Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002778.1 Hibiscus syriacus cultivar Beakdansim tig00005722_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: 121302
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:5009 original size:22 final size:22
Alignment explanation
Indices: 4981--5022 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
4971 GGTTAAAATA
4981 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
5003 AAAAATAATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
5023 CAAATTAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:6327 original size:28 final size:28
Alignment explanation
Indices: 6285--6349 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
6275 TCACACATAT
6285 CCGCTCAAAGTGTTTGGGGTAAATGGAA
1 CCGCTCAAAGTGTTTGGGGTAAATGGAA
*
6313 CTGCTCAAAGTGTTTGGGGTAAATGGAA
1 CCGCTCAAAGTGTTTGGGGTAAATGGAA
6341 CCGCTCAAA
1 CCGCTCAAA
6350 CCAAAACTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (28 bp):
CCGCTCAAAGTGTTTGGGGTAAATGGAA
Found at i:7601 original size:8 final size:8
Alignment explanation
Indices: 7588--7640 Score: 65
Period size: 8 Copynumber: 6.5 Consensus size: 8
7578 AAAGTTCGAT
7588 AAAAAATA
1 AAAAAATA
7596 AAAAAATTA
1 AAAAAA-TA
7605 AAAAAATTA
1 AAAAAA-TA
7614 AAAAAA-A
1 AAAAAATA
7621 TAAAAAA-A
1 -AAAAAATA
7629 AAAAAATA
1 AAAAAATA
7637 AAAA
1 AAAA
7641 CAAAAATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.17
8 18 0.43
9 17 0.40
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAAATA
Found at i:7632 original size:14 final size:14
Alignment explanation
Indices: 7588--7651 Score: 67
Period size: 14 Copynumber: 4.6 Consensus size: 14
7578 AAAGTTCGAT
7588 AAAAAATAAAAAAA
1 AAAAAATAAAAAAA
** **
7602 TTAAAA-AAATTAA
1 AAAAAATAAAAAAA
7615 AAAAAATAAAAAAA
1 AAAAAATAAAAAAA
*
7629 AAAAAATAAAAACA
1 AAAAAATAAAAAAA
*
7643 AAAATATAA
1 AAAAAATAA
7652 CGAAATGGGT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
13 9 0.23
14 30 0.77
ACGTcount: A:0.84, C:0.02, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAAATAAAAAAA
Found at i:7639 original size:9 final size:9
Alignment explanation
Indices: 7588--7648 Score: 72
Period size: 9 Copynumber: 6.9 Consensus size: 9
7578 AAAGTTCGAT
7588 AAAAAATAA
1 AAAAAATAA
*
7597 AAAAATTAA
1 AAAAAATAA
*
7606 AAAAATTAA
1 AAAAAATAA
7615 AAAAAATAA
1 AAAAAATAA
7624 AAAAAA-AA
1 AAAAAATAA
7632 AAATAAA-AA
1 AAA-AAATAA
*
7641 CAAAAATA
1 AAAAAATA
7649 TAACGAAATG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
8 8 0.17
9 39 0.83
ACGTcount: A:0.85, C:0.02, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAAATAA
Found at i:13251 original size:21 final size:22
Alignment explanation
Indices: 13218--13258 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
13208 GTTAAAATTA
13218 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
13240 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
13259 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:14065 original size:76 final size:75
Alignment explanation
Indices: 13922--14069 Score: 208
Period size: 76 Copynumber: 2.0 Consensus size: 75
13912 TTCTAAATCA
* * *
13922 TAATTAAAATACTAAAAATTGTTTAAACTAAAATACAAAGATAAAGATAAAATATAAAAATAATA
1 TAATTAAAATACTAAAAACTATTTAAACTAAAATAAAAAGATAAAGATAAAATATAAAAATAATA
13987 TCCTAAAATT
66 TCCTAAAATT
* * * *
13997 TAATTAAAATACTAAAAACCTATTTAAACTAAAATAAAAAGATAAA-ATATAATGTTTAAAATAT
1 TAATTAAAATACTAAAAA-CTATTTAAACTAAAATAAAAAGATAAAGATAAAAT-ATAAAAATAA
14061 TATCCTAAA
64 TATCCTAAA
14070 TTTGAGTTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
75 24 0.38
76 40 0.62
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.30
Consensus pattern (75 bp):
TAATTAAAATACTAAAAACTATTTAAACTAAAATAAAAAGATAAAGATAAAATATAAAAATAATA
TCCTAAAATT
Found at i:15320 original size:21 final size:22
Alignment explanation
Indices: 15291--15343 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
15281 ATGTATATAT
*
15291 ATATATATATGTAA-TTAAAAA
1 ATATGTATATGTAACTTAAAAA
*
15312 ATATGTATATATAACTTAAAAA
1 ATATGTATATGTAACTTAAAAA
*
15334 A-AAGTATATG
1 ATATGTATATG
15344 AAATGTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.36
Consensus pattern (22 bp):
ATATGTATATGTAACTTAAAAA
Found at i:30107 original size:16 final size:15
Alignment explanation
Indices: 30075--30119 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
30065 TTTGGAATAT
30075 TTAATTCATAA-TAA
1 TTAATTCATAATTAA
*
30089 TTAATTACATATTTAA
1 TTAATT-CATAATTAA
30105 TTAATTCATAATTAA
1 TTAATTCATAATTAA
30120 AAACCCTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 6 0.22
15 12 0.44
16 9 0.33
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAATTCATAATTAA
Found at i:32189 original size:17 final size:17
Alignment explanation
Indices: 32167--32217 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 17
32157 AAACATATAT
