Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168282.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_51, 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: 160351
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 1000 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:694 original size:161 final size:159
Alignment explanation
Indices: 263--735 Score: 705
Period size: 153 Copynumber: 3.0 Consensus size: 159
253 AAAATTTTAC
* * *
263 CAAGTAATTAGTTGTTGGAAATGATTCTCAATTGACTCTAATAC-TTTAGCAGAAAATTGAGAAA
1 CAAGTAATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAA
*
327 ATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGGGGCTCCGTCGTCGGA
66 ATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGA
*
392 TTTATTAAAGAAAAAAAAAATC---ATC-
131 TTAATTAAAGAAAAAAAAAATCAAAATCA
*
417 C----AATTAATTATTGGAAATTATATTCTCAATTAACTCTAATACTTTTAGCAGAAAATTGAGA
1 CAAGTAATTAATTATTGGAAA-T-TATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
*
478 AAATTCCCTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
64 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
543 GATTAATTAAAGAAAAAAAAAATCAAAATCA
129 GATTAATTAAAGAAAAAAAAAATCAAAATCA
*
574 GCAAAGTAATTAATTATCGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAG-
1 -C-AAGTAATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
* *
638 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTTTACTTGTAGAGGCTCCGTCGTC
64 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTG-TTTCACTTGCAGAGGCTCCGTCGTC
* **
703 GGATTGATTAAAGAAAAAAGAAAAAAAAAATCA
128 GGATTAATTAAAGAAAAAA-AAAATCAAAATCA
736 AGATCAAAAT
Statistics
Matches: 289, Mismatches: 15, Indels: 22
0.89 0.05 0.07
Matches are distributed among these distances:
150 14 0.05
151 1 0.00
152 20 0.07
153 104 0.36
154 1 0.00
156 3 0.01
158 1 0.00
160 38 0.13
161 80 0.28
162 12 0.04
163 15 0.05
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (159 bp):
CAAGTAATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAA
ATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGA
TTAATTAAAGAAAAAAAAAATCAAAATCA
Found at i:770 original size:1 final size:1
Alignment explanation
Indices: 766--799 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
756 TAAAAAAATC
766 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
800 CCTGGAGCGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:771 original size:9 final size:8
Alignment explanation
Indices: 753--799 Score: 57
Period size: 7 Copynumber: 6.4 Consensus size: 8
743 AATCAAAGTC
753 AAATAAAA
1 AAATAAAA
*
761 AAATCAAA
1 AAATAAAA
769 AAA-AAAA
1 AAATAAAA
776 AAA-AAAA
1 AAATAAAA
783 AAA-AAAA
1 AAATAAAA
790 AAA-AAAA
1 AAATAAAA
797 AAA
1 AAA
800 CCTGGAGCGG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
7 27 0.73
8 10 0.27
ACGTcount: A:0.94, C:0.02, G:0.00, T:0.04
Consensus pattern (8 bp):
AAATAAAA
Found at i:772 original size:12 final size:12
Alignment explanation
Indices: 723--795 Score: 55
Period size: 10 Copynumber: 5.8 Consensus size: 12
713 AAGAAAAAAG
723 AAAAAAAAAATC
1 AAAAAAAAAATC
735 AAGATCAAAATCAAAGTC
1 AA-A--AAAA--AAA-TC
753 AAATAAAAAAATC
1 AAA-AAAAAAATC
766 AAAAAAAAAA--
1 AAAAAAAAAATC
776 AAAAAAAAAA--
1 AAAAAAAAAATC
786 AAAAAAAAAA
1 AAAAAAAAAA
796 AAAACCTGGA
Statistics
Matches: 54, Mismatches: 1, Indels: 14
0.78 0.01 0.20
Matches are distributed among these distances:
10 20 0.37
12 9 0.17
13 6 0.11
14 3 0.06
15 4 0.07
16 4 0.07
17 4 0.07
18 4 0.07
ACGTcount: A:0.82, C:0.07, G:0.03, T:0.08
Consensus pattern (12 bp):
AAAAAAAAAATC
Found at i:1159 original size:20 final size:20
Alignment explanation
Indices: 1130--1175 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1120 GGAAGATTCA
*
1130 CCGGATTCTGGAAATTTTCG
1 CCGGAATCTGGAAATTTTCG
***
1150 CCGGAATCTGGGTTTTTTCG
1 CCGGAATCTGGAAATTTTCG
1170 CCGGAA
1 CCGGAA
1176 GTTGGCCGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (20 bp):
CCGGAATCTGGAAATTTTCG
Found at i:1270 original size:19 final size:19
Alignment explanation
Indices: 1248--1311 Score: 54
Period size: 19 Copynumber: 3.7 Consensus size: 19
1238 TGGGCAGGTC
1248 GCCGGAAACTTCAATGTTG
1 GCCGGAAACTTCAATGTTG
1267 GCCGG-AA--T---T-TTG
1 GCCGGAAACTTCAATGTTG
1279 GCCGGAAACTTCAA-GATTG
1 GCCGGAAACTTCAATG-TTG
*
1298 GCCGGAAAATTCAA
1 GCCGGAAACTTCAA
1312 CCGGAAACTG
Statistics
Matches: 36, Mismatches: 1, Indels: 16
0.68 0.02 0.30
Matches are distributed among these distances:
12 8 0.22
13 3 0.08
15 1 0.03
16 1 0.03
18 2 0.06
19 21 0.58
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (19 bp):
GCCGGAAACTTCAATGTTG
Found at i:2114 original size:10 final size:9
Alignment explanation
Indices: 2099--2195 Score: 104
Period size: 8 Copynumber: 11.7 Consensus size: 9
2089 CAACTCAACA
2099 TTTTTGATTT
1 TTTTTG-TTT
*
2109 TTTTTG-AT
1 TTTTTGTTT
*
2117 TTTTTG-AT
1 TTTTTGTTT
2125 TTTTT-TTT
1 TTTTTGTTT
2133 TTTTT-TTT
1 TTTTTGTTT
2141 TTTTT-TTT
1 TTTTTGTTT
2149 TTTTT-TTT
1 TTTTTGTTT
2157 TTTTT-TTT
1 TTTTTGTTT
2165 TTTTTGTTT
1 TTTTTGTTT
2174 TTTTT-TTT
1 TTTTTGTTT
2182 TTTTT-TTT
1 TTTTTGTTT
2190 TTTTTG
1 TTTTTG
2196 CCGAAGCTCC
Statistics
Matches: 82, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
8 68 0.83
9 8 0.10
10 6 0.07
ACGTcount: A:0.03, C:0.00, G:0.05, T:0.92
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:2122 original size:18 final size:15
Alignment explanation
Indices: 2099--2195 Score: 121
Period size: 14 Copynumber: 6.4 Consensus size: 15
2089 CAACTCAACA
2099 TTTTTGATTTTTTTTGAT
1 TTTTTG-TTTTTTTT--T
2117 TTTTTGATTTTTTTTT
1 TTTTTG-TTTTTTTTT
2133 TTTTT-TTTTTTTTT
1 TTTTTGTTTTTTTTT
2147 TTTTT-TTTTTTTTT
1 TTTTTGTTTTTTTTT
2161 TTTTT-TTTTGTTTTT
1 TTTTTGTTTT-TTTTT
2176 TTTTT-TTTTTTTTT
1 TTTTTGTTTTTTTTT
2190 TTTTTG
1 TTTTTG
2196 CCGAAGCTCC
Statistics
Matches: 77, Mismatches: 0, Indels: 7
0.92 0.00 0.08
Matches are distributed among these distances:
14 42 0.55
15 14 0.18
16 6 0.08
18 15 0.19
ACGTcount: A:0.03, C:0.00, G:0.05, T:0.92
Consensus pattern (15 bp):
TTTTTGTTTTTTTTT
Found at i:2128 original size:1 final size:1
Alignment explanation
Indices: 2124--2194 Score: 133
Period size: 1 Copynumber: 71.0 Consensus size: 1
2114 GATTTTTTGA
*
2124 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2189 TTTTTT
1 TTTTTT
2195 GCCGAAGCTC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.00, C:0.00, G:0.01, T:0.99
Consensus pattern (1 bp):
T
Found at i:2134 original size:25 final size:25
Alignment explanation
Indices: 2106--2195 Score: 139
Period size: 24 Copynumber: 3.7 Consensus size: 25
2096 ACATTTTTGA
** *
2106 TTTTTTTTGATTTTTTG-ATTTTTT
1 TTTTTTTTTTTTTTTTGTTTTTTTT
2130 TTTTTTTTTTTTTTTT-TTTTTTTT
1 TTTTTTTTTTTTTTTTGTTTTTTTT
2154 TTTTTTTTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTGTTTTTTTT
2179 TTTTTTTTTTTTTTTTG
1 TTTTTTTTTTTTTTTTG
2196 CCGAAGCTCC
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
24 36 0.59
25 25 0.41
ACGTcount: A:0.02, C:0.00, G:0.04, T:0.93
Consensus pattern (25 bp):
TTTTTTTTTTTTTTTTGTTTTTTTT
Found at i:2295 original size:41 final size:39
Alignment explanation
Indices: 2201--2754 Score: 459
Period size: 40 Copynumber: 14.0 Consensus size: 39
2191 TTTTGCCGAA
* *
2201 GCTCCTCTAAACAGAGACTCAACGACTTTTGAAAGTAAATT
1 GCTCCTCTAAACAGAG--GCAACGACTTTGGAAAGTAAATT
2242 GCTCCTCTAAACAGAGGCAACGGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAAC-GACTTTGGAAAGTAAATT
** *
2282 GCTCCTCTCAAACAGAGGCACCACGACTTTGCTAATTAAGA--
1 GCTCCTCT-AAACAGAGGCA--ACGACTTTGGAAAGTAA-ATT
* *** ***** *
2323 G------GAAA-A-A--CTTGGA-TTTGCCCTCTAAACT
1 GCTCCTCTAAACAGAGGCAACGACTTTGGAAAGTAAATT
2351 GCTCCTCT--ACAGAGGCAACGACTTTGGAAAAGATAAATT
1 GCTCCTCTAAACAGAGGCAACGACTTTGG-AAAG-TAAATT
*
2390 GCT-CTCTAAACAGA-GC-ACGAACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAGTAAATT
*
2427 GCTCCTCTAAACAGAGGCAACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCAACGACTTTGG-AAAGTAAATT
* * *
2467 GCTCCTACT-ACCAGAGGCATGACGAAC-TTGAAAAGTTAATT
1 GCTCCT-CTAAACAGAGGCA--ACG-ACTTTGGAAAGTAAATT
*
2508 GCCTCCTCT-AACAAGAGGCAGACGAACTTTGGAAAAAATAAATT
1 G-CTCCTCTAAAC-AGAGGCA-ACG-ACTTTGG--AAAGTAAATT
2552 GCTCCTCTAAACAAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAAC-AGAGGCA--ACGACTTTGGAAAGTAAATT
*
2594 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAGTAAATT
*
2634 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGG-AAAGTAAATT
2676 GCTCCTCTAAACAGAGGCAACGAAC-TTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGG-AAAGTAAATT
*
2716 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAAT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAGTAAAT
2755 ACTCCTAGAC
Statistics
Matches: 428, Mismatches: 41, Indels: 89
0.77 0.07 0.16
Matches are distributed among these distances:
26 1 0.00
27 8 0.02
28 3 0.01
30 1 0.00
32 2 0.00
33 2 0.00
34 4 0.01
36 3 0.01
37 13 0.03
38 22 0.05
39 31 0.07
40 143 0.33
41 68 0.16
42 85 0.20
43 12 0.03
44 27 0.06
45 3 0.01
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (39 bp):
GCTCCTCTAAACAGAGGCAACGACTTTGGAAAGTAAATT
Found at i:2645 original size:82 final size:82
Alignment explanation
Indices: 2345--2754 Score: 535
Period size: 82 Copynumber: 5.1 Consensus size: 82
2335 ATTTGCCCTC
*
2345 TAAACTGCTCCTCT--ACAGAGGCAACG-ACTTTGGAAAAGATAAATTGCT-CTCTAAACAGA-G
1 TAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGGAAAAG-TAAATTGCTCCTCTAAACAGAGG
*
2405 CACGA--ACTTTGAAAAG
65 CACCACGACTTTGAAAAG
* *
2421 TAAATTGCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAAATAAATTGCTCCTACT-ACCAGAGG
1 TAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGGAAAAGTAAATTGCTCCT-CTAAACAGAGG
**
2484 CATGACGAAC-TTGAAAAG
65 CACCACG-ACTTTGAAAAG
* *
2502 TTAATTGCCTCCTCT-AACAAGAGGCAGACGAACTTTGGAAAAAATAAATTGCTCCTCTAAACAA
1 TAAATTG-CTCCTCTAAAC-AGAGGCA-ACGAACTTTGG-AAAAGTAAATTGCTCCTCTAAAC-A
*
2566 GAGGCACCACGACTTTGGAAAG
61 GAGGCACCACGACTTTGAAAAG
2588 TAAATTGCTCCTCTAAACAGAGGCAACGAACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGC
1 TAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGC
*
2652 ACCACGACTTTGGAAAAA
66 ACCACGACTTT-GAAAAG
2670 TAAATTGCTCCTCTAAACAGAGGCAACGAAC-TTGGAAAAGTAAATTGCTCCTCTAAACAGAGGC
1 TAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGC
2734 A--ACGAACTTTGAAAAG
66 ACCACG-ACTTTGAAAAG
2750 TAAAT
1 TAAAT
2755 ACTCCTAGAC
Statistics
Matches: 300, Mismatches: 14, Indels: 36
0.86 0.04 0.10
Matches are distributed among these distances:
76 13 0.04
77 9 0.03
78 30 0.10
79 7 0.02
80 13 0.04
81 41 0.14
82 104 0.35
83 4 0.01
84 18 0.06
85 35 0.12
86 26 0.09
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (82 bp):
TAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGC
ACCACGACTTTGAAAAG
Found at i:2651 original size:167 final size:164
Alignment explanation
Indices: 2345--2754 Score: 535
