Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000344.1 Hibiscus syriacus cultivar Beakdansim tig00000635_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: 189575
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:260 original size:35 final size:37
Alignment explanation
Indices: 186--261 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 37
176 AACAAGTTAA
* *
186 AAAATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAATTTATATATTTTCTTTAAAAAATTAAAAATCAT
* *
223 AAAATTTATATA-TTTGTTTACAAAATTAAAAAT-AT
1 AAAATTTATATATTTTCTTTAAAAAATTAAAAATCAT
258 AAAA
1 AAAA
262 AAGTTTAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 6 0.17
36 17 0.49
37 12 0.34
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (37 bp):
AAAATTTATATATTTTCTTTAAAAAATTAAAAATCAT
Found at i:4940 original size:21 final size:22
Alignment explanation
Indices: 4916--4961 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
4906 TATTTATTGA
4916 ACTCAATTATTTCTTCG-TTTC
1 ACTCAATTATTTCTTCGTTTTC
*
4937 ACTCGATTATTTCTTCGTTTTC
1 ACTCAATTATTTCTTCGTTTTC
4959 ACT
1 ACT
4962 GTTTCTCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.52
Consensus pattern (22 bp):
ACTCAATTATTTCTTCGTTTTC
Found at i:13253 original size:13 final size:13
Alignment explanation
Indices: 13235--13261 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13225 CATAGTTAAA
13235 CAGTCTTCATATG
1 CAGTCTTCATATG
13248 CAGTCTTCATATG
1 CAGTCTTCATATG
13261 C
1 C
13262 GCGTCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:14220 original size:2 final size:2
Alignment explanation
Indices: 14213--14249 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
14203 GATAAAACTA
14213 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14250 ATTTATGTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15765 original size:14 final size:14
Alignment explanation
Indices: 15733--15759 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
15723 GAATGAACAT
15733 AAACGAACATAACG
1 AAACGAACATAACG
15747 AAACGAACATAAC
1 AAACGAACATAAC
15760 CGAACGTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.22, G:0.11, T:0.07
Consensus pattern (14 bp):
AAACGAACATAACG
Found at i:19855 original size:20 final size:21
Alignment explanation
Indices: 19830--19891 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
19820 ATGAGACCCA
19830 ATTTCTCTCATTTTC-TATTC
1 ATTTCTCTCATTTTCTTATTC
19850 ATTTCTCT-ATTTTCTTATTC
1 ATTTCTCTCATTTTCTTATTC
* *
19870 TTTTATCTCCATTTTTCTTATT
1 ATTTCTCT-CA-TTTTCTTATT
19892 GTGATTGGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
19 6 0.17
20 19 0.53
22 1 0.03
23 10 0.28
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTCTCTCATTTTCTTATTC
Found at i:20819 original size:2 final size:2
Alignment explanation
Indices: 20812--20849 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
20802 AGTCTGTCCA
20812 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
20850 GCAACGACCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:23143 original size:20 final size:20
Alignment explanation
Indices: 23103--23140 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23093 ATTCTTTTAC
23103 TATTTATATTATATTATAAT
1 TATTTATATTATATTATAAT
*
23123 TATTTATTTTAT-TTATAA
1 TATTTATATTATATTATAA
23141 ATTTAGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTATATTATATTATAAT
Found at i:23285 original size:34 final size:33
Alignment explanation
Indices: 23245--23318 Score: 130
Period size: 34 Copynumber: 2.2 Consensus size: 33
23235 TAAATATGTT
23245 TTTTTTTTGTCTAAACTCATTTTCCGAAACTAA
1 TTTTTTTTGTCTAAACTCATTTTCCGAAACTAA
*
23278 TATTTTTTTGTCTAAACTCATTTTCCGAAACTCA
1 T-TTTTTTTGTCTAAACTCATTTTCCGAAACTAA
23312 TTTTTTT
1 TTTTTTT
23319 AATTCTGAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
33 7 0.18
34 32 0.82
ACGTcount: A:0.24, C:0.18, G:0.05, T:0.53
Consensus pattern (33 bp):
TTTTTTTTGTCTAAACTCATTTTCCGAAACTAA
Found at i:25991 original size:69 final size:69
Alignment explanation
Indices: 25875--26028 Score: 249
