Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000011.1 Hibiscus syriacus cultivar Beakdansim tig00000017_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: 62787
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2295 original size:45 final size:45
Alignment explanation
Indices: 2209--2354 Score: 166
Period size: 45 Copynumber: 3.2 Consensus size: 45
2199 AGTTCACCAT
** * *
2209 TATGCATTTTCAATTATAACATCCCTTTCATGCCAATAATGCACCCA
1 TATGCA-TTTCAATTATGGCAT-CATTTCATACCAATAATGCACCCA
* * * * *
2256 TATGCATTTCATTTATGGCATTATTTCTTATCAATAATGCACTCA
1 TATGCATTTCAATTATGGCATCATTTCATACCAATAATGCACCCA
* * *
2301 TATGCATTTCAATTATGTCATCCTTTCATGCCAATAATGCACCCA
1 TATGCATTTCAATTATGGCATCATTTCATACCAATAATGCACCCA
2346 TATGCATTT
1 TATGCATTT
2355 TTTAATTCAT
Statistics
Matches: 82, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
45 64 0.78
46 12 0.15
47 6 0.07
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.39
Consensus pattern (45 bp):
TATGCATTTCAATTATGGCATCATTTCATACCAATAATGCACCCA
Found at i:3587 original size:20 final size:20
Alignment explanation
Indices: 3559--3607 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
3549 GTTGCCTGGA
3559 ATCGATACCCTTCTCTTAGT
1 ATCGATACCCTTCTCTTAGT
*
3579 ATTGATACCCTTCTCTTAGT
1 ATCGATACCCTTCTCTTAGT
3599 ATCGATACC
1 ATCGATACC
3608 ACTTACATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.22, C:0.29, G:0.10, T:0.39
Consensus pattern (20 bp):
ATCGATACCCTTCTCTTAGT
Found at i:15225 original size:3 final size:3
Alignment explanation
Indices: 15217--15278 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
15207 TTATGAATAT
15217 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
15265 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
15279 TTTGAATATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:18776 original size:3 final size:3
Alignment explanation
Indices: 18768--18867 Score: 193
Period size: 3 Copynumber: 33.7 Consensus size: 3
18758 CCCTTTTTTA
18768 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18815 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18863 TAT TA
1 TAT TA
18868 GGTAATGGCC
Statistics
Matches: 96, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 94 0.98
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:19641 original size:31 final size:31
Alignment explanation
Indices: 19606--19681 Score: 152
Period size: 31 Copynumber: 2.5 Consensus size: 31
19596 ATTCATATAT
19606 TCGGGTCAGGTCGGGTGAAACTTTATTTTGG
1 TCGGGTCAGGTCGGGTGAAACTTTATTTTGG
19637 TCGGGTCAGGTCGGGTGAAACTTTATTTTGG
1 TCGGGTCAGGTCGGGTGAAACTTTATTTTGG
19668 TCGGGTCAGGTCGG
1 TCGGGTCAGGTCGG
19682 TTTCTTTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.14, C:0.14, G:0.38, T:0.33
Consensus pattern (31 bp):
TCGGGTCAGGTCGGGTGAAACTTTATTTTGG
Found at i:22049 original size:41 final size:40
Alignment explanation
Indices: 21661--22081 Score: 238
Period size: 41 Copynumber: 10.3 Consensus size: 40
21651 AATGGTACAA
* * * **
21661 TTAGTGGCGTTTATACACAAACGCCATAATAG-GGCTCATCT
1 TTAGTGGCGTTTTTA-ACAAATGCCGTAATAGAGTATCA-CT
* *
21702 ATAGTGGCGTTTTTAAACAAACGCCGCT-ATA-ATGT-TCATCT
1 TTAGTGGCGTTTTT-AACAAATGCCG-TAATAGA-GTATCA-CT
* * * *
21743 ATAGTGGCATTTTTCAACAAACGCCATAATAGAGTAGT-ACT
1 TTAGTGGCGTTTTT-AACAAATGCCGTAATAGAGTA-TCACT
* *
21784 TTAGTGGCGTTTTTAAATAAATGCCGTAATAGAGT-TCATT
1 TTAGTGGCGTTTTT-AACAAATGCCGTAATAGAGTATCACT
* *
21824 TATAGTGGTGTTTTTCAACAAATGCCGCAATAGAGTAGTCA-T
1 T-TAGTGGCGTTTTT-AACAAATGCCGTAATAGAGTA-TCACT
** * *
21866 TT-GCAGCGTTTTTATACAAATGTCGTAATAGGGT-TCATCT
1 TTAGTGGCGTTTTTA-ACAAATGCCGTAATAGAGTATCA-CT
* * *
21906 ATAGTGGCATTTTTTAACAAATGCCGAAATAGAGTAGT-ACT
1 TTAGTGGC-GTTTTTAACAAATGCCGTAATAGAGTA-TCACT
* * *
21947 TTAGCGGTGTTTTTATACAAATGCCGTAATAGGGT-TCATCT
1 TTAGTGGCGTTTTTA-ACAAATGCCGTAATAGAGTATCA-CT
* * * * *
21988 ATAGTGACATTTTTCAAAAAATGTCGTAATAGAGTAGT-ACT
1 TTAGTGGCGTTTTT-AACAAATGCCGTAATAGAGTA-TCACT
* * * * *
22029 TTAGTGGCGTTTATAGAAAAATGCCGCAAAAGA-TATAATCT
1 TTAGTGGCGTTTTTA-ACAAATGCCGTAATAGAGTATCA-CT
