Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006466.1 Hibiscus syriacus cultivar Beakdansim tig00015667_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: 108623
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2257 original size:58 final size:58
Alignment explanation
Indices: 2195--2313 Score: 213
Period size: 58 Copynumber: 2.1 Consensus size: 58
2185 CTTATAAATC
2195 TTTAT-TATAATTTTAGATATTTTCTATTTTTAATAAAATTAATAAATTCCTTTGAAAA
1 TTTATATATAATTTTAGATATTTTCTATTTTTAAT-AAATTAATAAATTCCTTTGAAAA
*
2253 TTTATATATAATTTTGGATATTTTCTATTTTTAATAAATTAATAAATTCCTTTGAAAA
1 TTTATATATAATTTTAGATATTTTCTATTTTTAATAAATTAATAAATTCCTTTGAAAA
2311 TTT
1 TTT
2314 CACTTTTAGG
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
58 31 0.53
59 28 0.47
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.53
Consensus pattern (58 bp):
TTTATATATAATTTTAGATATTTTCTATTTTTAATAAATTAATAAATTCCTTTGAAAA
Found at i:9109 original size:30 final size:32
Alignment explanation
Indices: 9056--9130 Score: 120
Period size: 30 Copynumber: 2.4 Consensus size: 32
9046 TATATTTAGG
9056 GTTTAGGGTTTATGATATATATAAGTTAT-AA
1 GTTTAGGGTTTATGATATATATAAGTTATAAA
9087 GATTTAGGGTTTATG-T-TATATAAGTTATAAA
1 G-TTTAGGGTTTATGATATATATAAGTTATAAA
9118 GTTTAGGGTTTAT
1 GTTTAGGGTTTAT
9131 AATTTATGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
30 24 0.57
31 5 0.12
32 13 0.31
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (32 bp):
GTTTAGGGTTTATGATATATATAAGTTATAAA
Found at i:11467 original size:2 final size:2
Alignment explanation
Indices: 11460--11487 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11450 GAATAATTTA
11460 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
11488 TATTAGTATA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17026 original size:64 final size:61
Alignment explanation
Indices: 16952--17074 Score: 192
Period size: 64 Copynumber: 2.0 Consensus size: 61
16942 TTGGTCATCC
16952 AACTATCAAAAAGAATTATTAATATGCCATAAATCATCACACCTAATTTCTTAATTTATTTCCA
1 AACTATCAAAAAGAATTATTAATATGCCATAAATC-T-ACA-CTAATTTCTTAATTTATTTCCA
* * *
17016 AACTATCAAAAAGAATTATTAATATGCCATAAGTCTTCACTAATTTCTTAATTTTTTTC
1 AACTATCAAAAAGAATTATTAATATGCCATAAATCTACACTAATTTCTTAATTTATTTC
17075 TGCATTTAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
61 19 0.34
62 2 0.04
63 1 0.02
64 34 0.61
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.39
Consensus pattern (61 bp):
AACTATCAAAAAGAATTATTAATATGCCATAAATCTACACTAATTTCTTAATTTATTTCCA
Found at i:24213 original size:39 final size:39
Alignment explanation
Indices: 24152--24232 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
24142 TCAGATCAAC
*
24152 AATCATTGATTATATGACGAAATAAAATAATTGAATATA
1 AATCATTGATTATACGACGAAATAAAATAATTGAATATA
* *
24191 AATCATTGATTATACGATGAAATACAATAATTGAATATA
1 AATCATTGATTATACGACGAAATAAAATAATTGAATATA
24230 AAT
1 AAT
24233 TAAAATTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (39 bp):
AATCATTGATTATACGACGAAATAAAATAATTGAATATA
Found at i:30652 original size:34 final size:34
Alignment explanation
Indices: 30604--30671 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
30594 GGCCAAGATC
30604 AAAGACAAGGAGGGTATTCCACCAGATCAGCAGA
1 AAAGACAAGGAGGGTATTCCACCAGATCAGCAGA
*
30638 AAAGGCAAGGAGGGTATTCCACCAGATCAGCAGA
1 AAAGACAAGGAGGGTATTCCACCAGATCAGCAGA
30672 GGTTAATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.40, C:0.21, G:0.28, T:0.12
Consensus pattern (34 bp):
AAAGACAAGGAGGGTATTCCACCAGATCAGCAGA
Found at i:32567 original size:29 final size:29
Alignment explanation
Indices: 32516--32573 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
32506 ATGTTGGTCG
*
32516 TAGGTCGCCATGCCTTCAGGGCGACCTAC
1 TAGGTCGCCATGCCTTCACGGCGACCTAC
* * *
32545 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCACGGCGACCTAC
32574 AAGAGATTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.34, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCACGGCGACCTAC
Found at i:32643 original size:10 final size:9