Period size: 69 Copynumber: 2.2 Consensus size: 69
25865 TCTCTGGTAT
*
25875 AGTGACTGGGAAGAAAGCAAAACTGGAATGCATCCAAATTTATAACCTTGCCCATGTTGATCAAA
1 AGTGACTGGGAAGAAAGCAAAACTGGAATACATCCAAATTTATAACCTTGCCCATGTTGATCAAA
25940 GAAG
66 GAAG
* *
25944 AGTGGCTGGGAAGAAAGCAAAACTGGAATATAT-CAAGATTTATAACCTTGCCCATGTTGATCAA
1 AGTGACTGGGAAGAAAGCAAAACTGGAATACATCCAA-ATTTATAACCTTGCCCATGTTGATCAA
26008 AGAAG
65 AGAAG
26013 AGTGACTGAGG-AGAAA
1 AGTGACTG-GGAAGAAA
26029 CAGATTCAGG
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
68 3 0.04
69 74 0.94
70 2 0.03
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (69 bp):
AGTGACTGGGAAGAAAGCAAAACTGGAATACATCCAAATTTATAACCTTGCCCATGTTGATCAAA
GAAG
Found at i:32760 original size:17 final size:18
Alignment explanation
Indices: 32738--32771 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
32728 TTAGCCATTC
*
32738 AATAAAATTATT-TTTAA
1 AATAAAAATATTATTTAA
32755 AATAAAAATATTATTTA
1 AATAAAAATATTATTTA
32772 TATATTACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATAAAAATATTATTTAA
Found at i:33230 original size:19 final size:16
Alignment explanation
Indices: 33196--33226 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33186 TACAAAATCT
33196 AATAATTCATAATATA
1 AATAATTCATAATATA
*
33212 AATAATTCATTATAT
1 AATAATTCATAATAT
33227 TATATACATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATTCATAATATA
Found at i:34026 original size:18 final size:18
Alignment explanation
Indices: 34003--34038 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
33993 ATGAGGAGCA
34003 GGGTTTTACTTCTACTTC
1 GGGTTTTACTTCTACTTC
34021 GGGTTTTACTTCTACTTC
1 GGGTTTTACTTCTACTTC
34039 CTATTCCTGC
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:0.11, C:0.22, G:0.17, T:0.50
Consensus pattern (18 bp):
GGGTTTTACTTCTACTTC
Found at i:36927 original size:21 final size:21
Alignment explanation
Indices: 36880--36928 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
36870 TGAAAGGAAT
*
36880 GTGCAACCAACATAACAAAGA
1 GTGCATCCAACATAACAAAGA
36901 GTGCATCCAACATAACAAAGA
1 GTGCATCCAACATAACAAAGA
36922 GTGCATC
1 GTGCATC
36929 AAGCACAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.14
Consensus pattern (21 bp):
GTGCATCCAACATAACAAAGA
Found at i:41927 original size:22 final size:22
Alignment explanation
Indices: 41902--41948 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
41892 GTACCGAATT
*
41902 GCGATTTTGAAACGATCCGATC
1 GCGATTTTGAAACGATCCGAAC
41924 GCGATTTTGAAACGATCCGAAC
1 GCGATTTTGAAACGATCCGAAC
41946 GCG
1 GCG
41949 TTCGTACCGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (22 bp):
GCGATTTTGAAACGATCCGAAC
Found at i:46061 original size:6 final size:6
Alignment explanation
Indices: 46032--46076 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
46022 ATTTTTAACC
* *
46032 ATTTTA ATTTTCA ATATTA CATTTTA ATTTTA CTTTTA ATTTTA A
1 ATTTTA ATTTT-A ATTTTA -ATTTTA ATTTTA ATTTTA ATTTTA A
46077 AAAATATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 23 0.70
7 10 0.30
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (6 bp):
ATTTTA
Found at i:52581 original size:35 final size:35
Alignment explanation
Indices: 52535--52607 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
52525 CTTCTGCCAC
52535 TTTTAATATAGTATGTCTGCATATTTTTGTTATTT
1 TTTTAATATAGTATGTCTGCATATTTTTGTTATTT
52570 TTTTAATATAGTATGTCTGCATATTTTTGTTATTT
1 TTTTAATATAGTATGTCTGCATATTTTTGTTATTT
52605 TTT
1 TTT
52608 ATTTAAAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.22, C:0.05, G:0.11, T:0.62
Consensus pattern (35 bp):
TTTTAATATAGTATGTCTGCATATTTTTGTTATTT
Found at i:59492 original size:31 final size:31
Alignment explanation
Indices: 59454--59518 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
59444 AGAGTCGAGG
*
59454 GTTTACCTATG-TCTTTCGGGACATATGGACA
1 GTTTACCTAGGTTC-TTCGGGACATATGGACA
*
59485 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGGGACATATGGACA
59516 GTT
1 GTT
59519 GCCGAGGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGGGACATATGGACA
Found at i:59529 original size:30 final size:31