22070 TTAGTGGCGTTT
1 TTAGTGGCGTTT
22082 ATTTTAACAA
Statistics
Matches: 300, Mismatches: 52, Indels: 56
0.74 0.13 0.14
Matches are distributed among these distances:
38 3 0.01
39 4 0.01
40 41 0.14
41 230 0.77
42 16 0.05
43 6 0.02
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (40 bp):
TTAGTGGCGTTTTTAACAAATGCCGTAATAGAGTATCACT
Found at i:22051 original size:82 final size:82
Alignment explanation
Indices: 21735--22054 Score: 412
Period size: 82 Copynumber: 3.9 Consensus size: 82
21725 CCGCTATAAT
* * *
21735 GTTCATCTATAGTGGCATTTTTCAACAAACGCCATAATAGAGTAGTACTTTAGTGGCGTTTTTA-
1 GTTCATCTATAGTGGCATTTTTCAACAAATGCCGTAATAGAGTAGTACTTTAGCGGCGTTTTTAT
*
21799 AATAAATGCCGTAATAGA
66 AA-AAATGCCGTAATAGG
* ** * *
21817 GTTCATTTATAGTGGTGTTTTTCAACAAATGCCGCAATAGAGTAGT-CATTT-GCAGCGTTTTTA
1 GTTCATCTATAGTGGCATTTTTCAACAAATGCCGTAATAGAGTAGTAC-TTTAGCGGCGTTTTTA
* *
21880 TACAAATGTCGTAATAGG
65 TAAAAATGCCGTAATAGG
* * *
21898 GTTCATCTATAGTGGCATTTTTTAACAAATGCCGAAATAGAGTAGTACTTTAGCGGTGTTTTTAT
1 GTTCATCTATAGTGGCATTTTTCAACAAATGCCGTAATAGAGTAGTACTTTAGCGGCGTTTTTAT
*
21963 ACAAATGCCGTAATAGG
66 AAAAATGCCGTAATAGG
* * * * * *
21980 GTTCATCTATAGTGACATTTTTCAAAAAATGTCGTAATAGAGTAGTACTTTAGTGGCGTTTATAG
1 GTTCATCTATAGTGGCATTTTTCAACAAATGCCGTAATAGAGTAGTACTTTAGCGGCGTTTTTAT
22045 AAAAATGCCG
66 AAAAATGCCG
22055 CAAAAGATAT
Statistics
Matches: 205, Mismatches: 29, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
81 68 0.33
82 137 0.67
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.35
Consensus pattern (82 bp):
GTTCATCTATAGTGGCATTTTTCAACAAATGCCGTAATAGAGTAGTACTTTAGCGGCGTTTTTAT
AAAAATGCCGTAATAGG
Found at i:22075 original size:82 final size:82
Alignment explanation
Indices: 21707--22077 Score: 371
Period size: 82 Copynumber: 4.5 Consensus size: 82
21697 CATCTATAGT
* * *
21707 GGCGTTTTTA-AACAAACGCCGCT-ATAATG-TTCATCTATAGTGGCATTTTTCAACAAACGCCA
1 GGCGTTTTTATAA-AAATGCCG-TAATAA-GATTCATCTATAGTGGCATTTTTCAACAAATGCCG
*
21769 TAATAGAGTAGTACTTTAGT
63 TAATAGAGTAGTACTTTAGC
* ** *
21789 GGCGTTTTTA-AATAAATGCCGTAAT-AGAGTTCATTTATAGTGGTGTTTTTCAACAAATGCCGC
1 GGCGTTTTTATAA-AAATGCCGTAATAAGA-TTCATCTATAGTGGCATTTTTCAACAAATGCCGT
21852 AATAGAGTAGT-CATTT-GC
64 AATAGAGTAGTAC-TTTAGC
* * * * * * *
21870 AGCGTTTTTATACAAATGTCGTAATAGGGTTCATCTATAGTGGCATTTTTTAACAAATGCCGAAA
1 GGCGTTTTTATAAAAATGCCGTAATAAGATTCATCTATAGTGGCATTTTTCAACAAATGCCGTAA
21935 TAGAGTAGTACTTTAGC
66 TAGAGTAGTACTTTAGC
* * * * * * *
21952 GGTGTTTTTATACAAATGCCGTAATAGGGTTCATCTATAGTGACATTTTTCAAAAAATGTCGTAA
1 GGCGTTTTTATAAAAATGCCGTAATAAGATTCATCTATAGTGGCATTTTTCAACAAATGCCGTAA
*
22017 TAGAGTAGTACTTTAGT
66 TAGAGTAGTACTTTAGC
* * * * *
22034 GGCGTTTATAGAAAAATGCCGCAA-AAGATATAATCTTTAGTGGC
1 GGCGTTTTTATAAAAATGCCGTAATAAGAT-TCATCTATAGTGGC
22078 GTTTATTTTA
Statistics
Matches: 242, Mismatches: 38, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
80 1 0.00
81 70 0.29
82 171 0.71
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.35
Consensus pattern (82 bp):
GGCGTTTTTATAAAAATGCCGTAATAAGATTCATCTATAGTGGCATTTTTCAACAAATGCCGTAA
TAGAGTAGTACTTTAGC
Found at i:31176 original size:21 final size:21
Alignment explanation
Indices: 31152--31203 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 21
31142 TGAAGCAAGG
31152 GAAGCAGAGAGAGCAGCAACA
1 GAAGCAGAGAGAGCAGCAACA
* ** * * *
31173 GAAGTAGCCAGAGCAGTAGCG
1 GAAGCAGAGAGAGCAGCAACA
31194 GAAGCAGAGA
1 GAAGCAGAGA
31204 AAGAATCAGC
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.37, T:0.04
Consensus pattern (21 bp):
GAAGCAGAGAGAGCAGCAACA
Found at i:31814 original size:43 final size:43
Alignment explanation
Indices: 31648--31853 Score: 211
Period size: 43 Copynumber: 4.8 Consensus size: 43
31638 TTTTAGCAAC
* * * *
31648 AACGCCGCAAAACATCAACACCTACTGCGGCGTTTGTGAGAAA
1 AACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCAGAAA
* * * * *
31691 AATGCTGCAAAATATCAACACCTACTGCGGCGTTT-TAGAGAAA
1 AACGCCGCTAAATATCAACACCTATTGCGGCGTTTGT-CAGAAA
** * *
31734 AACGCTACTAAACATCATA-ACATATTGCGGCGTTTGTCAGAAA
