Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000114.1 Hibiscus syriacus cultivar Beakdansim tig00000205_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: 799156
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:12755 original size:10 final size:10
Alignment explanation
Indices: 12742--12774 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
12732 AGTGAAAATG
12742 AAAAAATAAAA
1 AAAAAAT-AAA
12753 AAAAAATAAA
1 AAAAAATAAA
12763 AAAAAATAAA
1 AAAAAATAAA
12773 AA
1 AA
12775 TGAAAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:12756 original size:11 final size:11
Alignment explanation
Indices: 12742--12774 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
12732 AGTGAAAATG
12742 AAAAAATAAAA
1 AAAAAATAAAA
12753 AAAAAAT-AAA
1 AAAAAATAAAA
12763 AAAAAATAAAA
1 AAAAAATAAAA
12774 A
1 A
12775 TGAAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:13805 original size:55 final size:55
Alignment explanation
Indices: 13722--14225 Score: 693
Period size: 55 Copynumber: 9.1 Consensus size: 55
13712 CAACGGTTAT
* * * *
13722 TGAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* * *
13777 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGACCAGACACGATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* * * *
13832 TAAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* *
13887 TGAAGATTGTTCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGACACGAGTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* *
13942 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGAGCAGACACGATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* * * * *
13997 TGAAAATTGTTCGAGTCTTATACTCTCTGCATAAATAGGGAGCAGACACGACTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* * *
14052 TGAAGATTGTTGGAGTCTTATACTCTCTGCAGAAATAGGAAGCAGACACGATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* * * * * *
14107 TGAAGATTGTTCAAGTTTTATATTCTCTGAAGGAATAGGGAGCAGACAAGATTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGA
* * * * *
14163 TGAGGATTGTTTGGGTCTTATACTCTCTGAGGAAATAGGGAGCAGACACAATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
14218 TGAAGATT
1 TGAAGATT
14226 CTTCAAGTTC
Statistics
Matches: 394, Mismatches: 54, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
55 350 0.89
56 44 0.11
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
Found at i:19037 original size:18 final size:18
Alignment explanation
Indices: 19014--19051 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
19004 TGAACAAATC
19014 AAAAAGTGTTAGTGATAA
1 AAAAAGTGTTAGTGATAA
19032 AAAAAGTGTTAGTGATAA
1 AAAAAGTGTTAGTGATAA
19050 AA
1 AA
19052 TGAAATGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (18 bp):
AAAAAGTGTTAGTGATAA
Found at i:23799 original size:3 final size:3
Alignment explanation
Indices: 23791--23855 Score: 67
Period size: 3 Copynumber: 20.7 Consensus size: 3
23781 ATTTTTTATT
** *
23791 TAA TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA TATA TTT TATT TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TA-A TAA
*
23839 TAA TAA TAA AAA TAA TA
1 TAA TAA TAA TAA TAA TA
23856 GAAAAAATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
3 45 0.85
4 8 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:23815 original size:19 final size:19
Alignment explanation
Indices: 23791--23829 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
23781 ATTTTTTATT
23791 TAATAATAATAATAATATA
1 TAATAATAATAATAATATA
23810 TAATAATAATAATAATATA
1 TAATAATAATAATAATATA
23829 T
1 T
23830 TTTATTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAATAATAATAATAATATA
Found at i:24070 original size:45 final size:45
Alignment explanation
Indices: 23962--24110 Score: 226
Period size: 45 Copynumber: 3.3 Consensus size: 45
23952 TCTTGAAATG
*
23962 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCTAAGGTTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
*
24008 TTGAAAACATCAAGCACTGAAGGGCTTACATATGACCCGAAGGTT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* * * * *
24053 TTGAAAATATCATGCACTGAAGGGCTTATAGACGACCCGAAGGCT
1 TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
24098 TTGAAAACATCAA
1 TTGAAAACATCAA
24111 AAAGCTCCCA
Statistics
Matches: 93, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
45 52 0.56
46 41 0.44
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (45 bp):
TTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
Found at i:25636 original size:76 final size:76
Alignment explanation
Indices: 24043--25609 Score: 2735
Period size: 76 Copynumber: 20.6 Consensus size: 76
24033 TTACATATGA
* * * * * * *
24043 CCCGAAGG--TTTTGAAAATATCATGCACTGAAGGGCTTATAGACGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
24106 ATCAAAAAGCT
66 ATCAAAAAGCT
* * *
24117 CCCAAAGGCTTTTTGAAAACATCATGCACTGTAAGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
*
24182 ATAAAAAAGCT
66 ATCAAAAAGCT
* *
24193 CCCGAAGGCTTTTTGGAAACATCACGCACTATAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
24258 ATCAAAAAGCT
66 ATCAAAAAGCT
* * *
24269 CCCGAAGGCTTTTTTTTTTGTAACATCATGCACTGTAGAACTTACAGATGACCCTAAGGCTTTGA
1 CCCGAAGGC----TTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGA
24334 AAACATCAAAAAGCT
62 AAACATCAAAAAGCT
* * *
24349 CCCGAAGGCTTTTTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
24414 ATCAAAAAGCT
66 ATCAAAAAGCT
*
24425 CCCGAAGACTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
24490 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
24501 CCCGAAGGCTTTTTGGAAACATCATGCACTGTACGACTTACAGATGACCCTAAGGCTTTGAAAGC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
24566 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
24577 CCCGAAGGCTTTTTGGAAACATCACGCACTATAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
24642 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
24653 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTATAGATGACCCTAAGGCTTTGAAAGC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
24718 ATCAAAAAGCT
66 ATCAAAAAGCT
24729 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
24794 ATCAAAAAGCT
66 ATCAAAAAGCT
*
24805 CCCGAAGGCTTTTTGGGAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
24870 ATCAAAAA-CT
66 ATCAAAAAGCT
24880 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
24945 ATCAAAAAGCT
66 ATCAAAAAGCT
* * *
24956 CCCGAAGGCTTTTTGGAAACATCATGCACTATAGGACTTACAGATAACCCTAAGACTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
25021 ATCAAAAAGCT
66 ATCAAAAAGCT
25032 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
25097 ATCAAAAAGCT
66 ATCAAAAAGCT
25108 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
25173 ATCAAAAAGCT
66 ATCAAAAAGCT
*
25184 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
25249 ATCAAAAAGCT
66 ATCAAAAAGCT
*
25260 CCTGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
25325 ATCAAAAAGCT
66 ATCAAAAAGCT
*
25336 CCTGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
25401 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
25412 CCCGAAGGCTTTTTGGGAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
25477 ATCAAAAAGCT
66 ATCAAAAAGCT
*
25488 CCTGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
25553 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
25564 CTCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
25610 TTGGAAATAG
Statistics
Matches: 1423, Mismatches: 63, Indels: 12
0.95 0.04 0.01
Matches are distributed among these distances:
74 7 0.00
75 74 0.05
76 1271 0.89
80 71 0.05
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
ATCAAAAAGCT
Found at i:26311 original size:22 final size:22
Alignment explanation
Indices: 26286--26345 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
26276 AATAAAGCTT
26286 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
26308 TCATCTTTAAAAAGATAATCTA
1 TCATCTTTGAAAAGAGAATCTA
26330 TCATCTTTGAAAAGAG
1 TCATCTTTGAAAAGAG
26346 TGTAAATGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:29112 original size:114 final size:114
Alignment explanation
Indices: 28912--29139 Score: 393
Period size: 114 Copynumber: 2.0 Consensus size: 114
28902 ACGATCATGC
* * *
28912 AATTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
*
28977 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGAA
66 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTACGAGAA
* * *
29026 AATTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
29091 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTACGAGAA
66 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTACGAGAA
29140 CATTGCACTT
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 107 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (114 bp):
AATTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTACGAGAA
Found at i:36414 original size:20 final size:20
Alignment explanation
Indices: 36389--36430 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
36379 CTCATAATAA
36389 AAAAATAAATTAATATATAC
1 AAAAATAAATTAATATATAC
*
36409 AAAAATAGATTAATATATAC
1 AAAAATAAATTAATATATAC
36429 AA
1 AA
36431 TTTTATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAATAAATTAATATATAC
Found at i:37880 original size:29 final size:29
Alignment explanation
Indices: 37838--37893 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
37828 TTTGTATTTT
*
37838 TTTTATTTAATAATAATAATAATAATATA
1 TTTTATTTAATAATAATAAAAATAATATA
37867 TTTTATTTAATAATAATAAAAATAATA
1 TTTTATTTAATAATAATAAAAATAATA
37894 GAAAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TTTTATTTAATAATAATAAAAATAATATA
Found at i:45400 original size:5 final size:5
Alignment explanation
Indices: 45386--45434 Score: 71
Period size: 5 Copynumber: 9.8 Consensus size: 5
45376 GTCCGTCCGT
* * *
45386 CTCGT CTCGG CTCGG CACGG CTCGG GTCGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