Period size: 167 Copynumber: 2.5 Consensus size: 164
2335 ATTTGCCCTC
* *
2345 TAAACTGCTCCTCT-AC-AGAGGCAACG-ACTTTGGAAAAGATAAATTGCT-CTCTAAACAGA-G
1 TAAATTGCTCCTCTAACAAGAGGCAACGAACTTTGGAAAAAATAAATTGCTCCTCTAAACAGAGG
2405 --CACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTTTGGAAAAATAAATTG
66 CACACG-ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTTTGGAAAAATAAATTG
* ** *
2468 CTCCTACTACCAGAGGCATGACGAAC-TT-GAAAAG
130 CTCCTACTAACAGAGGCACCACG-ACTTTGGAAAAA
*
2502 TTAATTGCCTCCTCTAACAAGAGGCAGACGAACTTTGGAAAAAATAAATTGCTCCTCTAAACAAG
1 TAAATTG-CTCCTCTAACAAGAGGCA-ACGAACTTTGGAAAAAATAAATTGCTCCTCTAAAC-AG
* *
2567 AGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAACTTT-GAAAAGTAA
63 AGGCA-CACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAAATAA
2631 ATTGCTCCT-CTAAACAGAGGCACCACGACTTTGGAAAAA
126 ATTGCTCCTACT-AACAGAGGCACCACGACTTTGGAAAAA
*
2670 TAAATTGCTCCTCTAA-ACAGAGGCAACGAAC-TTGG-AAAAGTAAATTGCTCCTCTAAACAGAG
1 TAAATTGCTCCTCTAACA-AGAGGCAACGAACTTTGGAAAAAATAAATTGCTCCTCTAAACAGAG
2732 GCA-ACGAACTTTGAAAAGTAAAT
65 GCACACG-ACTTTGAAAAGTAAAT
2755 ACTCCTAGAC
Statistics
Matches: 224, Mismatches: 12, Indels: 29
0.85 0.05 0.11
Matches are distributed among these distances:
157 5 0.02
158 7 0.03
159 2 0.01
160 7 0.03
161 6 0.03
162 36 0.16
163 15 0.07
164 25 0.11
165 5 0.02
166 11 0.05
167 85 0.38
168 20 0.09
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (164 bp):
TAAATTGCTCCTCTAACAAGAGGCAACGAACTTTGGAAAAAATAAATTGCTCCTCTAAACAGAGG
CACACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTTTGGAAAAATAAATTGC
TCCTACTAACAGAGGCACCACGACTTTGGAAAAA
Found at i:3897 original size:10 final size:10
Alignment explanation
Indices: 3882--3911 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3872 GACCTGAATC
3882 TTTTTTTTTG
1 TTTTTTTTTG
*
3892 TTTTTTTTTT
1 TTTTTTTTTG
3902 TTTTTTTTTG
1 TTTTTTTTTG
3912 GGTACCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:3990 original size:21 final size:21
Alignment explanation
Indices: 3961--4016 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
3951 CTTTTTTTCA
* *
3961 TTTTCTCATTTTTTCCTTCTT
1 TTTTTTCATTTTTTCATTCTT
*
3982 TTTTTTCATTTTTTCATTTTT
1 TTTTTTCATTTTTTCATTCTT
4003 TTTTTTCATTTTTT
1 TTTTTTCATTTTTT
4017 TTTTCATCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTTCATTTTTTCATTCTT
Found at i:3995 original size:8 final size:8
Alignment explanation
Indices: 3953--4016 Score: 59
Period size: 8 Copynumber: 8.8 Consensus size: 8
3943 TTGGATCTCT
3953 TTTTTTCA
1 TTTTTTCA
*
3961 TTTTCTCA
1 TTTTTTCA
3969 TTTTTTC-
1 TTTTTTCA
* *
3976 CTTCTT--
1 TTTTTTCA
3982 TTTTTTCA
1 TTTTTTCA
3990 TTTTTTCA
1 TTTTTTCA
3998 -TTTTT--
1 TTTTTTCA
4003 TTTTTTCA
1 TTTTTTCA
4011 TTTTTT
1 TTTTTT
4017 TTTTCATCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
6 9 0.20
7 9 0.20
8 27 0.60
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCA
Found at i:3995 original size:12 final size:12
Alignment explanation
Indices: 3990--4023 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
3980 TTTTTTTTCA
3990 TTTTTTCATTTTT
1 TTTTTTCA-TTTT
4003 TTTTTTCATTTT
1 TTTTTTCATTTT
4015 TTTTTTCAT
1 TTTTTTCAT
4024 CATCTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTCATTTT
Found at i:4006 original size:13 final size:13
Alignment explanation
Indices: 3990--4039 Score: 73
Period size: 13 Copynumber: 3.7 Consensus size: 13
3980 TTTTTTTTCA
3990 TTTTTTCATTTTT
1 TTTTTTCATTTTT
4003 TTTTTTCATTTTT
1 TTTTTTCATTTTT
*
4016 TTTTTCATCATCTTT
1 TTTTT--TCATTTTT
4031 TTTTTTCAT
1 TTTTTTCAT
4040 CCATTGTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
13 22 0.65
15 12 0.35
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTCATTTTT
Found at i:4014 original size:29 final size:29
Alignment explanation
Indices: 3953--4039 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 29
3943 TTGGATCTCT
* *
3953 TTTTTTCATTTTCTCATTTTTTCCTTCTT--
1 TTTTTTCATTTTATCATTTTTT--TTTTTCA
*
3982 TTTTTTCATTTTTTCATTTTTTTTTTTCA
1 TTTTTTCATTTTATCATTTTTTTTTTTCA
*
4011 TTTTTT--TTTTCATCATCTTTTTTTTTCA
1 TTTTTTCATTTT-ATCATTTTTTTTTTTCA
4039 T
1 T
4040 CCATTGTTGA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
27 8 0.16
28 16 0.31
29 27 0.53
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (29 bp):
TTTTTTCATTTTATCATTTTTTTTTTTCA
Found at i:4413 original size:1 final size:1
Alignment explanation
Indices: 4407--4439 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
4397 TTTTGTGGTG
*
4407 TTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4440 CAAAATTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:7963 original size:153 final size:155
Alignment explanation
Indices: 7685--8139 Score: 716
Period size: 153 Copynumber: 2.9 Consensus size: 155
7675 TTTACCAAGT
* * *
7685 AATTAGTTGTTGGAAATGATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
1 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
* *
7750 CTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGGGGCTCCGTCGTCGGATTTAT
66 CTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAAT
*
7815 TAAAGAAAAAAA-CAAAATCATC-C
131 TAAAGAAAAAAATCAAAATCAGCAC
*
7838 AATTAATTATTGGAAATTATTCTCAATTAACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
1 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
*
7903 CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAAT
66 CTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAAT
*
7968 TAAAGAAAAAAAAATCAAAATCAGCAAAGT
131 TAAAG--AAAAAAATCAAAATCAGC--A-C
**
7998 AATTAATTATCAGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
1 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
* * *
8063 CTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTTTACTTGTAGAGGCTCCGTCGTCGGATTGA
66 CTCACCTCAGGAGTATGCAAGAAAAACTACTG-TTTCACTTGCAGAGGCTCCGTCGTCGGATTAA
8128 TTAAAGAAAAAA
130 TTAAAGAAAAAA
8140 GAAAAAAAAA
Statistics
Matches: 278, Mismatches: 16, Indels: 10
0.91 0.05 0.03
Matches are distributed among these distances:
153 128 0.46
155 7 0.03
156 9 0.03
159 6 0.02
160 93 0.33
161 35 0.13
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (155 bp):
AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
CTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAAT
TAAAGAAAAAAATCAAAATCAGCAC
Found at i:8189 original size:1 final size:1
Alignment explanation
Indices: 8185--8216 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
8175 AAAAAAATTC
8185 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8217 CCTGGAGCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:8192 original size:14 final size:13
Alignment explanation
Indices: 8141--8216 Score: 52
Period size: 11 Copynumber: 5.7 Consensus size: 13
8131 AAGAAAAAAG
8141 AAAAAAAAAATCA
1 AAAAAAAAAATCA
*
8154 AGATCAAAATCAAAGTCA
1 A-A--AAAA--AAAATCA
*
8172 AATAAAAAAATTCA
1 AA-AAAAAAAATCA
8186 AAAAAAAAAA--A
1 AAAAAAAAAATCA
8197 AAAAAAAAAA--A
1 AAAAAAAAAATCA
8208 AAAAAAAAA
1 AAAAAAAAA
8217 CCTGGAGCGG
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
11 21 0.39
13 8 0.15
14 9 0.17
16 8 0.15
17 1 0.02
18 7 0.13
ACGTcount: A:0.82, C:0.07, G:0.03, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAATCA
Found at i:8578 original size:20 final size:20
Alignment explanation
Indices: 8549--8594 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
8539 GGAAGATTCA
*
8549 CCGGATTCTGGAAATTTTCG
1 CCGGAATCTGGAAATTTTCG
***
8569 CCGGAATCTGGGTTTTTTCG
1 CCGGAATCTGGAAATTTTCG
8589 CCGGAA
1 CCGGAA
8595 GTTGGCCGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (20 bp):
CCGGAATCTGGAAATTTTCG
Found at i:8637 original size:20 final size:20
Alignment explanation
Indices: 8612--8654 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
8602 GGAAATTTGA
8612 CGGTTTCTGGGATTCTTCGC
1 CGGTTTCTGGGATTCTTCGC
8632 CGGTTTCTGGGATTCTTCGC
1 CGGTTTCTGGGATTCTTCGC
8652 CGG
1 CGG
8655 AAACTGGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.05, C:0.26, G:0.33, T:0.37
Consensus pattern (20 bp):
CGGTTTCTGGGATTCTTCGC
Found at i:8661 original size:20 final size:20
Alignment explanation
Indices: 8618--8662 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
8608 TTGACGGTTT
***
8618 CTGGGATTCTTCGCCGGTTT
1 CTGGGATTCTTCGCCGGAAA
8638 CTGGGATTCTTCGCCGGAAA
1 CTGGGATTCTTCGCCGGAAA
8658 CTGGG
1 CTGGG
8663 CAGGTCGCCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.24, G:0.33, T:0.31
Consensus pattern (20 bp):
CTGGGATTCTTCGCCGGAAA
Found at i:8691 original size:19 final size:19
Alignment explanation
Indices: 8669--8732 Score: 54
Period size: 19 Copynumber: 3.7 Consensus size: 19
8659 TGGGCAGGTC
8669 GCCGGAAACTTCAATGTTG
1 GCCGGAAACTTCAATGTTG
8688 GCCGG-AA--T---T-TTG
1 GCCGGAAACTTCAATGTTG
8700 GCCGGAAACTTCAA-GATTG
1 GCCGGAAACTTCAATG-TTG
*
8719 GCCGGAAAATTCAA
1 GCCGGAAACTTCAA
8733 CCGGAAACTG
Statistics
Matches: 36, Mismatches: 1, Indels: 16
0.68 0.02 0.30
Matches are distributed among these distances:
12 8 0.22
13 3 0.08
15 1 0.03
16 1 0.03
18 2 0.06
19 21 0.58
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (19 bp):
GCCGGAAACTTCAATGTTG
Found at i:9328 original size:40 final size:41
Alignment explanation
Indices: 9227--9328 Score: 113
Period size: 40 Copynumber: 2.5 Consensus size: 41
9217 ACAAAAAAAA
* *
9227 AATAATAATAATAATAAATATATAACTATATACATATAAATCT
1 AATAATAATAA-AATAAATAAATAAATATATACATATAAA-CT
*
9270 AAT-CTAATAAAA-AAATAAATAAATATATACATA-ATAA-T
1 AATAATAATAAAATAAATAAATAAATATATACATATA-AACT
*
9308 AATAATAATAAAATACATAAA
1 AATAATAATAAAATAAATAAA
9329 ATACAAAAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
38 4 0.08
39 9 0.18
40 27 0.53
41 2 0.04
42 6 0.12
43 3 0.06
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (41 bp):
AATAATAATAAAATAAATAAATAAATATATACATATAAACT
Found at i:10277 original size:357 final size:354
Alignment explanation
Indices: 9539--11136 Score: 1845
Period size: 357 Copynumber: 4.5 Consensus size: 354
9529 TGAAAATATT
* * * * * * ** * ** *
9539 GCCACATAAATTCTAACACCATTATTGAAAGCATTTATCCAAGAAAGACACCTTTAATAATTCCT
1 GCCACACAAATTGTAACACTATTATTGAAGGCGTATATTTAAGATAGATGCCTTTAATAATTCTT
* * * *
9604 ATCACAGTTTGTAGT-TAATTACTGAAGGCAGTTGCAAAAAACAACGCTTTTAATAA-TTTCTCT
66 ATCACAGTTTGTA-TATAATTACTGAAGGCAGTTTCAGAAAACAACACCTTTAATAATTTTC-CT
* * * * *
9667 AAAAAAATTTTCTCAGATTATTAAAAGCATCTTTTATTATGACACA-CC-TCAATATACCACGAT
129 AAAAAATTTTTTTGA-ATTATTAAAGGCGTCTTTTATTAT-A-A-AGCCTTCAATATACCACGAT
* ** *
9730 GGTAATGAAAGGTGTTTATTAGAAAAGGTGCCTTTAATATACCTTTAAACTTAGTAAT-CATTAC
190 GGTAATGAAAGGCGTTTATTAGAAAAGGCACCTTCAATATACCTTTAAACTTAGTAATCCATTAC
* * * * *
9794 TAAAGGCGTTTGTTAATAATAGACGCCTTCAAAATTTTCCCACTAAATATTTTGGGAATTATTAA
255 TGAAGGCATTTGTTAATAACAAACGCCTTCAAAATTTTCCCACTAAATATTTTGAGAATTATTAA
* * *
9859 AAGCATTTTTTATTGTAAAATACTTTCTATATACC
320 AGGCATCTTTTATTGTAAAATGCTTTCTATATACC
* * * * * * *
