Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006143.1 Hibiscus syriacus cultivar Beakdansim tig00014578_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: 58502
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:282 original size:22 final size:21
Alignment explanation
Indices: 257--306 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
247 TTGTAAATAT
257 ATTCCAACCAATATGCTCTATC
1 ATTCC-ACCAATATGCTCTATC
* * *
279 ATTCCACCAGTTTGCTCTTTC
1 ATTCCACCAATATGCTCTATC
*
300 ATCCCAC
1 ATTCCAC
307 TTGCAAACGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.24, C:0.36, G:0.06, T:0.34
Consensus pattern (21 bp):
ATTCCACCAATATGCTCTATC
Found at i:941 original size:24 final size:24
Alignment explanation
Indices: 914--1007 Score: 100
Period size: 24 Copynumber: 3.8 Consensus size: 24
904 ATTAGTATCC
*
914 AATCATTATTAAATAATTATTAGT
1 AATCATTATTAAATAATTATTAAT
* * *
938 AATCATTATT-AGTAATCATTACT
1 AATCATTATTAAATAATTATTAAT
961 AAATCATATCATTAAATAATTATTAAT
1 -AATCAT-T-ATTAAATAATTATTAAT
* *
988 AATCATTACTAAATCATTAT
1 AATCATTATTAAATAATTAT
1008 ATCAAATCAT
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
23 10 0.17
24 27 0.47
25 2 0.03
26 9 0.16
27 10 0.17
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.43
Consensus pattern (24 bp):
AATCATTATTAAATAATTATTAAT
Found at i:947 original size:13 final size:11
Alignment explanation
Indices: 914--1019 Score: 86
Period size: 13 Copynumber: 8.7 Consensus size: 11
904 ATTAGTATCC
914 AATCATTATTA
1 AATCATTATTA
*
925 AATAATTATTA
1 AATCATTATTA
936 GTAATCATTATTA
1 --AATCATTATTA
*
949 GTAATCATTACTA
1 --AATCATTATTA
962 AATCATATCATTA
1 AATCAT-T-ATTA
*
975 AATAATTATTAA
1 AATCATTATT-A
*
987 TAATCATTACTA
1 -AATCATTATTA
999 AATCATTATATCA
1 AATCATTAT-T-A
1012 AATCATTA
1 AATCATTA
1020 ATATTAAAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
11 27 0.34
12 5 0.06
13 47 0.59
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (11 bp):
AATCATTATTA
Found at i:1074 original size:15 final size:16
Alignment explanation
Indices: 1044--1074 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1034 CATTATATTA
1044 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
1060 ATCATTACT-AATCAT
1 ATCATTACTAAATCAT
1075 TAAATATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (16 bp):
ATCATTACTAAATCAT
Found at i:4156 original size:47 final size:46
Alignment explanation
Indices: 4078--4172 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 46
4068 CCTTTTGGTG
4078 ATTTTGCATTGAATCTTCTCTCTGAGCCAATTGCATGCCCTATTGT
1 ATTTTGCATTGAATCTTCTCTCTGAGCCAATTGCATGCCCTATTGT
4124 ATTTTGCATTGAATCTTTCTCTCTGAGCCAATTGCATGCCCTATTGT
1 ATTTTGCATTGAATC-TTCTCTCTGAGCCAATTGCATGCCCTATTGT
4171 AT
1 AT
4173 AAGATTTATT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 15 0.31
47 33 0.69
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (46 bp):
ATTTTGCATTGAATCTTCTCTCTGAGCCAATTGCATGCCCTATTGT
Found at i:8546 original size:20 final size:20
Alignment explanation
Indices: 8510--8547 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
8500 AATTTAATTT
*
8510 TCAAATATAGTATTAATAAA
1 TCAAATATAATATTAATAAA
8530 TCAAATAGTAATA-TAATA
1 TCAAATA-TAATATTAATA
8548 TTTAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (20 bp):
TCAAATATAATATTAATAAA
Found at i:21774 original size:42 final size:42
Alignment explanation