45435 TGGTCGTGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.02, C:0.39, G:0.39, T:0.20
Consensus pattern (5 bp):
CTCGG
Found at i:45461 original size:6 final size:6
Alignment explanation
Indices: 45432--45462 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
45422 TCGGCTCGGC
*
45432 TCGTGG TCGTGC TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
45463 AATACGTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.19, G:0.45, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:47228 original size:30 final size:30
Alignment explanation
Indices: 47192--47250 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
47182 TGGTAAACTA
*
47192 CTTTTTTATGACTTTTTTATATTTAAGTTC
1 CTTTTTTATGACTTTTTTATATATAAGTTC
*
47222 CTTTTTTATGATTTTTTTATATATAAGTT
1 CTTTTTTATGACTTTTTTATATATAAGTT
47251 GTGTTACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.64
Consensus pattern (30 bp):
CTTTTTTATGACTTTTTTATATATAAGTTC
Found at i:48422 original size:19 final size:19
Alignment explanation
Indices: 48398--48450 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 19
48388 TATATGGTAA
48398 ACTATTTCACTATAAGTTT
1 ACTATTTCACTATAAGTTT
**
48417 ACTA-TT-A-T-TAAGTAA
1 ACTATTTCACTATAAGTTT
*
48432 ACTATTTCACTATTAGTTT
1 ACTATTTCACTATAAGTTT
48451 GGGGGTGTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 8
0.66 0.13 0.21
Matches are distributed among these distances:
15 9 0.36
16 3 0.12
17 2 0.08
18 3 0.12
19 8 0.32
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47
Consensus pattern (19 bp):
ACTATTTCACTATAAGTTT
Found at i:48599 original size:18 final size:18
Alignment explanation
Indices: 48576--48624 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
48566 ACTGTTAGTT
*
48576 GTGGGCCTAATGCTGAAA
1 GTGGGCCTAATGATGAAA
48594 GTGGGCCTAATGATGAAA
1 GTGGGCCTAATGATGAAA
*
48612 GTGGGCCTTATGA
1 GTGGGCCTAATGA
48625 AGGGGATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.24
Consensus pattern (18 bp):
GTGGGCCTAATGATGAAA
Found at i:49360 original size:36 final size:36
Alignment explanation
Indices: 49313--49385 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
49303 AGATAAGGGG
* *
49313 TAGTGTTGTAGAGGAGTTGAATAGGTTGTTTGATTA
1 TAGTGTTGTAGAGGAGTTCAATAGGCTGTTTGATTA
49349 TAGTGTTGTAGAGGAGTTCAATAGGCTGTTTGATTA
1 TAGTGTTGTAGAGGAGTTCAATAGGCTGTTTGATTA
49385 T
1 T
49386 GTCTTTGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.25, C:0.03, G:0.32, T:0.41
Consensus pattern (36 bp):
TAGTGTTGTAGAGGAGTTCAATAGGCTGTTTGATTA
Found at i:49843 original size:40 final size:38
Alignment explanation
Indices: 49768--49860 Score: 143
Period size: 40 Copynumber: 2.4 Consensus size: 38
49758 AATCACTTTG
* *
49768 ATTCAAATT-ATTTTTTTATTATTATCAATATTCACTA
1 ATTCAAATTGTTTTTTTTATTATTATCAATAATCACTA
49805 ATTCAAATTGTTTTCTTATTATTATTATCAATAATCACTA
1 ATTCAAATTGTTTT-TT-TTATTATTATCAATAATCACTA
49845 ATTCAAATTGTTTTTT
1 ATTCAAATTGTTTTTT
49861 GATTGAATAG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
37 9 0.18
38 3 0.06
39 4 0.08
40 35 0.69
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.54
Consensus pattern (38 bp):
ATTCAAATTGTTTTTTTTATTATTATCAATAATCACTA
Found at i:52269 original size:17 final size:17
Alignment explanation
Indices: 52256--52288 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
52246 CGAATGCATT
52256 CCATGCATCGATGCACA
1 CCATGCATCGATGCACA
*
52273 CCATGCACCGATGCAC
1 CCATGCATCGATGCAC
52289 TGAAGATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.39, G:0.18, T:0.15
Consensus pattern (17 bp):
CCATGCATCGATGCACA
Found at i:52386 original size:64 final size:63
Alignment explanation
Indices: 52240--52398 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
52230 GAATTAAATT
*
52240 GAACATCGAATGCATTCCATGCATCGATGCA-CACCATGCACCGATGCACTGAAGATTTTATAA
1 GAACATCGAATGCATT-GATGCATCGATGCACCACCATGCACCGATGCACTGAAGATTTTATAA
* * *
52303 GAACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCG-GGCTATTT-T
1 GAACATCGAATGCA-TTGATGCATCGATGCACCA-CCATGCACCGATGCACT-GAAGAT-TTTAT
52366 AA
62 AA
52368 -AACATCGAATGCACTTGATGCATCGATGCAC
1 GAACATCGAATGCA-TTGATGCATCGATGCAC
52399 TCTTAGTGCA
Statistics
Matches: 86, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
63 27 0.31
64 34 0.40
65 21 0.24
66 4 0.05
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (63 bp):
GAACATCGAATGCATTGATGCATCGATGCACCACCATGCACCGATGCACTGAAGATTTTATAA
Found at i:52398 original size:17 final size:19
Alignment explanation
Indices: 52370--52418 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
52360 TATTTTAAAA
52370 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
52388 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
52407 CACCGATGCACT
1 CATCGATGCACT
52419 AAGGTTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:52414 original size:64 final size:61
Alignment explanation
Indices: 52240--52418 Score: 177
Period size: 64 Copynumber: 2.8 Consensus size: 61
52230 GAATTAAATT
*
52240 GAACATCGAATGCATTCCATGCATCGATGCACACCA-TGCACCGATGCACTGAAGATTTTATAA
1 GAACATCGAATGCATT-GATGCATCGATG--CACCAGTGCACCGATGCACTGAAGATTTTATAA
* * *
52303 GAACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCG-GGCTATTT-T
1 GAACATCGAATGCA-TTGATGCATCGATGCACCAG---TGCACCGATGCACT-GAAGAT-TTTAT
52366 AA
60 AA
52368 -AACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 GAACATCGAATGCA-TTGATGCATCGATGCAC-C--AGTGCACCGATGCACT
52419 AAGGTTCCAA
Statistics
Matches: 100, Mismatches: 6, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
61 5 0.05
63 25 0.25
64 45 0.45
65 19 0.19
66 4 0.04
67 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (61 bp):
GAACATCGAATGCATTGATGCATCGATGCACCAGTGCACCGATGCACTGAAGATTTTATAA
Found at i:58314 original size:20 final size:20
Alignment explanation
Indices: 58289--58340 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
58279 GCCTTGAATG
58289 TGCATCGATGCACGGGGTCA
1 TGCATCGATGCACGGGGTCA
58309 TGCATCGATGCACGGGGTCA
1 TGCATCGATGCACGGGGTCA
58329 TGCATCGATGCA
1 TGCATCGATGCA
58341 TCCGTTGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.25, G:0.33, T:0.21
Consensus pattern (20 bp):
TGCATCGATGCACGGGGTCA
Found at i:60529 original size:19 final size:19
Alignment explanation
Indices: 60505--60542 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
60495 AAAGGGGGAG
60505 AAATGTTAAGTGTTGAAAT
1 AAATGTTAAGTGTTGAAAT
60524 AAATGTTAAGTGTTGAAAT
1 AAATGTTAAGTGTTGAAAT
60543 GTTTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (19 bp):
AAATGTTAAGTGTTGAAAT
Found at i:60989 original size:16 final size:16
Alignment explanation
Indices: 60968--60998 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60958 CGAATGCATT
*
60968 CCATGCATCGATGCAA
1 CCATGCACCGATGCAA
60984 CCATGCACCGATGCA
1 CCATGCACCGATGCA
60999 CTGAAGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.16
Consensus pattern (16 bp):
CCATGCACCGATGCAA
Found at i:61042 original size:46 final size:45
Alignment explanation
Indices: 60986--61092 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
60976 CGATGCAACC
* * *
60986 ATGCACCGATGCACT-GAAGAT-TTTATAAGAACATCGAATGCATTTG
1 ATGCATCGATGCACTCG-AGATATTT-TAA-AACATCAAATGCACTTG
* *
61032 ATGCATCGATGCACTCGGGCTATTTTAAAACATCAAATGCACTTG
1 ATGCATCGATGCACTCGAGATATTTTAAAACATCAAATGCACTTG
*
61077 ATGCATAGATGCACTC
1 ATGCATCGATGCACTC
61093 TTAGTGCACT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
45 30 0.57
46 19 0.36
47 4 0.08
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (45 bp):
ATGCATCGATGCACTCGAGATATTTTAAAACATCAAATGCACTTG
Found at i:69323 original size:20 final size:20
Alignment explanation
Indices: 69284--69338 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
69274 ATTTTCCATG
* *
69284 AATTTGTAAAACCCTAGGGT
1 AATTTGTAAATCCTTAGGGT
* *
69304 CATTTGTAAATCCTTCGGGT
1 AATTTGTAAATCCTTAGGGT
*
69324 AATTTGTGAATCCTT
1 AATTTGTAAATCCTT
69339 TAGATCATCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (20 bp):
AATTTGTAAATCCTTAGGGT
Found at i:72982 original size:23 final size:22
Alignment explanation
Indices: 72955--72999 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
72945 TGTTATGGCT
72955 GATTTGAATGATATGAGTCAATG
1 GATTTGAATGATATGA-TCAATG
*
72978 GATTTGAATGATATTATCAATG
1 GATTTGAATGATATGATCAATG
73000 CGTTAATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (22 bp):
GATTTGAATGATATGATCAATG
Found at i:74021 original size:19 final size:19
Alignment explanation
Indices: 73997--74033 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
73987 TCAAAATAGA
*
73997 AACAAAGTAAACTAACACT
1 AACAAAGCAAACTAACACT
74016 AACAAAGCAAACTAACAC
1 AACAAAGCAAACTAACAC
74034 CAATAAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.24, G:0.05, T:0.11
Consensus pattern (19 bp):
AACAAAGCAAACTAACACT
Found at i:76169 original size:20 final size:20
Alignment explanation
Indices: 76140--76179 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
76130 TAGTCAAAAC
*
76140 TAGGGGTGTAAATAAATAGA
1 TAGGGATGTAAATAAATAGA
*
76160 TAGGGATGTAAATGAATAGA
1 TAGGGATGTAAATAAATAGA
76180 AAGTTCGGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.25
Consensus pattern (20 bp):
TAGGGATGTAAATAAATAGA
Found at i:76622 original size:24 final size:24
Alignment explanation
Indices: 76595--76671 Score: 127
Period size: 24 Copynumber: 3.2 Consensus size: 24
76585 GAACGTGTTC
*
76595 ATGAACACGTTCGTGGACATATAA
1 ATGAACACGTTCGTGAACATATAA
*
76619 ATGAACACGTTTGTGAACATATAA
1 ATGAACACGTTCGTGAACATATAA
*
76643 ATGAACACATTCGTGAACATATAA
1 ATGAACACGTTCGTGAACATATAA
76667 ATGAA
1 ATGAA
76672 TATATTCACG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (24 bp):
ATGAACACGTTCGTGAACATATAA
Found at i:76684 original size:24 final size:24
Alignment explanation
Indices: 76611--76686 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 24
76601 ACGTTCGTGG
* ***
76611 ACATATAAATGAACACGTTTGTGA
1 ACATATAAATGAACACATTCACGA