32167 TAACTGTAAATATTTGA
1 TAACTGTAAATATTTGA
* *
32184 TAACTGAAAAATCATCTGA
1 TAACTG-TAAAT-ATTTGA
*
32203 TAACTGTAAACATTT
1 TAACTGTAAATATTT
32218 AGAATTCATG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 9 0.33
18 7 0.26
19 11 0.41
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TAACTGTAAATATTTGA
Found at i:47936 original size:18 final size:17
Alignment explanation
Indices: 47913--47986 Score: 60
Period size: 18 Copynumber: 4.2 Consensus size: 17
47903 TTAATTTGTG
47913 TTTGATAACTGTAAAGCA
1 TTTGATAACTGTAAA-CA
*
47931 TTTGATATCTGTAAA-A
1 TTTGATAACTGTAAACA
* * *
47947 CTCTGATAAGTAGAAAATCA
1 -TTTGATAACT-GTAAA-CA
*
47967 TTTGAAAACTGTAAACA
1 TTTGATAACTGTAAACA
47984 TTT
1 TTT
47987 AGAATTCATC
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
16 1 0.02
17 12 0.28
18 22 0.51
19 7 0.16
20 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.35
Consensus pattern (17 bp):
TTTGATAACTGTAAACA
Found at i:51560 original size:17 final size:17
Alignment explanation
Indices: 51535--51575 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
51525 ACTATTTTCA
51535 AAGGATTTAAAAATTTG
1 AAGGATTTAAAAATTTG
*
51552 AATGATTTAAAAATTTG
1 AAGGATTTAAAAATTTG
51569 AAGGATT
1 AAGGATT
51576 AAATTGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (17 bp):
AAGGATTTAAAAATTTG
Found at i:52937 original size:44 final size:44
Alignment explanation
Indices: 52889--53198 Score: 415
Period size: 44 Copynumber: 7.0 Consensus size: 44
52879 ATGTTACTGA
** * * *
52889 CATAAATGAAAATGTGTATCGGTGTATTATTGGCAGAAATGTGC
1 CATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGC
* * * *
52933 CATAAATGAAAATGAATAACGATGCATTATTGGAAGAAAGGTAC
1 CATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGC
* * * *
52977 CATAAATGAAAATGTATAACGGTGCATTATTGGTAGAAAGATGT
1 CATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGC
*
53021 CATAAAT-ACAAATGCATAATGGTGCATTATTGGCAGAAAGGTGC
1 CATAAATGA-AAATGCATAACGGTGCATTATTGGCAGAAAGGTGC
* * *
53065 CATGAATGAAAATGCATAACGGTGCATTATTGGAAGAAATGTGC
1 CATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGC
* * *
53109 CATAAATGAAAATGTATAATGGTGCATTATTGGCAGAAAGGTTC
1 CATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGC
*
53153 CATAAATGAAAATGCATAACGGTGTATTATTGGCAGAAAGGTGC
1 CATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGC
53197 CA
1 CA
53199 CTCATGGAAT
Statistics
Matches: 231, Mismatches: 33, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
43 1 0.00
44 229 0.99
45 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (44 bp):
CATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGC
Found at i:53055 original size:132 final size:132
Alignment explanation
Indices: 52889--53198 Score: 462
Period size: 132 Copynumber: 2.3 Consensus size: 132
52879 ATGTTACTGA
** * *
52889 CATAAATGAAAATGTGTATCGGTGTATTATTGGCAGAAATGTGCCATAAATGAAAATGAATAACG
1 CATAAATGAAAATGCATAACGGTGTATTATTGGCAGAAAGGTGCCATAAATGAAAATGAATAACG
*
52954 ATGCATTATTGGAAGAAAGGTACCATAAATGAAAATGTATAACGGTGCATTATTGGTAGAAAGAT
66 ATGCATTATTGGAAGAAAGGTACCATAAATGAAAATGTATAACGGTGCATTATTGGCAGAAAGAT
53019 GT-
131 -TC
* * * *
53021 CATAAAT-ACAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCCATGAATGAAAATGCATAAC
1 CATAAATGA-AAATGCATAACGGTGTATTATTGGCAGAAAGGTGCCATAAATGAAAATGAATAAC
* * * * *
53085 GGTGCATTATTGGAAGAAATGTGCCATAAATGAAAATGTATAATGGTGCATTATTGGCAGAAAGG
65 GATGCATTATTGGAAGAAAGGTACCATAAATGAAAATGTATAACGGTGCATTATTGGCAGAAAGA
53150 TTC
130 TTC
53153 CATAAATGAAAATGCATAACGGTGTATTATTGGCAGAAAGGTGCCA
1 CATAAATGAAAATGCATAACGGTGTATTATTGGCAGAAAGGTGCCA
53199 CTCATGGAAT
Statistics
Matches: 159, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
131 2 0.01
132 156 0.98
133 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (132 bp):
CATAAATGAAAATGCATAACGGTGTATTATTGGCAGAAAGGTGCCATAAATGAAAATGAATAACG
ATGCATTATTGGAAGAAAGGTACCATAAATGAAAATGTATAACGGTGCATTATTGGCAGAAAGAT
TC
Found at i:59441 original size:18 final size:19
Alignment explanation
Indices: 59393--59443 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
59383 TACGATGAAT
*
59393 AGTATCGATACTGATGCAATT
1 AGTATCGATACTGATG--ATG
*
59414 AGTATTGATACTGATG-TG
1 AGTATCGATACTGATGATG
59432 AGTATCGATACT
1 AGTATCGATACT
59444 AAGAGAAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 12 0.44
21 15 0.56
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (19 bp):
AGTATCGATACTGATGATG
Found at i:60055 original size:44 final size:44
Alignment explanation
Indices: 60005--60219 Score: 238
Period size: 44 Copynumber: 4.9 Consensus size: 44
59995 ATGTTACCGA
* *
60005 CATAAATGAAAATACATAGCGGTGCATTATTGACAGAAATGTGC
1 CATAAATGAAAATACATAACGGTGCATTATTGACAGAAAGGTGC
** * * * *
60049 CATAAATGAAAATGTATAACGGTGTATTATTGGCATAAAGGTTC
1 CATAAATGAAAATACATAACGGTGCATTATTGACAGAAAGGTGC
*
60093 CATAAATGAAAATGA-ATAACTGTGCATTATTGGA-AGAAAGGTGC
