATTTAAAGA
189902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
189932 TTAAATAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:191383 original size:3 final size:3
Alignment explanation
Indices: 191377--191423 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
191367 ATTATTTATT
*
191377 TAA TAA TAA TAA T-A TAA T-A TAA TAT TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
191421 TAA
1 TAA
191424 ATAAAACAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 4 0.10
3 32 0.82
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:191388 original size:25 final size:24
Alignment explanation
Indices: 191354--191417 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 24
191344 CCTGTAAAAT
*
191354 ATAATAATAATAAAT-TATTTATTTA
1 ATAATAATAATAAATATA-ATA-TTA
191379 ATAATAATAATATAATATAATATTA
1 ATAATAATAATA-AATATAATATTA
191404 ATAATAAATAATAA
1 ATAAT-AATAATAA
191418 TAATAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 21 0.60
26 12 0.34
27 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATAATAATAATAAATATAATATTA
Found at i:191398 original size:16 final size:16
Alignment explanation
Indices: 191379--191426 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
191369 TATTTATTTA
191379 ATAATAATAATATAAT
1 ATAATAATAATATAAT
*
191395 ATAATATTAATAATAA-
1 ATAATAATAAT-ATAAT
191411 ATAATAATAATA-AAT
1 ATAATAATAATATAAT
191426 A
1 A
191427 AAACAAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 2 0.07
15 2 0.07
16 20 0.71
17 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATAATAATATAAT
Found at i:191400 original size:13 final size:13
Alignment explanation
Indices: 191377--191427 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
191367 ATTATTTATT
191377 TAATAAT-AATAA
1 TAATAATAAATAA
*
191389 T-ATAATATAATAT
1 TAATAATA-AATAA
191402 TAATAATAAATAA
1 TAATAATAAATAA
191415 TAATAATAAATAA
1 TAATAATAAATAA
191428 AACAAATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 5 0.15
12 1 0.03
13 22 0.65
14 6 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TAATAATAAATAA
Found at i:198469 original size:3 final size:3
Alignment explanation
Indices: 198461--198502 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
198451 ATTAACCAAA
198461 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
198503 AATACATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:207071 original size:12 final size:12
Alignment explanation
Indices: 207054--207078 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
207044 AATACATAAG
207054 ATACAACCAACA
1 ATACAACCAACA
207066 ATACAACCAACA
1 ATACAACCAACA
207078 A
1 A
207079 AACACCCCAA
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:0.60, C:0.32, G:0.00, T:0.08
Consensus pattern (12 bp):
ATACAACCAACA
Found at i:212652 original size:14 final size:14
Alignment explanation
Indices: 212633--212668 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
212623 AAATAATGAG
212633 TTAAAGGAGAACTA
1 TTAAAGGAGAACTA
212647 TTAAAGCGGAGAACTA
1 TTAAA--GGAGAACTA
212663 TTAAAG
1 TTAAAG
212669 CACCCAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.30
16 14 0.70
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.22
Consensus pattern (14 bp):
TTAAAGGAGAACTA
Found at i:212659 original size:16 final size:16
Alignment explanation
Indices: 212638--212669 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
212628 ATGAGTTAAA