Alignment explanation
Indices: 59468--59530 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
59458 ACCTATGTCT
*
59468 TTCGGGACATATGGACAGTTTACCTAGGTTC
1 TTCGGGACATATGGACAGTTTACCGAGGTTC
* *
59499 TTCGGGACCTATGGACAG-TTGCCGAGGTTC
1 TTCGGGACATATGGACAGTTTACCGAGGTTC
59529 TT
1 TT
59531 TATGACCTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.32
Consensus pattern (31 bp):
TTCGGGACATATGGACAGTTTACCGAGGTTC
Found at i:59538 original size:30 final size:31
Alignment explanation
Indices: 59472--59543 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 31
59462 ATGTCTTTCG
* * *
59472 GGACATATGGACAGTTTACCTAGGTTCTTCG
1 GGACCTATGGACAGTTTACCGAGGTTCTTCA
* *
59503 GGACCTATGGACAG-TTGCCGAGGTTCTTTA
1 GGACCTATGGACAGTTTACCGAGGTTCTTCA
*
59533 TGACCTATGGA
1 GGACCTATGGA
59544 TAGGTCCTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 22 0.63
31 13 0.37
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (31 bp):
GGACCTATGGACAGTTTACCGAGGTTCTTCA
Found at i:60251 original size:21 final size:21
Alignment explanation
Indices: 60225--60265 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
60215 GAAATTTTAG
*
60225 TGCATCGGTGCACTGTAGCAA
1 TGCATCGATGCACTGTAGCAA
*
60246 TGCATCGATGGACTGTAGCA
1 TGCATCGATGCACTGTAGCA
60266 CTGTTCATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (21 bp):
TGCATCGATGCACTGTAGCAA
Found at i:65442 original size:30 final size:31
Alignment explanation
Indices: 65381--65443 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
65371 ATCTATGTCT
* *
65381 TTCGGGACATATGGACAATTTACCTAGGTTC
1 TTCGGGACATATGGACAAGTTACCGAGGTTC
* *
65412 TTCGGGACCTATGGAC-AGTTGCCGAGGTTC
1 TTCGGGACATATGGACAAGTTACCGAGGTTC
65442 TT
1 TT
65444 TATGACCTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 13 0.46
31 15 0.54
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.32
Consensus pattern (31 bp):
TTCGGGACATATGGACAAGTTACCGAGGTTC
Found at i:73154 original size:2 final size:2
Alignment explanation
Indices: 73147--73175 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
73137 AAACAAGCAG
73147 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73176 CATTGCCGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:84683 original size:96 final size:96
Alignment explanation
Indices: 84519--84715 Score: 367
Period size: 96 Copynumber: 2.1 Consensus size: 96
84509 GGCTAGAAAT
84519 TTGAAAATTAGGTAAGTAATTGTAATTTTAAATTTTGTTGCGGAAGACGGTTATCGGATAGAGCA
1 TTGAAAATTAGGTAAGTAATTGTAATTTTAAATTTTGTTGCGGAAGACGGTTATCGGATAGAGCA
84584 AAATCGCAACTGATAATTTGAGAAAATAAAA
66 AAATCGCAACTGATAATTTGAGAAAATAAAA
*
84615 TTGAAAATTAGGTAAGTAATTGTAATTTTAAATTTTGTTGCGGAAGACGGTTATCGGATAGAGTA
1 TTGAAAATTAGGTAAGTAATTGTAATTTTAAATTTTGTTGCGGAAGACGGTTATCGGATAGAGCA
*
84680 AAATTGCAACTGATAATTTGAGAAAATAAAA
66 AAATCGCAACTGATAATTTGAGAAAATAAAA
*
84711 ATGAA
1 TTGAA
84716 GATAAAAGAG
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (96 bp):
TTGAAAATTAGGTAAGTAATTGTAATTTTAAATTTTGTTGCGGAAGACGGTTATCGGATAGAGCA
AAATCGCAACTGATAATTTGAGAAAATAAAA
Found at i:86873 original size:23 final size:23
Alignment explanation
Indices: 86847--86947 Score: 103
Period size: 23 Copynumber: 4.3 Consensus size: 23
86837 CACCACAGCT
*
86847 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGTAGTGCCA
* *
86870 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGTAGTGCCA
* ** *
86893 CGTCGAATTGCACCGTAGTGCCG
1 CATATAATTGCACCGTAGTGCCA
* *
86916 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGTAGTGCCA
*
86939 TATAATAAT
1 CAT-ATAAT
86948 GTTCGTAAGG
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
23 62 0.94
24 4 0.06
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGTAGTGCCA
Found at i:87133 original size:103 final size:103
Alignment explanation
Indices: 86954--87274 Score: 556
Period size: 103 Copynumber: 3.1 Consensus size: 103
86944 TAATGTTCGT
*
86954 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTCACCA
*
87019 GACTTTACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
87057 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTCACCA
*
87122 GACTTCACACATGTTCCAAAGAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
87160 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCA-AGGATCAAGTA-GTTGTCTCAC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGA-GATCAAGTATG-TGTCTCAC
87223 CAGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
64 CAGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
87263 ATGGACCACATA
1 AAGGACCACATA
87275 GACCCTCGAC
Statistics
Matches: 209, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
102 2 0.01
103 207 0.99
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:91053 original size:21 final size:21
Alignment explanation
Indices: 91029--91073 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
91019 AAATGACCGG
* *
91029 ATTAACATAATATTTTAGGTA
1 ATTAACAGAAAATTTTAGGTA
*
91050 ATTACCAGAAAATTTTAGGTA
1 ATTAACAGAAAATTTTAGGTA
91071 ATT
1 ATT
91074 TTTACCGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (21 bp):
ATTAACAGAAAATTTTAGGTA
Found at i:98544 original size:22 final size:22
Alignment explanation
Indices: 98516--98570 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
98506 CAGTCTACAA
98516 GCAATCAGAAACCTTAGCAAAT
1 GCAATCAGAAACCTTAGCAAAT
98538 GCAATCAGAAACCTTAGCAAAT
1 GCAATCAGAAACCTTAGCAAAT
98560 GCAATCAGAAA
1 GCAATCAGAAA
98571 ATATGTTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.47, C:0.22, G:0.15, T:0.16
Consensus pattern (22 bp):
GCAATCAGAAACCTTAGCAAAT
Found at i:103930 original size:64 final size:64
Alignment explanation
Indices: 103861--103984 Score: 164
Period size: 64 Copynumber: 1.9 Consensus size: 64
103851 TAATGAAGGT
* *
103861 ATGCATCGATGCACT-ACTTGTGCATCGGTGCA-TAAAATGCATTCGATGTTT-TATTATTAATG
1 ATGCATCGATGCA-TGACTTATGCATCGATGCACT-AAATGCATTCGATGTTTATATT-TTAATG
103923 GA
63 GA
* *
103925 ATGCATCGATGCATGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTATATTTTAA
1 ATGCATCGATGCATGACTTATGCATCGATGCACTAAATGCATTCGATGTTTATATTTTAA
103985 ACAATTTATG
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
63 1 0.02
64 47 0.89
65 5 0.09
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (64 bp):
ATGCATCGATGCATGACTTATGCATCGATGCACTAAATGCATTCGATGTTTATATTTTAATGGA
Found at i:112261 original size:35 final size:34
Alignment explanation
Indices: 112176--112262 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
112166 ATTTTGTATT
*
112176 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
112210 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
112248 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
112263 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:112503 original size:18 final size:18
Alignment explanation
Indices: 112477--112524 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
112467 TCCTCGCTGT
*
112477 CATCATCGTCGTCGTCAC
1 CATCGTCGTCGTCGTCAC
112495 CATCGTCGTCGTCGTCAC
1 CATCGTCGTCGTCGTCAC
*
112513 CATCGTCATCGT
1 CATCGTCGTCGT
112525 TGTCGTAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.38, G:0.19, T:0.29
Consensus pattern (18 bp):
CATCGTCGTCGTCGTCAC
Found at i:112524 original size:15 final size:15
Alignment explanation
Indices: 112475--112507 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
112465 ACTCCTCGCT
*
112475 GTCATCATCGTCGTC
1 GTCACCATCGTCGTC
112490 GTCACCATCGTCGTC
1 GTCACCATCGTCGTC
112505 GTC
1 GTC
112508 GTCACCATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.36, G:0.21, T:0.30
Consensus pattern (15 bp):
GTCACCATCGTCGTC
Found at i:114593 original size:111 final size:111
Alignment explanation
Indices: 114399--114731 Score: 567
Period size: 111 Copynumber: 3.0 Consensus size: 111
114389 ATTACAAAAA
*
114399 TTAATTCTTATTCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
114464 AATTAAAACGTTAAAATGTTACTGTATTAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
114510 TTAATTCTTAAACTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * * *
114575 AATTAAAACATTAAAATGTTACCGTATCAACAAAATGTCGAGATGT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