1 CATAAATGAAAAT-ACATAACGGTGCATTATT-GACAGAAAGGTGC
* * *
60137 CATAAATGAAAATGCATAACTGTGCATTATTGGA-AGAAAGGTAC
1 CATAAATGAAAATACATAACGGTGCATTATT-GACAGAAAGGTGC
* * * *
60181 CATAAATAAAAATACATAAGGGTGCAGTATTGGCAGAAA
1 CATAAATGAAAATACATAACGGTGCATTATTGACAGAAA
60220 AGTTAAAATA
Statistics
Matches: 145, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
43 1 0.01
44 143 0.99
45 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.26
Consensus pattern (44 bp):
CATAAATGAAAATACATAACGGTGCATTATTGACAGAAAGGTGC
Found at i:60105 original size:88 final size:88
Alignment explanation
Indices: 60005--60219 Score: 274
Period size: 88 Copynumber: 2.4 Consensus size: 88
59995 ATGTTACCGA
* *
60005 CATAAATGAAAATACATAGCGGTGCATTATTGACAGAAATGTGCCATAAATGAAAATGTATAACG
1 CATAAATGAAAATACATAGCGGTGCATTATTGACAGAAAGGTGCCATAAATGAAAATGCATAACG
* * * *
60070 GTGTATTATTGGCATAAAGGTTC
66 GTGCATTATTGGAAGAAAGGTAC
* *
60093 CATAAATGAAAATGA-ATAACTGTGCATTATTGGA-AGAAAGGTGCCATAAATGAAAATGCATAA
1 CATAAATGAAAAT-ACATAGCGGTGCATTATT-GACAGAAAGGTGCCATAAATGAAAATGCATAA
*
60156 CTGTGCATTATTGGAAGAAAGGTAC
64 CGGTGCATTATTGGAAGAAAGGTAC
* * *
60181 CATAAATAAAAATACATAAG-GGTGCAGTATTGGCAGAAA
1 CATAAATGAAAATACAT-AGCGGTGCATTATTGACAGAAA
60220 AGTTAAAATA
Statistics
Matches: 108, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
87 2 0.02
88 102 0.94
89 4 0.04
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.26
Consensus pattern (88 bp):
CATAAATGAAAATACATAGCGGTGCATTATTGACAGAAAGGTGCCATAAATGAAAATGCATAACG
GTGCATTATTGGAAGAAAGGTAC
Found at i:61293 original size:11 final size:10
Alignment explanation
Indices: 61260--61293 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
61250 ATGGCCTAAG
*
61260 TTTCATGAAA
1 TTTCATGTAA
61270 TTTCATGTAA
1 TTTCATGTAA
61280 TTTCATGTTAA
1 TTTCATG-TAA
61291 TTT
1 TTT
61294 AACCATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 16 0.73
11 6 0.27
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TTTCATGTAA
Found at i:64825 original size:3 final size:3
Alignment explanation
Indices: 64817--64906 Score: 153
Period size: 3 Copynumber: 29.7 Consensus size: 3
64807 AATATAAATT
* *
64817 TAA TAA TAA TAA TAA TAA TGA TGA TAA TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
64863 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
64907 TGGATAAAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
3 81 0.96
4 3 0.04
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:65359 original size:113 final size:112
Alignment explanation
Indices: 65040--65791 Score: 1002
Period size: 114 Copynumber: 6.6 Consensus size: 112
65030 ATTGAATAAA
* * * * *
65040 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGG-GATGATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCT-CTGGAAAAGATAATCCATC
* * * *
65103 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
65 AATTGATGAATTC-AGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * * * *
65152 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATAATCC
* * * *
65216 ATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
62 ATCAATTGATGAATTC-AGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
65268 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
65333 ATTTGATGAATTCAGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 A-TTGATGAATTCAGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
65381 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
65446 ATTTGATGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 A-TTGATGAATTCAG-AAAAAGGTTGAACAAATTCTTCTCATTATGAAC
*
65495 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCTATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
*
65560 ATTTGATGAATTCAGGAAAAAGGTTGAATAAATTCTTCTCATTATGAAC
66 A-TTGATGAATTCA-GAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
65609 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA--TTGAC-CT--AACAATGCTGATCC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTT--CTCTGGAA-AA-GATAATCC
* * * *
65669 ATCAAGTGATAGAATT-AGGCAGAAGGTTGAACAAATTCTTCTCATTATGAAT
62 ATCAATTGAT-GAATTCA-GAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
65721 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATG-TCAATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAT-AATCCATC
*
65785 AAATGAT
65 AATTGAT
65792 AGATTTGAAT
Statistics
Matches: 592, Mismatches: 27, Indels: 41
0.90 0.04 0.06
Matches are distributed among these distances:
111 2 0.00
112 90 0.15
113 194 0.33
114 196 0.33
115 7 0.01
116 101 0.17
117 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (112 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
ATTGATGAATTCAGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
Found at i:66581 original size:83 final size:83
Alignment explanation
Indices: 66441--66914 Score: 749
Period size: 83 Copynumber: 5.7 Consensus size: 83