9894 GTCACATAAATTTTAATACCATTATTGAAGGCCTATATTTAAGATAGATGCCTTTAATAATTCCT
1 GCCACACAAATTGTAACACTATTATTGAAGGCGTATATTTAAGATAGATGCCTTTAATAATTCTT
* * * * *
9959 ATCACAGTTTGTATACAATTACTGAAGGTAATTTTAGAAAACAACATCTTTAATAATTTTCCTAA
66 ATCACAGTTTGTATATAATTACTGAAGGCAGTTTCAGAAAACAACACCTTTAATAATTTTCCTAA
* * * *
10024 AAAATTTTTTTTGAATTATTGAAGGCGTTTTTTATTATAAAGCGTCTTCAATATACCATGATGTT
131 AAAA-TTTTTTTGAATTATTAAAGGCGTCTTTTATTATAAAGC--CTTCAATATACCACGATGGT
* * **
10089 AATGGAAGGTGTTTATTAGAAAAGGTGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTGA
193 AATGAAAGGCGTTTATTAGAAAAGGCACCTTCAATATACCTTTAAACTTAGTAATCCATTACTGA
* *
10154 AGGCATTTGTTAATAACAAACGCCTTCAAAATTTTCTCACTAAATAGTTTGAGAATTATTAAAGG
258 AGGCATTTGTTAATAACAAACGCCTTCAAAATTTTCCCACTAAATATTTTGAGAATTATTAAAGG
*
10219 CATCTTTTATTGTAAAATG-TCTTCTATATATC
323 CATCTTTTATTGTAAAATGCT-TTCTATATACC
* *
10251 GCTACACAAATTGTAACACTATTATTGAAGGCGTATATTTAAGATAGATGCCTTTAACAATTCTT
1 GCCACACAAATTGTAACACTATTATTGAAGGCGTATATTTAAGATAGATGCCTTTAATAATTCTT
* ** * *
10316 ATCACAGTTTATATATAATTACTGAAGGCAGTTTTGGCAAACAACACCTTCAATAATTTTCCTAA
66 ATCACAGTTTGTATATAATTACTGAAGGCAGTTTCAGAAAACAACACCTTTAATAATTTTCCTAA
** * * * * *
10381 AAAAAATTTTTCAGATTATTAAAGGCATCTTTTATTATAAAACACCTTCAATATATCACAATGGT
131 AAAATTTTTTTGA-ATTATTAAAGGCGTCTTTTATTAT-AAA-GCCTTCAATATACCACGATGGT
* * *
10446 AATGGAAGGCGTTTATTAGAAAAGGCACCTTCAATATACCTTTAAACTTAGTAATCCATTATTGC
193 AATGAAAGGCGTTTATTAGAAAAGGCACCTTCAATATACCTTTAAACTTAGTAATCCATTACTGA
10511 AGGCATTTGTTAATAACAAACGCCTTCAAAAATTTT-CCACTAAATATTTT-AGGAATTATTAAA
258 AGGCATTTGTTAATAACAAACGCCTTC-AAAATTTTCCCACTAAATATTTTGA-GAATTATTAAA
** * *
10574 GGTGTCTTCTATTGTAAAATGCTTTCTATATACT
321 GGCATCTTTTATTGTAAAATGCTTTCTATATACC
* * ** *
10608 GCCACACAAATTCTAACACTGTTATTGAAGGCGTATATCCAAGAAAGATGCCTTTAATAATTCTT
1 GCCACACAAATTGTAACACTATTATTGAAGGCGTATATTTAAGATAGATGCCTTTAATAATTCTT
* * * ** * *
10673 TTCACAGTTTGTAGT-TAATTACTGAAGGCGGTTACAGAAAACAATGCCTTCAATAATTTCCCTA
66 ATCACAGTTTGTA-TATAATTACTGAAGGCAGTTTCAGAAAACAACACCTTTAATAATTTTCCTA
* * * * *
10737 CAAAAATTTTCTCGGATTATTAAAGGTGTCTTTTATTATGACATGCCTTCAATATACCACGATGG
130 -AAAAATTTTTTTGAATTATTAAAGGCGTCTTTTATTAT-A-AAGCCTTCAATATACCACGATGG
* * *
10802 TAATGAAAGGCATTTATTAGAAGAA-GCACTTTCAATATACGTTTAAACTTAGTAATCCATTACT
192 TAATGAAAGGCGTTTATTAGAA-AAGGCACCTTCAATATACCTTTAAACTTAGTAATCCATTACT
* * * * *
10866 GAAAGCATTTGTTAATAATATATGCCTTCAAAATTTTCCCACTAAATATTTTG-GTAGTTATTAA
256 GAAGGCATTTGTTAATAACAAACGCCTTCAAAATTTTCCCACTAAATATTTTGAG-AATTATTAA
** ** * *
10930 AGGTGTCTTTTACCGTAAAATACCTTCTATATACC
320 AGGCATCTTTTATTGTAAAATGCTTTCTATATACC
* *
10965 ACCACACAAATTGTAACACTATTATTGAAGGCGTATATTTAAGATAGATGCCTTTAATAATTTTT
1 GCCACACAAATTGTAACACTATTATTGAAGGCGTATATTTAAGATAGATGCCTTTAATAATTCTT
* * * *
11030 ATCATAGTTTGTATATAATTACTGAATGC-GATTTCA-AATAACAACGCCTTTAATAATTTCCCT
66 ATCACAGTTTGTATATAATTACTGAAGGCAG-TTTCAGAA-AACAACACCTTTAATAATTTTCCT
*
11093 AAAAAAATTTTTTTCGGATTATTAAAGGCGTCTTTTATTATAAA
129 -AAAAAATTTTTTT-GAATTATTAAAGGCGTCTTTTATTATAAA
11137 CCACCTTCAA
Statistics
Matches: 1070, Mismatches: 146, Indels: 53
0.84 0.12 0.04
Matches are distributed among these distances:
352 1 0.00
353 2 0.00
354 2 0.00
355 128 0.12
356 101 0.09
357 785 0.73
358 50 0.05
359 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (354 bp):
GCCACACAAATTGTAACACTATTATTGAAGGCGTATATTTAAGATAGATGCCTTTAATAATTCTT
ATCACAGTTTGTATATAATTACTGAAGGCAGTTTCAGAAAACAACACCTTTAATAATTTTCCTAA
AAAATTTTTTTGAATTATTAAAGGCGTCTTTTATTATAAAGCCTTCAATATACCACGATGGTAAT
GAAAGGCGTTTATTAGAAAAGGCACCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGG
CATTTGTTAATAACAAACGCCTTCAAAATTTTCCCACTAAATATTTTGAGAATTATTAAAGGCAT
CTTTTATTGTAAAATGCTTTCTATATACC
Found at i:14452 original size:58 final size:58
Alignment explanation
Indices: 14392--14609 Score: 274
Period size: 59 Copynumber: 3.7 Consensus size: 58
14382 TTGTACAGGG
* ** * ** *
14392 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTGAAGCTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAGA
*
14450 AAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTTTGAAAATTTATTTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCC-CCAAAA-ATATTTTTTTGAAAATTTA-TTTTTAAGA
* * ** **
14511 AAAATTGATACTTTCAACTTTTTCTCAAAAATCCTTTTTAAAAAATTTATTTTTAAGAA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAG-A
14570 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
14610 TTATTTAAAG
Statistics
Matches: 136, Mismatches: 20, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
58 32 0.24
59 56 0.41
60 20 0.15
61 28 0.21
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.44
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTATTTTTAAGA
Found at i:14667 original size:6 final size:6
Alignment explanation
Indices: 14638--14716 Score: 71
Period size: 6 Copynumber: 14.2 Consensus size: 6
14628 ATAATAAAAC
* * * *
14638 AAAATA AAAGTG AAAAT- -AAA-A AAAATA AAAAGA AAAGT- -AAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
14681 AAAATA AAAATA AAAAT- AAAATA AAGATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA A
14717 TATTAAATAA
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
4 6 0.10
5 8 0.14
6 44 0.76
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:14679 original size:16 final size:16
Alignment explanation
Indices: 14650--14694 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
14640 AATAAAAGTG
*
14650 AAAATAAAAA-AAATA
1 AAAAGAAAAATAAATA
*
14665 AAAAGAAAAGTAAATA
1 AAAAGAAAAATAAATA
*
14681 AAAATAAAAATAAA
1 AAAAGAAAAATAAA
14695 AATAAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.82, C:0.00, G:0.04, T:0.13
Consensus pattern (16 bp):
AAAAGAAAAATAAATA
Found at i:14710 original size:17 final size:17
Alignment explanation
Indices: 14620--14716 Score: 76
Period size: 17 Copynumber: 5.8 Consensus size: 17
14610 TTATTTAAAG
*
14620 AAAATAGAATAATAAAA-C
1 AAAATA-AA-AATAAAATA
*
14638 AAAATAAAAGTGAAAATA
1 AAAATAAAAAT-AAAATA
* *
14656 AAAA-AAATA-AAAAGA
1 AAAATAAAAATAAAATA
* *
14671 AAAGTAAATA-AAAATA
1 AAAATAAAAATAAAATA
14687 AAAATAAAAATAAAATA
1 AAAATAAAAATAAAATA
*
14704 AAGATAAAAATAA
1 AAAATAAAAATAA
14717 TATTAAATAA
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
15 8 0.12
16 20 0.31
17 27 0.42
18 10 0.15
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAATAAAAATAAAATA
Found at i:14723 original size:23 final size:22
Alignment explanation
Indices: 14620--14727 Score: 103
Period size: 22 Copynumber: 4.8 Consensus size: 22
14610 TTATTTAAAG
14620 AAAATAGAATAATAAA-ACAAAATA
1 AAAATA-AA-AATAAATA-AAAATA
* *
14644 AAAGTGAAAATAAA-AAAAATA
1 AAAATAAAAATAAATAAAAATA
* *
14665 AAAAGAAAAGTAAATAAAAATA
1 AAAATAAAAATAAATAAAAATA
*
14687 AAAATAAAAATAAAATAAAGATA
1 AAAATAAAAAT-AAATAAAAATA
* *
14710 AAAATAATATTAAATAAA
1 AAAATAAAAATAAATAAA
14728 CCCAATCTAA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
21 16 0.23
22 30 0.42
23 21 0.30
24 4 0.06
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.18
Consensus pattern (22 bp):
AAAATAAAAATAAATAAAAATA
Found at i:15261 original size:19 final size:19
Alignment explanation
Indices: 15239--15275 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
15229 GGCCAGAATC
15239 TTCACCGAAAAATGCAACT
1 TTCACCGAAAAATGCAACT
*
15258 TTCACCGAAAAATTCAAC
1 TTCACCGAAAAATGCAAC
15276 CGAAATCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.27, G:0.08, T:0.22
Consensus pattern (19 bp):
TTCACCGAAAAATGCAACT
Found at i:15639 original size:22 final size:21
Alignment explanation
Indices: 15614--15662 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
15604 AGCCTTCCAA
15614 AATAAAAATCAGATAAAAAAAT
1 AATAAAAATCAGA-AAAAAAAT
* * *
15636 AATAGATAATTAGAAAAATAAT
1 AATA-AAAATCAGAAAAAAAAT
15658 AATAA
1 AATAA
15663 GATAAATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.65
23 7 0.30
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.22
Consensus pattern (21 bp):
AATAAAAATCAGAAAAAAAAT
Found at i:15700 original size:9 final size:9
Alignment explanation
Indices: 15683--15819 Score: 54
Period size: 9 Copynumber: 14.3 Consensus size: 9
15673 CAATAATATT
*
15683 ATAAGATAA
1 ATAAAATAA
15692 ATAAAAT-A
1 ATAAAATAA
15700 ATAATAAT-A
1 ATAA-AATAA
15709 ATAATAAT-A
1 ATAA-AATAA
15718 ATAATAATAATA
1 ATAA-AAT-A-A
15730 ATAACAGATAA
1 ATAA-A-ATAA
15741 ATAAATATATA
1 ATAAA-ATA-A
* *
15752 ATTAGATAA
1 ATAAAATAA
15761 ATAAAAATACA
1 AT-AAAATA-A
15772 TATAAAATAA
1 -ATAAAATAA
15782 A-AAAATAA
1 ATAAAATAA
15790 A-AGGAAA-AA
1 ATA--AAATAA
*
15799 AGGAAAA-AA
1 A-TAAAATAA
15808 ATAAAATAA
1 ATAAAATAA
15817 ATA
1 ATA
15820 TATATATATT
Statistics
Matches: 106, Mismatches: 8, Indels: 28
0.75 0.06 0.20
Matches are distributed among these distances:
8 18 0.17
9 45 0.42
10 15 0.14
11 17 0.16
12 9 0.08
13 2 0.02
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.23
Consensus pattern (9 bp):
ATAAAATAA
Found at i:15704 original size:3 final size:3
Alignment explanation
Indices: 15691--15733 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
15681 TTATAAGATA
15691 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
15734 CAGATAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:15891 original size:13 final size:12
Alignment explanation
Indices: 15873--15924 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
15863 GATATAAAGG
*
15873 AAAATATATACAT
1 AAAATATA-AAAT
15886 AAAATATAAAAT
1 AAAATATAAAAT
*
15898 AAAA-ATAACA-
1 AAAATATAAAAT
15908 AAAATATAAAAT
1 AAAATATAAAAT
15920 AAAAT
1 AAAAT
15925 TGGGCTTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 4 0.12
11 10 0.29
12 12 0.35
13 8 0.24
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATATAAAAT
Found at i:15901 original size:25 final size:25
Alignment explanation
Indices: 15850--15924 Score: 84
Period size: 25 Copynumber: 3.1 Consensus size: 25
15840 AATAATAAAT
* ** **
15850 AATAAATACATAGGATATAAAGGAA
1 AATATATACATAAAATATAAAATAA
15875 AATATATACATAAAATATAAAATAA
1 AATATATACATAAAATATAAAATAA
15900 AA-ATA-ACA-AAAATATAAAATAA
1 AATATATACATAAAATATAAAATAA
15922 AAT
1 AAT
15925 TGGGCTTACC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
22 16 0.36
23 3 0.07
24 3 0.07
25 22 0.50
ACGTcount: A:0.68, C:0.04, G:0.05, T:0.23
Consensus pattern (25 bp):
AATATATACATAAAATATAAAATAA
Found at i:16081 original size:6 final size:6
Alignment explanation
Indices: 16072--16112 Score: 59
Period size: 6 Copynumber: 7.0 Consensus size: 6
16062 ACATTTTCAT
16072 TTTTTG TTTTTG TTTTT- TTTTTG TTTGTT- TTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTT-TTG TTTTTG TTTTTG
16113 ACTAAAGCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 7 0.22
6 23 0.72
7 2 0.06
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:16082 original size:8 final size:8
Alignment explanation
Indices: 16078--16111 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
16068 TCATTTTTTG