114621 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
114686 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTATAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
114732 ATGATTTCCA
Statistics
Matches: 206, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 206 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:114884 original size:20 final size:20
Alignment explanation
Indices: 114859--114913 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
114849 TAAAAAGAGG
114859 GAGTATTTGAGAGAAATTTA
1 GAGTATTTGAGAGAAATTTA
114879 GAGTATTTGAGAGAAATTTA
1 GAGTATTTGAGAGAAATTTA
*
114899 GA-TAAATTGAGAGAA
1 GAGT-ATTTGAGAGAA
114914 TTTGGTGTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (20 bp):
GAGTATTTGAGAGAAATTTA
Found at i:115347 original size:19 final size:19
Alignment explanation
Indices: 115319--115366 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
115309 AACTAAATCG
115319 CAATGCGATCGATAATTCA
1 CAATGCGATCGATAATTCA
* *
115338 CAATGTGATCGATAATTCG
1 CAATGCGATCGATAATTCA
*
115357 CAACGCGATC
1 CAATGCGATC
115367 TTCGGTATCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (19 bp):
CAATGCGATCGATAATTCA
Found at i:115423 original size:21 final size:21
Alignment explanation
Indices: 115397--115440 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
115387 TCCAGATTCA
115397 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTTCGACTATCG
115418 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTTCGACTATCG
115439 CA
1 CA
115441 TTGCAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.34, G:0.18, T:0.18
Consensus pattern (21 bp):
CAACGCGAACTTCGACTATCG
Found at i:115485 original size:21 final size:21
Alignment explanation
Indices: 115455--115545 Score: 107
Period size: 21 Copynumber: 4.4 Consensus size: 21
115445 AATTTACATA
*
115455 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
115476 TTCGCGTTGCGATAG-CCGAAG
1 TTCGCGTTGCGATAGTCC-AAG
* ** *
115497 TTCGCATTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
115518 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
115537 TTCGCGTTG
1 TTCGCGTTG
115546 AGCCTTAAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
19 15 0.26
20 2 0.04
21 38 0.67
22 2 0.04
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:116098 original size:19 final size:19
Alignment explanation
Indices: 116074--116114 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
116064 TCTTTTTAAA
116074 GAACTTCGACTATCACAAC
1 GAACTTCGACTATCACAAC
* *
116093 GAACTTGGACTATCGCAAC
1 GAACTTCGACTATCACAAC
116112 GAA
1 GAA
116115 TTTATAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.20
Consensus pattern (19 bp):
GAACTTCGACTATCACAAC
Found at i:116171 original size:20 final size:20
Alignment explanation
Indices: 116146--116197 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
116136 AATTTGGACT
116146 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
116166 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
116186 ATCGCAATGCGA
1 ATCGCAATGCGA
116198 TAGTCGAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:117135 original size:3 final size:3
Alignment explanation
Indices: 117127--117152 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
117117 ATAGGTATGC
117127 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
117153 GAGGAGGAGG
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:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:119546 original size:30 final size:30
Alignment explanation
Indices: 119512--119570 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
119502 CAGTTTCTTG
* **
119512 GGCTGATCAGCAATAGATGGAGAAGAATCT
1 GGCTGATCAGCAAAAGACAGAGAAGAATCT
119542 GGCTGATCAGCAAAAGACAGAGAAGAATC
1 GGCTGATCAGCAAAAGACAGAGAAGAATC
119571 AGTCATTCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.15, G:0.29, T:0.15
Consensus pattern (30 bp):
GGCTGATCAGCAAAAGACAGAGAAGAATCT
Found at i:121707 original size:39 final size:39
Alignment explanation
Indices: 121664--121763 Score: 173
Period size: 39 Copynumber: 2.6 Consensus size: 39