**
76635 ACATATAAATGAACACATTCGTGA
1 ACATATAAATGAACACATTCACGA
* *
76659 ACATATAAATGAATATATTCACGA
1 ACATATAAATGAACACATTCACGA
76683 ACAT
1 ACAT
76687 GTTCAAGAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (24 bp):
ACATATAAATGAACACATTCACGA
Found at i:76685 original size:48 final size:48
Alignment explanation
Indices: 76595--76686 Score: 112
Period size: 48 Copynumber: 1.9 Consensus size: 48
76585 GAACGTGTTC
* * * ***
76595 ATGAACACGTTCGTGGACATATAAATGAACACGTTTGTGAACATATAA
1 ATGAACACATTCGTGAACATATAAATGAACACATTCACGAACATATAA
* *
76643 ATGAACACATTCGTGAACATATAAATGAATATATTCACGAACAT
1 ATGAACACATTCGTGAACATATAAATGAACACATTCACGAACAT
76687 GTTCAAGAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 36 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (48 bp):
ATGAACACATTCGTGAACATATAAATGAACACATTCACGAACATATAA
Found at i:77359 original size:327 final size:322
Alignment explanation
Indices: 76711--77353 Score: 991
Period size: 327 Copynumber: 1.9 Consensus size: 322
76701 AATAAACGAA
* * *
76711 CATGAACACGATATTAAAAATTTAAACGAACACCTTAAAAAATAAATAAACGAACACAAACATAA
1 CATGAACACAATATTAAAAATGTAAACGAACACCTTAAAAAATAAACAAACGAACACAAACATAA
* * * *
76776 CCTTATTCGTTCAAGCTCGGTTCATTTACACCTTTAGTCAAAACAATCAACATCTAAGCTATAAT
66 CCTTATTCATTCAAGCCCGATTCATTCACACCTTTAGTCAAAACAATCAACATCTAAGCTATAAT
*
76841 GATGGGAAAATGAAATTATTAAACCTCATCCAAATAAGTCCAACTGCATTAAGTGAGATTGCTTT
131 GATGGGAAAATGAAATTATTAAACCTCATCCAAATAAGTCAAACTGCATTAAGTGAGATTGCTTT
76906 ATAGCCTTCAAATTAGGCCAAGTATATGGGCGAGAAAAATGAGTGAATGCAAAACTAAATTTTCT
196 ATAGCCTTCAAATTAGGCCAAGTATATGGGCGAGAAAAATGAGTGAATGCAAAACTAAATTTTCT
*
76971 CGTGGTGCAACATAAGCAAGAAAAAATATATGAAAAATATATCTAACACCTTAAAAAATTTAAAC
261 CGTGGGGCAACATAAGCAAGAAAAAATATATGAAAAATATATCT---A-CTT--AAAATTTAAAC
77036 TAG
320 TAG
* * * *
77039 CATGAGCACAATATTAAAAATGTAAACGAACGCCTT-AAAAATAAACAAATGAACACGAACATAA
1 CATGAACACAATATTAAAAATGTAAACGAACACCTTAAAAAATAAACAAACGAACACAAACATAA
77103 CCTTATTCATTCAAGCCCGATTCATTCACACCTTTAGTCAAAACAATCAACATCTAAGCTATAAT
66 CCTTATTCATTCAAGCCCGATTCATTCACACCTTTAGTCAAAACAATCAACATCTAAGCTATAAT
*
77168 GATGGGAAAATGAAATTGTTAAACCTCATATCCAAATAAGTCAAACTGCATTAAGTGAGATTGCT
131 GATGGGAAAATGAAATTATTAAACCTC--ATCCAAATAAGTCAAACTGCATTAAGTGAGATTGCT
77233 TTATAGCCTTCAAATTAGGCCAAGTATATGGGCCATTAAAGAGAAAAATGAGTGAATGCAAAGAC
194 TTATAGCCTTCAAATTAGGCCAAGTATATGGG-C------GAGAAAAATGAGTGAATGCAAA-AC
*
77298 TAAATTTTCTCGTGGGGCAACATAAGCAAGAAAAAAATATATGAAAAATATCTCTA
251 TAAATTTTCTCGTGGGGCAACATAAGCAAG-AAAAAATATATGAAAAATATATCTA
77354 AATTTAGTAT
Statistics
Matches: 289, Mismatches: 15, Indels: 15
0.91 0.05 0.05
Matches are distributed among these distances:
327 112 0.39
328 32 0.11
329 67 0.23
330 1 0.00
335 1 0.00
336 22 0.08
337 31 0.11
338 23 0.08
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.26
Consensus pattern (322 bp):
CATGAACACAATATTAAAAATGTAAACGAACACCTTAAAAAATAAACAAACGAACACAAACATAA
CCTTATTCATTCAAGCCCGATTCATTCACACCTTTAGTCAAAACAATCAACATCTAAGCTATAAT
GATGGGAAAATGAAATTATTAAACCTCATCCAAATAAGTCAAACTGCATTAAGTGAGATTGCTTT
ATAGCCTTCAAATTAGGCCAAGTATATGGGCGAGAAAAATGAGTGAATGCAAAACTAAATTTTCT
CGTGGGGCAACATAAGCAAGAAAAAATATATGAAAAATATATCTACTTAAAATTTAAACTAG
Found at i:78254 original size:60 final size:60
Alignment explanation
Indices: 78190--78303 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
78180 TTATAGGGTA
*
78190 TTGCTTTATTAAGTCCCTCAACTATTAAAAGTTACAAAATGGTCTTCCGACTATAAGATG
1 TTGCTTTATTAAGTCCCTCAACTATTAAAAGTTACAAAATGGTCATCCGACTATAAGATG
* * * * * *
78250 TTGCTTTGTTGAGTCTCTCGACTATTAAAAGTTACAAAATTGTCATCTGACTAT
1 TTGCTTTATTAAGTCCCTCAACTATTAAAAGTTACAAAATGGTCATCCGACTAT
78304 TCATTATGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (60 bp):
TTGCTTTATTAAGTCCCTCAACTATTAAAAGTTACAAAATGGTCATCCGACTATAAGATG
Found at i:82856 original size:16 final size:17
Alignment explanation
Indices: 82820--82857 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
82810 AGACTCCAAG
82820 AACAATCAATTAAAAAA
1 AACAATCAATTAAAAAA
* *
82837 AACAATC-ATTGAACAA
1 AACAATCAATTAAAAAA
82853 AACAA
1 AACAA
82858 GAGAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.66, C:0.16, G:0.03, T:0.16
Consensus pattern (17 bp):
AACAATCAATTAAAAAA
Found at i:96934 original size:21 final size:21
Alignment explanation
Indices: 96908--96970 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
96898 ATATATATAA
96908 TCCAAAGGACCA-A-ATATGT
1 TCCAAAGGACCACATATATGT
*
96927 GTCTCAAAGAACCACATATATGT
1 -TC-CAAAGGACCACATATATGT
**
96950 TCCAAAGGATTACATATATGT
1 TCCAAAGGACCACATATATGT
96971 CTTGAAGGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 2 0.06
21 25 0.69
22 3 0.08
23 6 0.17
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (21 bp):
TCCAAAGGACCACATATATGT
Found at i:96972 original size:42 final size:43
Alignment explanation
Indices: 96889--96972 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 43
96879 AAATCTCCTT
* *
96889 AAGAACCATATATATATAATCCAAAGGACCAAATATGTGTCTCA
1 AAGAACCACATATATAT-ATCCAAAGGACCAAATATATGTCTCA
* ** *
96933 AAGAACCACATATATGT-TCCAAAGGATTACATATATGTCT
1 AAGAACCACATATATATATCCAAAGGACCAAATATATGTCT
96973 TGAAGGACCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 19 0.56
44 15 0.44
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (43 bp):
AAGAACCACATATATATATCCAAAGGACCAAATATATGTCTCA
Found at i:97706 original size:29 final size:29
Alignment explanation
Indices: 97650--97731 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
97640 CGATTAGTAT
**
97650 ATATAAGTGAAATTC-TTTTTGCAGCAACA
1 ATATAAGTGAAATTCTTTTTTTTA-CAACA
*
97679 A-ATTAGTGAAATTCCTTTTTTTTACAACA
1 ATATAAGTGAAATT-CTTTTTTTTACAACA
*
97708 ATATAATTGAAATTCTTTTTTTTA
1 ATATAAGTGAAATTCTTTTTTTTA
97732 TCATTAAGCT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 11 0.24
29 18 0.40
30 16 0.36
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (29 bp):
ATATAAGTGAAATTCTTTTTTTTACAACA
Found at i:98053 original size:3 final size:3
Alignment explanation
Indices: 98045--98092 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
98035 CCTTTTATAA
* * ** *
98045 TAT TAT TAT TAT TAT TAT TAT TGT TGT TGC TGT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
98093 ATAACCAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:99781 original size:17 final size:17
Alignment explanation
Indices: 99729--99781 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
99719 TTAAAACATT
99729 TGATATCTGTAAAATATC
1 TGATATCTGT-AAATATC
* *
99747 TAATAACTGT-AATCATC
1 TGATATCTGTAAAT-ATC
*
99764 TGATATCTATAAATATC
1 TGATATCTGTAAATATC
99781 T
1 T
99782 AATAACTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 3 0.11
17 14 0.50
18 11 0.39
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.40
Consensus pattern (17 bp):
TGATATCTGTAAATATC
Found at i:99794 original size:17 final size:17
Alignment explanation
Indices: 99739--99794 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
99729 TGATATCTGT
99739 AAAATATCTAATAACT-
1 AAAATATCTAATAACTA
** * *
99755 GTAATCATCTGATATCTA
1 AAAAT-ATCTAATAACTA
*
99773 TAAATATCTAATAACTA
1 AAAATATCTAATAACTA
99790 AAAAT
1 AAAAT
99795 CATATGATAA
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
16 3 0.10
17 23 0.79
18 3 0.10
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (17 bp):
AAAATATCTAATAACTA
Found at i:99796 original size:35 final size:35
Alignment explanation
Indices: 99720--99803 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 35
99710 TCGATAACTT
* *
99720 TAAAA-CATTTGATATCTGTAAAATATCTAATAAC
1 TAAAATCATATGATATCTATAAAATATCTAATAAC
** *
99754 TGTAATCATCTGATATCTAT-AAATATCTAATAAC
1 TAAAATCATATGATATCTATAAAATATCTAATAAC
99788 TAAAAATCATATGATA
1 T-AAAATCATATGATA
99804 ATTGTAAACA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
34 18 0.44
35 23 0.56
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.36
Consensus pattern (35 bp):
TAAAATCATATGATATCTATAAAATATCTAATAAC
Found at i:100231 original size:65 final size:65
Alignment explanation
Indices: 100155--100316 Score: 204
Period size: 65 Copynumber: 2.5 Consensus size: 65
100145 AATTAAATTG
* * * *
100155 AACATCAAATGCATTTCATGCATCGATGCACTTA-CCATGCACCGATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTT-TG
100218 A
65 A
* * *
100219 AAGCATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTTTG
1 AA-CATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTTTG
100283 A
65 A
* *
100284 AACATCGAATGCACTTGATGCATCGTTGCACTC
1 AACATCGAATGCATTTGATGCATCGATGCACTC
100317 TTAGTGCACC
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 30 0.35
65 52 0.61
66 3 0.04
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTTTGA
Found at i:100330 original size:64 final size:63
Alignment explanation
Indices: 100157--100334 Score: 164
Period size: 65 Copynumber: 2.7 Consensus size: 63
100147 TTAAATTGAA
* * * * * *
100157 CATCAAATGCATTTCATGCATCGATGCACTTACCATGCACCGATGCACTGAGGATTTTATGAAAG
1 CATCGAATGCACTTGATGCATCGATGCAC-CAGC-TGCACCGATGCACTCAGGATTTTATGAAAG
* * * *
100222 CATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTT-TGAAA
1 CATCGAATGCACTTGATGCATCGATGCACCAG-C-TGCACCGATGCACTCAGGAT-TTTATGAAA
100286 -
63 G
*
100286 CATCGAATGCACTTGATGCATCGTTGCACTCTTAG-TGCACCGATGCACT
1 CATCGAATGCACTTGATGCATCGATGCAC-C--AGCTGCACCGATGCACT
100335 AAGGGTCCAA
Statistics
Matches: 97, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
64 41 0.42
65 51 0.53
66 3 0.03
67 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (63 bp):
CATCGAATGCACTTGATGCATCGATGCACCAGCTGCACCGATGCACTCAGGATTTTATGAAAG
Found at i:101936 original size:26 final size:27
Alignment explanation
Indices: 101900--101958 Score: 111
Period size: 26 Copynumber: 2.2 Consensus size: 27
101890 CAAACGGTTC
101900 AGAAAAATGATGAGACCTTACCGAGG-
1 AGAAAAATGATGAGACCTTACCGAGGA
101926 AGAAAAATGATGAGACCTTACCGAGGA
1 AGAAAAATGATGAGACCTTACCGAGGA
101953 AGAAAA
1 AGAAAA