66431 TAGTTCTTAC
* **
66441 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAA
66506 TTCAATGATTGGTTCTG-
66 TTCAATGATTGGTTCTGT
* *
66523 CTAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTCTAA
1 C-AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAA
*
66588 ATTCAATGATTTGTTCTGT
65 ATTCAATGATTGGTTCTGT
* *
66607 CCAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCAAATTCATCTTCTAA
66671 ATTCAATGATT-GTTCTG-
65 ATTCAATGATTGGTTCTGT
* * *
66688 CTAAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 C-AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAA
*
66753 ATTCAATGATTGATTCTGT
65 ATTCAATGATTGGTTCTGT
* * *
66772 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAA
66837 TTCAATGATTGGTTCTGT
66 TTCAATGATTGGTTCTGT
*
66855 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTT
66915 TCAGTTAATG
Statistics
Matches: 362, Mismatches: 23, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
81 2 0.01
82 74 0.20
83 282 0.78
84 4 0.01
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAA
TTCAATGATTGGTTCTGT
Found at i:66757 original size:165 final size:166
Alignment explanation
Indices: 66443--66914 Score: 781
Period size: 165 Copynumber: 2.8 Consensus size: 166
66433 GTTCTTACCA
* **
66443 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCATATTCATCTTCCCAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAAT
* *
66507 TCAATGATTGGTTCTGCTAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAA
65 TCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
*
66572 CAAATTCATCTTCTAAATTCAATGATTTG-TTCTGTCC
130 CAAATTCATCTTCCAAATTCAATGA-TTGATTCTGTCC
*
66609 AACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
* *
66674 CAATGATT-GTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGC
66 CAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGC
66738 AAATTCATCTTCCAAATTCAATGATTGATTCTGTCC
131 AAATTCATCTTCCAAATTCAATGATTGATTCTGTCC
**
66774 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
*
66839 CAATGATTGGTTCTG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
66 CAATGATTGGTTCTGCT-AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
66903 CAAATTCATCTT
130 CAAATTCATCTT
66915 TCAGTTAATG
Statistics
Matches: 287, Mismatches: 15, Indels: 8
0.93 0.05 0.03
Matches are distributed among these distances:
164 3 0.01
165 154 0.54
166 128 0.45
167 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.28
Consensus pattern (166 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
CAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGC
AAATTCATCTTCCAAATTCAATGATTGATTCTGTCC
Found at i:66880 original size:248 final size:248
Alignment explanation
Indices: 66442--66914 Score: 824
Period size: 248 Copynumber: 1.9 Consensus size: 248
66432 AGTTCTTACC
* *
66442 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCCAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAAT
*
66507 TCAATGATTGGTTCTGCTAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAA
66 TCAATGATTGATTCTGCTAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAA
*
66572 CAAATTCATCTTCTAAATTCAATGATTTGTTCTGTCCAACCAGATCAAATAACTCAAAGAACACT
131 CAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAAATAACTCAAAGAACACT
66637 TCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCT
196 TCCAGAAGATGCTA-TGAGCAAATTCATCTTCTAAATTCAATGATTGTTCTGCT
* *
66690 AAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAAT
* * *
66755 TCAATGATTGATTCTG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTA
66 TCAATGATTGATTCTGCT-AAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
*
66819 ACAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC
130 ACAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAAATAACTCAAAGAACAC
66884 TTCCAGAAGATGCTATGAGCAAATTCATCTT
195 TTCCAGAAGATGCTATGAGCAAATTCATCTT
66915 TCAGTTAATG
Statistics
Matches: 213, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
247 3 0.01
248 210 0.99
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.28
Consensus pattern (248 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAAT
TCAATGATTGATTCTGCTAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAA
CAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAAATAACTCAAAGAACACT
TCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATTCAATGATTGTTCTGCT
Found at i:79392 original size:20 final size:21
Alignment explanation
Indices: 79369--79407 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
79359 TATATGTATA
*
79369 TTTATGAATAT-ATAAAATTT
1 TTTATCAATATAATAAAATTT
79389 TTTATCAATATAATAAAAT
1 TTTATCAATATAATAAAAT
79408 AAAAATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (21 bp):
TTTATCAATATAATAAAATTT
Found at i:80331 original size:23 final size:23
Alignment explanation
Indices: 80301--80347 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