212638 GGAGAACTATTAAAGC
1 GGAGAACTATTAAAGC
212654 GGAGAACTATTAAAGC
1 GGAGAACTATTAAAGC
212670 ACCCAAATTA
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:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (16 bp):
GGAGAACTATTAAAGC
Found at i:213240 original size:15 final size:15
Alignment explanation
Indices: 213220--213252 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
213210 TGTTTTTGTT
213220 TTCATTCATCTTTTC
1 TTCATTCATCTTTTC
213235 TTCATTCATCTTTTC
1 TTCATTCATCTTTTC
213250 TTC
1 TTC
213253 TTTACCATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (15 bp):
TTCATTCATCTTTTC
Found at i:219663 original size:19 final size:20
Alignment explanation
Indices: 219641--219692 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
219631 AAATAAAAGA
*
219641 GAAAAAATGAAAAAATGA-G
1 GAAAAAAAGAAAAAATGATG
219660 GAAAAAAAG-AAAAATGATG
1 GAAAAAAAGAAAAAATGATG
* *
219679 GAGAAAACGAAAAA
1 GAAAAAAAGAAAAA
219693 GAAAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.29
19 16 0.57
20 4 0.14
ACGTcount: A:0.69, C:0.02, G:0.21, T:0.08
Consensus pattern (20 bp):
GAAAAAAAGAAAAAATGATG
Found at i:219684 original size:21 final size:18
Alignment explanation
Indices: 219628--219775 Score: 62
Period size: 19 Copynumber: 8.2 Consensus size: 18
219618 TTGCTTGAAG
*
219628 AAGAAATAAAAGAGAAAAA
1 AAGAAA-AAATGAGAAAAA
*
219647 ATGAAAAAATGAGGAAAAA
1 AAGAAAAAATGA-GAAAAA
*
219666 AAG-AAAAATGATGGAGAAA
1 AAGAAAAAATGA--GAAAAA
* *
219685 ACG-AAAAA-GAAAAAAAA
1 AAGAAAAAATG-AGAAAAA
*
219702 AAGAAGAAAAATG-GAAAAGGG
1 AAG-A-AAAAATGAGAAAA--A
219723 AAGAAAAAAT--G-AAAA
1 AAGAAAAAATGAGAAAAA
*
219738 ATGAAAAAA-GAG-AAAA
1 AAGAAAAAATGAGAAAAA
* *
219754 ATGAAAAAAAGAGAAATAA
1 AAGAAAAAATGAGAAA-AA
219773 AAG
1 AAG
219776 GAGGGTTCAA
Statistics
Matches: 102, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
15 8 0.08
16 14 0.14
17 12 0.12
18 17 0.17
19 41 0.40
20 6 0.06
21 4 0.04
ACGTcount: A:0.72, C:0.01, G:0.20, T:0.07
Consensus pattern (18 bp):
AAGAAAAAATGAGAAAAA
Found at i:219752 original size:16 final size:17
Alignment explanation
Indices: 219733--219769 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
219723 AAGAAAAAAT
219733 GAAAAATG-AAAAAAGA
1 GAAAAATGAAAAAAAGA
219749 GAAAAATGAAAAAAAGA
1 GAAAAATGAAAAAAAGA
219766 GAAA
1 GAAA
219770 TAAAAGGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (17 bp):
GAAAAATGAAAAAAAGA
Found at i:219770 original size:15 final size:15
Alignment explanation
Indices: 219660--219774 Score: 67
Period size: 15 Copynumber: 7.3 Consensus size: 15
219650 AAAAAATGAG
219660 GAAAAAAAGAAAAAT
1 GAAAAAAAGAAAAAT
*
219675 GATGGAGAAAACGAAAAA-
1 GA---A-AAAAAGAAAAAT
219693 GAAAAAAA-AAAGAA-
1 GAAAAAAAGAAA-AAT
** *
219707 GAAAAATGGAAAAGGGAA
1 GAAAAAAAGAAAA---AT
*
219725 GAAAAAATGAAAAAT
1 GAAAAAAAGAAAAAT
219740 GAAAAAAGAGAAAAAT
1 GAAAAAA-AGAAAAAT
*
219756 GAAAAAAAGAGAAAT
1 GAAAAAAAGAAAAAT
219771 -AAAA
1 GAAAA
219775 GGAGGGTTCA
Statistics
Matches: 80, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
13 3 0.04
14 17 0.21
15 21 0.26
16 14 0.17
17 1 0.01
18 14 0.17
19 10 0.12
ACGTcount: A:0.73, C:0.01, G:0.20, T:0.06
Consensus pattern (15 bp):
GAAAAAAAGAAAAAT
Found at i:220998 original size:37 final size:37
Alignment explanation
Indices: 220948--221059 Score: 145
Period size: 37 Copynumber: 3.0 Consensus size: 37
220938 TCGAAACAAG
* *
220948 TCAAACTTAAGCCTTCACGAAAGAGTTGTGAAGCAAT