101959 TTCAAACGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 26 0.81
27 6 0.19
ACGTcount: A:0.47, C:0.14, G:0.25, T:0.14
Consensus pattern (27 bp):
AGAAAAATGATGAGACCTTACCGAGGA
Found at i:108355 original size:2 final size:2
Alignment explanation
Indices: 108348--108375 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
108338 GCAGCTTAAG
108348 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
108376 CAATTGGCTA
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:108933 original size:64 final size:63
Alignment explanation
Indices: 108857--108978 Score: 149
Period size: 65 Copynumber: 1.9 Consensus size: 63
108847 ATGCACCAAT
*
108857 CCATGCATCGATGCACCATGA-ATTAAATTG-AACATCGAATGCATTTCATGCATCGATACACTT
1 CCATGCACCGATGCA-C-TGAGATTAAA-TGAAACATCGAATGCATTTCATGCATCGATACACTT
108920 A
63 A
** *
108921 CCATGCACCGATGCACTGAGGATTTTATGAAAACATCGAATGCATTTGATGCATCGAT
1 CCATGCACCGATGCACTGA-GATTAAATG-AAACATCGAATGCATTTCATGCATCGAT
108979 GCACCAGCCA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
62 3 0.06
63 3 0.06
64 18 0.36
65 26 0.52
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (63 bp):
CCATGCACCGATGCACTGAGATTAAATGAAACATCGAATGCATTTCATGCATCGATACACTTA
Found at i:108960 original size:65 final size:65
Alignment explanation
Indices: 108887--109048 Score: 195
Period size: 65 Copynumber: 2.5 Consensus size: 65
108877 AATTAAATTG
* * * * *
108887 AACATCGAATGCATTTCATGCATCGATACACTTA-CCATGCACCGATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGAACTCAGGATATTT-TG
108950 AA
65 -A
* * *
108952 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGAACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGAACTCAGGATATTTTGA
* *
109016 AACATCAAATGCACTTGATGCATCGATGCACTC
1 AACATCGAATGCATTTGATGCATCGATGCACTC
109049 TTAGTGTACC
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
64 31 0.37
65 50 0.60
66 3 0.04
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCAGCCATGCACCGATGAACTCAGGATATTTTGA
Found at i:112795 original size:18 final size:17
Alignment explanation
Indices: 112761--112818 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
112751 TAGCGTTAAA
*
112761 ATATATTTAATAAATAT
1 ATATATATAATAAATAT
*
112778 GTATAGTATAATATATATAT
1 ATATA-TATAATA-A-ATAT
*
112798 ATATATATGCATAAATAT
1 ATATATAT-AATAAATAT
112816 ATA
1 ATA
112819 AAGGTCCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
17 4 0.12
18 13 0.39
19 5 0.15
20 11 0.33
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (17 bp):
ATATATATAATAAATAT
Found at i:113035 original size:2 final size:2
Alignment explanation
Indices: 113030--113094 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
113020 AAGACATGAA
113030 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
113072 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
113095 ACAAAGGCAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:114742 original size:3 final size:3
Alignment explanation
Indices: 114729--114765 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
114719 GGCCTGTAGA
114729 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
114766 CAAGATCTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:120004 original size:17 final size:18
Alignment explanation
Indices: 119935--120032 Score: 78
Period size: 17 Copynumber: 5.6 Consensus size: 18
119925 AATTTGTCTG
* * *
119935 ATAACTGTAAAACATATG
1 ATAACTGTAAATCATCTA
* * *
119953 ATATCTGTAAAT-ATATG
1 ATAACTGTAAATCATCTA
119970 ATAA-T-TATAATCATCTA
1 ATAACTGTA-AATCATCTA
*
119987 ATATCTGTAAAT-ATCTA
1 ATAACTGTAAATCATCTA
* *
120004 ATAACTGAAAATCATCTG
1 ATAACTGTAAATCATCTA
120022 ATAACTGTAAA
1 ATAACTGTAAA
120033 CATTTAGAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
15 2 0.03
16 4 0.06
17 29 0.45
18 28 0.43
19 2 0.03
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (18 bp):
ATAACTGTAAATCATCTA
Found at i:120030 original size:35 final size:35
Alignment explanation
Indices: 119935--120032 Score: 110
Period size: 34 Copynumber: 2.8 Consensus size: 35
119925 AATTTGTCTG
* *
119935 ATAACTGTAAAA-CATATGATATCTGTAAATATATG
1 ATAACTG-AAAATCATCTGATATCTGTAAATATATA
* * * *
119970 ATAA-TTATAATCATCTAATATCTGTAAATATCTA
1 ATAACTGAAAATCATCTGATATCTGTAAATATATA
*
120004 ATAACTGAAAATCATCTGATAACTGTAAA
1 ATAACTGAAAATCATCTGATATCTGTAAA
120033 CATTTAGAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
33 3 0.06
34 24 0.47
35 24 0.47
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (35 bp):
ATAACTGAAAATCATCTGATATCTGTAAATATATA
Found at i:124621 original size:12 final size:12
Alignment explanation
Indices: 124604--124637 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
124594 GTATCGATAC
124604 GCTACAGTAACT
1 GCTACAGTAACT
124616 GCTACAGTAACT
1 GCTACAGTAACT
*
124628 ACTACAGTAA
1 GCTACAGTAA
124638 TTTCAGCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.24
Consensus pattern (12 bp):
GCTACAGTAACT
Found at i:125221 original size:40 final size:39
Alignment explanation
Indices: 125160--125276 Score: 164
Period size: 40 Copynumber: 3.0 Consensus size: 39
125150 CGTAGTGCTA
* *
125160 CACATAAGGTCATGCCGACCATATACACCGAAGTGTATT
1 CACATAAGGTCATACCCACCATATACACCGAAGTGTATT
* *
125199 GCACATAAGGTCATTCCCACCATATACACCGAAGTGTACT
1 -CACATAAGGTCATACCCACCATATACACCGAAGTGTATT
**
125239 -ACATAAGGTTGTACCCACCATATACACCGAAGTGTATT
1 CACATAAGGTCATACCCACCATATACACCGAAGTGTATT
125277 ATAAACCTGC
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
38 34 0.49
40 36 0.51
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.24
Consensus pattern (39 bp):
CACATAAGGTCATACCCACCATATACACCGAAGTGTATT
Found at i:128557 original size:7 final size:7
Alignment explanation
Indices: 128545--128603 Score: 57
Period size: 7 Copynumber: 8.3 Consensus size: 7
128535 GAAACAAATG
128545 AAAAGAA
1 AAAAGAA
128552 AAAAGAA
1 AAAAGAA
128559 AAAA-AA
1 AAAAGAA
*
128565 AAAAAAA
1 AAAAGAA
*
128572 AAAAAAA
1 AAAAGAA
128579 AAAATGACA
1 AAAA-GA-A
* *
128588 AAAATAG
1 AAAAGAA
128595 AAAAGAA
1 AAAAGAA
128602 AA
1 AA
128604 GGGGGATCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
6 6 0.14
7 31 0.70
8 2 0.05
9 5 0.11
ACGTcount: A:0.86, C:0.02, G:0.08, T:0.03
Consensus pattern (7 bp):
AAAAGAA
Found at i:128591 original size:1 final size:1
Alignment explanation
Indices: 128545--128582 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
128535 GAAACAAATG
* *
128545 AAAAGAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
128583 TGACAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.95, C:0.00, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:130228 original size:13 final size:13
Alignment explanation
Indices: 130210--130235 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
130200 GTTTTTAGGT
130210 CCATTACAAATAC
1 CCATTACAAATAC
130223 CCATTACAAATAC
1 CCATTACAAATAC
130236 AATCAATCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (13 bp):
CCATTACAAATAC
Found at i:131529 original size:20 final size:19
Alignment explanation
Indices: 131486--131529 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
131476 CTCTGTATTT
131486 ATTTATTTTATTTTCTTCA
1 ATTTATTTTATTTTCTTCA
*
131505 CTTTATTTTCATTATT-TTCA
1 ATTTATTTT-ATT-TTCTTCA
131525 ATTTA
1 ATTTA
131530 GTCACTAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 8 0.38
20 11 0.52
21 2 0.10
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTCTTCA
Found at i:131647 original size:32 final size:32
Alignment explanation
Indices: 131609--131733 Score: 123
Period size: 32 Copynumber: 3.9 Consensus size: 32
131599 AGTCACTAAT
131609 TTACTAACATTCTAACATTTATTTTATCGTTC
1 TTACTAACATTCTAACATTTATTTTATCGTTC
** * *
131641 GAACTAACATTCTAAC-TTTAATTTATTTGTTC
1 TTACTAACATTCTAACATTTATTTTA-TCGTTC
* *
131673 TTACTAACA--CTAACTTTTTATTTTTATAGTTC
1 TTACTAACATTCTAAC-ATTTA-TTTTATCGTTC
131705 TTACTAAC-TTACTAACATTGTATTTTATC
1 TTACTAACATT-CTAACATT-TATTTTATC
131734 ACACAAACTA
Statistics
Matches: 75, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
30 5 0.07
31 8 0.11
32 43 0.57
33 12 0.16
34 7 0.09
ACGTcount: A:0.30, C:0.17, G:0.04, T:0.50
Consensus pattern (32 bp):
TTACTAACATTCTAACATTTATTTTATCGTTC
Found at i:132475 original size:28 final size:29
Alignment explanation
Indices: 132443--132497 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
132433 CTTTGTTTTA
*
132443 CATTTTTTTATT-TTATTATTTTTTATCT
1 CATTTTATTATTATTATTATTTTTTATCT
* *
132471 CATTTTATTGTTATTGTTATTTTTTAT
1 CATTTTATTATTATTATTATTTTTTAT
132498 TTTTATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.18, C:0.05, G:0.04, T:0.73
Consensus pattern (29 bp):
CATTTTATTATTATTATTATTTTTTATCT
Found at i:134822 original size:4 final size:4
Alignment explanation
Indices: 134800--134835 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
134790 TCAACCCTCT
134800 TTTA TTT- TTTA -TT- TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
134836 TTGTGTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 7 0.24
4 22 0.76
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (4 bp):
TTTA
Found at i:134830 original size:18 final size:18
Alignment explanation
Indices: 134800--134874 Score: 68
Period size: 18 Copynumber: 4.2 Consensus size: 18
134790 TCAACCCTCT
*
134800 TTTATTT-TTTATTTTTA
1 TTTATTTATTTATTTTCA
134817 TTTATTTATTTA-TTT-A
1 TTTATTTATTTATTTTCA
* *
134833 TTTTTGTGTGTTTATTTTCA
1 TTTAT-T-TATTTATTTTCA
134853 TTTACTTTATTT-TTTTCA
1 TTTA-TTTATTTATTTTCA
134871 TTTA
1 TTTA
134875 CTTTTAATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
16 5 0.10
17 11 0.23
18 19 0.40
19 7 0.15
20 5 0.10
21 1 0.02
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (18 bp):
TTTATTTATTTATTTTCA
Found at i:134846 original size:22 final size:21
Alignment explanation
Indices: 134800--134850 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
134790 TCAACCCTCT
*
134800 TTTATTTTTTATTTTTATTTA