80291 GTTTAGTTGT
*
80301 TGTTTTTTTTTTTCC-TTTCTCTG
1 TGTTTTTTTTTCTCCGTTT-TCTG
80324 TGTTTTTTTTTCTCCGTTTTCTG
1 TGTTTTTTTTTCTCCGTTTTCTG
80347 T
1 T
80348 TTCTGTCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.00, C:0.17, G:0.11, T:0.72
Consensus pattern (23 bp):
TGTTTTTTTTTCTCCGTTTTCTG
Found at i:80863 original size:3 final size:3
Alignment explanation
Indices: 80855--80937 Score: 157
Period size: 3 Copynumber: 27.7 Consensus size: 3
80845 AATATAAATT
*
80855 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
80903 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
80938 TGGATAAAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:81644 original size:18 final size:18
Alignment explanation
Indices: 81593--81674 Score: 78
Period size: 17 Copynumber: 4.6 Consensus size: 18
81583 TTAATATGTT
* *
81593 TCTGATAACTGTAAAACA
1 TCTGATAACTGAAAAATA
* * *
81611 TCTTATATCTG-TAAATA
1 TCTGATAACTGAAAAATA
81628 TCTGATAACTGAAAAATCA
1 TCTGATAACTGAAAAAT-A
*
81647 TCTGATAAC-AAAAAATA
1 TCTGATAACTGAAAAATA
*
81664 TCTAATAACTG
1 TCTGATAACTG
81675 TAAACATTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
17 22 0.43
18 19 0.37
19 10 0.20
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.32
Consensus pattern (18 bp):
TCTGATAACTGAAAAATA
Found at i:81666 original size:17 final size:18
Alignment explanation
Indices: 81623--81673 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
81613 TTATATCTGT
*
81623 AAATATCTGATAACTGAA
1 AAATATCTGATAACTAAA
81641 AAATCATCTGATAAC-AAA
1 AAAT-ATCTGATAACTAAA
*
81659 AAATATCTAATAACT
1 AAATATCTGATAACT
81674 GTAAACATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 9 0.31
18 10 0.34
19 10 0.34
ACGTcount: A:0.53, C:0.14, G:0.06, T:0.27
Consensus pattern (18 bp):
AAATATCTGATAACTAAA
Found at i:87471 original size:42 final size:40
Alignment explanation
Indices: 87386--87482 Score: 113
Period size: 42 Copynumber: 2.4 Consensus size: 40
87376 TAGTTACAGT
* * **
87386 GGTTTAGAAACTAGGAAGAGGGTTTAGAAACTAGGCATGG
1 GGTTTTGAAACTAGGAAGAGGGTTTAGAAACTAGACAAAG
* *
87426 GGTTTTGAAACTAGGTATAGGGGGTTTAGAAACTAGATAAAG
1 GGTTTTGAAACTAGG-A-AGAGGGTTTAGAAACTAGACAAAG
87468 GGTTTTTGAAACTAG
1 GG-TTTTGAAACTAG
87483 AAAAGGGGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 14 0.29
41 1 0.02
42 21 0.44
43 12 0.25
ACGTcount: A:0.34, C:0.06, G:0.32, T:0.28
Consensus pattern (40 bp):
GGTTTTGAAACTAGGAAGAGGGTTTAGAAACTAGACAAAG
Found at i:87480 original size:21 final size:21
Alignment explanation
Indices: 87424--87494 Score: 90
Period size: 22 Copynumber: 3.4 Consensus size: 21
87414 AACTAGGCAT
* *
87424 GGGGTTTTGAAACTAGGTATAG
1 GGGGTTTTGAAACTAGATA-AA
*
87446 GGGGTTTAGAAACTAGATAAA
1 GGGGTTTTGAAACTAGATAAA
*
87467 GGGTTTTTGAAACTAGA-AAA
1 GGGGTTTTGAAACTAGATAAA
87487 GGGGTTTT
1 GGGGTTTT
87495 CCAAACCAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.23
21 16 0.37
22 17 0.40
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.31
Consensus pattern (21 bp):
GGGGTTTTGAAACTAGATAAA
Found at i:87490 original size:42 final size:40
Alignment explanation
Indices: 87386--87493 Score: 108
Period size: 42 Copynumber: 2.6 Consensus size: 40
87376 TAGTTACAGT
* * * * *
87386 GGTTTAGAAACTAGGAAGAGGGTTTAGAAACTAGGCATGG
1 GGTTTTGAAACTAGAAAGGGGGTTTAGAAACTAGGAAAGG
* *
87426 GGTTTTGAAACTAGGTATAGGGGGTTTAGAAACTAGATAAAGG
1 GGTTTTGAAACTA-G-AAAGGGGGTTTAGAAACTAG-GAAAGG
* *
87469 GTTTTTGAAACTAGAAAAGGGGTTT
1 GGTTTTGAAACTAGAAAGGGGGTTT
87494 TCCAAACCAG
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
40 12 0.22
41 10 0.18
42 18 0.33
43 15 0.27
ACGTcount: A:0.34, C:0.06, G:0.32, T:0.28
Consensus pattern (40 bp):
GGTTTTGAAACTAGAAAGGGGGTTTAGAAACTAGGAAAGG
Found at i:87494 original size:20 final size:20
Alignment explanation
Indices: 87386--87493 Score: 92
Period size: 20 Copynumber: 5.2 Consensus size: 20
87376 TAGTTACAGT
*
87386 GGTTTAGAAACTAG-GAAGAG
1 GGTTTAGAAACTAGAAAAG-G
** *
87406 GGTTTAGAAACTAGGCATGG
1 GGTTTAGAAACTAGAAAAGG
* * *
87426 GGTTTTGAAACTAGGTATAGGG
1 GGTTTAGAAACTA-G-AAAAGG
87448 GGTTTAGAAACTAGATAAAGG
1 GGTTTAGAAACTAGA-AAAGG
* *
87469 GTTTTTGAAACTAGAAAAGG
1 GGTTTAGAAACTAGAAAAGG
87489 GGTTT
1 GGTTT
87494 TCCAAACCAG
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
20 37 0.51
21 20 0.28
22 15 0.21
ACGTcount: A:0.34, C:0.06, G:0.32, T:0.28
Consensus pattern (20 bp):
GGTTTAGAAACTAGAAAAGG
Found at i:87500 original size:21 final size:21
Alignment explanation
Indices: 87455--87500 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
87445 GGGGGTTTAG
**
87455 AAACTAGATAAAGGGTTTTTG
1 AAACTAGATAAAGGGTTTTCC
87476 AAACTAGA-AAAGGGGTTTTCC
1 AAACTAGATAAA-GGGTTTTCC
87497 AAAC
1 AAAC
87501 CAGGCTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (21 bp):
AAACTAGATAAAGGGTTTTCC
Found at i:90280 original size:20 final size:20