16078 TTTTTGTT
1 TTTTTGTT
16086 TTTTT-TT
1 TTTTTGTT
*
16093 TGTTTGTT
1 TTTTTGTT
16101 TTTTTGTT
1 TTTTTGTT
16109 TTT
1 TTT
16112 GACTAAAGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (8 bp):
TTTTTGTT
Found at i:16093 original size:17 final size:17
Alignment explanation
Indices: 16071--16112 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
16061 AACATTTTCA
16071 TTTTTTGTTT-TTGTTTT
1 TTTTTTGTTTGTT-TTTT
16088 TTTTTTGTTTGTTTTTT
1 TTTTTTGTTTGTTTTTT
16105 TGTTTTTG
1 T-TTTTTG
16113 ACTAAAGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (17 bp):
TTTTTTGTTTGTTTTTT
Found at i:16212 original size:41 final size:40
Alignment explanation
Indices: 16119--16490 Score: 376
Period size: 41 Copynumber: 9.0 Consensus size: 40
16109 TTTGACTAAA
* * *
16119 GCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAACATAAATG
1 GCTCCTCTAAACAGAGGC-CAACGACTTTG-GAAA-ATAAATT
* *
16162 GCTCCTCTAATCAGAGGCTCAATGACTTTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGC-CAACGACTTTGGAAAATAAATT
* * *
16203 GCTCCTCTAAACAAAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGC-CAACGACTTTGGAAAATAAATT
* *
16244 GCTCCTTTAAACAGAGG-CAACGAAACTTTGGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCCAACG--ACTTT-GGAAAATAAATT
* *
16286 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGC-CAACGACTTTGGAAAATAAATT
* *
16327 GCTCATCTAAACAGAGG-CAATGAAACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCCAACG--ACTTTGGAAAA-TAAATT
* *
16369 GCTCC-CTAAACAGAGGTACC-ATGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGG--CCAACGACTTTGGAAAATAAATT
* * * *
16409 GCTCCTCTAAATAGATGCACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGC-CAACGACTTTGGAAAATAAATT
16450 GCTCCTCTAAACAGAGG-CAACGAAACTTTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGCCAACG--ACTTTGGAAAATAAATT
16491 ACTCATTGAC
Statistics
Matches: 283, Mismatches: 30, Indels: 34
0.82 0.09 0.10
Matches are distributed among these distances:
39 12 0.04
40 12 0.04
41 177 0.63
42 46 0.16
43 31 0.11
44 5 0.02
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (40 bp):
GCTCCTCTAAACAGAGGCCAACGACTTTGGAAAATAAATT
Found at i:16272 original size:82 final size:82
Alignment explanation
Indices: 16119--16490 Score: 434
Period size: 82 Copynumber: 4.5 Consensus size: 82
16109 TTTGACTAAA
* * * * * * * *
16119 GCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAACATAAATGGCTCCTCTAATCAGAGGC-TC-
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAA-GTAAATTGCTCCTCTAAACAGAGGCAACG
16182 AATGACTTTGGAAAATAAATT
64 AA--ACTTTGGAAAATAAATT
* *
16203 GCTCCTCTAAACAAAGGCACCACGACTTTGGAAAGTAAATTGCTCCTTTAAACAGAGGCAACGAA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAA
*
16268 ACTTTGGGAAAGTAAATT
66 ACTTT-GGAAAATAAATT
* *
16286 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCATCTAAACAGAGGCAATGAA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAA
16351 ACTTTGGAAAAGTAAATT
66 ACTTTGGAAAA-TAAATT
* * * *
16369 GCTCC-CTAAACAGAGGTACCATGACTTTGGAAAGTAAATTGCTCCTCTAAATAGATGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACG
*
16433 --ACTTTGAAAAATAAATT
64 AAACTTTGGAAAATAAATT
*
16450 GCTCCTCTAAACAGAGGCA--ACGAAACTTTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACG--ACTTTGGAAAGTAAATT
16491 ACTCATTGAC
Statistics
Matches: 253, Mismatches: 26, Indels: 20
0.85 0.09 0.07
Matches are distributed among these distances:
80 2 0.01
81 11 0.04
82 118 0.47
83 92 0.36
84 30 0.12
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (82 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAA
ACTTTGGAAAATAAATT
Found at i:17780 original size:18 final size:17
Alignment explanation
Indices: 17759--17816 Score: 66
Period size: 19 Copynumber: 3.3 Consensus size: 17
17749 AGTTTTCTCA
17759 TTTTTTCATTCATTCTTTT
1 TTTTTTC-TTCATTC-TTT
17778 TTTTTTCTTC-TT-TTT
1 TTTTTTCTTCATTCTTT
17793 TTTTTTCTTCATCATCTTT
1 TTTTTTCTTCAT--TCTTT
17812 TTTTT
1 TTTTT
17817 CTCATTTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 13 0.37
16 1 0.03
17 2 0.06
18 4 0.11
19 15 0.43
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTCTTCATTCTTT
Found at i:17794 original size:15 final size:15
Alignment explanation
Indices: 17774--17802 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17764 TCATTCATTC
17774 TTTTTTTTTTCTTCT
1 TTTTTTTTTTCTTCT
17789 TTTTTTTTTTCTTC
1 TTTTTTTTTTCTTC
17803 ATCATCTTTT
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:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTTCTTCT
Found at i:17817 original size:18 final size:17
Alignment explanation
Indices: 17759--17818 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
17749 AGTTTTCTCA
17759 TTTTTTCATTCAT-TCTT
1 TTTTTTC-TTCATCTCTT
* *
17776 TTTTTT-TTCTTCTTTTT
1 TTTTTTCTTCATC-TCTT
17793 TTTTTTCTTCATCATCTT
1 TTTTTTCTTCATC-TCTT
17811 TTTTTTCT
1 TTTTTTCT
17819 CATTTTTCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
15 4 0.11
17 15 0.43
18 16 0.46
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTTCTTCATCTCTT
Found at i:21786 original size:59 final size:59
Alignment explanation
Indices: 21723--22001 Score: 332
Period size: 58 Copynumber: 4.7 Consensus size: 59
21713 TTTTGTGCAG
* * ** **
21723 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTGAAGCTTTAA-TTTCGA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTAATTTTTAA
* * *
21781 GGAAAATTGATACTTTCAACTTTTCATCAAAAATTTATTTTTTTGAAAATTTATTTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTTGAAAATTTAATTTTTAA
* ** **
21842 GAAAAAATGATACTTTCAACTTTTCCTCAAAAATCCTTTTTAAAAAATTT-ATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTAATTTTTAA
* *
21900 GAAAAATTGACACTTTCAACTTTTCCTCAAAAACCT-TTTTTTTG-AAATTTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTTGAAAATTTAATTTTTAA
*
21959 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATAATTTTTTT
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTT
22002 TATTTTTATT
Statistics
Matches: 189, Mismatches: 24, Indels: 15
0.83 0.11 0.07
Matches are distributed among these distances:
57 1 0.01
58 74 0.39
59 64 0.34
60 16 0.08
61 34 0.18
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.44
Consensus pattern (59 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTAATTTTTAA
Found at i:21789 original size:58 final size:58
Alignment explanation
Indices: 21723--22001 Score: 344
Period size: 59 Copynumber: 4.7 Consensus size: 58
21713 TTTTGTGCAG
* * ** * **
21723 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTGAAGCTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTTAA
* *
21781 GGAAAATTGATACTTTCAACTTTTCATCAAAAATTTATTTTTTTGAAAATTTATTTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTTGAAAATTTA-TTTTTAA
* ** **
21842 GAAAAAATGATACTTTCAACTTTTCCTCAAAAATCCTTTTTAAAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTTAA
* *
21900 GAAAAATTGACACTTTCAACTTTTCCTCAAAAACCT-TTTTTTTGAAATTTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTTGAAAATTTATTTTTAA
*
21959 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATAATTTTTTT
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTT
22002 TATTTTTATT
Statistics
Matches: 190, Mismatches: 24, Indels: 13
0.84 0.11 0.06
Matches are distributed among these distances:
57 1 0.01
58 68 0.36
59 71 0.37
60 16 0.08
61 34 0.18
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.44
Consensus pattern (58 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTATTTTTAA
Found at i:21845 original size:17 final size:16
Alignment explanation
Indices: 21810--21846 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
21800 CTTTTCATCA
*
21810 AAAATTTATTTTTTTG
1 AAAATTTATTTTTTAG
21826 AAAATTTATTTTTTAAG
1 AAAATTTATTTTTT-AG
21843 AAAA
1 AAAA
21847 AATGATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (16 bp):
AAAATTTATTTTTTAG
Found at i:21873 original size:119 final size:116
Alignment explanation
Indices: 21723--21999 Score: 365
Period size: 119 Copynumber: 2.3 Consensus size: 116
21713 TTTTGTGCAG
** ** * *
21723 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTGAAGCTTTAATTTCGAGGAAAAT
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATT-TTTAAAAAATTTAATTTCAAGAAAAAT
* **
21788 TGATACTTTCAACTTTTCATCAAAAATTTATTTTTTTGAAAATTTATTTTTTAA
65 TGACACTTTCAACTTTTCATCAAAAACCT-TTTTTTTGAAAATTTA-TTTTTAA
* * * * *
21842 GAAAAAATGATACTTTCAACTTTTCCTCAAAAATCCTTTTTAAAAAATTTATTTTTAAGAAAAAT
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAAT-ATTTTTAAAAAATTTAATTTCAAGAAAAAT
* *
21907 TGACACTTTCAACTTTTCCTCAAAAACCTTTTTTTTGAAATTTTATTTTTAA
65 TGACACTTTCAACTTTTCATCAAAAACCTTTTTTTTGAAAATTTATTTTTAA
21959 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATAATTTTT
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAAT-ATTTTT
22000 TTTATTTTTA
Statistics
Matches: 137, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
117 44 0.32
118 15 0.11
119 76 0.55
120 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (116 bp):
GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTAAAAAATTTAATTTCAAGAAAAATT
GACACTTTCAACTTTTCATCAAAAACCTTTTTTTTGAAAATTTATTTTTAA
Found at i:22056 original size:34 final size:30
Alignment explanation
Indices: 22012--22103 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 30
22002 TATTTTTATT
*
22012 TAAAGAAAATAGAATAATAAAACAAAATAAAAG
1 TAAAAAAAATA-AA-AATAAAA-AAAATAAAAG
*
22045 TGAAAATAAAT-AAAAT-AAAAAAATAAAAG
1 T-AAAAAAAATAAAAATAAAAAAAATAAAAG
22074 TAAAAAAAATAAAAATAAAATAAAGATAAA
1 TAAAAAAAATAAAAATAAAA-AAA-ATAAA
22104 GATAATATTA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
28 8 0.16
29 16 0.31
30 6 0.12
31 6 0.12
32 7 0.14
33 1 0.02
34 7 0.14
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.16
Consensus pattern (30 bp):
TAAAAAAAATAAAAATAAAAAAAATAAAAG
Found at i:22060 original size:39 final size:38
Alignment explanation
Indices: 22012--22103 Score: 96
Period size: 39 Copynumber: 2.3 Consensus size: 38
22002 TATTTTTATT
* * * *
22012 TAAAGAAAATAGAATAATAAAA-CAAAATAAAAGTGAAAA
1 TAAATAAAATAAAAAAATAAAAGCAAAA-AAAA-TAAAAA
*
22051 TAAATAAAATAAAAAAATAAAAGTAAAAAAAATAAAAA
1 TAAATAAAATAAAAAAATAAAAGCAAAAAAAATAAAAA
22089 TAAAATAAAGATAAA
1 T-AAATAAA-ATAAA
22104 GATAATATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
38 6 0.13
39 30 0.67
40 9 0.20
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.16
Consensus pattern (38 bp):
TAAATAAAATAAAAAAATAAAAGCAAAAAAAATAAAAA
Found at i:22139 original size:5 final size:5
Alignment explanation
Indices: 22027--22119 Score: 77
Period size: 5 Copynumber: 18.2 Consensus size: 5
22017 AAAATAGAAT
*
22027 AATAA AACAA AATAA AAGTGAA AAT-A AATAA AAT-A AA-AA AATAA AAGTAA
1 AATAA AATAA AATAA AA-T-AA AATAA AATAA AATAA AATAA AATAA AA-TAA
* *
22077 AA-AA AATAAA AATAA AATAA AGATAA AGATAA TATTA AATAA A