1 TTTATTTTTTATTTTTATGTA
* *
134821 TTTATTTATTTATTTTTGTGTG
1 TTTATTT-TTTATTTTTATGTA
134843 TTTATTTT
1 TTTATTTT
134851 CATTTACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (21 bp):
TTTATTTTTTATTTTTATGTA
Found at i:135821 original size:5 final size:5
Alignment explanation
Indices: 135811--135853 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
135801 AATTGTTAAA
* *
135811 AAAAG AAAAG AAAAG ATAAG -AAAG GAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
135854 AATATCTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
4 3 0.09
5 31 0.91
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:135839 original size:19 final size:19
Alignment explanation
Indices: 135808--135852 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
135798 AGCAATTGTT
135808 AAAA-AAAGAAAAGAAAAG
1 AAAAGAAAGAAAAGAAAAG
* *
135826 ATAAGAAAGGAAAGAAAAG
1 AAAAGAAAGAAAAGAAAAG
135845 AAAAGAAA
1 AAAAGAAA
135853 AAATATCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (19 bp):
AAAAGAAAGAAAAGAAAAG
Found at i:144124 original size:59 final size:59
Alignment explanation
Indices: 144032--144145 Score: 192
Period size: 59 Copynumber: 1.9 Consensus size: 59
144022 AATAGATGGA
*
144032 TAAGTGTCCTATCAAACCCTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGACTT
1 TAAGTGTCCTATCAAACCCTCCTAGTCACAATGAAAAGGCAAACTCGATAATATGACTT
* * *
144091 TAAGTGTCCTGTCGAACCCTCCTAGTCACAATGAAAAGGCAAACTTGATAATATG
1 TAAGTGTCCTATCAAACCCTCCTAGTCACAATGAAAAGGCAAACTCGATAATATG
144146 GCTCTAACCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (59 bp):
TAAGTGTCCTATCAAACCCTCCTAGTCACAATGAAAAGGCAAACTCGATAATATGACTT
Found at i:151871 original size:26 final size:23
Alignment explanation
Indices: 151842--151889 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
151832 GTTTTTTTGA
151842 AAAAATAGAATACTCATAATTATTAC
1 AAAAATA-AAT-CT-ATAATTATTAC
*
151868 AAAAATAAATGTATAATTATTA
1 AAAAATAAATCTATAATTATTA
151890 ATCTATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 1 0.05
25 3 0.14
26 7 0.33
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAAATAAATCTATAATTATTAC
Found at i:156397 original size:196 final size:198
Alignment explanation
Indices: 156051--156575 Score: 576
Period size: 196 Copynumber: 2.7 Consensus size: 198
156041 TAAATCATGC
* * **
156051 ATTTAGTCACAATAACGTATTAAATTTGGTCAAAATAAAAATTTATGTTAAATTTATTTCGTCAT
1 ATTTAGTCACAATAACATAGTAAATTTAATCAAAATAAAAATTTATGTTAAATTTATTTCGTCAT
* * * ** * *
156116 AATATTTTCA-CAAAATAACAACTTTTGACAAATTTATTTTGTCATAATAACAATTTATAATAAA
66 AATATTTT-ATCAAAATAAAAAATTGTGACAAATTTATTTAATCAAAATAACAATTTATAACAAA
*
156180 TATTAATTCCTCTAAATAAAAAATTATGAAAAATAATATTCTTTCACAAT-ATAAAGTATAACAA
130 TATTAATTCCTCTAAATAAAAAATTATGAAAAATAATATTCTTTCACAATAACAAAGTATAACAA
* *
156244 ATTT
195 AATG
* ** * *
156248 ATTTAGTTACAATAACATAGTAAATTTAATCAAAAT-AATTTTTTTGTTAAATTTATTTGGTCAT
1 ATTTAGTCACAATAACATAGTAAATTTAATCAAAATAAAAATTTATGTTAAATTTATTTCGTCAT
* * ** *
156312 AATATTTTATCGAAATAAAAAATTGTAACAAATTTATTTAATCAAAATAGTATTTTATAACAAAT
66 AATATTTTATCAAAATAAAAAATTGTGACAAATTTATTTAATCAAAATAACAATTTATAACAAAT
* * * * * * *
156377 ATTAATTTCTC-ATTATAAAAAATTGTGACAAGTAATATTCTTTCACAATAACAAATTGTAACAA
131 ATTAATTCCTCTA-AATAAAAAATTATGAAAAATAATATTCTTTCACAATAACAAAGTATAACAA
156441 AATG
195 AATG
* * * * * * *
156445 ATTTAGTCACAATAATCCT-GTTAAGTTTTATCATAGTAAAAAATTATGTCAAATTTATTTCGTC
1 ATTTAGTCACAATAA-CATAG-TAAATTTAATCAAAATAAAAATTTATGTTAAATTTATTTCGTC
** * * * *
156509 CCAATATTTTATCAAAAT-GAAAATTGTGACAAATTTATTTAATTAAAATAAAAAATTATAACAA
64 ATAATATTTTATCAAAATAAAAAATTGTGACAAATTTATTTAATCAAAATAACAATTTATAACAA
156573 ATA
129 ATA
156576 ATATTCTTTC
Statistics
Matches: 269, Mismatches: 53, Indels: 11
0.81 0.16 0.03
Matches are distributed among these distances:
195 2 0.01
196 117 0.43
197 59 0.22
198 56 0.21
199 35 0.13
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (198 bp):
ATTTAGTCACAATAACATAGTAAATTTAATCAAAATAAAAATTTATGTTAAATTTATTTCGTCAT
AATATTTTATCAAAATAAAAAATTGTGACAAATTTATTTAATCAAAATAACAATTTATAACAAAT
ATTAATTCCTCTAAATAAAAAATTATGAAAAATAATATTCTTTCACAATAACAAAGTATAACAAA
ATG
Found at i:160673 original size:29 final size:28
Alignment explanation
Indices: 160607--160675 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
160597 AGGGCCATGC
* *
160607 CCCCCAAAATTAAAAAAAATTAGTTTTGA
1 CCCCC-AAATTTAAAAAAATTAGATTTGA
**
160636 CCCTTAAATTTAAAAAAATTCA-ATTTGA
1 CCCCCAAATTTAAAAAAATT-AGATTTGA
160664 TCCCCCAAATTT
1 -CCCCCAAATTT
160676 TTAGAAATTC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
28 19 0.59
29 13 0.41
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.32
Consensus pattern (28 bp):
CCCCCAAATTTAAAAAAATTAGATTTGA
Found at i:161999 original size:20 final size:20
Alignment explanation
Indices: 161976--162024 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
161966 TAATGAACAA
*
161976 TACCGATACTGTTCATATGG
1 TACCGATACTATTCATATGG
161996 TACCGATACTATTCATATGG
1 TACCGATACTATTCATATGG
162016 TACCGATAC
1 TACCGATAC
162025 CAAAGGTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (20 bp):
TACCGATACTATTCATATGG
Found at i:162185 original size:20 final size:21
Alignment explanation
Indices: 162160--162199 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
162150 TTATGTATAG
162160 TAGTATCGATACCA-TAGGCA
1 TAGTATCGATACCATTAGGCA
162180 TAGTATCGATACCATTAGGC
1 TAGTATCGATACCATTAGGC
162200 CCCAACAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCATTAGGCA
Found at i:164971 original size:18 final size:18
Alignment explanation
Indices: 164948--164995 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
164938 ATGCAAAAAA
164948 TGGTATCGATACCCAAAG
1 TGGTATCGATACCCAAAG
164966 TGGTATCGATACCCAAAG
1 TGGTATCGATACCCAAAG
*
164984 TGGTACCGATAC
1 TGGTATCGATAC
164996 TATTCTGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (18 bp):
TGGTATCGATACCCAAAG
Found at i:165203 original size:43 final size:43
Alignment explanation
Indices: 165143--165418 Score: 179
Period size: 43 Copynumber: 6.4 Consensus size: 43
165133 CAATAGGTTA
*
165143 TGATGTTTAGCGACGTTTTTCGCTA-AAACGCCGAAGTAGGTGT
1 TGATGTTTAGCGGCGTTTTTCGC-ACAAACGCCGAAGTAGGTGT
* * ** * *
165186 TGATGTTTTGTGGCGTTTTTTTCACAAATGCC-ACAGTAGGTAT
1 TGATGTTTAGCGGCGTTTTTCGCACAAACGCCGA-AGTAGGTGT
* * * * ** * * *
165229 TGATATTTAGCTGTGTTTGTCATAAAAACGTCGCAA-TATGTGT
1 TGATGTTTAGCGGCGTTTTTCGCACAAACGCCG-AAGTAGGTGT
* * * *
165272 TAATATTTAGCAGTGTTTTTCAG-ACAAACGCCGCAA-TAGGT-T
1 TGATGTTTAGCGGCGTTTTTC-GCACAAACGCCG-AAGTAGGTGT
* *
165314 ATGATGTTTAGCGGCATTTTTCGCTA-AAACGCCGTAGTAGGTGT
1 -TGATGTTTAGCGGCGTTTTTCGC-ACAAACGCCGAAGTAGGTGT
* * ** * *
165358 TGATGTTTTGTGGCGTTTTTTTCACAAACGCCGCAGTAGGTAT
1 TGATGTTTAGCGGCGTTTTTCGCACAAACGCCGAAGTAGGTGT
*
165401 TGATGTTTTGCGGCGTTT
1 TGATGTTTAGCGGCGTTT
165419 CTGATAAAAA
Statistics
Matches: 180, Mismatches: 42, Indels: 22
0.74 0.17 0.09
Matches are distributed among these distances:
42 6 0.03
43 170 0.94
44 3 0.02
45 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.38
Consensus pattern (43 bp):
TGATGTTTAGCGGCGTTTTTCGCACAAACGCCGAAGTAGGTGT
Found at i:165272 original size:86 final size:86
Alignment explanation
Indices: 165143--165433 Score: 239
Period size: 86 Copynumber: 3.4 Consensus size: 86
165133 CAATAGGTTA
* * * * *
165143 TGATGTTTAGCGACGTTTTTCGCTAAAACGCCG-AAGTAGGTGTTGATGTTTTGTGGCGTTTTTT
1 TGATATTTAGCGGCATTTGTCGATAAAACGCCGCAA-TAGGTGTTGATGTTTTGTGGCGTTTTTT
* *
165207 TCACAAATGCCACAGTAGGTAT
65 TCACAAACGCCGCAGTAGGTAT
* ** * * * * * ** * *
165229 TGATATTTAGCTGTGTTTGTC-ATAAAAACGTCGCAATATGTGTTAATATTTAGCAGTGTTTTTC
1 TGATATTTAGCGGCATTTGTCGAT-AAAACGCCGCAATAGGTGTTGATGTTTTGTGGCGTTTTTT
** *
165293 AGACAAACGCCGCAATAGGT-T
65 TCACAAACGCCGCAGTAGGTAT
* * * * *
165314 ATGATGTTTAGCGGCATTTTTCGCTAAAACGCCGTAGTAGGTGTTGATGTTTTGTGGCGTTTTTT
1 -TGATATTTAGCGGCATTTGTCGATAAAACGCCGCAATAGGTGTTGATGTTTTGTGGCGTTTTTT
165379 TCACAAACGCCGCAGTAGGTAT
65 TCACAAACGCCGCAGTAGGTAT
* * * *
165401 TGATGTTTTGCGGCGTTTCT-GATAAAAACGCCG
1 TGATATTTAGCGGCATTTGTCGAT-AAAACGCCG
165434 ATACAGGTTT
Statistics
Matches: 155, Mismatches: 44, Indels: 12
0.73 0.21 0.06
Matches are distributed among these distances:
85 4 0.03
86 147 0.95
87 4 0.03
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.36
Consensus pattern (86 bp):
TGATATTTAGCGGCATTTGTCGATAAAACGCCGCAATAGGTGTTGATGTTTTGTGGCGTTTTTTT
CACAAACGCCGCAGTAGGTAT
Found at i:165461 original size:41 final size:43
Alignment explanation
Indices: 165410--165503 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 43
165400 TTGATGTTTT
* *
165410 GCGGCGTTTCT-GATAAAAACGCCGATACAGGT-TTGTATATA
1 GCGGCGTTTCTAGATAAAAACGCCGATAAAGGTATGGTATATA
* * *
165451 GCGGCGTTTCTAGGATAAAAACGCCGCTAAATGTATGGTATATT
1 GCGGCGTTTCTA-GATAAAAACGCCGATAAAGGTATGGTATATA
165495 GCGGCGTTT
1 GCGGCGTTT
165504 TTTTTACAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 11 0.24
43 18 0.40
44 16 0.36
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (43 bp):
GCGGCGTTTCTAGATAAAAACGCCGATAAAGGTATGGTATATA
Found at i:165919 original size:25 final size:25
Alignment explanation
Indices: 165881--165928 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
165871 GCTTCTCTGC
165881 TGCTGTCTCTCTT-CCTCTGCTTCTT
1 TGCTGTCTCTCTTCCCT-TGCTTCTT
165906 TGCT-TCTCTGCTTCCCTTGCTTC
1 TGCTGTCTCT-CTTCCCTTGCTTC
165929 ATTTTCCGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 13 0.62
26 3 0.14
ACGTcount: A:0.00, C:0.38, G:0.12, T:0.50
Consensus pattern (25 bp):
TGCTGTCTCTCTTCCCTTGCTTCTT
Found at i:173320 original size:16 final size:16
Alignment explanation
Indices: 173286--173320 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
173276 CCAGACAAAT
*
173286 AAATTGAAACACCATA
1 AAATTGAAACACCACA
*
173302 AAATTGAAACACCGCA
1 AAATTGAAACACCACA
173318 AAA
1 AAA
173321 GTAGGTAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.20, G:0.09, T:0.14
Consensus pattern (16 bp):