Alignment explanation
Indices: 90249--90308 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
90239 CCGTTGGTAC
90249 AAAGGGTTTAGAAACTAGG-
1 AAAGGGTTTAGAAACTAGGT
*
90268 AAAGGGATTTAGAAAGTAGGT
1 AAAGGG-TTTAGAAACTAGGT
*
90289 ATAGTGGTTTAGAAACTAGG
1 AAAG-GGTTTAGAAACTAGG
90309 CAGGGGGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.17
20 12 0.34
21 15 0.43
22 2 0.06
ACGTcount: A:0.40, C:0.03, G:0.32, T:0.25
Consensus pattern (20 bp):
AAAGGGTTTAGAAACTAGGT
Found at i:90332 original size:41 final size:41
Alignment explanation
Indices: 90253--90332 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
90243 TGGTACAAAG
**
90253 GGTTTAGAAACTAGGAAAGGGATTTAGAAAGTAGGTATAGT
1 GGTTTAGAAACTAGGAAAGGGATTTAGAAACCAGGTATAGT
* * * * *
90294 GGTTTAGAAACTAGGCAGGGGGTTTTGAAACCATGTATA
1 GGTTTAGAAACTAGGAAAGGGATTTAGAAACCAGGTATA
90333 AGGGGTTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.35, C:0.06, G:0.31, T:0.28
Consensus pattern (41 bp):
GGTTTAGAAACTAGGAAAGGGATTTAGAAACCAGGTATAGT
Found at i:94770 original size:49 final size:49
Alignment explanation
Indices: 94694--94796 Score: 170
Period size: 49 Copynumber: 2.1 Consensus size: 49
94684 AACCGTTAAA
* * *
94694 GTCGTACACTTTGTTTGTGAGATCGTTAAGGCCTATGTTCCTACCAAAG
1 GTCGTACACTTTGTTGGCGAGAGCGTTAAGGCCTATGTTCCTACCAAAG
*
94743 GTCGTACGCTTTGTTGGCGAGAGCGTTAAGGCCTATGTTCCTACCAAAG
1 GTCGTACACTTTGTTGGCGAGAGCGTTAAGGCCTATGTTCCTACCAAAG
94792 GTCGT
1 GTCGT
94797 TCCTACCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.32
Consensus pattern (49 bp):
GTCGTACACTTTGTTGGCGAGAGCGTTAAGGCCTATGTTCCTACCAAAG
Found at i:94800 original size:16 final size:16
Alignment explanation
Indices: 94779--94815 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
94769 TAAGGCCTAT
94779 GTTCCTACCAAAGGTC
1 GTTCCTACCAAAGGTC
94795 GTTCCTACCAAAGGTC
1 GTTCCTACCAAAGGTC
94811 GTTCC
1 GTTCC
94816 AGTGTTGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.27
Consensus pattern (16 bp):
GTTCCTACCAAAGGTC
Found at i:94836 original size:64 final size:65
Alignment explanation
Indices: 94730--94853 Score: 196
Period size: 64 Copynumber: 1.9 Consensus size: 65
94720 TAAGGCCTAT
**
94730 GTTCCTACCAAAGGTCGTACGCTTTGTTGGCGAGAGCGTTAAGGCCTATGTTCCTACCAAAGGTC
1 GTTCCTACCAAAGGTCGTACGCAGTGTTGGCGAGAGCGTTAAGGCCTATGTTCCTACCAAAGGTC
* * *
94795 GTTCCTACCAAAGGTCGTTC-CAGTGTTGGTGAGAGCGTTAAGGCCTATGTTCCTGCCAA
1 GTTCCTACCAAAGGTCGTACGCAGTGTTGGCGAGAGCGTTAAGGCCTATGTTCCTACCAA
94854 GCAATTTCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
64 35 0.65
65 19 0.35
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (65 bp):
GTTCCTACCAAAGGTCGTACGCAGTGTTGGCGAGAGCGTTAAGGCCTATGTTCCTACCAAAGGTC
Found at i:97797 original size:16 final size:17
Alignment explanation
Indices: 97772--97808 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
97762 TAGTAAGATC
97772 AAAAGAAACTCGAACT-
1 AAAAGAAACTCGAACTG
*
97788 AAAAGTAACTCGAACTG
1 AAAAGAAACTCGAACTG
97805 AAAA
1 AAAA
97809 CAACCAGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.57, C:0.16, G:0.14, T:0.14
Consensus pattern (17 bp):
AAAAGAAACTCGAACTG
Found at i:98707 original size:3 final size:3
Alignment explanation
Indices: 98699--98769 Score: 133
Period size: 3 Copynumber: 23.7 Consensus size: 3
98689 AATATAAATT
*
98699 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
98747 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
98770 TGGATAAAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:99467 original size:35 final size:35
Alignment explanation
Indices: 99425--99509 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 35
99415 TTAATATGTT
* * **
99425 TCTGATAACTGTAAAA-CATCTTATATCTGTAAATA
1 TCTGATAACTGTAAAATCATCTGATAAC-AAAAATA
*
99460 TCTGATAACTGAAAAATCATCTGATAACAAAAATA
1 TCTGATAACTGTAAAATCATCTGATAACAAAAATA
*
99495 TCTAATAACTGTAAA
1 TCTGATAACTGTAAA
99510 CATTTAGAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 33 0.79
36 9 0.21
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (35 bp):
TCTGATAACTGTAAAATCATCTGATAACAAAAATA
Found at i:99483 original size:19 final size:18
Alignment explanation
Indices: 99425--99505 Score: 78
Period size: 17 Copynumber: 4.6 Consensus size: 18
99415 TTAATATGTT
* *
99425 TCTGATAACTGTAAAACA
1 TCTGATAACTGAAAAATA
* * *
99443 TCTTATATCTG-TAAATA
1 TCTGATAACTGAAAAATA
99460 TCTGATAACTGAAAAATCA
1 TCTGATAACTGAAAAAT-A
99479 TCTGATAAC--AAAAATA
1 TCTGATAACTGAAAAATA
*
99495 TCTAATAACTG
1 TCTGATAACTG
99506 TAAACATTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
16 9 0.18
17 19 0.37
18 13 0.25
19 10 0.20
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (18 bp):
TCTGATAACTGAAAAATA
Found at i:99497 original size:16 final size:17
Alignment explanation
Indices: 99455--99503 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