Indices: 21674--21757 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
21664 ATTTTAACAA
* *
21674 ACGAACA-TCTGCCTTTAATGAATCCACTTCCGCATATGCTTT
1 ACGAACAGTC-GCCTTCAACGAATCCACTTCCGCATATGCTTT
21716 ACGAACAGTCGCCTTCAACGAATCCACTTCCGCATATGCTTT
1 ACGAACAGTCGCCTTCAACGAATCCACTTCCGCATATGCTTT
21758 TTCTATATCG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 37 0.95
43 2 0.05
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30
Consensus pattern (42 bp):
ACGAACAGTCGCCTTCAACGAATCCACTTCCGCATATGCTTT
Found at i:29894 original size:15 final size:15
Alignment explanation
Indices: 29876--29905 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29866 AAAACCATGT
29876 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
29891 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
29906 GAAATAAATA
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:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:29912 original size:15 final size:15
Alignment explanation
Indices: 29879--29913 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29869 ACCATGTTAG
* *
29879 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
29894 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
29909 ATAAA
1 ATAAA
29914 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:30015 original size:8 final size:8
Alignment explanation
Indices: 29991--30114 Score: 52
Period size: 8 Copynumber: 14.5 Consensus size: 8
29981 AAATAGTAAG
*
29991 TAAAATAA
1 TAAAAAAA
29999 TATAAAAAA
1 TA-AAAAAA
30008 TAAAAAAAA
1 T-AAAAAAA
30017 TAAAGAAAA
1 TAAA-AAAA
* *
30026 -GAAGAAA
1 TAAAAAAA
* *
30033 TAAATATA
1 TAAAAAAA
* *
30041 GAAATAAA
1 TAAAAAAA
* *
30049 CAAATAAA
1 TAAAAAAA
*
30057 TAAAATAA
1 TAAAAAAA
30065 TAATAAAAA
1 TAA-AAAAA
30074 GTAAAAATAGTA
1 -TAAAAA-A--A
*
30086 TATATAAAA
1 TA-AAAAAA
30095 TAAAAAAA
1 TAAAAAAA
*
30103 TAAAAAAG
1 TAAAAAAA
30111 TAAA
1 TAAA
30115 TATATATATA
Statistics
Matches: 90, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
7 3 0.03
8 48 0.53
9 27 0.30
10 5 0.06
11 3 0.03
12 4 0.04
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.19
Consensus pattern (8 bp):
TAAAAAAA
Found at i:30037 original size:20 final size:20
Alignment explanation
Indices: 29993--30060 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
29983 ATAGTAAGTA
29993 AAATAATATAAA-AAAT-AA-
1 AAATAA-ATAAAGAAATAAAC
*
30011 AAA-AAATAAAGAAA-AGAAG
1 AAATAAATAAAGAAATA-AAC
*
30030 AAATAAATATAGAAATAAAC
1 AAATAAATAAAGAAATAAAC
30050 AAATAAATAAA
1 AAATAAATAAA
30061 ATAATAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
16 5 0.12
17 5 0.12
18 5 0.12
19 3 0.07
20 22 0.54
21 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.16
Consensus pattern (20 bp):
AAATAAATAAAGAAATAAAC
Found at i:30066 original size:20 final size:20
Alignment explanation
Indices: 30030--30067 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
30020 AGAAAAGAAG
*
30030 AAATAAATATAGAAATAAAC
1 AAATAAATATAAAAATAAAC
30050 AAATAAATA-AAATAATAA
1 AAATAAATATAAA-AATAA
30068 TAAAAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (20 bp):
AAATAAATATAAAAATAAAC
Found at i:30094 original size:33 final size:32
Alignment explanation
Indices: 30056--30140 Score: 91
Period size: 36 Copynumber: 2.5 Consensus size: 32
30046 AAACAAATAA
30056 ATAAAATAATAATAAAAAGTAAAAATAGTATAT
1 ATAAAATAATAATAAAAAGTAAAAATA-TATAT
* *
