Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015192.1 Kokia drynarioides strain JFW-HI SEQ_130236, 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: 216668
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 66 characters in sequence are not A, C, G, or T
Found at i:7874 original size:2 final size:2
Alignment explanation
Indices: 7867--7898 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
7857 TAAATTTACA
*
7867 CT CT CT CT CT CT CT CT CT CT CT CT CA CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
7899 ATATAATATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:15682 original size:31 final size:30
Alignment explanation
Indices: 15647--15708 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
15637 TGAGTTAATC
15647 AAGTTATTCGGATCAACTCGAATAAAAAATT
1 AAGTTATTCGGATCAACTCGAA-AAAAAATT
* * * *
15678 AAGTTTTTCGGTTTAACTCGAAAACAAATT
1 AAGTTATTCGGATCAACTCGAAAAAAAATT
15708 A
1 A
15709 CACAATTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (30 bp):
AAGTTATTCGGATCAACTCGAAAAAAAATT
Found at i:20634 original size:35 final size:35
Alignment explanation
Indices: 20587--20656 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
20577 CGTTATTCTG
*
20587 AATGTTTCAAGTTGAGCAACTTTCTGTTTCTATGT
1 AATGTTTCAAGTTGAGCAACTTTCTGTTGCTATGT
*
20622 AATGTTTGAAGTTGAGCAACTTTCTGTTGCTATGT
1 AATGTTTCAAGTTGAGCAACTTTCTGTTGCTATGT
20657 TTTGGAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.44
Consensus pattern (35 bp):
AATGTTTCAAGTTGAGCAACTTTCTGTTGCTATGT
Found at i:24737 original size:73 final size:70
Alignment explanation
Indices: 24637--24784 Score: 197
Period size: 73 Copynumber: 2.1 Consensus size: 70
24627 TCAAAGTTCT
* * * * *
24637 AAAGTCTCGATATAGTCTTGAAAACTTCAATAGTTAAGCATGTTAGCATACCAGATTAAACAAGA
1 AAAGTCTCGATATAGTCATGAAAACTTCAATACTTAAGCACGTTAGCATACCAAATCAAACAAGA
24702 TATTC
66 TATTC
* * *
24707 AAAGTGCTCGATATAGAGTCATGAAAACTTCGATACTTAAGCACGTTGGCATACCAAATCAAGCA
1 AAAGT-CTCGATAT--AGTCATGAAAACTTCAATACTTAAGCACGTTAGCATACCAAATCAAACA
24772 AGATATTC
63 AGATATTC
24780 AAAGT
1 AAAGT
24785 TTTAAAAGTC
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
70 5 0.07
71 8 0.12
73 54 0.81
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (70 bp):
AAAGTCTCGATATAGTCATGAAAACTTCAATACTTAAGCACGTTAGCATACCAAATCAAACAAGA
TATTC
Found at i:25447 original size:15 final size:15
Alignment explanation
Indices: 25427--25457 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
25417 ATGTCAATGC
25427 ACATGATATTAACCA
1 ACATGATATTAACCA
25442 ACATGATATTAACCA
1 ACATGATATTAACCA
25457 A
1 A
25458 GCTGAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (15 bp):
ACATGATATTAACCA
Found at i:32737 original size:22 final size:22
Alignment explanation
Indices: 32703--32755 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
32693 ATAATCTAGT
*
32703 TTTTATAAAAAAAAATTTAAAAA
1 TTTTA-AAAAAAAAATATAAAAA
*
32726 -TTTAAAAGAAAATATATAAAAA
1 TTTTAAAA-AAAAAATATAAAAA
32748 TTTTAAAA
1 TTTTAAAA
32756 TATAAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 3 0.12
22 16 0.62
23 7 0.27
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
TTTTAAAAAAAAAATATAAAAA
Found at i:32757 original size:18 final size:20
Alignment explanation
Indices: 32734--32773 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
32724 AATTTAAAAG
*
32734 AAAATATATAA-AAATT-TT
1 AAAATATAAAAGAAATTATT
32752 AAAATATAAAAGAAATTATT
1 AAAATATAAAAGAAATTATT
32772 AA
1 AA
32774 TTATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 5 0.26
20 4 0.21
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAATATAAAAGAAATTATT
Found at i:41732 original size:2 final size:2
Alignment explanation
Indices: 41725--41749 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41715 GAAAATTGGG
41725 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
41750 TTTTAATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:47005 original size:17 final size:17
Alignment explanation
Indices: 46970--47011 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
46960 GGAAAAAGTA
*
46970 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
46988 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
47005 GTTAAAG
1 GTTAAAG
47012 GTCAAGGGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:51299 original size:19 final size:19
Alignment explanation