1 AATAA AAT-AA AATAA AATAA A-ATAA A-ATAA AATAA AATAA A
22120 CCTAATCTAA
Statistics
Matches: 73, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
4 14 0.19
5 33 0.45
6 22 0.30
7 4 0.05
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:23063 original size:24 final size:21
Alignment explanation
Indices: 23000--23206 Score: 88
Period size: 21 Copynumber: 9.4 Consensus size: 21
22990 TAAAAATCAG
23000 ATAAAAA-AATTAAT-AGATAA
1 ATAAAAATAA-TAATAAGATAA
*
23020 TTAAAAAATAATAATAAGATAA
1 AT-AAAAATAATAATAAGATAA
*
23042 ATCAACAATAATATTATAAGATAA
1 AT-AAAAATAATA--ATAAGATAA
*
23066 ATAAAAATAATAATAATA-ACA
1 ATAAAAATAATAATAAGATA-A
* *
23087 GATAAATAAATATATAATTATATAA
1 -AT-AA-AAATA-ATAATAAGATAA
*
23112 ATAAAAATACAT-ATAAAATAAA
1 ATAAAAATA-ATAATAAGAT-AA
* * * *
23134 AAATAAAATAAAAAAAAGGAAAA
1 ATA-AAAATAATAATAA-GATAA
* *
23157 AT-AAAAT-A-AATATATATTA
1 ATAAAAATAATAATA-AGATAA
*
23176 ATAAATAGTAATAATAA-ATAA
1 ATAAA-AATAATAATAAGATAA
23197 ATAATAAATA
1 ATAA-AAATA
23207 CATAGGATAT
Statistics
Matches: 143, Mismatches: 23, Indels: 41
0.69 0.11 0.20
Matches are distributed among these distances:
19 7 0.05
20 6 0.04
21 37 0.26
22 35 0.24
23 29 0.20
24 19 0.13
25 9 0.06
26 1 0.01
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (21 bp):
ATAAAAATAATAATAAGATAA
Found at i:23089 original size:26 final size:24
Alignment explanation
Indices: 23010--23141 Score: 95
Period size: 24 Copynumber: 5.7 Consensus size: 24
23000 ATAAAAAAAT
*
23010 TAAT-AGAT-AATTAAAA-AATAA
1 TAATAAGATAAATAAAAATAATAA
*
23031 TAATAAGATAAATCAACAATAAT-A
1 TAATAAGATAAAT-AAAAATAATAA
*
23055 TTATAAGATAAATAAAAATAATAA
1 TAATAAGATAAATAAAAATAATAA
23079 TAATAACAGATAAAT--AAAT-AT-A
1 TAAT-A-AGATAAATAAAAATAATAA
* *
23101 TAATTATATAAATAAAAATACATATA
1 TAATAAGATAAATAAAAATA-ATA-A
*
23127 AAATAA-A-AAATAAAA
1 TAATAAGATAAATAAAA
23142 TAAAAAAAAG
Statistics
Matches: 89, Mismatches: 9, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
20 7 0.08
21 4 0.04
22 13 0.15
23 13 0.15
24 34 0.38
25 5 0.06
26 13 0.15
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (24 bp):
TAATAAGATAAATAAAAATAATAA
Found at i:23135 original size:18 final size:17
Alignment explanation
Indices: 23090--23150 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
23080 AATAACAGAT
*
23090 AAATAAATATATAATTATA
1 AAATAAA-AAATAA-TATA
23109 TAAAT-AAAAATACATATA
1 -AAATAAAAAATA-ATATA
*
23127 AAATAAAAAATAAAATA
1 AAATAAAAAATAATATA
23144 AAA-AAAA
1 AAATAAAA
23151 GGAAAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 4 0.11
17 11 0.30
18 15 0.41
19 3 0.08
20 4 0.11
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAAAAATAATATA
Found at i:23250 original size:25 final size:23
Alignment explanation
Indices: 23213--23284 Score: 76
Period size: 22 Copynumber: 3.1 Consensus size: 23
23203 AATACATAGG
* *
23213 ATATAAAGGAAAATATATACATAAA
1 ATATAAA-AAAAATATA-AAATAAA
23238 ATATAAAATAAAA-ATAAAATAAA
1 ATATAAAA-AAAATATAAAATAAA
*
23261 A-ATAACAAAAATATAAAATAAA
1 ATATAAAAAAAATATAAAATAAA
23283 AT
1 AT
23285 TGGGCTTACC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
21 4 0.10
22 16 0.39
23 7 0.17
24 3 0.07
25 11 0.27
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (23 bp):
ATATAAAAAAAATATAAAATAAA
Found at i:26183 original size:19 final size:20
Alignment explanation
Indices: 26156--26197 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
26146 TTATTTAATT
26156 TTTATAAAATTAATAAATAA
1 TTTATAAAATTAATAAATAA
* *
26176 TTTA-AAAATTCATAAATTA
1 TTTATAAAATTAATAAATAA
26195 TTT
1 TTT
26198 TATGTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTATAAAATTAATAAATAA
Found at i:26249 original size:10 final size:10
Alignment explanation
Indices: 26222--26251 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
26212 ATTTTTTGAT
26222 AAATAATAAA
1 AAATAATAAA
26232 AAACTAATAAA
1 AAA-TAATAAA
26243 AAATAATAA
1 AAATAATAA
26252 CTCAAATGTT
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:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (10 bp):
AAATAATAAA
Found at i:26378 original size:17 final size:17
Alignment explanation
Indices: 26358--26390 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
26348 GTTGTTAATT
*
26358 ATTTATATAATAATAAA
1 ATTTATAAAATAATAAA
26375 ATTTATAAAATAATAA
1 ATTTATAAAATAATAA
26391 TTTTTAATTC
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTTATAAAATAATAAA
Found at i:26396 original size:17 final size:17
Alignment explanation
Indices: 26353--26396 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
26343 ATTTAGTTGT
*
26353 TAATTATTTATATAATAA
1 TAATT-TTTATAAAATAA
**
26371 TAAAATTTATAAAATAA
1 TAATTTTTATAAAATAA
26388 TAATTTTTA
1 TAATTTTTA
26397 ATTCATAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATTTTTATAAAATAA
Found at i:29584 original size:52 final size:52
Alignment explanation
Indices: 29497--29653 Score: 201
Period size: 52 Copynumber: 3.0 Consensus size: 52
29487 TGGACAAGAA
* *
29497 GACTTGCAA-ATGAAGAATTCCAAGA-GAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGA-GAAGAATTCTAAGAGGAAAG-GGATTCTTAATAGGCAAGTTT
*
29549 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
* * ** * *
29601 GATTTACGGGAGAAGAATTCTAAGAGGAGAGGGATTCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
29653 G
1 G
29654 TATGGTTATA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
52 87 0.94
53 6 0.06
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.26
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
Found at i:30174 original size:31 final size:31
Alignment explanation
Indices: 30136--30220 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
30126 AGGCTTTTAA
* *
30136 CCCAACAAATAGTATCAGAGCTGTGGTATTC
1 CCCAACAAGTGGTATCAGAGCTGTGGTATTC
*
30167 CCCAACAAGTGGTATCAGAGCTGTGGTGTTC
1 CCCAACAAGTGGTATCAGAGCTGTGGTATTC
* *
30198 CTCAACAAGTGGTATCAAAGCTG
1 CCCAACAAGTGGTATCAGAGCTG
30221 AAGGTTTGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (31 bp):
CCCAACAAGTGGTATCAGAGCTGTGGTATTC
Found at i:30291 original size:25 final size:25
Alignment explanation
Indices: 30263--30317 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
30253 AAGATGTGGA
**
30263 AAGAGTTGATGGTTCGAGACATGGG
1 AAGAGTTGACAGTTCGAGACATGGG
*
30288 AAGAGTTGACAGTTCGAGATATGGG
1 AAGAGTTGACAGTTCGAGACATGGG
30313 AAGAG
1 AAGAG
30318 CTTGGTTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.38, T:0.22
Consensus pattern (25 bp):
AAGAGTTGACAGTTCGAGACATGGG
Found at i:30682 original size:52 final size:52
Alignment explanation
Indices: 30594--30750 Score: 192
Period size: 52 Copynumber: 3.0 Consensus size: 52
30584 TGGACAAGAA
* *
30594 GACTTGCAA-ATGAAGAATTCCAAGA-GAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGA-GAAGAATTCTAAGAGGAAAGA-GATTCTTAATAGGCAAGTTT
*
30646 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTT
* * ** * * *
30698 GATTTACGGGAGAAGAATTCTAAGAGGAGAGGGATTCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTT
30750 G
1 G
30751 TATGGTTATA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
52 85 0.92
53 7 0.08
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.26
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTT
Found at i:33234 original size:28 final size:29
Alignment explanation
Indices: 33203--33266 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
33193 ACTTTTGTAT
* **
33203 ATATATTTAAAATTTTTTAATTA-TTAAA
1 ATATATTAAAAAAATTTTAATTATTTAAA
33231 ATATATTAAAAAAATTTTAATTATTTAAA
1 ATATATTAAAAAAATTTTAATTATTTAAA
33260 ATA-ATTA
1 ATATATTA
33267 TTTTATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 24 0.75
29 8 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
ATATATTAAAAAAATTTTAATTATTTAAA
Found at i:33279 original size:20 final size:22
Alignment explanation
Indices: 33244--33301 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
33234 TATTAAAAAA
*
33244 ATTTTAATTATTTAAAATAATT
1 ATTTTAATTATTTAAAATAACT
33266 ATTTT-ATT-TTTAAAATAACT
1 ATTTTAATTATTTAAAATAACT
*
33286 ATTTTTTATTATTTAA
1 A-TTTTAATTATTTAA
33302 TTCATTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 12 0.38
21 7 0.22
22 8 0.25
23 5 0.16
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTTAATTATTTAAAATAACT
Found at i:33440 original size:20 final size:22
Alignment explanation
Indices: 33401--33462 Score: 83
Period size: 20 Copynumber: 2.9 Consensus size: 22
33391 TATATATTTA
*
33401 AATTTTTTTAATTATTTAAAAT
1 AATTATTTTAATTATTTAAAAT
33423 AATTATTTT-ATT-TTTAAAAT
1 AATTATTTTAATTATTTAAAAT
*
33443 AATTATTTTTTATTATTTAA
1 AATTA-TTTTAATTATTTAA
33463 TTCATTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 13 0.36
21 7 0.19
22 11 0.31
23 5 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
AATTATTTTAATTATTTAAAAT
Found at i:33604 original size:19 final size:19
Alignment explanation
Indices: 33582--33618 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
33572 TTTATATATA
*
33582 ATAGTTTAGTATGAAAAAT
1 ATAGTTTAATATGAAAAAT
*
33601 ATAGTTTAATATTAAAAA
1 ATAGTTTAATATGAAAAA
33619 GATTACAAGT
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:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
ATAGTTTAATATGAAAAAT
Found at i:33757 original size:21 final size:22
Alignment explanation
Indices: 33733--33781 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
33723 GATTTTAGAA
*
33733 AAAAAAATCATAGTCTAATA-T
1 AAAAAAATCATAATCTAATAGT
*
33754 AAAAAAATCGTAATCTAATAGT
1 AAAAAAATCATAATCTAATAGT
33776 AAAAAA
1 AAAAAA
33782 CCGTAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.24
Consensus pattern (22 bp):
AAAAAAATCATAATCTAATAGT
Found at i:33786 original size:21 final size:21
Alignment explanation
Indices: 33746--33788 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
33736 AAAATCATAG
*
33746 TCTAATATAAAAAAATCGTAA
1 TCTAATATAAAAAAACCGTAA
33767 TCTAATAGT-AAAAAACCGTAA
1 TCTAATA-TAAAAAAACCGTAA
33788 T
1 T
33789 TATTGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (21 bp):
TCTAATATAAAAAAACCGTAA
Found at i:35240 original size:18 final size:16
Alignment explanation
Indices: 35198--35252 Score: 74
Period size: 18 Copynumber: 3.2 Consensus size: 16
35188 AAAAACTTAA
35198 TTAATTATTTTTATTTT
1 TTAA-TATTTTTATTTT
35215 TTAATATTTTTATTTT
1 TTAATATTTTTATTTT
35231 TATCAATATTTTTATTTAT
1 T-T-AATATTTTTATTT-T
35250 TTA
1 TTA
35253 TTAGTATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
16 13 0.37
17 6 0.17
18 14 0.40
19 2 0.06
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (16 bp):
TTAATATTTTTATTTT
Found at i:35717 original size:21 final size:19
Alignment explanation
Indices: 35691--35737 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
35681 TCTATAATTT
35691 AAAAAATATA-ATTAAATGAA
1 AAAAAATATAGA-TAAAT-AA
*
35711 AATAAAAAATAGATAAATAA
1 AA-AAAATATAGATAAATAA
35731 AAAAAAT
1 AAAAAAT
35738 CAAAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 4 0.17