30089 ATAAAATAAAAAAATAAAAAAGTAAATATATATAT
1 ATAAAAT--AATAAT-AAAAAGTAAAAATATATAT
*
30124 AT-ATATAATTAATAAAA
1 ATAAAATAA-TAATAAAA
30141 CTGATAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
32 6 0.14
33 10 0.23
34 3 0.07
35 12 0.27
36 13 0.30
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (32 bp):
ATAAAATAATAATAAAAAGTAAAAATATATAT
Found at i:30107 original size:27 final size:30
Alignment explanation
Indices: 30063--30118 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 30
30053 TAAATAAAAT
* *
30063 AATAATAAAAAGTAAAAATAGTATATATAA
1 AATAATAAAAAGTAAAAAAAGTAAATATAA
30093 AATAA-AAAAA-T-AAAAAAGTAAATATA
1 AATAATAAAAAGTAAAAAAAGTAAATATA
30119 TATATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.54
28 1 0.04
29 5 0.21
30 5 0.21
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.23
Consensus pattern (30 bp):
AATAATAAAAAGTAAAAAAAGTAAATATAA
Found at i:30129 original size:41 final size:37
Alignment explanation
Indices: 30084--30191 Score: 108
Period size: 43 Copynumber: 2.7 Consensus size: 37
30074 GTAAAAATAG
*
30084 TATATATAAAATAAAAAAATAAAAAAGTAAATATATATA
1 TATATATAAAATAAAAAAATAAAAAA-T-AATATATTTA
30123 TATATATAATTAATAAAACTGATAATAAAAAATAATATATTTA
1 TATATATAA--AATAAAA---A-AATAAAAAATAATATATTTA
**
30166 TATATATAATCTAAAAAAAATAAAAA
1 TATATATAAAAT-AAAAAAATAAAAA
30192 TATATACTAA
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
38 8 0.14
39 10 0.17
41 8 0.14
42 4 0.07
43 18 0.31
44 2 0.03
45 9 0.15
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (37 bp):
TATATATAAAATAAAAAAATAAAAAATAATATATTTA
Found at i:30242 original size:23 final size:24
Alignment explanation
Indices: 30203--30248 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
30193 ATATACTAAA
30203 GTAAAAAAGAAAATACAT-AAAAT
1 GTAAAAAAGAAAATACATGAAAAT
*
30226 GTAAAAAA-ATAATTACATGAAAA
1 GTAAAAAAGA-AAATACATGAAAA
30249 AAAAGAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 15 0.75
24 4 0.20
ACGTcount: A:0.67, C:0.04, G:0.09, T:0.20
Consensus pattern (24 bp):
GTAAAAAAGAAAATACATGAAAAT
Found at i:30558 original size:37 final size:37
Alignment explanation
Indices: 30517--30621 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
30507 GTACTTGTGG
* * * * *
30517 ATCCTATCTTTAGGATTTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* * *
30554 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
30591 ATCCTATTTTTAGGAGTTTGAATCGTAGTAA
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAA
30622 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:31471 original size:105 final size:105
Alignment explanation
Indices: 31164--31794 Score: 934
Period size: 105 Copynumber: 6.0 Consensus size: 105
31154 GCATTGTTCC
* * *** *
31164 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCAGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * *
31228 ACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
31270 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
31330 CAGCGGTCCTTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
31370 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
31435 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
31475 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
31540 CAGCGGTCCCCTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
31580 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