1 AACGCCGCTAAATATCA-ACACCTATTGCGGCGTTTGTCAGAAA
* *
31777 AACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCACACA
1 AACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCAGAAA
* * *
31820 AAC-ACGCTAAATATCAATATCTATTGCGGCGTTT
1 AACGCCGCTAAATATCAACACCTATTGCGGCGTTT
31854 TTTGTTTAAA
Statistics
Matches: 140, Mismatches: 19, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
42 30 0.21
43 108 0.77
44 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (43 bp):
AACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCAGAAA
Found at i:36010 original size:29 final size:29
Alignment explanation
Indices: 35960--36015 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
35950 GAAAACGAAC
** *
35960 TAAAAGTTTAGTGATTGTACTGTAAGTTT
1 TAAAAGTTTAGTGATTAAACTGCAAGTTT
35989 TAAAAG-TTAGGTGATTAAACTGCAAGT
1 TAAAAGTTTA-GTGATTAAACTGCAAGT
36016 ACCTTAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.13
29 20 0.87
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (29 bp):
TAAAAGTTTAGTGATTAAACTGCAAGTTT
Found at i:37093 original size:16 final size:16
Alignment explanation
Indices: 37072--37102 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
37062 TAATAAATAG
37072 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
37088 ACGAACATAAACGAA
1 ACGAACATAAACGAA
37103 TAAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:37185 original size:10 final size:10
Alignment explanation
Indices: 37170--37228 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
37160 CATTTAATAA
37170 ATAAACGAAC
1 ATAAACGAAC
37180 ATAAACGAAC
1 ATAAACGAAC
** *
37190 ACGAAC-ATAA
1 ATAAACGA-AC
37200 ATGAACACGAAC
1 AT-AA-ACGAAC
37212 ATAAACGAAC
1 ATAAACGAAC
37222 ATAAACG
1 ATAAACG
37229 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 1 0.03
10 29 0.74
11 3 0.08
12 5 0.13
13 1 0.03
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:37195 original size:16 final size:16
Alignment explanation
Indices: 37174--37222 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
37164 TAATAAATAA
37174 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
37190 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
37206 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
37222 A
1 A
37223 TAAACGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:37984 original size:10 final size:10
Alignment explanation
Indices: 37969--38016 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
37959 ATAAATGAAT
37969 GAACATAAAC
1 GAACATAAAC
37979 GAACATAATCGAAC
1 GAACAT-A---AAC
37993 GAACATAAAC
1 GAACATAAAC
*
38003 GAACATAACC
1 GAACATAAAC
38013 GAAC
1 GAAC
38017 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:37993 original size:14 final size:14
Alignment explanation
Indices: 37976--38006 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
37966 AATGAACATA
*
37976 AACGAACATAATCG
1 AACGAACATAAACG
37990 AACGAACATAAACG
1 AACGAACATAAACG
38004 AAC
1 AAC
38007 ATAACCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:37996 original size:24 final size:24
Alignment explanation
Indices: 37956--38017 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
37946 GATTGGGTTA
*
37956 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
37980 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
*
38004 AACATAACCGAACG
1 AACATAATCGAACG
38018 TTCACGAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 3 0.09
24 32 0.91
ACGTcount: A:0.55, C:0.19, G:0.13, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:39730 original size:25 final size:25
Alignment explanation
Indices: 39702--39758 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
39692 TAAGCCTAAT
39702 GAACCCTTGAAGCTTAGGGTATTAG
1 GAACCCTTGAAGCTTAGGGTATTAG
39727 GAACCCTTGAAGCTTAGGGTATTAG
1 GAACCCTTGAAGCTTAGGGTATTAG
*
39752 AAACCCT
1 GAACCCT
39759 AGCAAGGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (25 bp):
GAACCCTTGAAGCTTAGGGTATTAG
Found at i:41606 original size:35 final size:35
Alignment explanation