Alignment explanation
Indices: 32630--32693 Score: 65
Period size: 10 Copynumber: 6.4 Consensus size: 9
32620 GGCCATCCGA
32630 CCGAGGCCAT
1 CCGAGG-CAT
32640 CCGAGAGCAT
1 CCGAG-GCAT
*
32650 CCGAAAGCAT
1 CCG-AGGCAT
32660 CCGAGGTCAT
1 CCGAGG-CAT
32670 CCGAGAGCAT
1 CCGAG-GCAT
32680 CCGAGGCCAT
1 CCGAGG-CAT
32690 CCGA
1 CCGA
32694 ACGAGCTATG
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
9 3 0.06
10 41 0.87
11 3 0.06
ACGTcount: A:0.27, C:0.34, G:0.28, T:0.11
Consensus pattern (9 bp):
CCGAGGCAT
Found at i:32660 original size:20 final size:20
Alignment explanation
Indices: 32637--32694 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
32627 CGACCGAGGC
32637 CATCCGAGAG-CATCCGAAAG
1 CATCCGAG-GCCATCCGAAAG
* *
32657 CATCCGAGGTCATCCGAGAG
1 CATCCGAGGCCATCCGAAAG
32677 CATCCGAGGCCATCCGAA
1 CATCCGAGGCCATCCGAA
32695 CGAGCTATGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 1 0.03
20 33 0.97
ACGTcount: A:0.29, C:0.33, G:0.26, T:0.12
Consensus pattern (20 bp):
CATCCGAGGCCATCCGAAAG
Found at i:32715 original size:33 final size:33
Alignment explanation
Indices: 32671--32751 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
32661 CGAGGTCATC
* *
32671 CGAGAGCATCCGAGGCCATCCGAACGAGCTATG
1 CGAGGGCATCCGAGGCCAACCGAACGAGCTATG
* *
32704 CGAGGGCATCCGAGGTCAACCGAGCGAGCTATG
1 CGAGGGCATCCGAGGCCAACCGAACGAGCTATG
*
32737 CGAGGGAATCCGAGG
1 CGAGGGCATCCGAGG
32752 GAAGCCGAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.26, C:0.27, G:0.36, T:0.11
Consensus pattern (33 bp):
CGAGGGCATCCGAGGCCAACCGAACGAGCTATG
Found at i:32760 original size:33 final size:33
Alignment explanation
Indices: 32678--32764 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 33
32668 ATCCGAGAGC
* * * *
32678 ATCCGAGGCCATCCGAACGAGCTATGCGAGGGC
1 ATCCGAGGTCAACCGAGCGAGCTATGCGAGGGA
32711 ATCCGAGGTCAACCGAGCGAGCTATGCGAGGGA
1 ATCCGAGGTCAACCGAGCGAGCTATGCGAGGGA
*
32744 ATCCGAGG-GAAGCCGAGCGAG
1 ATCCGAGGTCAA-CCGAGCGAG
32765 GGTAGGTCGC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 2 0.04
33 46 0.96
ACGTcount: A:0.26, C:0.26, G:0.37, T:0.10
Consensus pattern (33 bp):
ATCCGAGGTCAACCGAGCGAGCTATGCGAGGGA
Found at i:32842 original size:50 final size:49
Alignment explanation
Indices: 32767--32864 Score: 169
Period size: 50 Copynumber: 2.0 Consensus size: 49
32757 CGAGCGAGGG
* *
32767 TAGGTCGCCCGGAGGGTATGGCGACCTATTTGTTGGGACGTGCATGTGCA
1 TAGGTCGCCCGGAGGGCATGGCGACCTATGTGTT-GGACGTGCATGTGCA
32817 TAGGTCGCCCGGAGGGCATGGCGACCTATGTGTTGGACGTGCATGTGC
1 TAGGTCGCCCGGAGGGCATGGCGACCTATGTGTTGGACGTGCATGTGC
32865 CATGCAACAC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 14 0.30
50 32 0.70
ACGTcount: A:0.15, C:0.21, G:0.39, T:0.24
Consensus pattern (49 bp):
TAGGTCGCCCGGAGGGCATGGCGACCTATGTGTTGGACGTGCATGTGCA
Found at i:32944 original size:29 final size:29
Alignment explanation
Indices: 32902--32958 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
32892 GAGCAAGGGT
32902 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
*
32931 AGGTCGTCCGGAGTGCATGGCGACCTAC
1 AGGTCGCCCGGAGTGCATGGCGACCTAC
32959 GGCCAACACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.30, G:0.35, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:35357 original size:60 final size:60
Alignment explanation
Indices: 35230--35477 Score: 254
Period size: 60 Copynumber: 4.1 Consensus size: 60
35220 TTTGAATAAA
* * * * *
35230 TTTAGGGATGAAATT-GAAAGATTCAAAAGTTT-GGGACTAATTTAGAATGAGA-TCTATAG
1 TTTAGGGATAAAATTAGAATG-TTTAAAAGTTTAAGGACCAATTTAGAATGAGAGTC-ATAG
* ** *
35289 TTTGGGGATAAAATT-GAAATGTTTAAAAGTTTAAGGAATAATTTAGAATGAGAGTCATAA
1 TTTAGGGATAAAATTAG-AATGTTTAAAAGTTTAAGGACCAATTTAGAATGAGAGTCATAG
* * *
35349 TTTAGGGATGAAATTAGAATGTTTAAAAGTTGAAGGACCAATTTAAAATGAGAGTCATAG
1 TTTAGGGATAAAATTAGAATGTTTAAAAGTTTAAGGACCAATTTAGAATGAGAGTCATAG
* *
35409 TTTAAGGATATGATGCAATTAGAATGTTTAAAAATTTAAGGACCAATTT-GAGATGAGAGTCATA
1 TTTAGGGATA--A---AATTAGAATGTTTAAAAGTTTAAGGACCAATTTAGA-ATGAGAGTCATA