20 6 0.26
21 12 0.52
22 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (19 bp):
AAAAAATATAGATAAATAA
Found at i:35720 original size:13 final size:13
Alignment explanation
Indices: 35704--35762 Score: 64
Period size: 13 Copynumber: 4.2 Consensus size: 13
35694 AAATATAATT
35704 AAATGAAAATAAA
1 AAATGAAAATAAA
35717 AAATAGATAAATAAAAA
1 AAAT-GA-AAAT--AAA
*
35734 AAATCAAAATAAA
1 AAATGAAAATAAA
*
35747 AAAAGAAAATAAA
1 AAATGAAAATAAA
35760 AAA
1 AAA
35763 AAAACTTAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 21 0.54
14 2 0.05
15 8 0.21
16 1 0.03
17 7 0.18
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.14
Consensus pattern (13 bp):
AAATGAAAATAAA
Found at i:35730 original size:15 final size:14
Alignment explanation
Indices: 35710--35763 Score: 67
Period size: 15 Copynumber: 3.8 Consensus size: 14
35700 AATTAAATGA
35710 AAATAAAAAATAGAT
1 AAATAAAAAA-AGAT
35725 AAATAAAAAAA-AT
1 AAATAAAAAAAGAT
35738 CAAAATAAAAAAAGA-
1 --AAATAAAAAAAGAT
35753 AAATAAAAAAA
1 AAATAAAAAAA
35764 AAACTTAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
13 13 0.36
14 1 0.03
15 21 0.58
16 1 0.03
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (14 bp):
AAATAAAAAAAGAT
Found at i:35745 original size:19 final size:18
Alignment explanation
Indices: 35723--35766 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
35713 TAAAAAATAG
35723 ATAAATAAAA-AAAATCAAA
1 ATAAA-AAAAGAAAAT-AAA
35742 ATAAAAAAAGAAAATAAA
1 ATAAAAAAAGAAAATAAA
35760 A-AAAAAA
1 ATAAAAAA
35767 CTTAACTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.25
18 8 0.33
19 10 0.42
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.11
Consensus pattern (18 bp):
ATAAAAAAAGAAAATAAA
Found at i:35765 original size:15 final size:14
Alignment explanation
Indices: 35708--35764 Score: 71
Period size: 14 Copynumber: 4.0 Consensus size: 14
35698 ATAATTAAAT
*
35708 GAAAATAAAAAATA
1 GAAAATAAAAAAAA
35722 GATAAATAAAAAAAA
1 GA-AAATAAAAAAAA
*
35737 TCAAAAT-AAAAAAA
1 -GAAAATAAAAAAAA
35751 GAAAATAAAAAAAA
1 GAAAATAAAAAAAA
35765 AACTTAACTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
13 5 0.14
14 16 0.43
15 15 0.41
16 1 0.03
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (14 bp):
GAAAATAAAAAAAA
Found at i:35766 original size:30 final size:30
Alignment explanation
Indices: 35704--35764 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
35694 AAATATAATT
*
35704 AAATGAAAATAAAAAATAGATAAATAAAAA
1 AAATCAAAATAAAAAATAGATAAATAAAAA
35734 AAATCAAAATAAAAAA-AGA-AAATAAAAA
1 AAATCAAAATAAAAAATAGATAAATAAAAA
35762 AAA
1 AAA
35765 AACTTAACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 12 0.40
29 3 0.10
30 15 0.50
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.13
Consensus pattern (30 bp):
AAATCAAAATAAAAAATAGATAAATAAAAA
Found at i:36434 original size:23 final size:25
Alignment explanation
Indices: 36393--36442 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
36383 GTTTACCCAA
36393 ATGAAATCATAAAATATTATT-TTT
1 ATGAAATCATAAAATATTATTCTTT
36417 ATGAAATCAT-AAATATTATTCTTT
1 ATGAAATCATAAAATATTATTCTTT
36441 AT
1 AT
36443 TTAATTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (25 bp):
ATGAAATCATAAAATATTATTCTTT
Found at i:39136 original size:16 final size:16
Alignment explanation
Indices: 39092--39137 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
39082 TTCTTCTTTT
39092 GTATT-TTATGTATT-
1 GTATTATTATGTATTA
39106 GTATTATTTAT-TATTA
1 GTATTA-TTATGTATTA
*
39122 TTATTATTATGTATTA
1 GTATTATTATGTATTA
39138 ATATATGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 5 0.19
15 8 0.30
16 14 0.52
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (16 bp):
GTATTATTATGTATTA
Found at i:40232 original size:18 final size:16
Alignment explanation
Indices: 40199--40322 Score: 85
Period size: 16 Copynumber: 7.6 Consensus size: 16
40189 TTTTATTTGT
40199 TTTTTATTTATTATTA
1 TTTTTATTTATTATTA
40215 TTTTTATTTATTAGATTA
1 TTTTTATTTATT--ATTA
** * *
40233 GGTTTATTTAATATTC
1 TTTTTATTTATTATTA
40249 TTTTTATCTTTATT-TTA
1 TTTTTA--TTTATTATTA
* *
40266 TTTTTATTTTTGTTTTA
1 TTTTTATTTAT-TATTA
* *
40283 CTTTTCTTT-TT-TTA
1 TTTTTATTTATTATTA
40297 TTTTT-TTTATTATCTA
1 TTTTTATTTATTAT-TA
*
40313 TTTTTCTTTA
1 TTTTTATTTA
40323 AATAAAAAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
13 3 0.03
14 9 0.10
15 6 0.07
16 28 0.33
17 22 0.26
18 18 0.21
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (16 bp):
TTTTTATTTATTATTA
Found at i:40232 original size:21 final size:21
Alignment explanation
Indices: 40191--40232 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
40181 TTGAATTTTT
* *
40191 TTATTTGTTTTTTATTTATTA
1 TTATTTGTTATTTATTGATTA
40212 TTATTT-TTATTTATTAGATTA
1 TTATTTGTTATTTATT-GATTA
40233 GGTTTATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TTATTTGTTATTTATTGATTA
Found at i:40271 original size:17 final size:16
Alignment explanation
Indices: 40249--40301 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
40239 TTTAATATTC
40249 TTTTTATCTTTATTTTA
1 TTTTTATCTTT-TTTTA
*
40266 TTTTTATTTTTGTTTTA
1 TTTTTATCTTT-TTTTA
*
40283 -CTTT-TCTTTTTTTA
1 TTTTTATCTTTTTTTA
40297 TTTTT
1 TTTTT
40302 TTTATTATCT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 3 0.10
17 15 0.50
ACGTcount: A:0.11, C:0.06, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTTATCTTTTTTTA
Found at i:40282 original size:22 final size:22
Alignment explanation
Indices: 40257--40317 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 22
40247 TCTTTTTATC
40257 TTTATTTTATTTTTATT-TTTGT
1 TTTATTTTATTTTT-TTATTTGT
* *
40279 TTTACTTTTCTTTTTTTATTTTT
1 TTTA-TTTTATTTTTTTATTTGT
40302 TTTATTATCTATTTTT
1 TTTATT-T-TATTTTT
40318 CTTTAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 8 0.25
23 18 0.56
24 6 0.19
ACGTcount: A:0.13, C:0.05, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTATTTTATTTTTTTATTTGT
Found at i:40558 original size:59 final size:59
Alignment explanation
Indices: 40362--40680 Score: 441
Period size: 59 Copynumber: 5.4 Consensus size: 59
40352 CTATTTTTAG
* ** * *
40362 GGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTAAAAAAAAAAACATTTTTGG
1 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAA-GTTTTTGA
*
40422 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAACAAAATTTCAAAAAAAAAAGGTTTTTGA
1 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC-AAAAAAAAA-GTTTTTGA
*
40483 GGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTCAAAAAAAAAGTTTTTGA
1 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAAGTTTTTGA
* * * *
40542 GGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAGTTTC-CAAAAAATG-TTTTGA
1 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAAGTTTTTGA
* *
40598 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTCCAAAAAAATA-TTTTTTA
1 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTT-CAAAAAAAAAGTTTTTGA
40656 GGGAAAAGTTGAAAGTATCAATTTT
1 -GGAAAAGTTGAAAGTATCAATTTT
40681 TCCCACACAA
Statistics
Matches: 236, Mismatches: 18, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
56 44 0.19
57 8 0.03
58 16 0.07
59 66 0.28
60 47 0.20
61 55 0.23
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (59 bp):
GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAAGTTTTTGA
Found at i:40622 original size:115 final size:117
Alignment explanation
Indices: 40362--40680 Score: 439
Period size: 115 Copynumber: 2.7 Consensus size: 117
40352 CTATTTTTAG
* ** *
40362 GGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTAAAAAAAAAAACATTTTTGGGGAAA
1 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATT-TCAAAAAAAA-ATTTTTGAGGAAA
40427 AGTTGAAAGTATCAATTTTCCTTAAAAACAAAATTTCAAAAAAAAAAGGTTTTTGA
64 AGTTGAAAGTATCAATTTTCCTTAAAAACAAAATTTC--AAAAAAAAGGTTTTTGA
*
40483 GGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTCAAAAAAAAAGTTTTTGAGGAAAA
1 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAA-TTTTTGAGGAAAA
* * * * *
40548 GTTGAAAGTATCAATTTTCCTTGAAAA-TAAGTTTC-CAAAAAATG-TTTTGA
65 GTTGAAAGTATCAATTTTCCTTAAAAACAAAATTTCAAAAAAAAGGTTTTTGA
* *
40598 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTCCAAAAAAATATTTTTTAGGGAAA
1 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTT-CAAAAAAAAATTTTTGA-GGAAA
40662 AGTTGAAAGTATCAATTTT
64 AGTTGAAAGTATCAATTTT
40681 TCCCACACAA
Statistics
Matches: 182, Mismatches: 13, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
114 12 0.07
115 72 0.40
116 7 0.04
119 7 0.04
120 46 0.25
121 38 0.21
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (117 bp):
GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAATTTTTGAGGAAAAG
TTGAAAGTATCAATTTTCCTTAAAAACAAAATTTCAAAAAAAAGGTTTTTGA
Found at i:44552 original size:17 final size:16
Alignment explanation
Indices: 44532--44582 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
44522 AAAAATGAGG
44532 AAAAAAAGATGATGAAA
1 AAAAAAAGA-GATGAAA
44549 AAAAAAA-AGA-GAAA
1 AAAAAAAGAGATGAAA
*
44563 AAAGAAAGAAAGATGAAA
1 AAA-AAA-AGAGATGAAA
44581 AA
1 AA
44583 TTAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 7 0.23
15 5 0.17
16 2 0.07
17 10 0.33
18 6 0.20
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (16 bp):
AAAAAAAGAGATGAAA
Found at i:44555 original size:18 final size:16
Alignment explanation
Indices: 44532--44582 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 16
44522 AAAAATGAGG
44532 AAAAAAAGATGATGAAAA
1 AAAAAAAGATGA--AAAA
44550 AAAAAAAGA-GAAAAA
1 AAAAAAAGATGAAAAA
44565 AGAAAGAAAGATGAAAAA
1 A-AAA-AAAGATGAAAAA
44583 TTAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.17
16 3 0.10
17 7 0.23
18 15 0.50
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (16 bp):
AAAAAAAGATGAAAAA
Found at i:44562 original size:14 final size:14
Alignment explanation
Indices: 44522--44565 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
44512 ACAATAGATG
*
44522 AAAAATGAGGAAAA
1 AAAAATGAGAAAAA
*
44536 AAAGATGATGAAAAA
1 AAAAATGA-GAAAAA
*
44551 AAAAAAGAGAAAAA
1 AAAAATGAGAAAAA
44565 A
1 A
44566 GAAAGAAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (14 bp):
AAAAATGAGAAAAA
Found at i:45931 original size:14 final size:14
Alignment explanation
Indices: 45912--45941 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
45902 GCGAGGCAAC
45912 TTTACTTTTCAAAG
1 TTTACTTTTCAAAG
45926 TTTACTTTTCAAAG
1 TTTACTTTTCAAAG
45940 TT
1 TT
45942 CGTTGCCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (14 bp):
TTTACTTTTCAAAG
Found at i:45992 original size:42 final size:42
Alignment explanation
Indices: 45926--46214 Score: 457
Period size: 42 Copynumber: 7.0 Consensus size: 42
45916 CTTTTCAAAG
45926 TTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAA
1 TTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAA
* *
45966 TTTATTTTTCCAAAGTCGTGGTGCCTCTATTTAGAGGAGCAA