AAATTGAAACACCACA
Found at i:174532 original size:41 final size:41
Alignment explanation
Indices: 174468--174601 Score: 112
Period size: 41 Copynumber: 3.3 Consensus size: 41
174458 AAAAAAATGG
* * * *
174468 CGGCGTTTA-TATTAAAAACGCCAC-AATGGGATAAACTATTA
1 CGGCGTTTATTA-CAAAAACGCCACTAACGAGA-AAACAATTA
* * *
174509 CGGCGTTTATTACGAAAATGCCACTAACGAGAAAACAATTG
1 CGGCGTTTATTACAAAAACGCCACTAACGAGAAAACAATTA
* * * *
174550 CGGCGTTTATTACAAAAA-GGCACTAAAGGAGAATACAATTG
1 CGGCGTTTATTACAAAAACGCCACT-AACGAGAAAACAATTA
*
174591 CGGAGTTTATT
1 CGGCGTTTATT
174602 TAAAAATGCC
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 5 0.06
41 66 0.85
42 7 0.09
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25
Consensus pattern (41 bp):
CGGCGTTTATTACAAAAACGCCACTAACGAGAAAACAATTA
Found at i:174640 original size:41 final size:41
Alignment explanation
Indices: 174595--174698 Score: 129
Period size: 44 Copynumber: 2.5 Consensus size: 41
174585 CAATTGCGGA
174595 GTTTATTTAAAAATGCCACAAAATAATATATCTATTG-TGGC
1 GTTTATTTAAAAATGCCACAAAATAATATATCTATTGCT-GC
* *
174636 GTTTATCTAAAAAAAATGCCACAAAATATTATATCTATTGCTGC
1 GTTTAT-T--TAAAAATGCCACAAAATAATATATCTATTGCTGC
* *
174680 GTTTATCTAAAAACGCCAC
1 GTTTATTTAAAAATGCCAC
174699 TAAAGTACAA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
41 16 0.30
42 1 0.02
44 36 0.67
45 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (41 bp):
GTTTATTTAAAAATGCCACAAAATAATATATCTATTGCTGC
Found at i:174658 original size:44 final size:44
Alignment explanation
Indices: 174603--174692 Score: 155
Period size: 44 Copynumber: 2.0 Consensus size: 44
174593 GAGTTTATTT
174603 AAAAATGCCACAAAATAATATATCTATTG-TGGCGTTTATCTAAA
1 AAAAATGCCACAAAATAATATATCTATTGCT-GCGTTTATCTAAA
*
174647 AAAAATGCCACAAAATATTATATCTATTGCTGCGTTTATCTAAA
1 AAAAATGCCACAAAATAATATATCTATTGCTGCGTTTATCTAAA
174691 AA
1 AA
174693 CGCCACTAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 43 0.98
45 1 0.02
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.32
Consensus pattern (44 bp):
AAAAATGCCACAAAATAATATATCTATTGCTGCGTTTATCTAAA
Found at i:174829 original size:42 final size:41
Alignment explanation
Indices: 174669--175013 Score: 354
Period size: 41 Copynumber: 8.4 Consensus size: 41
174659 AAATATTATA
* * * * *
174669 TCTATTGCTGCGTTTATCTAAAAACGCCACTAAAGTACAAG
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
* * *
174710 TCTATAGCGACGTTTGTATAAAAACACCACTAAAGTACTAG
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
* * * *
174751 TCTATCGCGACGTTTATATAAAAACGCTACTAAAGTACGAG
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
* *
174792 TCTTTAGCGGCGTTT-TCATTCAAAACGCCACTAAAGTACGAG
1 TCTATAGCGGCGTTTGT-A-TAAAAACGCCACTAAAGTACGAG
* * *
174834 TTTATAGCGGCGTTTAG-ATTCAAAACGCCACTAAAGTATGAG
1 TCTATAGCGGCGTTT-GTA-TAAAAACGCCACTAAAGTACGAG
* * * *
174876 TATATAGCGGCGTTTGTATAGAAATGCCACTAAAGTACTAG
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
* * * * *
174917 TATATAGCGACGTTTGTATAAAAACGCCACTAACGTACAAT
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
* * *
174958 TCTATAGCGGCATTTGTATAAAAATGCCACTAAATTACGTA-
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACG-AG
*
174999 CCTATAGCGGCGTTT
1 TCTATAGCGGCGTTT
175014 ATTGGAAAAA
Statistics
Matches: 257, Mismatches: 41, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
40 1 0.00
41 182 0.71
42 74 0.29
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (41 bp):
TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
Found at i:176469 original size:41 final size:40
Alignment explanation
Indices: 176424--176603 Score: 132
Period size: 41 Copynumber: 4.4 Consensus size: 40
176414 AAAAAATGCC
* *
176424 ACTATTGTGGCGTTTGTTAAAAAATGCCACTATTGATTAAA
1 ACTATTGCGGCGTTT-TTAAAAAACGCCACTATTGATTAAA
* * * * * *
176465 ACTATTGTGGTGTTTTTCTAAAAACGTCATTATTGATTAAT
1 ACTATTGCGGCGTTTTT-AAAAAACGCCACTATTGATTAAA
* * **
176506 ACTATTGCGGTGTTTATCT-AAAAACGCCACTATTTATTATC
1 ACTATTGCGGCGTTT-T-TAAAAAACGCCACTATTGATTAAA
* *
176547 ACTATTGCGGCGTTTTAAGAATAAATGCCACTATATG-TGT-AA
1 ACTATTGCGGCGTTTTTA-AA-AAACGCCACTAT-TGAT-TAAA
*
176589 TCTATTGCGGCGTTT
1 ACTATTGCGGCGTTT
176604 GTGGTATAAA
Statistics
Matches: 112, Mismatches: 19, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
40 3 0.03
41 79 0.71
42 27 0.24
43 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.39
Consensus pattern (40 bp):
ACTATTGCGGCGTTTTTAAAAAACGCCACTATTGATTAAA
Found at i:176594 original size:42 final size:39
Alignment explanation
Indices: 176548--176684 Score: 125
Period size: 42 Copynumber: 3.4 Consensus size: 39
176538 TTTATTATCA
176548 CTATTGCGGCGTTTTAAGAATAAATGCCACTATATGTGTAAT
1 CTATTGCGGCGTTTT--GAATAAATGCCACTATATGT-TAAT
* * **
176590 CTATTGCGGCGTTTGTGGTATAAATACCGTTA-AT-TTACGAT
1 CTATTGCGGCGTTT-T-GAATAAATGCCACTATATGTTA--AT
** *
176631 CTATTGCGGCGTTTTGGCTAAAACGCCACTATATGTTAAT
1 CTATTGCGGCGTTTTGAAT-AAATGCCACTATATGTTAAT
176671 CTATTGCGGCGTTT
1 CTATTGCGGCGTTT
176685 GTGGTATAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 14
0.76 0.11 0.14
Matches are distributed among these distances:
39 4 0.05
40 25 0.32
41 20 0.26
42 28 0.36
43 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (39 bp):
CTATTGCGGCGTTTTGAATAAATGCCACTATATGTTAAT
Found at i:176684 original size:40 final size:41
Alignment explanation
Indices: 176548--176697 Score: 157
Period size: 41 Copynumber: 3.7 Consensus size: 41
176538 TTTATTATCA
* * *
176548 CTATTGCGGCGTTT-TAAGAATAAATGCCACTATATGTGTAAT
1 CTATTGCGGCGTTTGT-GGTATAAACGCCACTATATGT-TAAT
** **
176590 CTATTGCGGCGTTTGTGGTATAAATACCGTTA-AT-TTACGAT
1 CTATTGCGGCGTTTGTGGTATAAACGCCACTATATGTTA--AT
176631 CTATTGCGGCGTTT-TGGCTA-AAACGCCACTATATGTTAAT
1 CTATTGCGGCGTTTGTGG-TATAAACGCCACTATATGTTAAT
176671 CTATTGCGGCGTTTGTGGTATAAACGC
1 CTATTGCGGCGTTTGTGGTATAAACGC
176698 GATAATTTAC
Statistics
Matches: 91, Mismatches: 9, Indels: 17
0.78 0.08 0.15
Matches are distributed among these distances:
39 2 0.02
40 29 0.32
41 31 0.34
42 28 0.31
43 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (41 bp):
CTATTGCGGCGTTTGTGGTATAAACGCCACTATATGTTAAT
Found at i:176715 original size:41 final size:39
Alignment explanation
Indices: 176588--176727 Score: 144
Period size: 41 Copynumber: 3.5 Consensus size: 39
176578 TATATGTGTA
*
176588 ATCTATTGCGGCGTTTGTGGTATAAATAC-CGTTAATTTAC
1 ATCTATTGCGGCGTTTGTGGTAT-AA-ACGCGATAATTTAC
*
176628 GATCTATTGCGGCGTTT-TGGCTA-AAACGCCACTATATGTTA-
1 -ATCTATTGCGGCGTTTGTGG-TATAAACGCGA-TA-AT-TTAC
176669 ATCTATTGCGGCGTTTGTGGTATAAACGCGATAATTTACC
1 ATCTATTGCGGCGTTTGTGGTATAAACGCGATAATTTA-C
*
176709 ACTCTATTGTGGCGTTTGT
1 A-TCTATTGCGGCGTTTGT
176728 TAAAAAACGC
Statistics
Matches: 85, Mismatches: 4, Indels: 20
0.78 0.04 0.18
Matches are distributed among these distances:
38 5 0.06
39 5 0.06
40 26 0.31
41 46 0.54
42 3 0.04
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (39 bp):
ATCTATTGCGGCGTTTGTGGTATAAACGCGATAATTTAC
Found at i:176738 original size:81 final size:82
Alignment explanation
Indices: 176573--176725 Score: 240
Period size: 81 Copynumber: 1.9 Consensus size: 82
176563 AAGAATAAAT
* *
176573 GCCACTATATGTGTAATCTATTGCGGCGTTTGTGGTATAAATACCGTTAATTTACGATCTATTGC
1 GCCACTATATGTGTAATCTATTGCGGCGTTTGTGGTATAAATACCGATAATTTACCATCTATTGC
176638 GGCGTTTTGGCTAAAAC
66 GGCGTTTTGGCTAAAAC
176655 GCCACTATATGT-TAATCTATTGCGGCGTTTGTGGTAT-AA-ACGCGATAATTTACCACTCTATT
1 GCCACTATATGTGTAATCTATTGCGGCGTTTGTGGTATAAATAC-CGATAATTTACCA-TCTATT
*
176717 GTGGCGTTT
64 GCGGCGTTT
176726 GTTAAAAAAC
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
79 2 0.03
80 13 0.20
81 39 0.59
82 12 0.18
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.37
Consensus pattern (82 bp):
GCCACTATATGTGTAATCTATTGCGGCGTTTGTGGTATAAATACCGATAATTTACCATCTATTGC
GGCGTTTTGGCTAAAAC
Found at i:178299 original size:21 final size:21
Alignment explanation
Indices: 178252--178293 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
178242 TTTTAGATAG
* *
178252 AAAATTAATTTGATAATTAAT
1 AAAATTAATATGATAATAAAT
178273 AAAATTAATATGATAATAAAT
1 AAAATTAATATGATAATAAAT
178294 TTAATTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
AAAATTAATATGATAATAAAT
Found at i:179673 original size:4 final size:4
Alignment explanation
Indices: 179664--179690 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
179654 AAAAGGTTAA
179664 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
179691 ATCATATTAA
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:179763 original size:16 final size:15
Alignment explanation
Indices: 179742--179773 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
179732 ATTTAAAGGA
179742 AATAAATAAACAAAAT
1 AATAAATAAA-AAAAT
179758 AATAAATAAAAAAAT
1 AATAAATAAAAAAAT
179773 A
1 A
179774 TTAATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
AATAAATAAAAAAAT
Found at i:181135 original size:20 final size:20
Alignment explanation
Indices: 181107--181146 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
181097 TTTTATATAT
*
181107 TTTCTAAAACATTTTCAAAA
1 TTTCAAAAACATTTTCAAAA
181127 TTTCAAAAACATTTTCAAAA
1 TTTCAAAAACATTTTCAAAA
181147 CTATATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTCAAAAACATTTTCAAAA
Found at i:181178 original size:36 final size:36
Alignment explanation
Indices: 181138--181447 Score: 275
Period size: 36 Copynumber: 8.6 Consensus size: 36
181128 TTCAAAAACA
*
181138 TTTTCAAAACTATATATTATATATATTTAAAAAATG
1 TTTTCAAAACTATATATTATATATATTTTAAAAATG
* *
181174 TTTTCAAAAAAACTATATATATATATATATATTCAAAATG
1 TTTTC---AAAACTATATAT-TATATATATTTTAAAAATG
181214 TTTTCAAAAACTATATA-TATATATA---T-----TG
1 TTTTC-AAAACTATATATTATATATATTTTAAAAATG
* *
181242 TTTTCAAAACTATATATTATATATGTTTTTAAAATG
1 TTTTCAAAACTATATATTATATATATTTTAAAAATG
* * *
181278 TTTTCGAAACTATATATTATATATGTTTTCAAAATG
1 TTTTCAAAACTATATATTATATATATTTTAAAAATG
* * *
181314 TTTTCAAAAACTATTTATTATATATATATATTCAAATTG