35473 G
60 G
35474 TTTA
1 TTTA
35478 TGTGATAGCT
Statistics
Matches: 160, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
59 24 0.15
60 83 0.52
61 3 0.02
62 1 0.01
64 1 0.01
65 48 0.30
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (60 bp):
TTTAGGGATAAAATTAGAATGTTTAAAAGTTTAAGGACCAATTTAGAATGAGAGTCATAG
Found at i:35532 original size:40 final size:40
Alignment explanation
Indices: 35488--35565 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
35478 TGTGATAGCT
**
35488 CATAATCAGTGATGGAGTCGCACATAATTGCGGGTGAGTA
1 CATAATCAGTGACAGAGTCGCACATAATTGCGGGTGAGTA
* *
35528 CATAATCAGTGGCAGAGTCGCACATAGTTGCGGGTGAG
1 CATAATCAGTGACAGAGTCGCACATAATTGCGGGTGAG
35566 CACGTAAGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (40 bp):
CATAATCAGTGACAGAGTCGCACATAATTGCGGGTGAGTA
Found at i:43489 original size:12 final size:12
Alignment explanation
Indices: 43472--43506 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
43462 ATTTCCCTTT
43472 TTCATTTTCTTC
1 TTCATTTTCTTC
43484 TTCATTTTTCTTC
1 TTCA-TTTTCTTC
43497 TTCATTTTCT
1 TTCATTTTCT
43507 CTCCATCGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.09, C:0.23, G:0.00, T:0.69
Consensus pattern (12 bp):
TTCATTTTCTTC
Found at i:44859 original size:43 final size:43
Alignment explanation
Indices: 44806--45106 Score: 333
Period size: 43 Copynumber: 7.0 Consensus size: 43
44796 AAAATAAAGC
* ** *
44806 CAAAATGGTCAATATCTATAGCAACGTTTTTGGAACAAACGCCA
1 CAAAA-GGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCG
* * * * *
44850 CAAAAGGTCAATACCTATAGCGCCATTTTTGGAACAAATGCCG
1 CAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCG
* * *
44893 CAAAAGATAAAGATCTATAGAGGCGTTTTTTGGAACAAACGCCG
1 CAAAAGGTCAAGATCTATAGCGGCG-TTTTTGGAACAAACGCCG
* *
44937 CAAAAGG-CCAGATCTATAGAGGCG-TTTTGGAACAAATC-CCG
1 CAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAACAAA-CGCCG
* * *
44978 CAAAAGGTC-AGATCTATAGCGTCCTTTTTGGAACAAACGCTG
1 CAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCG
* ** *
45020 CAAAAGATTGAGATCTATAGCGGCGTTTTTGGAACAAACACCG
1 CAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCG
*
45063 CAAAAGGTC-AGATCTATAGCGACGTTTTTGGATACAAACGCCG
1 CAAAAGGTCAAGATCTATAGCGGCGTTTTTGGA-ACAAACGCCG
45106 C
1 C
45107 TAATTACCTT
Statistics
Matches: 219, Mismatches: 31, Indels: 15
0.83 0.12 0.06
Matches are distributed among these distances:
41 35 0.16
42 45 0.21
43 111 0.51
44 28 0.13
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (43 bp):
CAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCG
Found at i:45054 original size:85 final size:84
Alignment explanation
Indices: 44819--45106 Score: 319
Period size: 85 Copynumber: 3.4 Consensus size: 84
44809 AATGGTCAAT
* * * * * * *
44819 ATCTATAGCAACGTTTTTGGAACAAACGCCACAAAAGGTCAATACCTATAGCGCCATTTTTGGAA
1 ATCTATAGCGACCTTTTTGGAACAAACGCCGCAAAA-GTCAAGATCTATAGCGGCGTTTTTGGAA
* * *
44884 CAAATGCCGCAAAAGATAAAG
65 CAAATCCCGCAAAAGGT-CAG
* * * * * *
44905 ATCTATAGAGGCGTTTTTTGGAACAAACGCCGCAAAAGGCCAGATCTATAGAGGCG-TTTTGGAA
1 ATCTATAGCGAC-CTTTTTGGAACAAACGCCGCAAAAGTCAAGATCTATAGCGGCGTTTTTGGAA
44969 CAAATCCCGCAAAAGGTCAG
65 CAAATCCCGCAAAAGGTCAG
* * **
44989 ATCTATAGCGTCCTTTTTGGAACAAACGCTGCAAAAGATTGAGATCTATAGCGGCGTTTTTGGAA
1 ATCTATAGCGACCTTTTTGGAACAAACGCCGCAAAAG-TCAAGATCTATAGCGGCGTTTTTGGAA
45054 CAAA-CACCGCAAAAGGTCAG
65 CAAATC-CCGCAAAAGGTCAG
*
45074 ATCTATAGCGACGTTTTTGGATACAAACGCCGC
1 ATCTATAGCGACCTTTTTGGA-ACAAACGCCGC
45107 TAATTACCTT
Statistics
Matches: 171, Mismatches: 26, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
83 23 0.13
84 27 0.16
85 68 0.40
86 31 0.18
87 22 0.13
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (84 bp):
ATCTATAGCGACCTTTTTGGAACAAACGCCGCAAAAGTCAAGATCTATAGCGGCGTTTTTGGAAC
AAATCCCGCAAAAGGTCAG
Found at i:45092 original size:127 final size:128
Alignment explanation
Indices: 44819--45104 Score: 393
Period size: 127 Copynumber: 2.2 Consensus size: 128
44809 AATGGTCAAT
*