121654 CTTGGGTCAA
121664 CAACTGAGATTTTTCTTCAGTGTATGCCATAGGTATAAG
1 CAACTGAGATTTTTCTTCAGTGTATGCCATAGGTATAAG
* *
121703 CAACTGAGATTTTTCTTCATTGTATGCCATAGGTGTAAG
1 CAACTGAGATTTTTCTTCAGTGTATGCCATAGGTATAAG
*
121742 CAACTGAAATTTTTCTTCAGTG
1 CAACTGAGATTTTTCTTCAGTG
121764 CACTCTTTCG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (39 bp):
CAACTGAGATTTTTCTTCAGTGTATGCCATAGGTATAAG
Found at i:124858 original size:18 final size:17
Alignment explanation
Indices: 124837--124876 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
124827 CCAAAAAAGC
124837 ACCAGAAGGAAAAACGGA
1 ACCAG-AGGAAAAACGGA
*
124855 ACCAGCGGAAAAACGGA
1 ACCAGAGGAAAAACGGA
124872 ACCAG
1 ACCAG
124877 CTAAGGGGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.50, C:0.23, G:0.28, T:0.00
Consensus pattern (17 bp):
ACCAGAGGAAAAACGGA
Found at i:124864 original size:17 final size:17
Alignment explanation
Indices: 124844--124877 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
124834 AGCACCAGAA
124844 GGAAAAACGGAACCAGC
1 GGAAAAACGGAACCAGC
124861 GGAAAAACGGAACCAGC
1 GGAAAAACGGAACCAGC
124878 TAAGGGGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.24, G:0.29, T:0.00
Consensus pattern (17 bp):
GGAAAAACGGAACCAGC
Found at i:125181 original size:25 final size:22
Alignment explanation
Indices: 125128--125178 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
125118 AAGTTACTGT
*
125128 TTTTATTTAATAAAAATAATAG
1 TTTTATTGAATAAAAATAATAG
*
125150 TTTTATTGAATAAAAATAATAT
1 TTTTATTGAATAAAAATAATAG
125172 TTTTATT
1 TTTTATT
125179 ATTATTTCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
TTTTATTGAATAAAAATAATAG
Found at i:126211 original size:21 final size:22
Alignment explanation
Indices: 126185--126225 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
126175 CCAGGAAAGG
126185 GAGTATCGGTACTT-CTTTAAT
1 GAGTATCGGTACTTCCTTTAAT
126206 GAGTATCGGTACTTCCTTTA
1 GAGTATCGGTACTTCCTTTA
126226 TAATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (22 bp):
GAGTATCGGTACTTCCTTTAAT
Found at i:128299 original size:20 final size:20
Alignment explanation
Indices: 128270--128309 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
128260 GCTACCTCAT
* *
128270 TCTTCTTCTTATTTTTCTTC
1 TCTTCATCTTATTCTTCTTC
*
128290 TCTTCATCTTCTTCTTCTTC
1 TCTTCATCTTATTCTTCTTC
128310 CTTTACCATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.30, G:0.00, T:0.65
Consensus pattern (20 bp):
TCTTCATCTTATTCTTCTTC
Found at i:129611 original size:21 final size:22
Alignment explanation
Indices: 129585--129625 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
129575 ATAGGATAGG
129585 GAGTATCGATAC-TCCTTTAAT
1 GAGTATCGATACTTCCTTTAAT
129606 GAGTATCGATACTTCCTTTA
1 GAGTATCGATACTTCCTTTA
129626 TAATTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (22 bp):
GAGTATCGATACTTCCTTTAAT
Found at i:130070 original size:15 final size:15
Alignment explanation
Indices: 130050--130079 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
130040 TTCAACAGTC
130050 TTTTAAACAATTTTA
1 TTTTAAACAATTTTA
130065 TTTTAAACAATTTTA
1 TTTTAAACAATTTTA
130080 AGACAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTAAACAATTTTA
Found at i:133962 original size:24 final size:24
Alignment explanation
Indices: 133930--133993 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
133920 TTTTATGATC
* *
133930 GTTTATGTTTGTTTATACTCATTT
1 GTTTGTGTTCGTTTATACTCATTT
** **
133954 GTTTGTGTTCGTTTACGCTTGTTT
1 GTTTGTGTTCGTTTATACTCATTT
133978 GTTTGTGTTCGTTTAT
1 GTTTGTGTTCGTTTAT
133994 CATTTTAACG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.09, C:0.09, G:0.20, T:0.61
Consensus pattern (24 bp):
GTTTGTGTTCGTTTATACTCATTT
Found at i:135774 original size:23 final size:23
Alignment explanation
Indices: 135706--135766 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
135696 ACATCTTATA
* *
135706 TGGCACTACGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
135729 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
135752 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