Indices: 41557--41627 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
41547 AAGAAATAAG
*
41557 TTTATGAGCCCTGCTTTTAATTTAGTTTATTAATA
1 TTTATGAGCCCTGCTTTTAATTTAGTATATTAATA
* *
41592 TTTATGGGCTCTGCTTTTAATTTAGTATATTAATA
1 TTTATGAGCCCTGCTTTTAATTTAGTATATTAATA
41627 T
1 T
41628 AGTTTTTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.25, C:0.10, G:0.13, T:0.52
Consensus pattern (35 bp):
TTTATGAGCCCTGCTTTTAATTTAGTATATTAATA
Found at i:43586 original size:20 final size:21
Alignment explanation
Indices: 43561--43608 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
43551 ACCAACAAAT
*
43561 TCGCAACGCGAATTT-GTAAA
1 TCGCAACGCGAATTTAGAAAA
43581 TCGCAACGCGAATTTAGAAAA
1 TCGCAACGCGAATTTAGAAAA
43602 TCGCAAC
1 TCGCAAC
43609 AAAGAAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (21 bp):
TCGCAACGCGAATTTAGAAAA
Found at i:43675 original size:19 final size:19
Alignment explanation
Indices: 43637--43746 Score: 139
Period size: 19 Copynumber: 5.6 Consensus size: 19
43627 ACGCGTTTGC
43637 CAAATTCGCAACACTGAATTT
1 CAAATTCGC-A-ACTGAATTT
*
43658 CAAATTCGCAATTGAATTT
1 CAAATTCGCAACTGAATTT
*
43677 CAAATTCACAACTGAATTT
1 CAAATTCGCAACTGAATTT
43696 CAAATTCGCAACTGAATTT
1 CAAATTCGCAACTGAATTT
* *
43715 CAAATTCGAAACTCGATTTT
1 CAAATTCGCAACT-GAATTT
* *
43735 CGAATTCACAAC
1 CAAATTCGCAAC
43747 ACGAATTTAA
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
19 55 0.70
20 15 0.19
21 9 0.11
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (19 bp):
CAAATTCGCAACTGAATTT
Found at i:43957 original size:16 final size:15
Alignment explanation
Indices: 43922--43960 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
43912 TCCCCATCTC
*
43922 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
43937 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
43953 TAATTTTT
1 TAATTTTT
43961 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:44728 original size:24 final size:24
Alignment explanation
Indices: 44701--44778 Score: 120
Period size: 24 Copynumber: 3.2 Consensus size: 24
44691 GTATTCGAAA
*
44701 TTTGATCTTAGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
*
44725 TTTGATCTTGGTCAATACCCGAAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
44749 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
44773 TTTGAT
1 TTTGAT
44779 GATGTTTCAG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:47056 original size:18 final size:18
Alignment explanation
Indices: 47033--47068 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
47023 AAGCAAAAGG
*
47033 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
47051 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
47069 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:47484 original size:20 final size:20
Alignment explanation
Indices: 47406--47477 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
47396 ATCACAACGT
**
47406 GAATTTGACTTTCGCGTTGC
1 GAATTTGACTTTAACGTTGC
*
47426 GAATTTGACTTTAATGTTGC
1 GAATTTGACTTTAACGTTGC
47446 GAATTTGACTTTAACGTTGC
1 GAATTTGACTTTAACGTTGC
47466 GAATTTGACTTT
1 GAATTTGACTTT
47478 TGCGTTGTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.43
Consensus pattern (20 bp):
GAATTTGACTTTAACGTTGC
Found at i:47617 original size:64 final size:65
Alignment explanation
Indices: 47543--47701 Score: 266
Period size: 65 Copynumber: 2.4 Consensus size: 65
47533 TTGAATAAAC
* *
47543 AACAAATCAACTTTTTCAAATCAATTAAACAAGC-AGAAAATAATTCTTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
* *
47607 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
47672 AACAAATCAACTTTTACAAATCAATGTAAA
1 AACAAATCAACTTTTACAAATCAAT-TAAA
47702 ATTCAATTAA
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
64 33 0.37
65 52 0.58
66 4 0.04
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.30
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
Found at i:49032 original size:21 final size:21
Alignment explanation
Indices: 49006--49099 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 21
48996 GTGAATCGGG
*
49006 CTCTTGAATGGTGGAAGGGAC