44819 ATCTATAGCAACGTTTTTGGAACAAACGCCACAAAAGGTCAATACCTATAGCGCCATTTTTGGAA
1 ATCTATAGCGACGTTTTTGGAACAAACGCCACAAAAGGTCAATA-CTATAGCGCCATTTTTGGAA
* *
44884 CAAATGCCGCAAAAGATAAAGATCTATAGAGGCGTTTTTTGGAACAAACGCCGCAAAAGGCCAG
65 CAAACGCCGCAAAAGATAAAGATCTATAGAGGCGTTTTTTGGAACAAACACCGCAAAAGGCCAG
* * *
44948 ATCTATAGAGGCG-TTTTGGAACAAATC-CCGCAAAAGGTCAGAT-CTATAGCGTCC-TTTTTGG
1 ATCTATAGCGACGTTTTTGGAACAAA-CGCCACAAAAGGTCA-ATACTATAGCG-CCATTTTTGG
* ** * *
45009 AACAAACGCTGCAAAAGATTGAGATCTATAGCGGCG-TTTTTGGAACAAACACCGCAAAAGGTCA
63 AACAAACGCCGCAAAAGATAAAGATCTATAGAGGCGTTTTTTGGAACAAACACCGCAAAAGGCCA
45073 G
128 G
45074 ATCTATAGCGACGTTTTTGGATACAAACGCC
1 ATCTATAGCGACGTTTTTGGA-ACAAACGCC
45105 GCTAATTACC
Statistics
Matches: 138, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
126 38 0.28
127 54 0.39
128 33 0.24
129 13 0.09
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (128 bp):
ATCTATAGCGACGTTTTTGGAACAAACGCCACAAAAGGTCAATACTATAGCGCCATTTTTGGAAC
AAACGCCGCAAAAGATAAAGATCTATAGAGGCGTTTTTTGGAACAAACACCGCAAAAGGCCAG
Found at i:46523 original size:18 final size:18
Alignment explanation
Indices: 46500--46543 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
46490 CAATAGAATT
*
46500 TGTGTGTGTATATATACA
1 TGTGTGTGTAAATATACA
**
46518 TGTGTGTGTAAATATATT
1 TGTGTGTGTAAATATACA
46536 TGTGTGTG
1 TGTGTGTG
46544 ATAGAGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.23, C:0.02, G:0.27, T:0.48
Consensus pattern (18 bp):
TGTGTGTGTAAATATACA
Found at i:47980 original size:30 final size:30
Alignment explanation
Indices: 47934--48171 Score: 244
Period size: 30 Copynumber: 7.9 Consensus size: 30
47924 TGTAGTTTCG
*
47934 ATCTGCATGAGATTAATTCCCCGTTCTGAC
1 ATCTGCATGGGATTAATTCCCCGTTCTGAC
* ** *
47964 ATCTCCATGGGATTAATTCCATGTTTTGAC
1 ATCTGCATGGGATTAATTCCCCGTTCTGAC
*
47994 ATCTGCATGAGATTAATTCCCCGTTCTGAC
1 ATCTGCATGGGATTAATTCCCCGTTCTGAC
* * * * *
48024 ATCTGTATGAGATTAGTTCCTCGTTTTGAC
1 ATCTGCATGGGATTAATTCCCCGTTCTGAC
* * *
48054 ATCTTCATGGGATTAGTTCCCCGTTTTGAC
1 ATCTGCATGGGATTAATTCCCCGTTCTGAC
* * * *
48084 ATATGCATGGGATTAGTTCCCCATTTTGAC
1 ATCTGCATGGGATTAATTCCCCGTTCTGAC
* * * * *
48114 TTTTGCATGGGATTAGTTTCCCGTTCTAAC
1 ATCTGCATGGGATTAATTCCCCGTTCTGAC
*
48144 ATCTACATGGGA-TAAGTTCCCCGTTCTG
1 ATCTGCATGGGATTAA-TTCCCCGTTCTG
48172 TTTATCTACA
Statistics
Matches: 174, Mismatches: 33, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
29 2 0.01
30 172 0.99
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (30 bp):
ATCTGCATGGGATTAATTCCCCGTTCTGAC
Found at i:48162 original size:90 final size:90
Alignment explanation
Indices: 47934--48168 Score: 276
Period size: 90 Copynumber: 2.6 Consensus size: 90
47924 TGTAGTTTCG
* * * ** *
47934 ATCTGCATGAGATTAATTCCCCGTTCTGACATCTCCATGGGATTAA-TTCCATGTTTTGACATCT
1 ATCTGCATGAGATTAGTTTCCCGTTCTGACATCTACATGGGA-TAAGTTCCCCGTTTTGACATAT
*
47998 GCATGAGATTAATTCCCCGTTCTGAC
65 GCATGAGATTAATTCCCCATTCTGAC
* * * *
48024 ATCTGTATGAGATTAG-TTCCTCGTTTTGACATCTTCATGGGATTAGTTCCCCGTTTTGACATAT
1 ATCTGCATGAGATTAGTTTCC-CGTTCTGACATCTACATGGGATAAGTTCCCCGTTTTGACATAT
* * *
48088 GCATGGGATTAGTTCCCCATTTTGAC
65 GCATGAGATTAATTCCCCATTCTGAC
* * * *
48114 TTTTGCATGGGATTAGTTTCCCGTTCTAACATCTACATGGGATAAGTTCCCCGTT
1 ATCTGCATGAGATTAGTTTCCCGTTCTGACATCTACATGGGATAAGTTCCCCGTT
48169 CTGTTTATCT
Statistics
Matches: 121, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
89 5 0.04
90 112 0.93
91 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (90 bp):
ATCTGCATGAGATTAGTTTCCCGTTCTGACATCTACATGGGATAAGTTCCCCGTTTTGACATATG
CATGAGATTAATTCCCCATTCTGAC
Found at i:52577 original size:2 final size:2
Alignment explanation
Indices: 52570--52599 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52560 ATACATACAC
52570 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
52600 GCAAAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53707 original size:19 final size:19
Alignment explanation
Indices: 53643--53722 Score: 90
Period size: 19 Copynumber: 4.0 Consensus size: 19