1 TTTTC-AAAACTATATATTATATATAT-T-TTAAAAATG
* * * *
181353 TTTTAAAAAACTATATAATATATATA-TTCAAAAATCA
1 TTTT-CAAAACTATATATTATATATATTTTAAAAAT-G
*
181390 TTTTCAAAACTATATA--ATAAATATTTTCAAAAATCG
1 TTTTCAAAACTATATATTATATATATTTT-AAAAAT-G
*
181426 TTTTCAAAACTATATAATATAT
1 TTTTCAAAACTATATATTATAT
181448 TTTCAAAAAC
Statistics
Matches: 230, Mismatches: 22, Indels: 42
0.78 0.07 0.14
Matches are distributed among these distances:
27 11 0.05
28 14 0.06
31 1 0.00
33 1 0.00
34 6 0.03
35 2 0.01
36 93 0.40
37 23 0.10
38 16 0.07
39 42 0.18
40 21 0.09
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (36 bp):
TTTTCAAAACTATATATTATATATATTTTAAAAATG
Found at i:181212 original size:40 final size:38
Alignment explanation
Indices: 181138--181239 Score: 147
Period size: 38 Copynumber: 2.7 Consensus size: 38
181128 TTCAAAAACA
181138 TTTTC-AAAACTATATAT-TATATATATTTAAAAAATG
1 TTTTCAAAAACTATATATATATATATATTTAAAAAATG
*
181174 TTTTCAAAAAAACTATATATATATATATATATT-CAAAATG
1 TTTTC--AAAAACTATATATATATATATAT-TTAAAAAATG
181214 TTTTCAAAAACTATATATATATATAT
1 TTTTCAAAAACTATATATATATATAT
181240 TGTTTTCAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
36 5 0.08
38 21 0.35
39 12 0.20
40 20 0.33
41 2 0.03
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (38 bp):
TTTTCAAAAACTATATATATATATATATTTAAAAAATG
Found at i:181231 original size:30 final size:28
Alignment explanation
Indices: 181195--181263 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
181185 ACTATATATA
181195 TATATATATATTCAAAATGTTTTCAAAAAC
1 TATATATATATT-AAAATGTTTTC-AAAAC
* *
181225 TATATATATA-TATATTGTTTTCAAAAC
1 TATATATATATTAAAATGTTTTCAAAAC
181252 TATATATTATAT
1 TATATA-TATAT
181264 ATGTTTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 11 0.31
28 13 0.37
29 1 0.03
30 10 0.29
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.46
Consensus pattern (28 bp):
TATATATATATTAAAATGTTTTCAAAAC
Found at i:181236 original size:140 final size:141
Alignment explanation
Indices: 181126--181447 Score: 364
Period size: 148 Copynumber: 2.2 Consensus size: 141
181116 CATTTTCAAA
181126 ATTTCAAAAACATTTTCAAAACTATATATTATATATATTTAAAAAATGTTTTCAAAAAAACTATA
1 ATTTCAAAAACATTTTCAAAACTATATATTATATATATTTAAAAAATGTTTTC--AAAAACTATA
* *
181191 TA-TATATATATATATTCAAAATGTTTTCAAAAACTATAT-ATATATA-TATTGTTTTCAAAACT
64 TATTATATATATATATTCAAAATGTTTTAAAAAACTATATAATATATATTATTATTTTCAAAACT
181253 ATATATTATATAT
129 ATATATTATATAT
* ** ** * * ** *
181266 GTTTTTAAAATGTTTTCGAAACTATATATTATATATGTTTTCAAAATGTTTTCAAAAACTATTTA
1 ATTTCAAAAACATTTTCAAAACTATATATTATATATATTTAAAAAATGTTTTCAAAAACTATATA
* *
181331 TTATATATATATATTCAAATTGTTTTAAAAAACTATATAATATATATATTCAAAAATCATTTTCA
66 TTATATATATATATTCAAAATGTTTTAAAAAACTATAT-A-ATATATATT-----ATTATTTTCA
* *
181396 AAACTATATAATAAATAT
124 AAACTATATATTATATAT
* *
181414 -TTTCAAAAATCGTTTTCAAAACTATATAATATAT
1 ATTTCAAAAA-CATTTTCAAAACTATATATTATAT
181448 TTTCAAAAAC
Statistics
Matches: 150, Mismatches: 21, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
138 11 0.07
139 35 0.23
140 44 0.29
142 7 0.05
143 1 0.01
147 7 0.05
148 45 0.30
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (141 bp):
ATTTCAAAAACATTTTCAAAACTATATATTATATATATTTAAAAAATGTTTTCAAAAACTATATA
TTATATATATATATTCAAAATGTTTTAAAAAACTATATAATATATATTATTATTTTCAAAACTAT
ATATTATATAT
Found at i:181265 original size:28 final size:28
Alignment explanation
Indices: 181212--181275 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 28
181202 ATATTCAAAA
181212 TGTTTTCAAAAACTATATATATATATAT
1 TGTTTTCAAAAACTATATATATATATAT
181240 TGTTTTC-AAAACTATATAT-TATATA-
1 TGTTTTCAAAAACTATATATATATATAT
*
181265 TGTTTTTAAAA
1 TGTTTTCAAAA
181276 TGTTTTCGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
25 6 0.18
26 9 0.26
27 12 0.35
28 7 0.21
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (28 bp):
TGTTTTCAAAAACTATATATATATATAT
Found at i:181456 original size:34 final size:34
Alignment explanation
Indices: 181359--181463 Score: 156
Period size: 36 Copynumber: 3.0 Consensus size: 34
181349 ATTGTTTTAA
181359 AAAACTATATAATATATATATTCAAAAATCATTTTC
1 AAAACTATATAATATAT-T-TTCAAAAATCATTTTC
*
181395 AAAACTATATAATAAATATTTTCAAAAATCGTTTTC
1 AAAACTATATAAT--ATATTTTCAAAAATCATTTTC
*
181431 AAAACTATATAATATATTTTCAAAAACCATTTT
1 AAAACTATATAATATATTTTCAAAAATCATTTT
181464 TTTAAAAAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
34 18 0.28
36 41 0.64
37 1 0.02
38 4 0.06
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (34 bp):
AAAACTATATAATATATTTTCAAAAATCATTTTC
Found at i:182254 original size:85 final size:84
Alignment explanation
Indices: 182081--182581 Score: 664
Period size: 85 Copynumber: 5.9 Consensus size: 84
182071 TACCATGCGG
* * * * **
182081 TTGATATGTCATCGAGCTGAATGGGATCAAACTCGAAAGTTTTTTGTTGACAAATAAACCTTCTC
1 TTGATATGTCATTGAGCTGAATGGAATCAAACTCG-AAGGTTTTTGTTGACAGATAGCCCTTCTC
182146 GCCTTGAGCTATGCTGTAAAT
65 GCCTTGAGCTATGCTG-AAAT
* * *
182167 TTGATATGTCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTCGTTGACAGATAGCCCTTCTCG
1 TTGATATGTCATTGAGCTGAATGGAATCAAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
* *
182232 CTTTGAGTTATGCTAGAAAT
66 CCTTGAGCTATGCT-GAAAT
* * *
182252 TTGATATGTCATTGAGCTGAATGGAATCGAACTCGAAGTTTTTTGTTGACAGATAACCCTTCTCG
1 TTGATATGTCATTGAGCTGAATGGAATCAAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
182317 CCTTGAGCTATGCTGTAAAT
66 CCTTGAGCTATGCTG-AAAT
* *
182337 TTGATATGTCATTGAGCTGAATAGAATCAAACTCGAAGGTTTTTGTTGACAGATAGCCCTTTTCG
1 TTGATATGTCATTGAGCTGAATGGAATCAAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
*
182402 CCTTGATCTGATG-T-AAAT
66 CCTTGAGCT-ATGCTGAAAT
* * * * *
182420 TTGATATGTCCTTGAGTTGAATGGAATCGAACTCGTAGGTTTTTTGTTGACAGATAGCCCTTCTA
1 TTGATATGTCATTGAGCTGAATGGAATCAAACTCGAAGG-TTTTTGTTGACAGATAGCCCTTCTC
*
182485 GCCTTGAGCTATGCTATAAAT
65 GCCTTGAGCTATGCT-GAAAT
* * * * * *
182506 TTGATATGCCCTTGAGCTGAATGTAATCAAACTCGAAGGTTTTTGCTAACAGATAGCCCTTCCCG
1 TTGATATGTCATTGAGCTGAATGGAATCAAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
182571 CCTTGAGCTAT
66 CCTTGAGCTAT
182582 TTTTGCGAAT
Statistics
Matches: 368, Mismatches: 40, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
83 41 0.11
84 34 0.09
85 220 0.60
86 73 0.20
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (84 bp):
TTGATATGTCATTGAGCTGAATGGAATCAAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
CCTTGAGCTATGCTGAAAT
Found at i:184290 original size:96 final size:96
Alignment explanation
Indices: 184125--184312 Score: 288
Period size: 96 Copynumber: 2.0 Consensus size: 96
184115 GTAATTTGTC
* * * *
184125 TTTATCAGGCTAGCTGAATCTTATCCATAAAGTCGGGGCAATTAACCAATTGCTCTAGAGGGATA
1 TTTATAAGGCTAGCTGAATCTTATCCACAAAGTCGGGACAATTAACCAATTGCTCTAGAGGGACA
*
184190 GCTCAAGCATTATTATATATATTATAATCACG
66 GCTCAAGCATTATTATATACA-TATAATCACG
*
184222 TTTATAAGGCTAGCTGAATCTTATCCACAAAG-CGGGACATTTAACCAATTGCTCTAGAGGGACA
1 TTTATAAGGCTAGCTGAATCTTATCCACAAAGTCGGGACAATTAACCAATTGCTCTAGAGGGACA
* *
184286 GCTCAAGCTTTATTGTATACATATAAT
66 GCTCAAGCATTATTATATACATATAAT
184313 ATTATAATAT
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
95 6 0.07
96 47 0.57
97 30 0.36
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (96 bp):
TTTATAAGGCTAGCTGAATCTTATCCACAAAGTCGGGACAATTAACCAATTGCTCTAGAGGGACA
GCTCAAGCATTATTATATACATATAATCACG
Found at i:186493 original size:97 final size:96
Alignment explanation
Indices: 186289--186506 Score: 262
Period size: 97 Copynumber: 2.2 Consensus size: 96
186279 AAAACAGAAA
* *
186289 ACCATAGTTTACAAACCAGTAAATTCCATGATTCCATAAATCAGGAACAATTCATATTTTCCAAT
1 ACCATAGTTCATAAACCAGTAAATTCCATGATTCCATAAATCAGGAACAATTCATATTTTCCAAT
* **
186354 GAAAACAGGAAACCTGATAACACATTTCAGGT
66 GAAAACA-GAAACATGATAACACATACCAGGT
* * *
186386 ACCATAGTTCATAAACTAGTAAATTCCATGATTCCATAAATCATGAACAATTCATAGTTTT-CGA
1 ACCATAGTTCATAAACCAGTAAATTCCATGATTCCATAAATCAGGAACAATTCATA-TTTTCCAA
* *
186450 TGAAAACCA-AAATCAT-ATATCACATACCATGTT
65 TGAAAA-CAGAAA-CATGATAACACATACCA-GGT
* *
186483 TCCATGGTTCATAAACCAGTAAAT
1 ACCATAGTTCATAAACCAGTAAAT
186507 CAATACTTTC
Statistics
Matches: 104, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
96 13 0.12
97 85 0.82
98 6 0.06
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (96 bp):
ACCATAGTTCATAAACCAGTAAATTCCATGATTCCATAAATCAGGAACAATTCATATTTTCCAAT
GAAAACAGAAACATGATAACACATACCAGGT
Found at i:187492 original size:28 final size:27
Alignment explanation
Indices: 187460--187519 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
187450 AATTCCAGGG
*
187460 TTTAGAGGTACTTTAGGCCATTTTACAC
1 TTTAGAGGCA-TTTAGGCCATTTTACAC
* * *
187488 TTTAGGGGCATTTTGGTCATTTTACAC
1 TTTAGAGGCATTTAGGCCATTTTACAC
187515 TTTAG
1 TTTAG
187520 GGTTATTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 20 0.71
28 8 0.29
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (27 bp):
TTTAGAGGCATTTAGGCCATTTTACAC
Found at i:191104 original size:97 final size:96
Alignment explanation
Indices: 190900--191117 Score: 242
Period size: 97 Copynumber: 2.2 Consensus size: 96
190890 AAAATAGAAA
* **
190900 ACCATAGTTCATAAACCAGTAAATTCCATGGTTCCATAAATCAGGAACAATTCATATTTTTTAGC
1 ACCATAGTTCATAAACCAGTAAATTCCATGATTCCATAAATCAGGAACAATTCATATTTTCGAGC
* * **
190965 GACAACAGGAAACCCGATAACATATTTCAGGT
66 GAAAACA-GAAACCAGATAACATATACCAGGT
*
190997 ACCATAGTTCATAAACCAGTAAATTCCATGATTCCATAAATCATGAACAATTCATAGTTTTCGA-
1 ACCATAGTTCATAAACCAGTAAATTCCATGATTCCATAAATCAGGAACAATTCATA-TTTTCGAG
* * * * *
191061 TGAAAACCA-AAATCAGATATCATATACCTTGTT
65 CGAAAA-CAGAAACCAGATAACATATACC-AGGT
* * *
191094 GCCATGGTTCATAAACTAGTAAAT
1 ACCATAGTTCATAAACCAGTAAAT
191118 CAATACTTTC
Statistics
Matches: 102, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
96 14 0.14
97 81 0.79
98 7 0.07
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (96 bp):
ACCATAGTTCATAAACCAGTAAATTCCATGATTCCATAAATCAGGAACAATTCATATTTTCGAGC
GAAAACAGAAACCAGATAACATATACCAGGT