1 TTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
* *
46008 TTTACTTTTCCAAAGTTGTGGTACCTCTGTTTAGAGGAGCAA
1 TTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
*
46050 TTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAA
1 TTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
46092 TTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAA
1 TTTACTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAA
*
46132 TTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAA
1 TTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
46174 TTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
1 TTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
46215 CTCTGTTTAG
Statistics
Matches: 232, Mismatches: 10, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
40 45 0.19
41 50 0.22
42 137 0.59
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.37
Consensus pattern (42 bp):
TTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
Found at i:46155 original size:82 final size:83
Alignment explanation
Indices: 45926--46214 Score: 478
Period size: 82 Copynumber: 3.5 Consensus size: 83
45916 CTTTTCAAAG
* *
45926 TTTACTTTTCAAAGTTCGT-TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTGC
1 TTTACTTTTCAAAGTTCGTGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTAC
*
45990 CTCTATTTAGAGGAGCAA
66 CTCTGTTTAGAGGAGCAA
*
46008 TTTACTTTTCCAAAGTT-GTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGT
1 TTTACTTTT-CAAAGTTCGT-GTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGT
46072 ACCTCTGTTTAGAGGAGCAA
64 ACCTCTGTTTAGAGGAGCAA
46092 TTTACTTTTCAAAGTTCGT-TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTAC
1 TTTACTTTTCAAAGTTCGTGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTAC
46156 CTCTGTTTAGAGGAGCAA
66 CTCTGTTTAGAGGAGCAA
*
46174 TTTACTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAA
1 TTTACTTTTCAAAGTTCGT-GTGCCTCTGTTTAGAGGAGCAA
46215 CTCTGTTTAG
Statistics
Matches: 195, Mismatches: 6, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
81 4 0.02
82 86 0.44
83 35 0.18
84 70 0.36
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.37
Consensus pattern (83 bp):
TTTACTTTTCAAAGTTCGTGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTAC
CTCTGTTTAGAGGAGCAA
Found at i:46220 original size:18 final size:18
Alignment explanation
Indices: 46197--46232 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
46187 GTCGTGGTGC
46197 CTCTGTTTAGAGGAGCAA
1 CTCTGTTTAGAGGAGCAA
46215 CTCTGTTTAGAGGAGCAA
1 CTCTGTTTAGAGGAGCAA
46233 TTTACTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (18 bp):
CTCTGTTTAGAGGAGCAA
Found at i:46287 original size:99 final size:100
Alignment explanation
Indices: 46114--46313 Score: 341
Period size: 99 Copynumber: 2.0 Consensus size: 100
46104 AGTTCGTTGC
46114 CTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTAC
1 CTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGT-GTACCTCTGTTTAGAGGAGCAATTTAC
*
46179 TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA
65 TTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAA
* *
46215 CTCTGTTTAGAGGAGCAATTTACTTTTTC-AAGTTCGT-TGCCTCTGTTTAGAGGAGCAATTTAC
1 CTCTGTTTAGAGGAGCAATTTACTTTTCCAAAG-TCGTGTACCTCTGTTTAGAGGAGCAATTTAC
46278 TTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAA
65 TTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAA
46314 TTTACTTTCC
Statistics
Matches: 95, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
99 60 0.63
100 3 0.03
101 32 0.34
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (100 bp):
CTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGTACCTCTGTTTAGAGGAGCAATTTACT
TTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAA
Found at i:46311 original size:41 final size:41
Alignment explanation
Indices: 46215--46394 Score: 276
Period size: 41 Copynumber: 4.4 Consensus size: 41
46205 AGAGGAGCAA
* *
46215 CTCTGTTTAGAGGAGCAATTTACTTTTTC-AAGTTCGT--TGC
1 CTCTGTTTAGAGGAGCAATTTAC-TTTCCAAAG-TCGTGGTAC
46255 CTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTAC
1 CTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTAC
46296 CTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTAC
1 CTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTAC
* *
46337 CTCTGTTTAGAGGAGTAATTTACTTTCCAAAAGTCGTGGTGC
1 CTCTGTTTAGAGGAGCAATTTACTTTCC-AAAGTCGTGGTAC
46379 CTCTGTTTAGAGGAGC
1 CTCTGTTTAGAGGAGC
46395 TTTGGTAAAA
Statistics
Matches: 131, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
39 8 0.06
40 26 0.20
41 70 0.53
42 27 0.21
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (41 bp):
CTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTAC
Found at i:46342 original size:140 final size:141
Alignment explanation
Indices: 46074--46351 Score: 524
Period size: 140 Copynumber: 2.0 Consensus size: 141
46064 GTCGTGGTAC
46074 CTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTT
1 CTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTT
*
46139 TTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTT
66 TTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTACCTCTGTT
46204 TAGAGGAGCAA
131 TAGAGGAGCAA
46215 CTCTGTTTAGAGGAGCAATTTACTTTTTC-AAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTAC-
1 CTCTGTTTAGAGGAGCAATTTAC-TTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACT
46278 TTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTACCTCTGT
65 TTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTACCTCTGT
46343 TTAGAGGAG
130 TTAGAGGAG
46352 TAATTTACTT
Statistics
Matches: 135, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
140 73 0.54
141 57 0.42
142 5 0.04
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (141 bp):
CTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTT
TTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTACCTCTGTT
TAGAGGAGCAA
Found at i:46635 original size:12 final size:12
Alignment explanation
Indices: 46615--46702 Score: 58
Period size: 12 Copynumber: 7.2 Consensus size: 12
46605 CTTTTGTATT
*
46615 TTATGTATTGTA
1 TTATTTATTGTA
*
46627 TTATTTATTATTA
1 TTATTTATT-GTA
46640 TTA-TTA-TGTA
1 TTATTTATTGTA
*
46650 TTA-ATATATGTA
1 TTATTTAT-TGTA
46662 TATATTTATT-TA
1 T-TATTTATTGTA
46674 TTTATTTATTGTTA
1 -TTATTTATTG-TA
*
46688 ATATTTATGTGTA
1 TTATTTAT-TGTA
46701 TT
1 TT
46703 TTATTATTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
10 7 0.12
11 1 0.02
12 26 0.43
13 19 0.32
14 7 0.12
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (12 bp):
TTATTTATTGTA
Found at i:46683 original size:16 final size:15
Alignment explanation
Indices: 46614--46727 Score: 72
Period size: 16 Copynumber: 7.2 Consensus size: 15
46604 TCTTTTGTAT
46614 TTTATGTATTGTATTA
1 TTTATGTATT-TATTA
46630 TTTAT-TA-TTATTA
1 TTTATGTATTTATTA
*
46643 -TTATGTATTAATATA
1 TTTATGTATTTAT-TA
* *
46658 TGTATATATTTATTTA
1 TTTATGTATTTA-TTA
* *
46674 TTTATTTATTGTTAATA
1 TTTATGTA-T-TTATTA
46691 TTTATGTGTATTTTATTA
1 TTTA--TGTA-TTTATTA
*
46709 TTTATGTATATATATA
1 TTTATGTATTTAT-TA
46725 TTT
1 TTT
46728 TTTATCTTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
12 4 0.05
13 7 0.09
14 4 0.05
15 8 0.10
16 30 0.38
17 8 0.10
18 12 0.15
19 5 0.06
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (15 bp):
TTTATGTATTTATTA
Found at i:46778 original size:59 final size:59
Alignment explanation
Indices: 46638--46780 Score: 143
Period size: 59 Copynumber: 2.4 Consensus size: 59
46628 TATTTATTAT
*
46638 TATTATTATGTATTAATATATGTATATATTTATTTATTTATTTATTGTTAATATTTATGTG
1 TATT-TTAT-TATTAATATATATATATATTTATTTATTTATTTATTGTTAATATTTATGTG
* * * *
46699 TATTTTATTATTTATGTATATATATATTT-TTTATCTTTTTTATT-TTATTCATTT-T-TG
1 TATTTTATTATTAATATATATATATATTTATTTAT-TTATTTATTGTTAAT-ATTTATGTG
46756 TATTTTTACTTATCTAAT-TATATAT
1 TA-TTTTA-TTAT-TAATATATATAT
46781 CTGATATATT
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
57 4 0.06
58 15 0.21
59 41 0.58
60 7 0.10
61 4 0.06
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (59 bp):
TATTTTATTATTAATATATATATATATTTATTTATTTATTTATTGTTAATATTTATGTG
Found at i:47770 original size:18 final size:16
Alignment explanation
Indices: 47737--47812 Score: 73
Period size: 16 Copynumber: 4.6 Consensus size: 16
47727 TTAATTTGTT
47737 TTTTTATTTATTATTA
1 TTTTTATTTATTATTA
47753 TTTTTATTTATTAGATTA
1 TTTTTATTTATT--ATTA
** * *
47771 GGTTTATTTAATATTC
1 TTTTTATTTATTATTA
47787 TTTTTATCTTTATT-TTA
1 TTTTTA--TTTATTATTA
47804 TTTTTATTT
1 TTTTTATTT
47813 TTCTTTTACT
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
15 3 0.06
16 19 0.40
17 8 0.17
18 18 0.38
ACGTcount: A:0.22, C:0.03, G:0.04, T:0.71
Consensus pattern (16 bp):
TTTTTATTTATTATTA
Found at i:47804 original size:11 final size:11
Alignment explanation
Indices: 47788--47860 Score: 50
Period size: 11 Copynumber: 7.0 Consensus size: 11
47778 TTAATATTCT
47788 TTTTATCTTTA
1 TTTTATCTTTA
*
47799 TTTTATTTTTA
1 TTTTATCTTTA
47810 TTTT-TCTTTTA
1 TTTTATC-TTTA
*
47821 CTTT-TCTTT-
1 TTTTATCTTTA
*
47830 TTTTAT-TTTT
1 TTTTATCTTTA
*
47840 TTATTAT-TCTA
1 TT-TTATCTTTA
47851 TTTT-TCTTTA
1 TTTTATCTTTA
47861 AATAAAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
9 7 0.14
10 12 0.24
11 31 0.62
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTATCTTTA
Found at i:47819 original size:17 final size:17
Alignment explanation
Indices: 47787--47849 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 17
47777 TTTAATATTC
* *
47787 TTTTTATCTTTATTTTA
1 TTTTTATTTTTCTTTTA
47804 TTTTTATTTTTCTTTTA
1 TTTTTATTTTTCTTTTA
* *
47821 CTTTTCTTTTT-TTATT-
1 TTTTTATTTTTCTT-TTA
*
47837 TTTTTATTATTCT
1 TTTTTATTTTTCT
47850 ATTTTTCTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 10 0.27
17 27 0.73
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTATTTTTCTTTTA
Found at i:47820 original size:22 final size:21
Alignment explanation
Indices: 47795--47855 Score: 59
Period size: 25 Copynumber: 2.7 Consensus size: 21
47785 TCTTTTTATC
47795 TTTATTTTATTTTTATTTTTCT
1 TTTATTTTATTTTTATTTTT-T
*
47817 TTTACTTTTCTTTTTTTATTTTTT
1 TTTA--TTT-TATTTTTATTTTTT
*
47841 TATTATTCTATTTTT
1 T-TTATTTTATTTTT
47856 CTTTAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
22 10 0.31
23 2 0.06
24 5 0.16
25 15 0.47
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTATTTTATTTTTATTTTTT
Found at i:47962 original size:60 final size:59
Alignment explanation
Indices: 47866--48220 Score: 463
Period size: 60 Copynumber: 6.0 Consensus size: 59
47856 CTTTAAATAA
* *
47866 AAAAATCAAAAGTTCCAAAAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTT
1 AAAAAT-AAAA-TTTCAAAAAAAAAATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTT
*
47927 AAAAATAAAATTTCAAAAAAAAACATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT
1 AAAAATAAAATTTCAAAAAAAAA-ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