31645 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
31685 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * *
31750 CCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
31791 GAGT
1 GAGT
31795 GTCACGATAT
Statistics
Matches: 488, Mismatches: 29, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
99 1 0.00
100 82 0.17
101 1 0.00
102 7 0.01
104 5 0.01
105 306 0.63
106 86 0.18
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:32040 original size:36 final size:36
Alignment explanation
Indices: 31993--32068 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
31983 TGTTTGGAGA
* * *
31993 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
32029 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
32065 GAAA
1 GAAA
32069 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:32178 original size:104 final size:104
Alignment explanation
Indices: 31968--32285 Score: 525
Period size: 104 Copynumber: 3.1 Consensus size: 104
31958 TTCGTTAAAT
* ** *
31968 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
32030 AAACTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
32069 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
32134 AAACTATCTCAAGAGAGAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
*
32173 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAATGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
32238 AAACTATCTCAGGAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
32277 TGTTTTCAA
1 TGTTTTCAA
32286 GAGAAACTGT
Statistics
Matches: 203, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
101 46 0.23
103 3 0.01
104 154 0.76
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:32442 original size:36 final size:36
Alignment explanation
Indices: 32409--32516 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 36
32399 GTGAAAACGG
*
32409 TCTCAAGCGAAACAAATCTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAAACAAATCTTGTTTTAAGAAAAACAA
** * * ** *
32445 TCTTGAGTGAAATAAATCTTCTTTCGAGAAAAACAT
1 TCTCAAGTGAAACAAATCTTGTTTTAAGAAAAACAA
* *
32481 TCTCAAGTGAGACAAAGT-ATGTTTTAAGAAAAACAA
1 TCTCAAGTGAAACAAA-TCTTGTTTTAAGAAAAACAA
32517 ATTTGAGTGA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
36 53 0.98
37 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (36 bp):
TCTCAAGTGAAACAAATCTTGTTTTAAGAAAAACAA
Found at i:32504 original size:72 final size:74
Alignment explanation
Indices: 32356--32531 Score: 198
Period size: 72 Copynumber: 2.4 Consensus size: 74
32346 TAAAATCTTC
* ** * *
32356 TTAAAAAAAACAGCCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAAA
1 TTAAGAAAAACAATCTTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAAA
*
32421 CAAATCTTGTT
64 CAAATCATGTT
* * *
32432 TTAAGAAAAACAATCTTGAGTGAAATAAAT-CTTCTTTCGAG-AAAAACATTCTCAAGTGAGACA
1 TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAAACA
32495 AAGT-ATGTT
66 AA-TCATGTT
*
32504 TTAAGAAAAACAAAT-TTGAGTGAGATAA
1 TTAAGAAAAAC-AATCTTGAGTGAAATAA
32532 TCATCTGCAT
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
72 46 0.52
73 15 0.17
75 4 0.05
76 23 0.26
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (74 bp):
TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAAACA
AATCATGTT
Found at i:33980 original size:183 final size:183
Alignment explanation
Indices: 33672--34208 Score: 959
Period size: 183 Copynumber: 2.9 Consensus size: 183