1 TCAAACTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
* *
220985 TCAAACTTAAGCCTTCACGGAAGAGTGGTGAAGCAAA
1 TCAAACTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
* * *
221022 TC-ATCTATAAGCCTTCAGGAAAGAATAGTGAAGCAAA
1 TCAAACT-TAAGCCTTCACGAAAGAGTAGTGAAGCAAA
221059 T
1 T
221060 ACGTTTGATG
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
36 3 0.05
37 63 0.95
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (37 bp):
TCAAACTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
Found at i:221120 original size:55 final size:55
Alignment explanation
Indices: 221061--221383 Score: 483
Period size: 55 Copynumber: 5.9 Consensus size: 55
221051 GAAGCAAATA
* * * *
221061 CGTTTGATGAAGATTGTTCGAGTTCTATACTCCCTGAATGAATAGGGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
*
221116 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
* *
221171 CGTTTTACGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
*
221226 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAAT--AGAGCGGATC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
* * *
221279 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAATGAATAGAGAGCAGACA
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
* *
221334 CATTTTATGAAGATTGTTCGAG-TCTTATACT-TCCTGAAGGAATAGGGAGC
1 CGTTTTATGAAGATTGTTCGAGTTC-TATACTCT-CTGAAGGAATAGAGAGC
221384 AGGCTCGTCA
Statistics
Matches: 246, Mismatches: 18, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
53 50 0.20
54 3 0.01
55 193 0.78
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (55 bp):
CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
Found at i:221190 original size:110 final size:110
Alignment explanation
Indices: 221069--221385 Score: 489
Period size: 108 Copynumber: 2.9 Consensus size: 110
221059 TACGTTTGAT
* *
221069 GAAGATTGTTCGAGTTCTATACTCCCTGAATGAATAGGGAGCGGACCCGTTTTATGAAGATTGTT
1 GAAGATTGTTCGAGTTCTATACTCTCTGAATGAATAGAGAGCGGACCCGTTTTATGAAGATTGTT
221134 CGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGTTTTAC
66 CGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGTTTTAC
* *
221179 GAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTATGAAGATTGTT
1 GAAGATTGTTCGAGTTCTATACTCTCTGAATGAATAGAGAGCGGACCCGTTTTATGAAGATTGTT
* * *
221244 CGAGTTCTATACTCTCTGAAGGAAT--AGAGCGGATCCGTTTTAT
66 CGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGTTTTAC
* * *
221287 GAAGATTGTTCGAGTTCTATACTCTCTGAATGAATAGAGAGCAGACACATTTTATGAAGATTGTT
1 GAAGATTGTTCGAGTTCTATACTCTCTGAATGAATAGAGAGCGGACCCGTTTTATGAAGATTGTT
*
221352 CGAG-TCTTATACT-TCCTGAAGGAATAGGGAGCAG
66 CGAGTTC-TATACTCT-CTGAAGGAATAGAGAGCAG
221386 GCTCGTCATT
Statistics
Matches: 189, Mismatches: 14, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
107 3 0.02
108 95 0.50
110 91 0.48
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (110 bp):
GAAGATTGTTCGAGTTCTATACTCTCTGAATGAATAGAGAGCGGACCCGTTTTATGAAGATTGTT
CGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGTTTTAC
Found at i:221348 original size:163 final size:164
Alignment explanation
Indices: 221061--221383 Score: 517
Period size: 163 Copynumber: 2.0 Consensus size: 164
221051 GAAGCAAATA
*
221061 CGTTTGATGAAGATTGTTCGAGTTCTATACTCCCTGAATGAATAGGGAGCGGACCCGTTTTATGA
1 CGTTTGATGAAGATTGTTCGAGTTCTATACTCCCTGAAGGAATA-GGAGCGGACCCGTTTTATGA
* *
221126 AGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGTTTTACGAAGATTGTTCG
65 AGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACACATTTTACGAAGATTGTTCG
221191 AGT-TCTATAC-TCTCTGAAGGAATAGAGAGCGAACC
130 AGTCT-TATACTTC-CTGAAGGAATAGAGAGCGAACC
* * *
221226 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATA-GAGCGGATCCGTTTTATGAA
1 CGTTTGATGAAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGAGCGGACCCGTTTTATGAA
* *
221290 GATTGTTCGAGTTCTATACTCTCTGAATGAATAGAGAGCAGACACATTTTATGAAGATTGTTCGA
66 GATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACACATTTTACGAAGATTGTTCGA
*
221355 GTCTTATACTTCCTGAAGGAATAGGGAGC
131 GTCTTATACTTCCTGAAGGAATAGAGAGC
221384 AGGCTCGTCA
Statistics
Matches: 147, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
163 103 0.70
164 3 0.02
165 41 0.28
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (164 bp):
CGTTTGATGAAGATTGTTCGAGTTCTATACTCCCTGAAGGAATAGGAGCGGACCCGTTTTATGAA
GATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACACATTTTACGAAGATTGTTCGA
GTCTTATACTTCCTGAAGGAATAGAGAGCGAACC
Found at i:226946 original size:21 final size:23
Alignment explanation
Indices: 226898--226947 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
226888 AGGTAAACTG
226898 ATAAAAGAATATCCATCACAAGA
1 ATAAAAGAATATCCATCACAAGA
*
226921 ATAAATAGAGTATCCA-C-CAA-A
1 ATAAA-AGAATATCCATCACAAGA
226942 ATAAAA
1 ATAAAA
226948 TATAACACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.04
21 6 0.24
22 3 0.12
23 6 0.24
24 9 0.36
ACGTcount: A:0.58, C:0.16, G:0.08, T:0.18
Consensus pattern (23 bp):
ATAAAAGAATATCCATCACAAGA
Found at i:229891 original size:15 final size:15
Alignment explanation
Indices: 229871--229927 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
229861 AAATGGGTAT
229871 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
**
229886 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
229903 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
229918 CGGGTACCCG
1 CGGGTACCCG
229928 TAACATCCGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 21 0.58
16 4 0.11
17 11 0.31
ACGTcount: A:0.21, C:0.35, G:0.28, T:0.16
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:229907 original size:17 final size:16
Alignment explanation
Indices: 229871--229939 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 16
229861 AAATGGGTAT
**
229871 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
229886 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AAAATC
**
229903 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
*
229918 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
229935 CGGGT
1 CGGGT
229940 CGGGACACGG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
15 21 0.48
16 6 0.14
17 17 0.39
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:229912 original size:32 final size:32
Alignment explanation
Indices: 229871--229939 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
229861 AAATGGGTAT
229871 CGGGTACCCGATTACCGGGTACCCGCAAAATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
* *
229903 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
229935 CGGGT
1 CGGGT
229940 CGGGACACGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGCAAAATC
Found at i:231212 original size:20 final size:20
Alignment explanation
Indices: 231169--231212 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
231159 CAATACCACC
**
231169 CAGTCTCGAGACCAACATGG
1 CAGTCTCGAGACCAACATCA
* *