1 CTCTTGAATGGTGGAAGGGGC
* *
49027 CTCTTGAACGAT-GACAGGGGC
1 CTCTTGAATGGTGGA-AGGGGC
* *
49048 TTCTTGAATGGTGGGAGGGGC
1 CTCTTGAATGGTGGAAGGGGC
** *
49069 CTCTTGAGCGAT-GAGAGGGGC
1 CTCTTGAATGGTGGA-AGGGGC
49090 CTCTTGAATG
1 CTCTTGAATG
49100 ATAGGAGATG
Statistics
Matches: 56, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
20 3 0.05
21 52 0.93
22 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.38, T:0.24
Consensus pattern (21 bp):
CTCTTGAATGGTGGAAGGGGC
Found at i:49061 original size:42 final size:41
Alignment explanation
Indices: 49003--49099 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 41
48993 CATGTGAATC
49003 GGGCTCTTGAATGGTGGAAGGGACCTCTTGAACGATGACAG
1 GGGCTCTTGAATGGTGGAAGGGACCTCTTGAACGATGACAG
* * * *
49044 GGGCTTCTTGAATGGTGGGAGGGGCCTCTTGAGCGATGAGAG
1 GGGC-TCTTGAATGGTGGAAGGGACCTCTTGAACGATGACAG
49086 GGGCCTCTTGAATG
1 GGG-CTCTTGAATG
49100 ATAGGAGATG
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
41 4 0.08
42 45 0.90
43 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (41 bp):
GGGCTCTTGAATGGTGGAAGGGACCTCTTGAACGATGACAG
Found at i:49112 original size:21 final size:21
Alignment explanation
Indices: 49088--49143 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
49078 GATGAGAGGG
*
49088 GCCTCTTGAATGATAGGAGAT
1 GCCTCTTGAATGATAGGAGAC
49109 GCCTCTTGAATGATAGGAGAC
1 GCCTCTTGAATGATAGGAGAC
*
49130 ACCTCTTGAATGAT
1 GCCTCTTGAATGAT
49144 GACAGGTGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (21 bp):
GCCTCTTGAATGATAGGAGAC
Found at i:49113 original size:42 final size:42
Alignment explanation
Indices: 49026--49118 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
49016 GTGGAAGGGA
* * * *
49026 CCTCTTGAACGATGACAGGGGCTTCTTGAATGGTGGGAGGGG
1 CCTCTTGAACGATGACAGGGGCCTCTTGAATGATAGGAGAGG
* * *
49068 CCTCTTGAGCGATGAGAGGGGCCTCTTGAATGATAGGAGATG
1 CCTCTTGAACGATGACAGGGGCCTCTTGAATGATAGGAGAGG
49110 CCTCTTGAA
1 CCTCTTGAA
49119 TGATAGGAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.25
Consensus pattern (42 bp):
CCTCTTGAACGATGACAGGGGCCTCTTGAATGATAGGAGAGG
Found at i:49310 original size:4 final size:4
Alignment explanation
Indices: 49289--49322 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
49279 GGGCCGCTGA
* *
49289 AAAT AAAT TAAT ACAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
49323 TGTTGAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:51300 original size:20 final size:20
Alignment explanation
Indices: 51277--51342 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
51267 AAACTTAAAT
* *
51277 TCGCAATGCGAAAATGAAAA
1 TCGCAACGCGAACATGAAAA
51297 TCGCAACGCGAACATGAAAA
1 TCGCAACGCGAACATGAAAA
*
51317 TCACAACGCGAACATGAAAA
1 TCGCAACGCGAACATGAAAA
51337 TCGCAA
1 TCGCAA
51343 TGACAAAATC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAACATGAAAA
Found at i:51920 original size:20 final size:20
Alignment explanation
Indices: 51895--52019 Score: 135
Period size: 20 Copynumber: 6.2 Consensus size: 20
51885 ATAAACACGC
51895 TTTGACTTCTGTGTTGCGAA
1 TTTGACTTCTGTGTTGCGAA
* *
51915 TTTGACTTCCGTGTTACGAA
1 TTTGACTTCTGTGTTGCGAA
*
51935 TTTGACTTTTTGTGTTGCGAA
1 TTTGAC-TTCTGTGTTGCGAA
*
51956 TTTGACTTCTGTGTTGTGAA
1 TTTGACTTCTGTGTTGCGAA
* * *
51976 TTTGACTTATGAGTTGCAAAA
1 TTTGACTTCTGTGTTGC-GAA
* * *
51997 TTGGAGTTC-GCGTTGCGAA
1 TTTGACTTCTGTGTTGCGAA
52016 TTTG
1 TTTG
52020 TTGGTCATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
19 5 0.06
20 56 0.65
21 25 0.29
ACGTcount: A:0.18, C:0.13, G:0.25, T:0.44
Consensus pattern (20 bp):
TTTGACTTCTGTGTTGCGAA
Found at i:51952 original size:41 final size:41
Alignment explanation
Indices: 51895--51983 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 41
51885 ATAAACACGC
51895 TTTGAC-TTCTGTGTTGCGAATTTGACTTCCGTGTTACGAA
1 TTTGACTTTCTGTGTTGCGAATTTGACTTCCGTGTTACGAA
* * **
51935 TTTGACTTTTTGTGTTGCGAATTTGACTTCTGTGTTGTGAA
1 TTTGACTTTCTGTGTTGCGAATTTGACTTCCGTGTTACGAA
51976 TTTGACTT
1 TTTGACTT
51984 ATGAGTTGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 6 0.14
41 38 0.86