99445 TTATATCTGT
99455 AAATATCTGATAACTGAA
1 AAATATCTGATAAC-GAA
99473 AAATCATCTGATAAC-AA
1 AAAT-ATCTGATAACGAA
*
99490 AAATATCTAATAAC
1 AAATATCTGATAAC
99504 TGTAAACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 9 0.31
17 6 0.21
18 4 0.14
19 10 0.34
ACGTcount: A:0.53, C:0.14, G:0.06, T:0.27
Consensus pattern (17 bp):
AAATATCTGATAACGAA
Found at i:105301 original size:42 final size:40
Alignment explanation
Indices: 105216--105312 Score: 113
Period size: 42 Copynumber: 2.4 Consensus size: 40
105206 TAGTTACAGT
* * **
105216 GGTTTAGAAACTAGGAAGAGGGTTTAGAAACTAGGCATGG
1 GGTTTTGAAACTAGGAAGAGGGTTTAGAAACTAGACAAAG
* *
105256 GGTTTTGAAACTAGGTATAGGGGGTTTAGAAACTAGATAAAG
1 GGTTTTGAAACTAGG-A-AGAGGGTTTAGAAACTAGACAAAG
105298 GGTTTTTGAAACTAG
1 GG-TTTTGAAACTAG
105313 AAAAGGGGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 14 0.29
41 1 0.02
42 21 0.44
43 12 0.25
ACGTcount: A:0.34, C:0.06, G:0.32, T:0.28
Consensus pattern (40 bp):
GGTTTTGAAACTAGGAAGAGGGTTTAGAAACTAGACAAAG
Found at i:105310 original size:21 final size:21
Alignment explanation
Indices: 105254--105324 Score: 90
Period size: 22 Copynumber: 3.4 Consensus size: 21
105244 AACTAGGCAT
* *
105254 GGGGTTTTGAAACTAGGTATAG
1 GGGGTTTTGAAACTAGATA-AA
*
105276 GGGGTTTAGAAACTAGATAAA
1 GGGGTTTTGAAACTAGATAAA
*
105297 GGGTTTTTGAAACTAGA-AAA
1 GGGGTTTTGAAACTAGATAAA
105317 GGGGTTTT
1 GGGGTTTT
105325 CCAAACCAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.23
21 16 0.37
22 17 0.40
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.31
Consensus pattern (21 bp):
GGGGTTTTGAAACTAGATAAA
Found at i:105320 original size:42 final size:40
Alignment explanation
Indices: 105216--105323 Score: 108
Period size: 42 Copynumber: 2.6 Consensus size: 40
105206 TAGTTACAGT
* * * * *
105216 GGTTTAGAAACTAGGAAGAGGGTTTAGAAACTAGGCATGG
1 GGTTTTGAAACTAGAAAGGGGGTTTAGAAACTAGGAAAGG
* *
105256 GGTTTTGAAACTAGGTATAGGGGGTTTAGAAACTAGATAAAGG
1 GGTTTTGAAACTA-G-AAAGGGGGTTTAGAAACTAG-GAAAGG
* *
105299 GTTTTTGAAACTAGAAAAGGGGTTT
1 GGTTTTGAAACTAGAAAGGGGGTTT
105324 TCCAAACCAG
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
40 12 0.22
41 10 0.18
42 18 0.33
43 15 0.27
ACGTcount: A:0.34, C:0.06, G:0.32, T:0.28
Consensus pattern (40 bp):
GGTTTTGAAACTAGAAAGGGGGTTTAGAAACTAGGAAAGG
Found at i:105324 original size:20 final size:20
Alignment explanation
Indices: 105216--105323 Score: 92
Period size: 20 Copynumber: 5.2 Consensus size: 20
105206 TAGTTACAGT
*
105216 GGTTTAGAAACTAG-GAAGAG
1 GGTTTAGAAACTAGAAAAG-G
** *
105236 GGTTTAGAAACTAGGCATGG
1 GGTTTAGAAACTAGAAAAGG
* * *
105256 GGTTTTGAAACTAGGTATAGGG
1 GGTTTAGAAACTA-G-AAAAGG
105278 GGTTTAGAAACTAGATAAAGG
1 GGTTTAGAAACTAGA-AAAGG
* *
105299 GTTTTTGAAACTAGAAAAGG
1 GGTTTAGAAACTAGAAAAGG
105319 GGTTT
1 GGTTT
105324 TCCAAACCAG
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
20 37 0.51
21 20 0.28
22 15 0.21
ACGTcount: A:0.34, C:0.06, G:0.32, T:0.28
Consensus pattern (20 bp):
GGTTTAGAAACTAGAAAAGG
Found at i:105330 original size:21 final size:21
Alignment explanation
Indices: 105285--105330 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
105275 GGGGGTTTAG
**
105285 AAACTAGATAAAGGGTTTTTG
1 AAACTAGATAAAGGGTTTTCC
105306 AAACTAGA-AAAGGGGTTTTCC
1 AAACTAGATAAA-GGGTTTTCC
105327 AAAC
1 AAAC
105331 CAGGCTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (21 bp):
AAACTAGATAAAGGGTTTTCC
Found at i:108109 original size:20 final size:20
Alignment explanation
Indices: 108078--108137 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
108068 CCGTTGGTAC
108078 AAAGGGTTTAGAAACTAGG-
1 AAAGGGTTTAGAAACTAGGT
*
108097 AAAGGGATTTAGAAAGTAGGT
1 AAAGGG-TTTAGAAACTAGGT
*
108118 ATAGTGGTTTAGAAACTAGG
1 AAAG-GGTTTAGAAACTAGG
108138 CAGGGGGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.17
20 12 0.34
21 15 0.43
22 2 0.06
ACGTcount: A:0.40, C:0.03, G:0.32, T:0.25
Consensus pattern (20 bp):
AAAGGGTTTAGAAACTAGGT
Found at i:108161 original size:41 final size:41
Alignment explanation
Indices: 108082--108161 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
108072 TGGTACAAAG
**
108082 GGTTTAGAAACTAGGAAAGGGATTTAGAAAGTAGGTATAGT
1 GGTTTAGAAACTAGGAAAGGGATTTAGAAACCAGGTATAGT
* * * * *
108123 GGTTTAGAAACTAGGCAGGGGGTTTTGAAACCATGTATA
1 GGTTTAGAAACTAGGAAAGGGATTTAGAAACCAGGTATA
108162 AGGGGTTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.35, C:0.06, G:0.31, T:0.28
Consensus pattern (41 bp):
GGTTTAGAAACTAGGAAAGGGATTTAGAAACCAGGTATAGT
Found at i:112598 original size:49 final size:49
Alignment explanation
Indices: 112522--112624 Score: 170
Period size: 49 Copynumber: 2.1 Consensus size: 49
112512 AACCGTTAAA
* * *
112522 GTCGTACACTTTGTTTGTGAGATCGTTAAGGCCTATGTTCCTACCAAAG
1 GTCGTACACTTTGTTGGCGAGAGCGTTAAGGCCTATGTTCCTACCAAAG
*
112571 GTCGTACGCTTTGTTGGCGAGAGCGTTAAGGCCTATGTTCCTACCAAAG