Found at i:191955 original size:27 final size:27
Alignment explanation
Indices: 191898--191965 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
191888 AATTCCAGGG
* *
191898 TTTAGAGGTACTTTAGGCCATTTTACTC
1 TTTAGGGGTA-TTTAGGCCATTTTACAC
* *
191926 TTTAGGGGTATTTTGGTCATTTTACAC
1 TTTAGGGGTATTTAGGCCATTTTACAC
191953 TTTAGGGGTATTT
1 TTTAGGGGTATTT
191966 CTATAATTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 27 0.75
28 9 0.25
ACGTcount: A:0.19, C:0.12, G:0.22, T:0.47
Consensus pattern (27 bp):
TTTAGGGGTATTTAGGCCATTTTACAC
Found at i:192881 original size:11 final size:11
Alignment explanation
Indices: 192859--192889 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
192849 AAAGGTCAAA
192859 GTCAAC-GTCG
1 GTCAACGGTCG
192869 GTCAACGGTCG
1 GTCAACGGTCG
192880 GTCAACGGTC
1 GTCAACGGTC
192890 AACGCTGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.19, C:0.29, G:0.32, T:0.19
Consensus pattern (11 bp):
GTCAACGGTCG
Found at i:195949 original size:96 final size:97
Alignment explanation
Indices: 195784--195967 Score: 361
Period size: 96 Copynumber: 1.9 Consensus size: 97
195774 CCGGCCACCA
195784 CCACCGGTGGATGGAAAAAAAATCCTTCTTTTTACACCTTCTAACCCCCTGAAGCCAAATCTGAC
1 CCACCGGTGGATGGAAAAAAAATCCTTCTTTTTACACCTTCTAACCCCCTGAAGCCAAATCTGAC
195849 CCTCAAACCCCCAAAAATCACCTACTCGCAAT
66 CCTCAAACCCCCAAAAATCACCTACTCGCAAT
195881 CCACCGGTGGATGG-AAAAAAATCCTTCTTTTTACACCTTCTAACCCCCTGAAGCCAAATCTGAC
1 CCACCGGTGGATGGAAAAAAAATCCTTCTTTTTACACCTTCTAACCCCCTGAAGCCAAATCTGAC
195945 CCTCAAACCCCCAAAAATCACCT
66 CCTCAAACCCCCAAAAATCACCT
195968 TAATCGTCGC
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
96 73 0.84
97 14 0.16
ACGTcount: A:0.33, C:0.35, G:0.10, T:0.22
Consensus pattern (97 bp):
CCACCGGTGGATGGAAAAAAAATCCTTCTTTTTACACCTTCTAACCCCCTGAAGCCAAATCTGAC
CCTCAAACCCCCAAAAATCACCTACTCGCAAT
Found at i:196108 original size:23 final size:23
Alignment explanation
Indices: 196078--196128 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
196068 ATTCATGTTC
196078 CTTTTGATGAGAAAAGGCCTTGG
1 CTTTTGATGAGAAAAGGCCTTGG
196101 CTTTTGATGAGAAAAGGCCTTGG
1 CTTTTGATGAGAAAAGGCCTTGG
*
196124 TTTTT
1 CTTTT
196129 TCAGTTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (23 bp):
CTTTTGATGAGAAAAGGCCTTGG
Found at i:196697 original size:22 final size:21
Alignment explanation
Indices: 196644--196708 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 21
196634 AAGAAAAAAC
*
196644 AAAATAAACAA-AATAAATAA
1 AAAATAAAAAATAATAAATAA
**
196664 AAACGAAGAAAATAATAAATAA
1 AAAATAA-AAAATAATAAATAA
*
196686 ATAAATAAAAAATACTAAA-AA
1 A-AAATAAAAAATAATAAATAA
196707 AA
1 AA
196709 GATTTTTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
20 6 0.17
21 6 0.17
22 20 0.56
23 4 0.11
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (21 bp):
AAAATAAAAAATAATAAATAA
Found at i:196767 original size:20 final size:21
Alignment explanation
Indices: 196742--196783 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
196732 TATATATTAT
* *
196742 ATTTTCTAAAACGTTTT-AAA
1 ATTTTCAAAAACATTTTCAAA
196762 ATTTTCAAAAACATTTTCAAA
1 ATTTTCAAAAACATTTTCAAA
196783 A
1 A
196784 CTATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTTTCAAAAACATTTTCAAA
Found at i:196822 original size:38 final size:37
Alignment explanation
Indices: 196775--197094 Score: 372
Period size: 38 Copynumber: 8.6 Consensus size: 37
196765 TTCAAAAACA
* **
196775 TTTTC-AAAACTATTTATTATATATATTTAAAAAATG
1 TTTTCAAAAACTATATATTATATATATTTTCAAAATG
* *
196811 TTTTAAAAAAACTATATA-TATATATATATTCAAAATG
1 TTTT-CAAAAACTATATATTATATATATTTTCAAAATG
* *
196848 TTCTCAAAAACTTTATATTATATATATGTTTTCAAAATG
1 TTTTCAAAAACTATATATTATATATA--TTTTCAAAATG
*
196887 TTTTC-AAAACTATATATTATATATGTTTTCAAAATG
1 TTTTCAAAAACTATATATTATATATATTTTCAAAATG
*
196923 TTTTCGAAAACTATATATTATATATATATTTTCAAAATG
1 TTTTCAAAAACTATATA-T-TATATATATTTTCAAAATG
196962 TTTTCAAAAACTAT-TATATATTATATATTTTCAAAATG
1 TTTTCAAAAACTATATAT-TA-TATATATTTTCAAAATG
197000 TTTTCAAAAACTATATA--ATATATA--TTCAAAAATTG
1 TTTTCAAAAACTATATATTATATATATTTTC-AAAA-TG
*
197035 TTTTC-AAAACTATATAATAT-TATATTTTCAAAAATCG
1 TTTTCAAAAACTATATATTATATATATTTTC-AAAAT-G
*
197072 TTTTCAAAAACTATATAATATAT
1 TTTTCAAAAACTATATATTATAT
197095 TTTCAAAAAC
Statistics
Matches: 251, Mismatches: 14, Indels: 35
0.84 0.05 0.12
Matches are distributed among these distances:
33 3 0.01
34 15 0.06
35 17 0.07
36 35 0.14
37 56 0.22
38 77 0.31
39 48 0.19
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (37 bp):
TTTTCAAAAACTATATATTATATATATTTTCAAAATG
Found at i:196889 original size:11 final size:11
Alignment explanation
Indices: 196873--196932 Score: 50
Period size: 11 Copynumber: 5.1 Consensus size: 11
196863 TATTATATAT
196873 ATGTTTTCAAA
1 ATGTTTTCAAA
196884 ATGTTTTCAAA
1 ATGTTTTCAAA
* *
196895 ACTATATATT-ATAT
1 A-TGT-T-TTCA-AA
196909 ATGTTTTCAAA
1 ATGTTTTCAAA
196920 ATGTTTTCGAAA
1 ATGTTTTC-AAA
196932 A
1 A
196933 CTATATATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
11 23 0.59
12 8 0.21
13 4 0.10
14 4 0.10
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.45
Consensus pattern (11 bp):
ATGTTTTCAAA
Found at i:197451 original size:24 final size:24
Alignment explanation
Indices: 197423--197470 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
197413 ATAAGATAAC
*
197423 TAAAACAATAAAAATA-TTTTATT
1 TAAAAAAATAAAAATATTTTTATT
*
197446 TAAAAATATAAAAATATTTTTATT
1 TAAAAAAATAAAAATATTTTTATT
197470 T
1 T
197471 TTATATTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAAAAAATAAAAATATTTTTATT
Found at i:198391 original size:36 final size:36
Alignment explanation
Indices: 198358--198479 Score: 102
Period size: 36 Copynumber: 3.2 Consensus size: 36
198348 TAGTATACAT
198358 ATTTCTCTTTCCAACTGAAACAAAATGAATATACTA
1 ATTTCTCTTTCCAACTGAAACAAAATGAATATACTA
**** * * * *
198394 ATTTCTCTGAAGAACTTAATATTAAGTAACATTAGTATAC-A
1 ATTTCTCTTTCCAACTGAA-A--CA--AA-ATGAATATACTA
198435 TATTTCTCTTTCCAACTGAAACAAAATGAATATACTA
1 -ATTTCTCTTTCCAACTGAAACAAAATGAATATACTA
198472 ATTTCTCT
1 ATTTCTCT
198480 GAAGAACTTA
Statistics
Matches: 62, Mismatches: 16, Indels: 16
0.66 0.17 0.17
Matches are distributed among these distances:
36 30 0.48
37 4 0.06
39 2 0.03
41 4 0.06
42 22 0.35
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (36 bp):
ATTTCTCTTTCCAACTGAAACAAAATGAATATACTA
Found at i:198473 original size:78 final size:78
Alignment explanation
Indices: 198344--198500 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
198334 TCCCTAAAAT
198344 ACATTAGTATACATATTTCTCTTTCCAACTGAAACAAAATGAATATACTAATTTCTCTGAAGAAC
1 ACATTAGTATACATATTTCTCTTTCCAACTGAAACAAAATGAATATACTAATTTCTCTGAAGAAC
198409 TTAATATTAAGTA
66 TTAATATTAAGTA
198422 ACATTAGTATACATATTTCTCTTTCCAACTGAAACAAAATGAATATACTAATTTCTCTGAAGAAC
1 ACATTAGTATACATATTTCTCTTTCCAACTGAAACAAAATGAATATACTAATTTCTCTGAAGAAC
198487 TTAATATTAAGTA
66 TTAATATTAAGTA
198500 A
1 A
198501 TTTGATCAGT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (78 bp):
ACATTAGTATACATATTTCTCTTTCCAACTGAAACAAAATGAATATACTAATTTCTCTGAAGAAC
TTAATATTAAGTA
Found at i:201042 original size:3 final size:3
Alignment explanation
Indices: 201034--201074 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
201024 TTCTTTTATG
* * *
201034 TAA TAA TAA TAA TAA TAA CAA TAA CAA TAA AAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
201075 CAACCCATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:207156 original size:168 final size:168
Alignment explanation
Indices: 206878--207214 Score: 665
Period size: 168 Copynumber: 2.0 Consensus size: 168
206868 CAATTTCACT
*
206878 TGTATTAGAGATATAGGTGGTTGACACAATACTGATGTGCTACTGTTGTGGAGCTGTTGCACATT
1 TGTATTAGAGATATAAGTGGTTGACACAATACTGATGTGCTACTGTTGTGGAGCTGTTGCACATT
206943 TGGGAAATTGTTAAAAATGTTATTAAATTTGTTAGGCTTGCCAGCTAGGCCTATAGGTAGTTACA
66 TGGGAAATTGTTAAAAATGTTATTAAATTTGTTAGGCTTGCCAGCTAGGCCTATAGGTAGTTACA
207008 GTATACCTATATAAACATGTTAGTGTGTTGTAGAAAAA
131 GTATACCTATATAAACATGTTAGTGTGTTGTAGAAAAA
207046 TGTATTAGAGATATAAGTGGTTGACACAATACTGATGTGCTACTGTTGTGGAGCTGTTGCACATT
1 TGTATTAGAGATATAAGTGGTTGACACAATACTGATGTGCTACTGTTGTGGAGCTGTTGCACATT
207111 TGGGAAATTGTTAAAAATGTTATTAAATTTGTTAGGCTTGCCAGCTAGGCCTATAGGTAGTTACA
66 TGGGAAATTGTTAAAAATGTTATTAAATTTGTTAGGCTTGCCAGCTAGGCCTATAGGTAGTTACA
207176 GTATACCTATATAAACATGTTAGTGTGTTGTAGAAAAA
131 GTATACCTATATAAACATGTTAGTGTGTTGTAGAAAAA
207214 T
1 T
207215 AAGAGTAAGA
Statistics
Matches: 168, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 168 1.00
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (168 bp):
TGTATTAGAGATATAAGTGGTTGACACAATACTGATGTGCTACTGTTGTGGAGCTGTTGCACATT
TGGGAAATTGTTAAAAATGTTATTAAATTTGTTAGGCTTGCCAGCTAGGCCTATAGGTAGTTACA
GTATACCTATATAAACATGTTAGTGTGTTGTAGAAAAA
Found at i:211817 original size:18 final size:19
Alignment explanation
Indices: 211796--211831 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
211786 ATATATTAAA
211796 CTTGAC-ATTTCTATTTGC
1 CTTGACAATTTCTATTTGC
*
211814 CTTGACAATTTTTATTTG
1 CTTGACAATTTCTATTTG
211832 TTTACTCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
CTTGACAATTTCTATTTGC
Found at i:213609 original size:20 final size:20
Alignment explanation
Indices: 213569--213607 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
213559 CACTGCAGGA
213569 ATTTATGGCCTCAACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
213589 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
213608 GACCTTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:215023 original size:24 final size:24
Alignment explanation
Indices: 214970--215023 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
214960 CACCATTGCT
*
214970 CATATAATTTTCACCGAAGTGCCA
1 CATAGAATTTTCACCGAAGTGCCA
**
214994 TGTAGAATTTTCACCGAAGTGCCA
1 CATAGAATTTTCACCGAAGTGCCA
215018 CATAGA
1 CATAGA
215024 TATGTCTCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (24 bp):
CATAGAATTTTCACCGAAGTGCCA
Done.