33662 ATCAGGTTTA
* *
33672 ACTGAAGGGTTCATCTCATCCCAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* * **
33737 GCCAAGTATCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
33801 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAAAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAAAGGGACAAATC
*
33855 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
33920 GCCAAGTGTCTGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
33985 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAAAGGGACAAATC
*
34038 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCAAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
34103 GCCAAGTGTCCGAGCAGTATCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
34168 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
34209 CGGATTTAAT
Statistics
Matches: 340, Mismatches: 13, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
183 339 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAAAGGGACAAATC
Found at i:38124 original size:15 final size:15
Alignment explanation
Indices: 38106--38135 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38096 AAAACCATGT
38106 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
38121 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
38136 GAAATAAATA
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:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:38142 original size:15 final size:15
Alignment explanation
Indices: 38109--38143 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
38099 ACCATGTTAG
* *
38109 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
38124 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
38139 ATAAA
1 ATAAA
38144 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:38246 original size:9 final size:9
Alignment explanation
Indices: 38222--38351 Score: 50
Period size: 9 Copynumber: 13.4 Consensus size: 9
38212 AAATAGTAAG
*
38222 TAAAATAAA
1 TAAAAAAAA
*
38231 TATAAAAAA
1 TAAAAAAAA
38240 T-AAAAAAA
1 TAAAAAAAA
38248 TAAAGAAAAA
1 TAAA-AAAAA
*
38258 GAAGAAATAAA
1 TAA-AAA-AAA
* *
38269 T-ATAGAAA
1 TAAAAAAAA
*
38277 TAAAACAAA
1 TAAAAAAAA
38286 TAAATAAAATAA
1 T-AA-AAAA-AA
38298 TAATAAAAAA
1 TAA-AAAAAA
38308 GTAAAAATAGTATA
1 -TAAAAA-A--A-A
* *
38322 TATATAAAA
1 TAAAAAAAA
38331 T-AAAAAAA
1 TAAAAAAAA
*
38339 TAAAAAAAG
1 TAAAAAAAA
38348 TAAA
1 TAAA
38352 TATATATATA
Statistics
Matches: 92, Mismatches: 15, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
8 17 0.18
9 29 0.32
10 18 0.20
11 18 0.20
12 4 0.04
13 5 0.05
14 1 0.01
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.19
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:38249 original size:21 final size:21
Alignment explanation
Indices: 38223--38312 Score: 64
Period size: 21 Copynumber: 4.4 Consensus size: 21
38213 AATAGTAAGT
38223 AAAATAAATATAAAAAATAAA
1 AAAATAAATATAAAAAATAAA
* *
38244 AAAAT-AA-A-GAAAAA-GAA
1 AAAATAAATATAAAAAATAAA
* *
38261 GAAATAAATAT-AGAAATAAA
1 AAAATAAATATAAAAAATAAA
*
38281 ACAAATAAATAAAATAATAATAAA
1 A-AAATAAATATAA-AA-AATAAA
*
38305 AAAGTAAA
1 AAAATAAA
38313 AATAGTATAT
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
17 6 0.12
18 7 0.13
19 6 0.12
20 4 0.08
21 14 0.27
22 1 0.02
23 7 0.13
24 7 0.13
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.17
Consensus pattern (21 bp):
AAAATAAATATAAAAAATAAA