53633 TTATGTATTT
53643 TATTTTACCTTATTTAGGG
1 TATTTTACCTTATTTAGGG
* *
53662 TGTTATTATC-TACTGTCTAGTGG
1 TATT-TTACCTTA-T-T-TAG-GG
53685 TATTTTACCTTATTTAGGG
1 TATTTTACCTTATTTAGGG
53704 TATTTTACCTTATTTAGGG
1 TATTTTACCTTATTTAGGG
53723 ACGAGTTAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
19 26 0.51
20 8 0.16
21 2 0.04
22 8 0.16
23 7 0.14
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.51
Consensus pattern (19 bp):
TATTTTACCTTATTTAGGG
Found at i:54059 original size:83 final size:84
Alignment explanation
Indices: 53965--54119 Score: 258
Period size: 83 Copynumber: 1.9 Consensus size: 84
53955 TTTTCCCGAA
* * * *
53965 TTCTCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC-GTGTTTGTTTTACGTAAT
1 TTCTCGTGTTTGTTTCACGTAATTCATTTTCCGAAAAATATTTTCCAGTGTTTATTTTACGTAAT
54029 TCGTTTTCCGAAAAATGTT
66 TCGTTTTCCGAAAAATGTT
54048 TTCTCGTGTTTGTTTCACGTAATTCATTTTCCGAAAAATATTTTCCAGTGTTTATTTTACGTAAT
1 TTCTCGTGTTTGTTTCACGTAATTCATTTTCCGAAAAATATTTTCCAGTGTTTATTTTACGTAAT
*
54113 TGGTTTT
66 TCGTTTT
54120 TTTGAACGTA
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
83 43 0.65
84 23 0.35
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.50
Consensus pattern (84 bp):
TTCTCGTGTTTGTTTCACGTAATTCATTTTCCGAAAAATATTTTCCAGTGTTTATTTTACGTAAT
TCGTTTTCCGAAAAATGTT
Found at i:54069 original size:42 final size:41
Alignment explanation
Indices: 53969--54119 Score: 221
Period size: 42 Copynumber: 3.6 Consensus size: 41
53959 CCCGAATTCT
*
53969 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTTC
*
54010 CGTGTTTGTTTTACGTAATTCGTTTTCCGAAAAATGTTTTC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTTC
* *
54051 TCGTGTTTGTTTCACGTAATTCATTTTCCGAAAAATATTTTC
1 -CGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTTC
* * *
54093 CAGTGTTTATTTTACGTAATTGGTTTT
1 C-GTGTTTGTTTCACGTAATTCGTTTT
54120 TTTGAACGTA
Statistics
Matches: 99, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
41 40 0.40
42 59 0.60
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.49
Consensus pattern (41 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTTC
Found at i:54402 original size:19 final size:20
Alignment explanation
Indices: 54380--54425 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
54370 TTATATTTTT
54380 TTTATAATATATAAA-AAAA
1 TTTATAATATATAAATAAAA
* *
54399 TTTAT-ATATTTAAATAATA
1 TTTATAATATATAAATAAAA
54418 TTT-TAATA
1 TTTATAATA
54426 AAGATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTATAATATATAAATAAAA
Found at i:54447 original size:23 final size:23
Alignment explanation
Indices: 54421--54465 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
54411 AATAATATTT
54421 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
54444 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
54466 ATATGACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:54810 original size:14 final size:15
Alignment explanation
Indices: 54789--54840 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
54779 TTCCAGAAAT
54789 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
54804 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
*
54818 GTAATTCATTTTTCA
1 GTAATTCATTTTCCA
54833 GTAATTCA
1 GTAATTCA
54841 AATTCCAGCC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:54814 original size:20 final size:20
Alignment explanation
Indices: 54777--54815 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54767 TCGGAAAATG
**
54777 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
54797 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
54816 CAGTAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:54825 original size:15 final size:15
Alignment explanation
Indices: 54789--54848 Score: 68
Period size: 15 Copynumber: 4.1 Consensus size: 15
54779 TTCCAGAAAT
**
54789 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
54804 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
** *
54818 GTAATTCATTTTTCA
1 GTAATTCAAATTCCA