135767 TTTATACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:136305 original size:3 final size:3
Alignment explanation
Indices: 136297--136378 Score: 164
Period size: 3 Copynumber: 27.3 Consensus size: 3
136287 TTCCTAATTC
136297 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
136345 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
136379 CATGTATATC
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:150283 original size:18 final size:18
Alignment explanation
Indices: 150260--150299 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
150250 GGAATTACAG
150260 TTTCCTAAAAACTATCAT
1 TTTCCTAAAAACTATCAT
150278 TTTCCTAAAAACTATCAT
1 TTTCCTAAAAACTATCAT
150296 TTTC
1 TTTC
150300 AAATGCAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTCCTAAAAACTATCAT
Found at i:164455 original size:21 final size:21
Alignment explanation
Indices: 164376--164456 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
164366 GCACTGAAAT
164376 TTGTCCCGAAGGACCAC--TA
1 TTGTCCCGAAGGACCACTGTA
* *
164395 -TGTCCC-ATAGGACCATTGCA
1 TTGTCCCGA-AGGACCACTGTA
164415 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
*
164436 TTGTCCCGAATGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
164457 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
17 1 0.02
18 13 0.25
20 1 0.02
21 36 0.69
22 1 0.02
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTGTA
Found at i:164954 original size:2 final size:2
Alignment explanation
Indices: 164947--164974 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
164937 CTTATGTAAG
164947 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
164975 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:164979 original size:2 final size:2
Alignment explanation
Indices: 164974--165013 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
164964 ACACACACAC
164974 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
165014 CATACAACGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:165385 original size:21 final size:20
Alignment explanation
Indices: 165356--165394 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
165346 TTTTATTTAC
165356 GGGGGAATC-GATACCCCCAA
1 GGGGGAATCTG-TACCCCCAA
165376 GGGGAGAATCTGTACCCCC
1 GGGG-GAATCTGTACCCCC
165395 TGTACAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.26, C:0.31, G:0.31, T:0.13
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCAA
Found at i:167810 original size:3 final size:3
Alignment explanation
Indices: 167802--167858 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
167792 TGGAGGGGGA
* * * * * * *
167802 GGT GGT GGT GCT GGT GCT GGT GCT GGT GGT GGT GGT GGC GGG GGC GGA
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
167850 GGT GGT GGT
1 GGT GGT GGT
167859 AATTTTGGTT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.02, C:0.09, G:0.63, T:0.26
Consensus pattern (3 bp):
GGT
Found at i:167817 original size:12 final size:12
Alignment explanation
Indices: 167802--167835 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
167792 TGGAGGGGGA
167802 GGTGGTGGTGCT
1 GGTGGTGGTGCT
*
167814 GGTGCTGGTGCT
1 GGTGGTGGTGCT
167826 GGTGGTGGTG
1 GGTGGTGGTG
167836 GTGGCGGGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.09, G:0.59, T:0.32
Consensus pattern (12 bp):
GGTGGTGGTGCT
Found at i:167918 original size:12 final size:12
Alignment explanation
Indices: 167899--167938 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
167889 GGGGGAGGGG
167899 GAGG-TGGGGAT
1 GAGGATGGGGAT
167910 GAGGATGGGGAT
1 GAGGATGGGGAT
* *
167922 GGGGATGGGGAG
1 GAGGATGGGGAT
167934 GAGGA
1 GAGGA
167939 GGAGGAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.23, C:0.00, G:0.65, T:0.12
Consensus pattern (12 bp):
GAGGATGGGGAT
Found at i:172504 original size:33 final size:30
Alignment explanation
Indices: 172456--172560 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 30
172446 TTAGTATATA
172456 ATTAAAATAAAAATAAATTTAAAAGTTAGAGTG
1 ATTAAAATAAAAAT-AA-TTAAAAGTT-GAGTG
* * *