* * *
47987 GAAAACAAAATTTCAAAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
1 AAAAATAAAATTTCAAAAAAAAA--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
*
48048 GAAAATAAAATTTCAAAAAAAAAAGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
1 AAAAATAAAATTTCAAAAAAAAAA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
* * *
48108 GAAAAT-AAGTTTC---CAAAAAATGTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
1 AAAAATAAAATTTCAAAAAAAAAAT-TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
* *
48164 AAAAAT-AAATTTCCAAAAAAATATTTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCC
1 AAAAATAAAATTT-CAAAAAAAAAATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCC
48221 CCACACAAAA
Statistics
Matches: 267, Mismatches: 17, Indels: 22
0.87 0.06 0.07
Matches are distributed among these distances:
55 1 0.00
56 50 0.19
57 1 0.00
58 2 0.01
59 46 0.17
60 105 0.39
61 62 0.23
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.32
Consensus pattern (59 bp):
AAAAATAAAATTTCAAAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
Found at i:48025 original size:121 final size:115
Alignment explanation
Indices: 47899--48220 Score: 484
Period size: 121 Copynumber: 2.7 Consensus size: 115
47889 ATATTTTTAG
47899 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAACATTTTTGGGGAAA
1 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAA-ATTTTTGGGGAAA
47964 AGTTGAAAGTATCAATTTTCCTTGAAAACAAAATTTCAAAAAAAAAGGGTTTTTGA
65 AGTTGAAAGTATCAATTTTCCTTGAAAA-AAAATTTC--AAAAAAA-GG-TTTTGA
* *
48020 GGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTCAAAAAAAAAAGTTTTTGAGGAAA
1 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAAA-TTTTTGGGGAAA
* * * *
48085 AGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTCCAAAAAATGTTTTGA
65 AGTTGAAAGTATCAATTTTCCTTGAAAAAAAATTTCAAAAAAAGGTTTTGA
* * *
48136 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTCCAAAAAAATATTTTTTGGGAAAA
1 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTT-CAAAAAAAAAATTTTTGGGGAAA
48200 AGTTGAAAGTATCAATTTTCC
65 AGTTGAAAGTATCAATTTTCC
48221 CCACACAAAA
Statistics
Matches: 188, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
115 37 0.20
116 48 0.26
117 1 0.01
118 6 0.03
120 7 0.04
121 89 0.47
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.32
Consensus pattern (115 bp):
GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAAAATTTTTGGGGAAAA
GTTGAAAGTATCAATTTTCCTTGAAAAAAAATTTCAAAAAAAGGTTTTGA
Found at i:53258 original size:18 final size:19
Alignment explanation
Indices: 53237--53272 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
53227 TAACATTTAT
53237 AAAATT-AATAAATTATTG
1 AAAATTCAATAAATTATTG
*
53255 AAAATTCATTAAATTATT
1 AAAATTCAATAAATTATT
53273 TTATATCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (19 bp):
AAAATTCAATAAATTATTG
Found at i:53849 original size:13 final size:12
Alignment explanation
Indices: 53831--53869 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
53821 ATTTTTTTAT
53831 TAAAAATATTAAA
1 TAAAAAT-TTAAA
*
53844 TAAAAATTTATAT
1 TAAAAATTTA-AA
53857 TAAAAATTTAAA
1 TAAAAATTTAAA
53869 T
1 T
53870 TGATGAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAAAATTTAAA
Found at i:60524 original size:153 final size:153
Alignment explanation
Indices: 60246--60540 Score: 527
Period size: 153 Copynumber: 1.9 Consensus size: 153
60236 TCGAGACTTA
** *
60246 AGCTCCGAACCCGCGCGGCTCCGGGACCCGGGCATTCACTCTTTCGACGTCCCAGATCAACTTTC
1 AGCTCCGAACCCGCGCGGCTCCACGACCCGGGCATTCACTCTTCCGACGTCCCAGATCAACTTTC
*
60311 TTGCCACGGTTCACATCCTTGTGAGATATTGTCCGCTCTGGCCCCCTTGGCCTCATGGTTTTGTC
66 TTGCCACGGTTCACACCCTTGTGAGATATTGTCCGCTCTGGCCCCCTTGGCCTCATGGTTTTGTC
60376 CTACAAAAGGCGTCTCACAAGGC
131 CTACAAAAGGCGTCTCACAAGGC
* *
60399 AGCTCCGAACCCGCGCGGCTCCACGACCCGGGCATTCACTCTTCCGGCGTCCCAGATCAGCTTTC
1 AGCTCCGAACCCGCGCGGCTCCACGACCCGGGCATTCACTCTTCCGACGTCCCAGATCAACTTTC
*
60464 TTGCCACGGTTCACACCCTTGTGAGGTATTGTCCGCTCTGGCCCCCTTGGCCTCATGGTTTTGTC
66 TTGCCACGGTTCACACCCTTGTGAGATATTGTCCGCTCTGGCCCCCTTGGCCTCATGGTTTTGTC
60529 CTACAAAAGGCG
131 CTACAAAAGGCG
60541 CGCAGAGGTG
Statistics
Matches: 135, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
153 135 1.00
ACGTcount: A:0.16, C:0.36, G:0.23, T:0.25
Consensus pattern (153 bp):
AGCTCCGAACCCGCGCGGCTCCACGACCCGGGCATTCACTCTTCCGACGTCCCAGATCAACTTTC
TTGCCACGGTTCACACCCTTGTGAGATATTGTCCGCTCTGGCCCCCTTGGCCTCATGGTTTTGTC
CTACAAAAGGCGTCTCACAAGGC
Found at i:61486 original size:13 final size:12
Alignment explanation
Indices: 61468--61501 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
61458 ACAGATAAAC
61468 ATAAAATAAAATA
1 ATAAAA-AAAATA
*
61481 ATAAAAGAAATA
1 ATAAAAAAAATA
61493 ATAAAAAAA
1 ATAAAAAAA
61502 GTAGAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (12 bp):
ATAAAAAAAATA
Found at i:66788 original size:23 final size:25
Alignment explanation
Indices: 66762--66811 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
66752 ATAATTTTAG
66762 TTTGGGAA-AA-AATGTTTTGTATT
1 TTTGGGAATAATAATGTTTTGTATT
** *
66785 TTTGTTAATAATTATGTTTTGTATT
1 TTTGGGAATAATAATGTTTTGTATT
66810 TT
1 TT
66812 ATTAGCTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 6 0.27
24 2 0.09
25 14 0.64
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (25 bp):
TTTGGGAATAATAATGTTTTGTATT
Found at i:71571 original size:144 final size:144
Alignment explanation
Indices: 70715--71512 Score: 1429
Period size: 144 Copynumber: 5.5 Consensus size: 144
70705 CCAGAAAACA
* * *
70715 TATTTTGATTCAACTCAAACTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCA
1 TATTATGACTCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCA
* **
70780 GAAAACATATTTCGATGAAGGTGGAGAGTGGACAAGCAAGTCAAGTTTCCTATGGAAGCAGGGAT
66 GAAAACATATTTCGATGAAGGTAGAGAGTGGACAAGCTGGTCAAGTTTCCTATGGAAGCAGGGAT
70845 TGAACCAGAGAAAT
131 TGAACCAGAGAAAT
*
70859 TATTATGACTCAACTTAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCA
1 TATTATGACTCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCA
70924 GAAAACATATTTCGATGAAGGTAGAGAGTGGACAAGCTGGTCAAGTTTCCTATGGAAGCAGGGAT
66 GAAAACATATTTCGATGAAGGTAGAGAGTGGACAAGCTGGTCAAGTTTCCTATGGAAGCAGGGAT
70989 TGAACCAGAGAAAT
131 TGAACCAGAGAAAT
*
71003 TATTATGACTCAACTTAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCA
1 TATTATGACTCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCA
*
71068 GAAAACATATTTCGATGAAGGTAGAGAGTGGA-TAGACTGGTCAAGTTTCCTATGGAAGCAGGGA
66 GAAAACATATTTCGATGAAGGTAGAGAGTGGACAAG-CTGGTCAAGTTTCCTATGGAAGCAGGGA
71132 TTGAACCAGAGAAAT
130 TTGAACCAGAGAAAT
* *
71147 TATTATGACGCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCCCTTGAGGTATCGACCCA
1 TATTATGACTCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCA
71212 GAAAACATATTTCGATGAAGGTAGAGAGTGGACAAGCTGGTCAAGTTTCCTATGGAAGCAGGGAT
66 GAAAACATATTTCGATGAAGGTAGAGAGTGGACAAGCTGGTCAAGTTTCCTATGGAAGCAGGGAT
71277 TGAACCAGAGAAAT
131 TGAACCAGAGAAAT
71291 TATTATGACTCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCA
1 TATTATGACTCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCA
*
71356 GAAAACATATTTCGATGAAGGTAGAGAGTGGA-TAGACTGGTCAAGTTTCCTATGGAAGCAGGGA
66 GAAAACATATTTCGATGAAGGTAGAGAGTGGACAAG-CTGGTCAAGTTTCCTATGGAAGCAGGGA
71420 TTGAACCAGAGAAAT
130 TTGAACCAGAGAAAT
* * *
71435 TATTTTGACTCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTCAGGTATTGACCCA
1 TATTATGACTCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCA
71500 GAAAACATATTTC
66 GAAAACATATTTC
71513 CATAGAGATG
Statistics
Matches: 633, Mismatches: 18, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
143 4 0.01
144 627 0.99
145 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (144 bp):
TATTATGACTCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCA
GAAAACATATTTCGATGAAGGTAGAGAGTGGACAAGCTGGTCAAGTTTCCTATGGAAGCAGGGAT
TGAACCAGAGAAAT
Found at i:74410 original size:14 final size:14
Alignment explanation
Indices: 74391--74420 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
74381 CTTGGACCCA
74391 CGAACCTAGAACCT
1 CGAACCTAGAACCT
*
74405 CGAACCTGGAACCT
1 CGAACCTAGAACCT
74419 CG
1 CG
74421 CTCTGATACC
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:0.30, C:0.37, G:0.20, T:0.13
Consensus pattern (14 bp):
CGAACCTAGAACCT
Found at i:77450 original size:29 final size:30
Alignment explanation
Indices: 77418--77481 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
77408 TAACTTTTGT
* **
77418 ATATATTTTAAAATTTTTTAATTA-TTAAA
1 ATATATTTAAAAAAATTTTAATTATTTAAA
77447 ATATA-TTAAAAAAATTTTAATTATTTAAA
1 ATATATTTAAAAAAATTTTAATTATTTAAA
77476 AT-TATT
1 ATATATT
77482 ATTTATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 17 0.57
29 13 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
ATATATTTAAAAAAATTTTAATTATTTAAA
Found at i:77492 original size:19 final size:18
Alignment explanation
Indices: 77452--77507 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
77442 TTAAAATATA
*
77452 TTAAAAAAATT-TTAATTAT
1 TTAAAATAATTATT-ATT-T
*
77471 TTAAAATTATTATTTATTT
1 TTAAAATAATTA-TTATTT
77490 TTAAAATAATTATTATTT
1 TTAAAATAATTATTATTT
77508 ATTATTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 6 0.19
19 21 0.66
20 3 0.09
21 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAAAATAATTATTATTT
Found at i:77658 original size:19 final size:19
Alignment explanation
Indices: 77636--77672 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
77626 TTTATATATA
*
77636 ATAGTTTAGTATGAAAAAT
1 ATAGTTTAATATGAAAAAT
*
77655 ATAGTTTAATATTAAAAA
1 ATAGTTTAATATGAAAAA
77673 AATTACAAGT
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:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
ATAGTTTAATATGAAAAAT
Found at i:80516 original size:23 final size:24
Alignment explanation
Indices: 80468--80516 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
80458 GTTTACCCAA
***
80468 ATGAAATCATAAAATATTATTTTT
1 ATGAAATCATAAAATATTAACCTT
80492 ATGAAATCAT-AAATATTAACCTT
1 ATGAAATCATAAAATATTAACCTT
80515 AT
1 AT
80517 TTTACTTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (24 bp):
ATGAAATCATAAAATATTAACCTT
Found at i:87818 original size:3 final size:3
Alignment explanation
Indices: 87810--87835 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
87800 AGTTATATAT
87810 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
87836 TTTGTAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:88436 original size:20 final size:20
Alignment explanation
Indices: 88413--88456 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
88403 TGCCCAGTTT
*
88413 CCGGCGAAGAATCCCAGAAA
1 CCGGCAAAGAATCCCAGAAA
88433 CCGGCAAAGAATCCCAGAAA
1 CCGGCAAAGAATCCCAGAAA
88453 CCGG
1 CCGG
88457 TGAATTTCCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.32, G:0.25, T:0.05
Consensus pattern (20 bp):
CCGGCAAAGAATCCCAGAAA
Done.