54833 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
54848 G
1 G
54849 CCAATAATTC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
14 12 0.33
15 24 0.67
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.40
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:54865 original size:34 final size:29
Alignment explanation
Indices: 54789--54848 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 29
54779 TTCCAGAAAT
*
54789 GTAATTCATTTTCCAGAATTCAAATTCCA
1 GTAATTCATTTTTCAGAATTCAAATTCCA
54818 GTAATTCATTTTTCAGTAATTCAAATTCCA
1 GTAATTCATTTTTCAG-AATTCAAATTCCA
54848 G
1 G
54849 CCAATAATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 15 0.52
30 14 0.48
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.40
Consensus pattern (29 bp):
GTAATTCATTTTTCAGAATTCAAATTCCA
Found at i:55563 original size:29 final size:29
Alignment explanation
Indices: 55528--55609 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
55518 AAACTAAATT
*
55528 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
55557 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
55586 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
55610 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:60352 original size:29 final size:29
Alignment explanation
Indices: 60289--60372 Score: 132
Period size: 29 Copynumber: 2.8 Consensus size: 29
60279 CAAACTAAAT
*
60289 TGATGTCATTACTTACATCATTTTAATTAA
1 TGATGTCATTGCTTACATCA-TTTAATTAA
*
60319 AGATGTCATTGCTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
60348 TGATGTCATTGCTTACATCAATTTA
1 TGATGTCATTGCTTACATC-ATTTA
60373 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
29 27 0.54
30 23 0.46
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (29 bp):
TGATGTCATTGCTTACATCATTTAATTAA
Found at i:65572 original size:19 final size:19
Alignment explanation
Indices: 65545--65611 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
65535 AATGTTTTTA
*
65545 TGAATAGTAATTTACTATT
1 TGAACAGTAATTTACTATT
*
65564 TGAACAGTAAATTACTATT
1 TGAACAGTAATTTACTATT
* *
65583 TGAACAGTAATTCACTGTT
1 TGAACAGTAATTTACTATT
65602 TGAACAGTAA
1 TGAACAGTAA
65612 CCCGATGCTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.37
Consensus pattern (19 bp):
TGAACAGTAATTTACTATT
Found at i:65742 original size:21 final size:21
Alignment explanation
Indices: 65716--65757 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
65706 ATTTGAATAT
*
65716 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
65737 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
65758 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:65824 original size:20 final size:22
Alignment explanation
Indices: 65786--65825 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
65776 TTTTAGTATA
65786 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
65808 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
65826 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:67483 original size:2 final size:2
Alignment explanation
Indices: 67476--67509 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
67466 TCTTTGAATG
* *
67476 CT CT CT CT CT TT CT CT CT CT CT TT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
67510 GTCTTCATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
CT
Found at i:67493 original size:12 final size:12
Alignment explanation
Indices: 67476--67509 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
67466 TCTTTGAATG
67476 CTCTCTCTCTTT
1 CTCTCTCTCTTT
67488 CTCTCTCTCTTT
1 CTCTCTCTCTTT
67500 CTCTCTCTCT
1 CTCTCTCTCT
67510 GTCTTCATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (12 bp):
CTCTCTCTCTTT
Found at i:72966 original size:31 final size:31
Alignment explanation
Indices: 72931--73023 Score: 177
Period size: 31 Copynumber: 3.0 Consensus size: 31
72921 AATAAAAGTG
*
72931 GTATAAATATAAAAGATAGGTGACTATTCTC
1 GTATAAATATAAAAGATAGGTGACAATTCTC
72962 GTATAAATATAAAAGATAGGTGACAATTCTC
1 GTATAAATATAAAAGATAGGTGACAATTCTC