Found at i:38259 original size:50 final size:48
Alignment explanation
Indices: 38175--38351 Score: 130
Period size: 50 Copynumber: 3.6 Consensus size: 48
38165 AAGGGAAAAC
* * * * *
38175 AAATTAAATAAAAGATAAGATAAAGAAAACAAAGATAAAATAGTAAGTA-
1 AAATAAAATAAAAAATAA-AAAAATAAAAAAAAGATAAAATAGTAA-TAG
*
38224 AAATAAATATAAAAAATAAAAAAATAAAGAAAAAGA-AGAAATA-AATATAG
1 AAATAAA-ATAAAAAATAAAAAAATAAA-AAAAAGATA-AAATAGTA-ATAG
* * *
38274 AAATAAAACAAATAAATAAAATAATAATAAAAAAG-TAAAAATAGT-ATAT
1 AAATAAAATAAA-AAATAAAAAAATAA-AAAAAAGAT-AAAATAGTAATAG
*
38323 ATATAAAATAAAAAAATAAAAAAAGTAAA
1 AAATAAAAT-AAAAAATAAAAAAA-TAAA
38352 TATATATATA
Statistics
Matches: 103, Mismatches: 13, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
49 42 0.41
50 59 0.57
51 2 0.02
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (48 bp):
AAATAAAATAAAAAATAAAAAAATAAAAAAAAGATAAAATAGTAATAG
Found at i:38303 original size:53 final size:50
Alignment explanation
Indices: 38170--38304 Score: 114
Period size: 53 Copynumber: 2.5 Consensus size: 50
38160 AAATAAAGGG
* *
38170 AAAACAAATTAAATAAAAGATAAGATAAAGAAAACAAAGATAAAATAGTAAGT
1 AAAACAAA-TAAAT-AAA-ATAAAATAAAGAAAACAAAGATAAAATAGTAAAT
*
38223 AAAATAAATATAA-AAAATAAAAAAATAAAGAAAA-AGAAGAAATAAATATAG-AAAT
1 AAAACAAATA-AATAAAAT---AAAATAAAGAAAACA-AAG--ATAAA-ATAGTAAAT
38278 AAAACAAATAAATAAAATAATAATAAA
1 AAAACAAATAAATAAAATAA-AATAAA
38305 AAAGTAAAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
50 2 0.03
51 3 0.04
52 5 0.07
53 30 0.44
54 2 0.03
55 22 0.32
56 4 0.06
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.17
Consensus pattern (50 bp):
AAAACAAATAAATAAAATAAAATAAAGAAAACAAAGATAAAATAGTAAAT
Found at i:38329 original size:36 final size:37
Alignment explanation
Indices: 38287--38365 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 37
38277 TAAAACAAAT
38287 AAATAAAATAATAATAAAAAAGTAAAAATAGTATATATATA
1 AAATAAAA-AAT-A-AAAAAAGTAAAAATA-TATATATATA
*
38328 AAATAAAAAAATAAAAAAAGTAAATATATATATATATA
1 AAAT-AAAAAATAAAAAAAGTAAAAATATATATATATA
38366 TATATAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
38 10 0.28
39 14 0.39
40 1 0.03
41 7 0.19
42 4 0.11
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.27
Consensus pattern (37 bp):
AAATAAAAAATAAAAAAAGTAAAAATATATATATATA
Found at i:38333 original size:30 final size:31
Alignment explanation
Indices: 38274--38357 Score: 100
Period size: 30 Copynumber: 2.7 Consensus size: 31
38264 ATAAATATAG
*
38274 AAATAAAACAAA-TAAATAAAATAATAATAAAA
1 AAATAAAA-AAAGTAAAT-ATATAATAATAAAA
* * *
38306 AAGTAAAAATAGTATATATATAA-AATAAAA
1 AAATAAAAAAAGTAAATATATAATAATAAAA
38336 AAATAAAAAAAGTAAATATATA
1 AAATAAAAAAAGTAAATATATA
38358 TATATATATA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 26 0.59
31 7 0.16
32 11 0.25
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.23
Consensus pattern (31 bp):
AAATAAAAAAAGTAAATATATAATAATAAAA
Found at i:38366 original size:44 final size:46
Alignment explanation
Indices: 38318--38415 Score: 121
Period size: 48 Copynumber: 2.1 Consensus size: 46
38308 GTAAAAATAG
*
38318 TATATATATAAAATAA-AAAA-ATAA-AAAAAGTAAATATATATATA
1 TATATATATAAAATAATAAAACATAATAAAAAAT-AATATATATATA
* *
38362 TATATATATAAATTAATAAAACTGATAATAAAAAATAATATATTTATA
1 TATATATATAAAATAATAAAAC--ATAATAAAAAATAATATATATATA
38410 TATATA
1 TATATA
38416 ATCTAAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 15 0.33