172489 ATTAAAATCAGAATAATTGAAAGTTGAGTG
1 ATTAAAATAAAAATAATTAAAAGTTGAGTG
* * *
172519 ATTAAATTAAAAA-AATT-AAATTTTAGTG
1 ATTAAAATAAAAATAATTAAAAGTTGAGTG
* *
172547 ATCAAAATAGAAAT
1 ATTAAAATAAAAAT
172561 GAAAAAATAA
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
28 19 0.32
29 4 0.07
30 15 0.25
31 8 0.13
32 2 0.03
33 12 0.20
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.31
Consensus pattern (30 bp):
ATTAAAATAAAAATAATTAAAAGTTGAGTG
Found at i:174126 original size:26 final size:26
Alignment explanation
Indices: 174076--174126 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
174066 TAAAATAAGA
* * *
174076 AATAAGTTTATTCATAAAGTGACATT
1 AATAAGTATATTCACAAAGTAACATT
*
174102 AATAAGTATATTCACATAGTAACAT
1 AATAAGTATATTCACAAAGTAACAT
174127 GACTTATGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (26 bp):
AATAAGTATATTCACAAAGTAACATT
Found at i:175414 original size:23 final size:26
Alignment explanation
Indices: 175364--175415 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
175354 TAAAAAACAT
175364 ATATCAATACTATAAAAACAATATTA
1 ATATCAATACTATAAAAACAATATTA
* *
175390 ATATTAATA-TATAATAA-AATA-TA
1 ATATCAATACTATAAAAACAATATTA
175413 ATA
1 ATA
175416 ATACGTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.21
24 4 0.17
25 7 0.29
26 8 0.33
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (26 bp):
ATATCAATACTATAAAAACAATATTA
Found at i:176670 original size:14 final size:14
Alignment explanation
Indices: 176651--176685 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
176641 TCACACAAAA
*
176651 CTCCACTAGTAACC
1 CTCCACTAGCAACC
176665 CTCCACTAGCAACC
1 CTCCACTAGCAACC
176679 CTCCACT
1 CTCCACT
176686 TTAGTCATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.49, G:0.06, T:0.20
Consensus pattern (14 bp):
CTCCACTAGCAACC
Found at i:183795 original size:34 final size:34
Alignment explanation
Indices: 183752--183818 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
183742 CAAACACATG
*
183752 AGATACTAATGCTATTGTAAATACGCAAAAGGTC
1 AGATACTAATGCTATTGAAAATACGCAAAAGGTC
* *
183786 AGATACTAATGTTATTGAAAATACGTAAAAGGT
1 AGATACTAATGCTATTGAAAATACGCAAAAGGT
183819 AATGCTTGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.28
Consensus pattern (34 bp):
AGATACTAATGCTATTGAAAATACGCAAAAGGTC
Found at i:187463 original size:21 final size:21
Alignment explanation
Indices: 187375--187456 Score: 128
Period size: 21 Copynumber: 3.9 Consensus size: 21
187365 AATATGTAAA
*
187375 TCGCAATGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
187396 TCGCACTGCGATAGTCTAAGT
1 TCGCATTGCGATAGTCCAAGT
*
187417 TCGCATTGCGATAATCCAAGT
1 TCGCATTGCGATAGTCCAAGT
187438 TCGCATTGCGATAGTCCAA
1 TCGCATTGCGATAGTCCAA
187457 AATCGCAACG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:187463 original size:42 final size:42
Alignment explanation
Indices: 187372--187464 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
187362 GCGAATATGT
* *
187372 AAATCGCAATGCGATAGTCCAAGTTCGCACTGCGATAGTCTA
1 AAATCGCAATGCGATAATCCAAGTTCGCACTGCGATAGTCCA
** * *
187414 AGTTCGCATTGCGATAATCCAAGTTCGCATTGCGATAGTCCA
1 AAATCGCAATGCGATAATCCAAGTTCGCACTGCGATAGTCCA
187456 AAATCGCAA
1 AAATCGCAA
187465 CGACTGGTTG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (42 bp):
AAATCGCAATGCGATAATCCAAGTTCGCACTGCGATAGTCCA
Found at i:188050 original size:6 final size:6
Alignment explanation
Indices: 188037--188072 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
188027 GCCGTCCGTC
188037 TCGT-G TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
188073 AATACATGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.00, C:0.17, G:0.47, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:188185 original size:19 final size:19
Alignment explanation
Indices: 188161--188197 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
188151 TGCGATTTTG
188161 GACTATCGCAACGAACTTC
1 GACTATCGCAACGAACTTC
188180 GACTATCGCAACGAACTT
1 GACTATCGCAACGAACTT
188198 GGAATAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
GACTATCGCAACGAACTTC
Done.