72993 GTATAAATATAAAAGATAGGTGACAATTCTC
1 GTATAAATATAAAAGATAGGTGACAATTCTC
73024 ATAGTTTACC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (31 bp):
GTATAAATATAAAAGATAGGTGACAATTCTC
Found at i:78783 original size:5 final size:5
Alignment explanation
Indices: 78703--78781 Score: 104
Period size: 5 Copynumber: 15.8 Consensus size: 5
78693 GAAATCCTTT
*
78703 TAATG TAATG TAATG TAATA TAATG TAATG TAATG TAATG TAATG TAATG
1 TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG
* * * * *
78753 TAATA TAATA TAATA TAATA TAATA TAAT
1 TAATG TAATG TAATG TAATG TAATG TAAT
78782 ATTTATTTAG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 71 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (5 bp):
TAATG
Found at i:81026 original size:21 final size:21
Alignment explanation
Indices: 81002--81043 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
80992 AAATAATTAC
* *
81002 ATATTTCATTAAATTATAAAA
1 ATATTTCAGTAAATAATAAAA
*
81023 ATATTTTAGTAAATAATAAAA
1 ATATTTCAGTAAATAATAAAA
81044 TAATGATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
ATATTTCAGTAAATAATAAAA
Found at i:81045 original size:20 final size:20
Alignment explanation
Indices: 80992--81045 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
80982 ATTATTGTAA
* * *
80992 AAATAATTACATATTTCATT
1 AAATAATAAAATATTTCAGT
* *
81012 AAATTATAAAAATATTTTAGT
1 AAATAAT-AAAATATTTCAGT
81033 AAATAATAAAATA
1 AAATAATAAAATA
81046 ATGATATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (20 bp):
AAATAATAAAATATTTCAGT
Found at i:81469 original size:4 final size:4
Alignment explanation
Indices: 81460--81486 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
81450 TTAAAAATTT
81460 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
81487 TACTTCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:86454 original size:61 final size:61
Alignment explanation
Indices: 86320--86481 Score: 190
Period size: 61 Copynumber: 2.7 Consensus size: 61
86310 CGTATAATTT
* * *
86320 AGGAT-AAAATTGAAATATTCAAAAAGTTTAGGGACCAATTTAGAATGAATATCACAGTTTG
1 AGGATGAAAAATGAAAGATTC-AAAAGTTTAGGGACCAATTTAGAATGAATATCACAGTTTA
* *
86381 AGGATG-AAAATGAAAGATTCAAAAGTTT-GAGGACTAATTTAGAATG-ATAGTCATAGTTTA
1 AGGATGAAAAATGAAAGATTCAAAAGTTTAG-GGACCAATTTAGAATGAATA-TCACAGTTTA
* *
86441 AGGATGAAAAATGAAATG-TTTAAAAGTTTAGGGATCAATTT
1 AGGATGAAAAATGAAA-GATTCAAAAGTTTAGGGACCAATTT
86482 GAAATGATGG
Statistics
Matches: 87, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
59 4 0.05
60 37 0.43
61 44 0.51
62 2 0.02
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (61 bp):
AGGATGAAAAATGAAAGATTCAAAAGTTTAGGGACCAATTTAGAATGAATATCACAGTTTA
Found at i:86668 original size:31 final size:30
Alignment explanation
Indices: 86606--86668 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
86596 TAATTAGTTT
* * *
86606 TATCCACCTTTTACTTTTTGGTGCATTAAG
1 TATCCAACTTTTACTTTTTGCTACATTAAG
*
86636 TATCCAACTTTTAGTTTTTGCTACAATTAAG
1 TATCCAACTTTTACTTTTTGCTAC-ATTAAG
86667 TA
1 TA
86669 GTTAACTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.46
Consensus pattern (30 bp):
TATCCAACTTTTACTTTTTGCTACATTAAG
Found at i:86897 original size:31 final size:30
Alignment explanation
Indices: 86861--86952 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 30
86851 ATAATTGAAC
86861 AAAAAAA-TAGGTACCTAGATGCACCATTA
1 AAAAAAATTAGGTACCTAGATGCACCATTA
* * *
86890 AAGAAAAATTAAGTACCTAAATGCATCATTA
1 AA-AAAAATTAGGTACCTAGATGCACCATTA
* * *
86921 AAAAGAGTTAGGTACCTAGATGCAACA-TA
1 AAAAAAATTAGGTACCTAGATGCACCATTA
86950 AAA
1 AAA
86953 TGATTAAGTA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 7 0.13
30 25 0.47
31 21 0.40
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.22
Consensus pattern (30 bp):
AAAAAAATTAGGTACCTAGATGCACCATTA
Found at i:92121 original size:17 final size:18
Alignment explanation
Indices: 92094--92129 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
92084 TTAAATATAA
92094 TAATATTTAAAAAAAAAT
1 TAATATTTAAAAAAAAAT