ACGTcount: A:0.16, C:0.13, G:0.22, T:0.48
Consensus pattern (41 bp):
TTTGACTTTCTGTGTTGCGAATTTGACTTCCGTGTTACGAA
Found at i:53661 original size:66 final size:66
Alignment explanation
Indices: 53575--53724 Score: 210
Period size: 66 Copynumber: 2.3 Consensus size: 66
53565 TGACACCGAG
* * * * *
53575 TGATCTGTGCAGTATTCAATTATCACTCCACCTTATGCATTACAAAGATACACGAGTCACATCGA
1 TGATCTGTACAATATTCAATTAACACTCCACCTTATACATCACAAAGATACACGAGTCACATCGA
53640 A
66 A
* *
53641 TGATCTGTACAATATTCAATTAACACTTCACCTTATACATCACAAAGGTACACGAGTCACATCGA
1 TGATCTGTACAATATTCAATTAACACTCCACCTTATACATCACAAAGATACACGAGTCACATCGA
*
53706 G
66 A
**
53707 TGATCAATACAATATTCA
1 TGATCTGTACAATATTCA
53725 GTAATCAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 74 1.00
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (66 bp):
TGATCTGTACAATATTCAATTAACACTCCACCTTATACATCACAAAGATACACGAGTCACATCGA
A
Found at i:56842 original size:17 final size:17
Alignment explanation
Indices: 56791--56845 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 17
56781 CCTAAAAAGT
56791 TAAAATAAACTTAAATAA
1 TAAAATAAA-TTAAATAA
*
56809 TAAAATAAAAT-AA-AA
1 TAAAATAAATTAAATAA
56824 TAAAA-AATATTAAATAA
1 TAAAATAA-ATTAAATAA
56841 TAAAA
1 TAAAA
56846 GAACTAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 2 0.06
15 9 0.28
16 4 0.12
17 8 0.25
18 9 0.28
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
TAAAATAAATTAAATAA
Found at i:58009 original size:5 final size:5
Alignment explanation
Indices: 57989--58049 Score: 61
Period size: 5 Copynumber: 11.4 Consensus size: 5
57979 GACTTGGACC
*
57989 TAAAA TAAGA -AAAA TAAAA TAAAAA TTAAAA TAAAA TAAAA TAAAAA
1 TAAAA TAAAA TAAAA TAAAA T-AAAA -TAAAA TAAAA TAAAA T-AAAA
58036 TGGAAAA TAAAA TA
1 T--AAAA TAAAA TA
58050 CTAATAATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 3 0.06
5 26 0.54
6 13 0.27
7 6 0.12
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:58021 original size:17 final size:17
Alignment explanation
Indices: 57998--58047 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 17
57988 CTAAAATAAG
57998 AAAAATAAAATAAAAAT
1 AAAAATAAAATAAAAAT
*
58015 TAAAATAAAAT-AAAAT
1 AAAAATAAAATAAAAAT
58031 AAAAATGGAAAATAAAA
1 AAAAAT--AAAATAAAA
58048 TACTAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 10 0.36
17 10 0.36
18 5 0.18
19 3 0.11
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (17 bp):
AAAAATAAAATAAAAAT
Found at i:58035 original size:23 final size:23
Alignment explanation
Indices: 57999--58049 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 23
57989 TAAAATAAGA
*
57999 AAAATAAAATAAAAAT-TAAAAT
1 AAAATAAAATAAAAATGGAAAAT
58021 AAAATAAAATAAAAATGGAAAAT
1 AAAATAAAATAAAAATGGAAAAT
58044 AAAATA
1 AAAATA
58050 CTAATAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (23 bp):
AAAATAAAATAAAAATGGAAAAT
Found at i:58113 original size:34 final size:35
Alignment explanation
Indices: 58070--58149 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 35
58060 TATGTATATA
*
58070 TTTCAAAAAATATTT-AAAAACTATACGTTATATGT
1 TTTC-AAAAATATTTAAAAAACTATACATTATATGT
*
58105 TTTCAAAAATATTTAAAAAACTATATATTATATGT
1 TTTCAAAAATATTTAAAAAACTATACATTATATGT
58140 TTTCAAAAAT
1 TTTCAAAAAT
58150 TCGTTTTCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
34 10 0.24
35 32 0.76
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.41
Consensus pattern (35 bp):
TTTCAAAAATATTTAAAAAACTATACATTATATGT
Found at i:58240 original size:37 final size:36
Alignment explanation
Indices: 58082--58254 Score: 136
Period size: 35 Copynumber: 4.6 Consensus size: 36
58072 TCAAAAAATA
* ** * *
58082 TTTAAAAACTATACGTTATATGTTTTCAAAAA-TAT
1 TTTAAAAATTATATATTATATGTTTTAAAAAATTGT
* * *
58117 TTAAAAAACTATATATTATATGTTTTCAAAAATTCGT
1 TTTAAAAATTATATATTATATGTTTTAAAAAATT-GT
* *
58154 TTTCAAAAACTATAT-TATATACGTTTTCAAAAAGAAATT-T
1 TTT-AAAAATTATATAT-TATATGTTTT---AAA-AAATTGT
*
58194 TTAAAAAAATTATATATTATATGTTTTAAAAAATGTGT
1 TT-TAAAAATTATATATTATATGTTTTAAAAAAT-TGT
*
58232 TTTTAAAATTATATATTATATGT
1 TTTAAAAATTATATATTATATGT