231189 CAGTCTCGAGACCGATATCA
1 CAGTCTCGAGACCAACATCA
231209 CAGT
1 CAGT
231213 AGGCAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.18
Consensus pattern (20 bp):
CAGTCTCGAGACCAACATCA
Found at i:232078 original size:26 final size:25
Alignment explanation
Indices: 232049--232127 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 25
232039 TCATATTTAC
232049 TTATTAAATATATTTTATTTTTAACT
1 TTATTAAATATATTTTATTTTTAA-T
*
232075 TTATTTAAAAATATTTATTTTAATTTTAAT
1 TTA-TT--AAATA--TATTTTATTTTTAAT
**
232105 TTAAGAATATATATTTTATTTTT
1 TTATTAA-ATATATTTTATTTTT
232128 TCTAAACTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
26 14 0.33
27 4 0.09
28 3 0.07
29 5 0.12
30 4 0.09
31 13 0.30
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (25 bp):
TTATTAAATATATTTTATTTTTAAT
Found at i:232123 original size:31 final size:27
Alignment explanation
Indices: 232054--232126 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 27
232044 TTTACTTATT
232054 AAATATATTTTATTTTTAACTTTATTTA
1 AAATATATTTTA-TTTTAACTTTATTTA
*
232082 AAA-ATA-TTTATTTTAATTTTAATTTAA
1 AAATATATTTTATTTTAACTTT-ATTT-A
232109 GAATATATATTTTATTTT
1 -AA-ATATATTTTATTTT
232127 TTCTAAACTA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
25 9 0.24
26 8 0.21
27 4 0.11
28 5 0.13
29 1 0.03
30 3 0.08
31 8 0.21
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (27 bp):
AAATATATTTTATTTTAACTTTATTTA
Found at i:232191 original size:27 final size:30
Alignment explanation
Indices: 232161--232236 Score: 74
Period size: 30 Copynumber: 2.6 Consensus size: 30
232151 TACTATTAAT
232161 CTAACTTT-TTAAAT-TA-TATAT-TTTATC
1 CTAA-TTTATTAAATATATTATATGTTTATC
232188 CTAATTTATTAAATATATTATATGTTTA-C
1 CTAATTTATTAAATATATTATATGTTTATC
*
232217 TTTACA-TTATTAAATATATT
1 -CTA-ATTTATTAAATATATT
232237 TTATTCTTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
26 3 0.07
27 10 0.24
28 2 0.05
29 6 0.14
30 20 0.48
31 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.54
Consensus pattern (30 bp):
CTAATTTATTAAATATATTATATGTTTATC
Found at i:232284 original size:20 final size:20
Alignment explanation
Indices: 232259--232297 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
232249 TAACTTCAAA
232259 ATATTTTA-ATATAAAAATAT
1 ATATTTTATA-ATAAAAATAT
232279 ATATTTTATAATAAAAATA
1 ATATTTTATAATAAAAATA
232298 AACATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATTTTATAATAAAAATAT
Found at i:233725 original size:81 final size:81
Alignment explanation
Indices: 233531--234146 Score: 959
Period size: 81 Copynumber: 7.6 Consensus size: 81
233521 TTTACCTATT
* *
233531 GCATGATTGACACTTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTATTT-
1 GCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTATTTA
233595 ACCGTTCATCTAACTG
66 ACCGTTCATCTAACTG
* *
233611 GCATAATTGGCACCTTTCTGCCAAATACACAGCTAGGCCATTTATCTTTTACTCAACGGTATTTA
1 GCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTATTTA
*
233676 ACCATTCATCTAACTG
66 ACCGTTCATCTAACTG
* * *
233692 AG-ATAATTGACACCTTTTTGCTAAATACACAGCTAGGCCATTTATCTTTTACTCAACGGTATTT
1 -GCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTATTT
*
233756 AACCGTTCATCTAATTG
65 AACCGTTCATCTAACTG
** * *
233773 GCATAATTGACACCTTTCTGCCAAATGCACTTCTATGCCATTTATCTTTTACTCAACGTTATTTA
1 GCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTATTTA
233838 ACCGTTCATCTAACTG
66 ACCGTTCATCTAACTG
* * *
233854 GCATAATTAACACATTTCTGCCAAATGCATAGCTAGGCCATTTATCTTTTACTCAACGGTATTTA