*
92112 TAAT-TTTAAATAAAAAT
1 TAATATTTAAAAAAAAAT
92129 T
1 T
92130 TTAAATTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATATTTAAAAAAAAAT
Found at i:95076 original size:21 final size:21
Alignment explanation
Indices: 95051--95091 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
95041 TTTATTATAT
*
95051 AAAAATAATATTAATAAATTCG
1 AAAAA-AATATCAATAAATTCG
*
95073 AAAAAAATATCAGTAAATT
1 AAAAAAATATCAATAAATT
95092 GTTTGAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (21 bp):
AAAAAAATATCAATAAATTCG
Found at i:96705 original size:20 final size:20
Alignment explanation
Indices: 96666--96705 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
96656 ATTTGATAAT
** *
96666 TTTAAAAAATTTATTTAAAA
1 TTTAAAAAAAATATTAAAAA
96686 TTTAAAAAAAATATTAAAAA
1 TTTAAAAAAAATATTAAAAA
96706 ATACATAAAT
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAAAAAAAATATTAAAAA
Found at i:98794 original size:39 final size:35
Alignment explanation
Indices: 98715--98805 Score: 105
Period size: 39 Copynumber: 2.5 Consensus size: 35
98705 AGTCATATAT
98715 TCGGGTCGGGTCGGGTCGGGTGAAACCTTAATTTCG
1 TCGGGTCGGGTCGGGTCGGGTGAAACCTT-ATTTCG
98751 TCGGGTCGGGTCGGGTCACGGGTGAAAACCCCTT-TCTTC-
1 TCGGGTCGGGTCGGGT--CGGGTG-AAA--CCTTAT-TTCG
98790 TCGGGTCGGGTCGGGT
1 TCGGGTCGGGTCGGGT
98806 GACCCAAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
36 16 0.33
38 6 0.12
39 20 0.41
40 3 0.06
41 4 0.08
ACGTcount: A:0.11, C:0.23, G:0.40, T:0.26
Consensus pattern (35 bp):
TCGGGTCGGGTCGGGTCGGGTGAAACCTTATTTCG
Found at i:99633 original size:20 final size:20
Alignment explanation
Indices: 99605--99645 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
99595 TACTTATCTT
* *
99605 ATTTGTAATAAAAATATTAG
1 ATTTATAATAAAAATAATAG
99625 ATTTATAATAAAAATAATAG
1 ATTTATAATAAAAATAATAG
99645 A
1 A
99646 AAACAACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (20 bp):
ATTTATAATAAAAATAATAG
Found at i:105739 original size:29 final size:30
Alignment explanation
Indices: 105675--105732 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
105665 ATAAGATGTG
*
105675 ATCACTTTTGCTTTTATTTAATTAAGATAGA
1 ATCA-TTTTGCTTTTATTTAATTAAGAGAGA
*
105706 ATCATTTTGTTTTTA-TTAATTAAGAGA
1 ATCATTTTGCTTTTATTTAATTAAGAGA
105733 TAGTCATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.44
30 10 0.40
31 4 0.16
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (30 bp):
ATCATTTTGCTTTTATTTAATTAAGAGAGA
Found at i:105912 original size:24 final size:25
Alignment explanation
Indices: 105858--105914 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
105848 TAAATAAATT
*
105858 TTAACATAAAAATATATTTTAATAAG
1 TTAATATAAAAATATATTTT-ATAAG
105884 TTAATATAACAAATAT-TTTT-TAAG
1 TTAATATAA-AAATATATTTTATAAG
105908 TTAATAT
1 TTAATAT
105915 TTATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 11 0.38
26 12 0.41
27 6 0.21
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (25 bp):
TTAATATAAAAATATATTTTATAAG
Found at i:106773 original size:36 final size:36
Alignment explanation
Indices: 106679--106775 Score: 160
Period size: 35 Copynumber: 2.7 Consensus size: 36
106669 CAACTAGAGT
*
106679 TTCATCTGTAATGCTCGTATCATTGGTGTCAGCAGC
1 TTCATCTGTAATGCTCGCATCATTGGTGTCAGCAGC
*
106715 TTCATCTGT-ATGCTCGCATCATTGGTTTCAGCAGC
1 TTCATCTGTAATGCTCGCATCATTGGTGTCAGCAGC
*
106750 TTCATCTGTAACGCTCGCATCATTGG
1 TTCATCTGTAATGCTCGCATCATTGG
106776 CTGCTGTGGC
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
35 33 0.58
36 24 0.42
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.36
Consensus pattern (36 bp):
TTCATCTGTAATGCTCGCATCATTGGTGTCAGCAGC
Found at i:108459 original size:17 final size:18
Alignment explanation
Indices: 108437--108470 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
108427 CCCTCAAGCT
*
108437 TTGCATTTCGA-TTCGAA
1 TTGCATCTCGAGTTCGAA
108454 TTGCATCTCGAGTTCGA
1 TTGCATCTCGAGTTCGA
108471 GTCTTGTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (18 bp):
TTGCATCTCGAGTTCGAA
Done.