58255 CTTCCAAAAC
Statistics
Matches: 114, Mismatches: 12, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
35 29 0.25
36 5 0.04
37 27 0.24
38 23 0.20
40 22 0.19
41 3 0.03
42 5 0.04
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.45
Consensus pattern (36 bp):
TTTAAAAATTATATATTATATGTTTTAAAAAATTGT
Found at i:58263 original size:78 final size:76
Alignment explanation
Indices: 58111--58263 Score: 186
Period size: 78 Copynumber: 2.0 Consensus size: 76
58101 ATGTTTTCAA
*
58111 AAATATTTAAAAAACTATATATTATATGTTTTCAAAAATTCGTTTTCAAAAACTATATTATATAC
1 AAATATTTAAAAAACTATATATTATATGTTTTAAAAAATTCGTTTTCAAAAACTATATTATATA-
*
58176 GTTTTCAAAAAG
65 GTTTCCAAAAAG
* * *
58188 AAATTTTTAAAAAAATTATATATTATATGTTTTAAAAAATGT-GTTTTTAAAATTA-TATATTAT
1 AAATATTT-AAAAAACTATATATTATATGTTTTAAAAAAT-TCGTTTTCAAAA--ACTATATTAT
58251 AT-GTCTTCCAAAA
62 ATAGT-TTCCAAAA
58264 CCGATTTTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
77 9 0.14
78 45 0.68
79 11 0.17
80 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (76 bp):
AAATATTTAAAAAACTATATATTATATGTTTTAAAAAATTCGTTTTCAAAAACTATATTATATAG
TTTCCAAAAAG
Found at i:58340 original size:37 final size:37
Alignment explanation
Indices: 58070--58459 Score: 262
Period size: 37 Copynumber: 10.4 Consensus size: 37
58060 TATGTATATA
**
58070 TTTCAAAAA-ATA-TTTAAAAACTATACGTTATATGT
1 TTTCAAAAATATATTTTAAAAACTATATATTATATGT
*
58105 TTTC-AAAA-ATATTTAAAAAACTATATATTATATGT
1 TTTCAAAAATATATTTTAAAAACTATATATTATATGT
* *
58140 TTTCAAAAAT-TCGTTTTCAAAAACTATAT-TATATACGT
1 TTTCAAAAATAT-ATTTT-AAAAACTATATAT-TATATGT
* * *
58178 TTTCAAAAAGAAATTTTTAAAAAAATTATATATTATATGT
1 TTTCAAAAATATA-TTTT--AAAAACTATATATTATATGT
* * * * *
58218 TTTAAAAAATGTGTTTTTAAAATTATATATTATATGT
1 TTTCAAAAATATATTTTAAAAACTATATATTATATGT
* * *** * * *
58255 CTTCCAAAACCGATTTTAAAAAACCATATATCAGATGCTT
1 TTTCAAAAATATATTTT-AAAAACTATATATTATATG--T
* * *
58295 TTTTAAAAATATATTTTCAAAACTATATATTATACGT
1 TTTCAAAAATATATTTTAAAAACTATATATTATATGT
** * * * *
58332 TTTCAAAAACGTATTTTCAAAACCATATTATATACATAT
1 TTTCAAAAATATATTTTAAAAACTATA-TAT-TATATGT
*
58371 TTTCAAAAATCA-ATTTTTAAAA--AT-TA-TATATGT
1 TTTCAAAAAT-ATATTTTAAAAACTATATATTATATGT
* *
58404 TTTCAAAAAAACTATCTTCTAAAAATTATATATTATATGT
1 TTTCAAAAATA-TAT-TT-TAAAAACTATATATTATATGT
*
58444 TTTCAAAAATAAATTT
1 TTTCAAAAATATATTT
58460 ACAAATTATA
Statistics
Matches: 274, Mismatches: 57, Indels: 45
0.73 0.15 0.12
Matches are distributed among these distances:
32 1 0.00
33 14 0.05
34 9 0.03
35 32 0.12
36 10 0.04
37 59 0.22
38 47 0.17
39 48 0.18
40 53 0.19
41 1 0.00
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (37 bp):
TTTCAAAAATATATTTTAAAAACTATATATTATATGT
Found at i:58397 original size:35 final size:34
Alignment explanation
Indices: 58358--58459 Score: 89
Period size: 35 Copynumber: 2.8 Consensus size: 34
58348 TCAAAACCAT
*
58358 ATTATATACATATTTTCAAAAATCAATTTTTAAAA
1 ATTATATA-ATATTTTCAAAAATCAATTTCTAAAA
* * *
58393 ATTATAT-ATGTTTTCAAAAAAACTATCTTCTAAAA
1 ATTATATAATATTTTC-AAAAATCAAT-TTCTAAAA
*
58428 ATTATATATTATATGTTTTCAAAAATAAATTT
1 ATTATATA--ATA--TTTTCAAAAATCAATTT
58460 ACAAATTATA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
33 7 0.13
34 8 0.15
35 21 0.40
38 4 0.08
39 7 0.13
40 5 0.10
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (34 bp):
ATTATATAATATTTTCAAAAATCAATTTCTAAAA
Found at i:58399 original size:77 final size:75
Alignment explanation
Indices: 58065--58401 Score: 198
Period size: 77 Copynumber: 4.5 Consensus size: 75
58055 AATAATATGT
* ** * * *
58065 ATATATTTCAAAAA--ATATTTAAAAACTATACGTTATATGTTTTCAAAAA-TATTTAAAAAACT
1 ATAT-TTTCAAAAATCATTTTTAAAAACTATATATTATACGTTTTCAAAAAGTATTTTAAAAACC
*
58127 ATA-TAT-TAT
65 ATATTATATAC
* * * *
58136 ATGTTTTCAAAAATTCGTTTTCAAAAACTATAT-TATATACGTTTTCAAAAAGAAATTTTTAAAA
1 ATATTTTCAAAAA-TCATTTTTAAAAACTATATAT-TATACGTTTTCAAAAAG-TA-TTTTAAAA
*
58200 A--A-ATTATATATT
62 ACCATATTATATA-C
* * * * * * *
58212 ATATGTTTTAAAAAAT-GTGTTTTTAAAATTATATATTATATGTCTTCCAAAACCG-ATTTTAAA
1 ATA--TTTTCAAAAATCAT-TTTTAAAAACTATATATTATACGT-TTTCAAAA-AGTATTTT-AA