1 GCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTATTTA
*
233919 ACCGTTAATCTAACTG
66 ACCGTTCATCTAACTG
* * *
233935 ACATAATTGACACATTTCTGCCAAAT-CACAACTAGGCCATTTATCTTTTACTCAACGGTATTTA
1 GCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTATTTA
233999 ACCGTTCATCTAACTG
66 ACCGTTCATCTAACTG
* * * * *
234015 ACATAAATGACACCTTTCTGTCAAATGCACAACTAGGCCATTTATCTTTTACTCAATGGTATTTA
1 GCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTATTTA
234080 ACCGTTCATCTAACTG
66 ACCGTTCATCTAACTG
* *
234096 GCATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTA
1 GCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTA
234147 ATCTTAGAAT
Statistics
Matches: 493, Mismatches: 39, Indels: 7
0.91 0.07 0.01
Matches are distributed among these distances:
80 135 0.27
81 357 0.72
82 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (81 bp):
GCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTATTTA
ACCGTTCATCTAACTG
Found at i:233993 original size:242 final size:243
Alignment explanation
Indices: 233531--234146 Score: 984
Period size: 242 Copynumber: 2.5 Consensus size: 243
233521 TTTACCTATT
* * *
233531 GCATGATTGACACTTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTATTT-
1 GCATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATTTATCTTTTACTCAACGGTATTTA
* *
233595 ACCGTTCATCTAACTGGCATAATTGGCACCTTTCTGCCAAATACACAGCTAGGCCATTTATCTTT
66 ACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTT
* * * * * *
233660 TACTCAACGGTATTTAACCATTCATCTAACTGAGATAATTGACACCTTTTTGCTAAATACACAGC
131 TACTCAACGGTATTTAACCATTAATCTAACTGACATAATTGACACATTTCTGCCAAATACACAAC
*
233725 TAGGCCATTTATCTTTTACTCAACGGTATTTAACCGTTCATCTAATTG
196 TAGGCCATTTATCTTTTACTCAACGGTATTTAACCGTTCATCTAACTG
** * *
233773 GCATAATTGACACCTTTCTGCCAAATGCACTTCTATGCCATTTATCTTTTACTCAACGTTATTTA
1 GCATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATTTATCTTTTACTCAACGGTATTTA
* * *
233838 ACCGTTCATCTAACTGGCATAATTAACACATTTCTGCCAAATGCATAGCTAGGCCATTTATCTTT
66 ACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTT
*
233903 TACTCAACGGTATTTAACCGTTAATCTAACTGACATAATTGACACATTTCTGCCAAAT-CACAAC
131 TACTCAACGGTATTTAACCATTAATCTAACTGACATAATTGACACATTTCTGCCAAATACACAAC
233967 TAGGCCATTTATCTTTTACTCAACGGTATTTAACCGTTCATCTAACTG
196 TAGGCCATTTATCTTTTACTCAACGGTATTTAACCGTTCATCTAACTG
* * * *
234015 ACATAAATGACACCTTTCTGTCAAATGCACAACTAGGCCATTTATCTTTTACTCAATGGTATTTA
1 GCATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATTTATCTTTTACTCAACGGTATTTA
* *
234080 ACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATTAATCTTT
66 ACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTT
234145 TA
131 TA
234147 ATCTTAGAAT
Statistics
Matches: 341, Mismatches: 32, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
242 229 0.67
243 112 0.33
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (243 bp):
GCATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCATTTATCTTTTACTCAACGGTATTTA
ACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTT
TACTCAACGGTATTTAACCATTAATCTAACTGACATAATTGACACATTTCTGCCAAATACACAAC
TAGGCCATTTATCTTTTACTCAACGGTATTTAACCGTTCATCTAACTG
Found at i:234145 original size:323 final size:323
Alignment explanation
Indices: 233531--234146 Score: 1011
Period size: 323 Copynumber: 1.9 Consensus size: 323
233521 TTTACCTATT
* * *
233531 GCATGATTGACACTTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTATTTA
1 GCATAATTAACACATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTATTTA
* * * * *
233596 CCGTTCATCTAACTGGCATAATTGGCACCTTTCTGCCAAATACACAGCTAGGCCATTTATCTTTT
66 CCGTTAATCTAACTGACATAATTGACACATTTCTGCCAAATACACAACTAGGCCATTTATCTTTT
* * * *
233661 ACTCAACGGTATTTAACCATTCATCTAACTGAGATAATTGACACCTTTTTGCTAAATACACAGCT
131 ACTCAACGGTATTTAACCATTCATCTAACTGACATAAATGACACCTTTCTGCTAAATACACAACT
*
233726 AGGCCATTTATCTTTTACTCAACGGTATTTAACCGTTCATCTAATTGGCATAATTGACACCTTTC
196 AGGCCATTTATCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTC
** * *
233791 TGCCAAATGCACTTCTATGCCATTTATCTTTTACTCAACGTTATTTAACCGTTCATCTAACTG
261 TGCCAAATGCACAACTAGGCCATTAATCTTTTACTCAACGTTATTTAACCGTTCATCTAACTG
*
233854 GCATAATTAACACATTTCTGCCAAATGCATAGCTAGGCCATTTATCTTTTACTCAACGGTATTTA
1 GCATAATTAACACATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTATTT-
233919 ACCGTTAATCTAACTGACATAATTGACACATTTCTGCCAAAT-CACAACTAGGCCATTTATCTTT
65 ACCGTTAATCTAACTGACATAATTGACACATTTCTGCCAAATACACAACTAGGCCATTTATCTTT
* *
233983 TACTCAACGGTATTTAACCGTTCATCTAACTGACATAAATGACACCTTTCTG-TCAAATGCACAA
130 TACTCAACGGTATTTAACCATTCATCTAACTGACATAAATGACACCTTTCTGCT-AAATACACAA
*
234047 CTAGGCCATTTATCTTTTACTCAATGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTT
194 CTAGGCCATTTATCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTT
234112 TCTGCCAAATGCACAACTAGGCCATTAATCTTTTA
259 TCTGCCAAATGCACAACTAGGCCATTAATCTTTTA
234147 ATCTTAGAAT
Statistics
Matches: 270, Mismatches: 21, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
322 1 0.00
323 231 0.86
324 38 0.14
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (323 bp):
GCATAATTAACACATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTATTTA
CCGTTAATCTAACTGACATAATTGACACATTTCTGCCAAATACACAACTAGGCCATTTATCTTTT
ACTCAACGGTATTTAACCATTCATCTAACTGACATAAATGACACCTTTCTGCTAAATACACAACT
AGGCCATTTATCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTC
TGCCAAATGCACAACTAGGCCATTAATCTTTTACTCAACGTTATTTAACCGTTCATCTAACTG
Found at i:234385 original size:55 final size:54
Alignment explanation
Indices: 234318--234513 Score: 248
Period size: 55 Copynumber: 3.6 Consensus size: 54
234308 GCCTACTTGT
* * * * * * *
234318 TATGAACTTCTTATATTTGTACATATATTTCCGATACGGAAATTCATACACTTAG
1 TATGAATTTCTTAT-TTTGCACACATAGTGCCCATACGAAAATTCATACACTTAG
* * ** *
234373 TATGAATTTCTTAGTTCGCACACCGAGTGCCCATACGAAAATTCATACATTTAG
1 TATGAATTTCTTATTTTGCACACATAGTGCCCATACGAAAATTCATACACTTAG
234427 TATGAATTTCTTAGTTTTGCACACATAGTGCCCATACGAAAATTCATACACTTAG
1 TATGAATTTCTTA-TTTTGCACACATAGTGCCCATACGAAAATTCATACACTTAG
*
234482 TATGAATTCCTTAGTTTTGCACACATAGTGCC
1 TATGAATTTCTTA-TTTTGCACACATAGTGCC
234514 ATTTGGTAGT
Statistics
Matches: 122, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
54 43 0.35
55 79 0.65
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (54 bp):
TATGAATTTCTTATTTTGCACACATAGTGCCCATACGAAAATTCATACACTTAG
Found at i:234899 original size:19 final size:21
Alignment explanation
Indices: 234855--234906 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
234845 ACGCCACCAT
*
234855 GGTATCGATACTACTATACTAT
1 GGTATCGATACTACTATA-TAC
234877 GGTATCGATACT-CTAT-TAC
1 GGTATCGATACTACTATATAC
*
234896 GGTACCGATAC
1 GGTATCGATAC
234907 CATTTTTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.43
21 4 0.14
22 12 0.43
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (21 bp):
GGTATCGATACTACTATATAC
Done.