1 GTCGTACACTTTGTTGGCGAGAGCGTTAAGGCCTATGTTCCTACCAAAG
112620 GTCGT
1 GTCGT
112625 TCCTACCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.32
Consensus pattern (49 bp):
GTCGTACACTTTGTTGGCGAGAGCGTTAAGGCCTATGTTCCTACCAAAG
Found at i:112628 original size:16 final size:16
Alignment explanation
Indices: 112607--112643 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
112597 TAAGGCCTAT
112607 GTTCCTACCAAAGGTC
1 GTTCCTACCAAAGGTC
112623 GTTCCTACCAAAGGTC
1 GTTCCTACCAAAGGTC
112639 GTTCC
1 GTTCC
112644 AGTGTTGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.27
Consensus pattern (16 bp):
GTTCCTACCAAAGGTC
Found at i:112664 original size:64 final size:65
Alignment explanation
Indices: 112558--112681 Score: 196
Period size: 64 Copynumber: 1.9 Consensus size: 65
112548 TAAGGCCTAT
**
112558 GTTCCTACCAAAGGTCGTACGCTTTGTTGGCGAGAGCGTTAAGGCCTATGTTCCTACCAAAGGTC
1 GTTCCTACCAAAGGTCGTACGCAGTGTTGGCGAGAGCGTTAAGGCCTATGTTCCTACCAAAGGTC
* * *
112623 GTTCCTACCAAAGGTCGTTC-CAGTGTTGGTGAGAGCGTTAAGGCCTATGTTCCTGCCAA
1 GTTCCTACCAAAGGTCGTACGCAGTGTTGGCGAGAGCGTTAAGGCCTATGTTCCTACCAA
112682 GCAATTTCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
64 35 0.65
65 19 0.35
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (65 bp):
GTTCCTACCAAAGGTCGTACGCAGTGTTGGCGAGAGCGTTAAGGCCTATGTTCCTACCAAAGGTC
Found at i:115621 original size:16 final size:17
Alignment explanation
Indices: 115596--115632 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
115586 TAGTAAGATC
115596 AAAAGAAACTCGAACT-
1 AAAAGAAACTCGAACTG
*
115612 AAAAGTAACTCGAACTG
1 AAAAGAAACTCGAACTG
115629 AAAA
1 AAAA
115633 CAACCAGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.57, C:0.16, G:0.14, T:0.14
Consensus pattern (17 bp):
AAAAGAAACTCGAACTG
Found at i:116380 original size:105 final size:108
Alignment explanation
Indices: 116178--116392 Score: 375
Period size: 106 Copynumber: 2.0 Consensus size: 108
116168 TTATATTAAT
116178 TGGTATTAGAGATTAGGCGATTAAATAAGAAGTTAATTTTCTCTCTCCCGGGTTAGTATTAAAAA
1 TGGTATTAGAGATTAGGCGATTAAATAAGAAGTT-ATTTTCTCTCTCCCGGGTTAGTATTAAAAA
116243 ATTAAAAAAAATCAAAAGCAAAATTTTTAAAGATGGAAGAAGCAA
65 ATTAAAAAAAATCAAAAGCAAAATTTTTAAAGATGG-AGAAGCAA
*
116288 TGGTATTAGAGATTAGGCGATT-AATAAGAAGTT-TTTTTTCTCTCCC-GGTTAGTATTAAAAAA
1 TGGTATTAGAGATTAGGCGATTAAATAAGAAGTTATTTTCTCTCTCCCGGGTTAGTATTAAAAAA
116350 TTAAAAAAAATC-AAAGCAAAATTTTTAAAGATGGAGAAGCAA
66 TTAAAAAAAATCAAAAGCAAAATTTTTAAAGATGGAGAAGCAA
116392 T
1 T
116393 CTTTCAGCTT
Statistics
Matches: 104, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
104 9 0.09
105 22 0.21
106 28 0.27
107 12 0.12
109 11 0.11
110 22 0.21
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (108 bp):
TGGTATTAGAGATTAGGCGATTAAATAAGAAGTTATTTTCTCTCTCCCGGGTTAGTATTAAAAAA
TTAAAAAAAATCAAAAGCAAAATTTTTAAAGATGGAGAAGCAA
Found at i:117391 original size:14 final size:14
Alignment explanation
Indices: 117368--117402 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
117358 TAATTGGAGA
*
117368 TGAAACGTTGAAGT
1 TGAAAAGTTGAAGT
*
117382 TGAAAAGTTGGAGT
1 TGAAAAGTTGAAGT
117396 TGAAAAG
1 TGAAAAG
117403 AATGAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.31, T:0.26
Consensus pattern (14 bp):
TGAAAAGTTGAAGT
Found at i:118269 original size:19 final size:20
Alignment explanation
Indices: 118239--118308 Score: 94
Period size: 19 Copynumber: 3.7 Consensus size: 20
118229 TGTACAGTTG
*
118239 AAATGTATAATAAATAAAAT
1 AAATATATAATAAATAAAAT
*
118259 AAATA-ATAATAAATAAAAG
1 AAATATATAATAAATAAAAT
118278 AAA-ATATAATAAAT--AAT
1 AAATATATAATAAATAAAAT
118295 AAATATATAATAAA
1 AAATATATAATAAA
118309 GATAAAAGGG
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
17 5 0.11
18 11 0.24
19 25 0.56
20 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (20 bp):
AAATATATAATAAATAAAAT
Found at i:119096 original size:17 final size:17
Alignment explanation
Indices: 119063--119097 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
119053 TAAAAATAAT
*
119063 ATCCTAAACTTAATTAA
1 ATCCTAAACCTAATTAA
*
119080 ATCCTAAACCTATTTAA
1 ATCCTAAACCTAATTAA
119097 A
1 A
119098 CTAAATACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (17 bp):
ATCCTAAACCTAATTAA
Found at i:121213 original size:55 final size:53
Alignment explanation
Indices: 121147--121255 Score: 155
Period size: 55 Copynumber: 2.0 Consensus size: 53
121137 CATAACCATA
*
121147 CAACCCGTCACGAACAGTAAGGCCCTGAGCACAAAGCCAAGGAACCTACAAGTT
1 CAACCCGTCACGAACAGTAAGGCCCTCAGCACAAAGCCAAGG-ACCTACAAGTT
* ** *
121201 CAACCCTGTCACGAACAGTAAGGCTCTCAGCACAAAGCTGAGGACCTGCAAGTT
1 CAACCC-GTCACGAACAGTAAGGCCCTCAGCACAAAGCCAAGGACCTACAAGTT
121255 C
1 C
121256 TTCTTCTCTA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
54 17 0.35
55 32 0.65
ACGTcount: A:0.34, C:0.31, G:0.21, T:0.14
Consensus pattern (53 bp):
CAACCCGTCACGAACAGTAAGGCCCTCAGCACAAAGCCAAGGACCTACAAGTT
Done.