* *
58275 AAACCATATATCAGATGC
60 AAACCATAT-T-ATATAC
* * *
58293 -T-TTTTTAAAAAT-ATATTTTCAAAACTATATATTATACGTTTTCAAAAACGTATTTTCAAAAC
1 ATATTTTCAAAAATCAT-TTTTAAAAACTATATATTATACGTTTTCAAAAA-GTATTTTAAAAAC
58355 CATATTATATAC
64 CATATTATATAC
*
58367 ATATTTTCAAAAATCAATTTTTAAAAATTATATAT
1 ATATTTTCAAAAATC-ATTTTTAAAAACTATATAT
58402 GTTTTCAAAA
Statistics
Matches: 205, Mismatches: 33, Indels: 50
0.71 0.11 0.17
Matches are distributed among these distances:
70 9 0.04
71 3 0.01
72 1 0.00
73 29 0.14
74 8 0.04
75 5 0.02
76 45 0.22
77 77 0.38
78 19 0.09
79 2 0.01
80 3 0.01
81 1 0.00
82 3 0.01
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (75 bp):
ATATTTTCAAAAATCATTTTTAAAAACTATATATTATACGTTTTCAAAAAGTATTTTAAAAACCA
TATTATATAC
Found at i:58410 original size:33 final size:35
Alignment explanation
Indices: 58370--58436 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
58360 TATATACATA
* *
58370 TTTTC-AAAAATCAAT-TTTTAAAAATTATATATG
1 TTTTCAAAAAAACAATCTTCTAAAAATTATATATG
*
58403 TTTTCAAAAAAACTATCTTCTAAAAATTATATAT
1 TTTTCAAAAAAACAATCTTCTAAAAATTATATAT
58437 TATATGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 8 0.28
35 16 0.55
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.43
Consensus pattern (35 bp):
TTTTCAAAAAAACAATCTTCTAAAAATTATATATG
Found at i:62700 original size:295 final size:292
Alignment explanation
Indices: 61999--62787 Score: 906
Period size: 295 Copynumber: 2.7 Consensus size: 292
61989 ATGCACAAAT
* * * * * * * * *
61999 TTTATAGATACAATTGTTTAACTTAAGACTTTAGGAGAGAACAAGACACCCTTTCATTACTGAAG
1 TTTATAGATACAATTGTTTAAATTGAGACTTTA-AAGATAAC-A-ATACTCTTTTATCACTGAAC
* * *
62064 TCATTTAAAATGTTCTAAAATTCTAATCTTAAATAAAAGATTATT-A-ATCATTTAATAAGTGAA
63 TCATTTAACATGTTCTAAAA-TCTAATCTTAAATAAAAGAATATTAATATCATTTAATCAGTGAA
* * * *
62127 ACTATCAACAATGTAATAATGAAGTTTGTTT-TTTGTTGCTCAAATATTAGTTCCAAGGTATATA
127 ACTATCAACAATGTAATAATGAAATTTGTTTATTTGTTGCTCAAATACTAGTTCCAAGTTCTATA
* *
62191 TTTGCAAAGCAATTATAAAAGCCAAAGAAGAAAGCTAAGACGAAAATTCAATATTAGTTAGGGTA
192 TTTGCAAAGCAATTATAAAAGCCAAAGAAGAAAACAAAGACGAAAATTCAATATTAGTTAGGGTA
* * *
62256 AAAATTTTCTTAGTTCATAGATAATGAACGCACACG
257 AAAATTTTCTTAGCTCATAGATAATGAACACACACA
* ** * *
62292 TCTTATAGATACAATTACTCGAATTTGAGACCTTAATAGATAACAATACACTCTTTTATCACTGA
1 T-TTATAGATACAATT-GTTTAAATTGAGACTTTAA-AGATAACAAT--ACTCTTTTATCACTGA
* * *
62357 ACTCATTTAACATGATCTAGATTCTAATCTTAAATAAAAGAA-ATTAATATCATTTAATCAGTGA
61 ACTCATTTAACATGTTCTAAAATCTAATCTTAAATAAAAGAATATTAATATCATTTAATCAGTGA
* * *
62421 AACTATCAACAGTGTAATAATAAAATTTGTTTATTGGTTGCTCAAATACTAGTTCCAA-TTCTAT
126 AACTATCAACAATGTAATAATGAAATTTGTTTATTTGTTGCTCAAATACTAGTTCCAAGTTCTAT
* * *
62485 ATCTGCAAAGC-ATTAT-AAAGCCACAGAAGAAAACAAATAC-AAAATTCAATATT-GTT-GAGG
191 ATTTGCAAAGCAATTATAAAAGCCAAAGAAGAAAACAAAGACGAAAATTCAATATTAGTTAG-GG
* * * *
62545 TAAATTTCACAAATTTTCTTAGCTCATAGATGATTAGCACATACA
255 T--A----A-AAATTTTCTTAGCTCATAGATAATGAACACACACA
*
62590 TTTATAGATACAATTGTTTAAATATGAGACTTTAAAGATAACAATACTGTTTTATCACTGAACTC
1 TTTATAGATACAATTGTTTAAAT-TGAGACTTTAAAGATAACAATACTCTTTTATCACTGAACTC
*
62655 A-TTAACATGTTCTAAAAT-TAATCTTAAATAAGAAAAAATATTAATATCATTT-ATCA-TGAAA
65 ATTTAACATGTTCTAAAATCTAATCTTAAAT-A-AAAGAATATTAATATCATTTAATCAGTGAAA
*
62716 CTATCAACAATGTAATAATGAAATTTGTTTATTTG-TGATCAAATACTAGTTCCCAAGTTCTATA
128 CTATCAACAATGTAATAATGAAATTTGTTTATTTGTTGCTCAAATACTAGTT-CCAAGTTCTATA
62780 TTTGCAAA
192 TTTGCAAA
Statistics
Matches: 421, Mismatches: 53, Indels: 43
0.81 0.10 0.08
Matches are distributed among these distances:
290 1 0.00
291 6 0.01
292 39 0.09
293 82 0.19
294 83 0.20
295 119 0.28
296 37 0.09
297 25 0.06
298 29 0.07
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (292 bp):
TTTATAGATACAATTGTTTAAATTGAGACTTTAAAGATAACAATACTCTTTTATCACTGAACTCA
TTTAACATGTTCTAAAATCTAATCTTAAATAAAAGAATATTAATATCATTTAATCAGTGAAACTA
TCAACAATGTAATAATGAAATTTGTTTATTTGTTGCTCAAATACTAGTTCCAAGTTCTATATTTG
CAAAGCAATTATAAAAGCCAAAGAAGAAAACAAAGACGAAAATTCAATATTAGTTAGGGTAAAAA
TTTTCTTAGCTCATAGATAATGAACACACACA
Done.