45 4 0.09
48 21 0.46
49 6 0.13
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (46 bp):
TATATATATAAAATAATAAAACATAATAAAAAATAATATATATATA
Found at i:38484 original size:23 final size:24
Alignment explanation
Indices: 38445--38490 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
38435 ATATACTAAA
38445 GTAAAAAAGAAAATACAT-AAAAT
1 GTAAAAAAGAAAATACATGAAAAT
*
38468 GTAAAAAA-ATAATTACATGAAAA
1 GTAAAAAAGA-AAATACATGAAAA
38491 AAAGAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 15 0.75
24 4 0.20
ACGTcount: A:0.67, C:0.04, G:0.09, T:0.20
Consensus pattern (24 bp):
GTAAAAAAGAAAATACATGAAAAT
Found at i:38799 original size:37 final size:37
Alignment explanation
Indices: 38758--38862 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
38748 GTACTTGTGG
* * * *
38758 ATCCTATCTTTAGGATTTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* * * *
38795 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
*
38832 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
38863 GACGAAAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
Found at i:43457 original size:31 final size:33
Alignment explanation
Indices: 43416--43478 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
43406 AAAAATTATA
43416 GGCTGTTTTTT-GCTAGTTGTAAGGGGCGTAGG
1 GGCTGTTTTTTGGCTAGTTGTAAGGGGCGTAGG
* *
43448 GGCT-TTTTTTGGCTGGTTGTAAGGGGTGTAG
1 GGCTGTTTTTTGGCTAGTTGTAAGGGGCGTAG
43479 TTGTATTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 6 0.21
32 22 0.79
ACGTcount: A:0.11, C:0.08, G:0.41, T:0.40
Consensus pattern (33 bp):
GGCTGTTTTTTGGCTAGTTGTAAGGGGCGTAGG
Found at i:43936 original size:11 final size:11
Alignment explanation
Indices: 43920--43991 Score: 60
Period size: 11 Copynumber: 6.5 Consensus size: 11
43910 TCCTATGATC
43920 TTATTTTTAAT
1 TTATTTTTAAT
*
43931 TTA-TTTTAAA
1 TTATTTTTAAT
43941 TTAGTTTTTCAAT
1 TTA-TTTTT-AAT
*
43954 TTCATTGTT-AT
1 TT-ATTTTTAAT
* *
43965 TCA-TTTTAAC
1 TTATTTTTAAT
43975 TTATTTTTAAT
1 TTATTTTTAAT
43986 TTATTT
1 TTATTT
43992 AATTTTCTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 3 0.06
10 13 0.28
11 18 0.38
12 4 0.09
13 8 0.17
14 1 0.02
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (11 bp):
TTATTTTTAAT
Found at i:43939 original size:10 final size:10
Alignment explanation
Indices: 43924--44005 Score: 53
Period size: 9 Copynumber: 7.9 Consensus size: 10
43914 ATGATCTTAT
43924 TTTTAATTTA
1 TTTTAATTTA
*
43934 TTTTAAATTA
1 TTTTAATTTA
43944 GTTTTTCAATTTCA
1 --TTTT-AATTT-A
*
43958 TTGTT-ATTCA
1 TT-TTAATTTA
*
43968 TTTTAACTTA
1 TTTTAATTTA
43978 TTTTTAATTTA
1 -TTTTAATTTA
43989 -TTTAATTT-
1 TTTTAATTTA
*
43997 TCTTAATTT
1 TTTTAATTT
44006 GATAGACTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
9 17 0.30
10 15 0.26
11 12 0.21
12 6 0.11
13 6 0.11
14 1 0.02
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTAATTTA
Found at i:44099 original size:27 final size:26
Alignment explanation
Indices: 44069--44131 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
44059 ATTTGCTAGA
44069 ATTTTGTTAACTTCCTTTTTAAGTTTT
1 ATTTTGTTAACTTCCTTTTTAA-TTTT
* ** *
44096 ATTTTATTTCCTTCTTTTTTAATTTT
1 ATTTTGTTAACTTCCTTTTTAATTTT
44122 ATTTCTGTTA
1 ATTT-TGTTA
44132 CTCATTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.17, C:0.11, G:0.05, T:0.67
Consensus pattern (26 bp):
ATTTTGTTAACTTCCTTTTTAATTTT
Found at i:44278 original size:16 final size:16
Alignment explanation
Indices: 44231--44280 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
44221 TTACGTTAAG
44231 TTATTT-TTTATTCATAT
1 TTATTTGTTTATT--TAT
* *
44248 TTA-TGGTTCATTTAT
1 TTATTTGTTTATTTAT
44263 TTATTTGTTTATTTAT
1 TTATTTGTTTATTTAT
44279 TT
1 TT
44281 TGGATATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
15 6 0.22
16 13 0.48
17 8 0.30
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.70
Consensus pattern (16 bp):
TTATTTGTTTATTTAT
Found at i:46738 original size:21 final size:21
Alignment explanation
Indices: 46701--46740 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
46691 ACTTTAATGA
*
46701 GGAGGATAAGTCCAGACAAAT
1 GGAGGATAAGTCAAGACAAAT
46722 GGAGGATAAGAT-AAGACAA
1 GGAGGATAAG-TCAAGACAA
46741 TTTGAGGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.47, C:0.10, G:0.30, T:0.12
Consensus pattern (21 bp):
GGAGGATAAGTCAAGACAAAT
Found at i:47857 original size:74 final size:74
Alignment explanation
Indices: 47767--48107 Score: 287
Period size: 74 Copynumber: 4.6 Consensus size: 74
47757 TCTTGTAAAG
* * * *
47767 GGGATTCGTCTTATTTGACTTAAACTCGCGAAGGGGATTCATCCAAAAAATCAAGATTGGCTTAA
1 GGGATTCGTCTTATTTGACTTAAACCCGCGAAGGGGAGTCATCCAAAAAATCAAGACTAGCTTAA
47832 ATCGCGAAA
66 ATCGCGAAA
* ** ** * *
47841 GGGATTCGTCTCATTTGACTTAAACCCGCGAAAAGGAGTCATTGAAAAAAAATCAAAACTAGCAT
1 GGGATTCGTCTTATTTGACTTAAACCCGCGAAGGGGAGTCA-T-CCAAAAAATCAAGACTAGCTT
** *
47906 AGACCCACG-AA
64 A-AATCGCGAAA
* * * *
47917 GGAAAGTT-GTCTTATTTGACTTAAACCCGCGAAGGGGAATAATCCAAAAAAAT-AAGACTGGCT
1 GG-GA-TTCGTCTTATTTGACTTAAACCCGCGAAGGGGAGTCATCC-AAAAAATCAAGACTAGCT
*
47980 TAAATTGC-AAA
63 TAAATCGCGAAA
* * **
47991 GAGGAGTCATCTTATTTGACTTAAACCCATGAAGGGGAGTCATCCAAAAAATCAAGACTAGCTTA
1 G-GGATTCGTCTTATTTGACTTAAACCCGCGAAGGGGAGTCATCCAAAAAATCAAGACTAGCTT-
*
48056 AAAT-GCGAAG
64 AAATCGCGAAA
* * * *** * *
48066 GGGAGTCATCTCACAAGACTTAAGCCCACGAAGGGGAGTCAT
1 GGGATTCGTCTTATTTGACTTAAACCCGCGAAGGGGAGTCAT
48108 TCGAAGAACC
Statistics
Matches: 211, Mismatches: 44, Indels: 24
0.76 0.16 0.09
Matches are distributed among these distances:
73 8 0.04
74 121 0.57
75 18 0.09
76 28 0.13
77 34 0.16
78 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (74 bp):
GGGATTCGTCTTATTTGACTTAAACCCGCGAAGGGGAGTCATCCAAAAAATCAAGACTAGCTTAA
ATCGCGAAA
Found at i:48238 original size:36 final size:36
Alignment explanation
Indices: 48147--48245 Score: 110
Period size: 36 Copynumber: 2.8 Consensus size: 36
48137 ATAATTTCAC
** *
48147 ATGACTTAAACCTATGAA-GGAGTCATCCAAAGAAA
1 ATGACTTAAACCCGTGAAGGGGGTCATCCAAAGAAA
* ** *
48182 ATGACTTAAACTCGCAAAGGGGGTCATCCAAAGAAC
1 ATGACTTAAACCCGTGAAGGGGGTCATCCAAAGAAA
*
48218 CTGACTTAAACCCGTGAAGGGGAGTCAT
1 ATGACTTAAACCCGTGAAGGGG-GTCAT
48246 TCGGAGCATA
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
35 13 0.25
36 33 0.65
37 5 0.10
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.19
Consensus pattern (36 bp):
ATGACTTAAACCCGTGAAGGGGGTCATCCAAAGAAA
Found at i:55671 original size:21 final size:21
Alignment explanation
Indices: 55645--55686 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
55635 CTCAAGAAAA
*
55645 AATATTGGGT-CATATGACTGT
1 AATATTGGCTACA-ATGACTGT
55666 AATATTGGCTACAATGACTGT
1 AATATTGGCTACAATGACTGT
55687 CAACCGAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (21 bp):
AATATTGGCTACAATGACTGT
Done.