Indices: 51275--51313 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
51265 CAATGGTTAA
51275 ATCATTCTTTCAAATTATT
1 ATCATTCTTTCAAATTATT
51294 ATCATTCTTTCAAATTATT
1 ATCATTCTTTCAAATTATT
51313 A
1 A
51314 CATAATTCAA
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:0.33, C:0.15, G:0.00, T:0.51
Consensus pattern (19 bp):
ATCATTCTTTCAAATTATT
Found at i:63787 original size:63 final size:63
Alignment explanation
Indices: 63621--63779 Score: 284
Period size: 63 Copynumber: 2.5 Consensus size: 63
63611 CACACCTGTT
63621 CCTCCACCTGCACAAGTCCACATACCAACGTCCTTACCCACTATTGTACCTCTCACAACTACC
1 CCTCCACCTGCACAAGTCCACATACCAACGTCCTTACCCACTATTGTACCTCTCACAACTACC
63684 CCTCCACCTGCACAAGTCCACATACCAACGTCCTTACCCACTATTGTACCTCTCACAACTACC
1 CCTCCACCTGCACAAGTCCACATACCAACGTCCTTACCCACTATTGTACCTCTCACAACTACC
* *
63747 CCTCCACCTGAACAA-TTCACTATACCAACGTCC
1 CCTCCACCTGCACAAGTCCAC-ATACCAACGTCC
63780 CAACCCACCA
Statistics
Matches: 93, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
62 4 0.04
63 89 0.96
ACGTcount: A:0.28, C:0.44, G:0.06, T:0.22
Consensus pattern (63 bp):
CCTCCACCTGCACAAGTCCACATACCAACGTCCTTACCCACTATTGTACCTCTCACAACTACC
Found at i:71728 original size:26 final size:26
Alignment explanation
Indices: 71697--71752 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 26
71687 GGTACATAAG
71697 TGCTGGGGAAACAGAAGCACACACAA
1 TGCTGGGGAAACAGAAGCACACACAA
* *
71723 TGCT-GGGTAACAGAAGCACACACAG
1 TGCTGGGGAAACAGAAGCACACACAA
71748 TGCTG
1 TGCTG
71753 AACAAAAGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.36, C:0.23, G:0.29, T:0.12
Consensus pattern (26 bp):
TGCTGGGGAAACAGAAGCACACACAA
Found at i:90294 original size:17 final size:17
Alignment explanation
Indices: 90261--90294 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
90251 TAAATTTAAG
*
90261 TTTATTATAATATTATT
1 TTTATTATAATACTATT
*
90278 TTTATTATATTACTATT
1 TTTATTATAATACTATT
90295 CAGTAAGTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTATTATAATACTATT
Found at i:93687 original size:20 final size:20
Alignment explanation
Indices: 93662--93701 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
93652 TAATTTTTTT
93662 TATTTTTATA-ATTTTGTTGA
1 TATTTTTATACATTTT-TTGA
93682 TATTTTTATACATTTTTTGA
1 TATTTTTATACATTTTTTGA
93702 GAAATTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (20 bp):
TATTTTTATACATTTTTTGA
Found at i:99859 original size:23 final size:27
Alignment explanation
Indices: 99800--99861 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 27
99790 TTTTGATAAA
*
99800 TTTAGAATTTAATCTTTATATTTTTAT
1 TTTAGAATTTAATCTTTATATTATTAT
99827 TTTCAGGAATTTAAT-TTT-T-TTATT-T
1 TTT-A-GAATTTAATCTTTATATTATTAT
99852 TTTAGAATTT
1 TTTAGAATTT
99862 CAAAATTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
23 6 0.19
24 1 0.03
25 4 0.12
26 4 0.12
27 4 0.12
28 4 0.12
29 9 0.28
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.63
Consensus pattern (27 bp):
TTTAGAATTTAATCTTTATATTATTAT
Found at i:100172 original size:11 final size:11
Alignment explanation
Indices: 100156--100181 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
100146 TGACACGTGT
100156 TTTTATTATTA
1 TTTTATTATTA
100167 TTTTATTATTA
1 TTTTATTATTA
100178 TTTT
1 TTTT
100182 TATATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:100543 original size:4 final size:4
Alignment explanation
Indices: 100524--100576 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
100514 AAATAAACGG
* * * *
100524 GAAA AAAA GAAAA GAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
100574 GAA
1 GAA
100577 TAATTATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 33 0.80
5 8 0.20
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:102782 original size:21 final size:20
Alignment explanation
Indices: 102743--102783 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
102733 GTAACTCAGG
*
102743 TATTGATATTTTTCGTAAAA
1 TATTGATATTTTGCGTAAAA
*
102763 TATTGATACTTTTGCTTAAAA
1 TATTGATA-TTTTGCGTAAAA
102784 ACGGTACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (20 bp):
TATTGATATTTTGCGTAAAA
Found at i:103725 original size:23 final size:23
Alignment explanation
Indices: 103616--103717 Score: 118
Period size: 23 Copynumber: 4.4 Consensus size: 23
103606 TGTTGGGCAA
* *
103616 CAGTAAACACACACAGTGCTAAT
1 CAGTAAGCACACACAGTGCGAAT
103639 CAGTAAGCACACACAGTGCTG-AT
1 CAGTAAGCACACACAGTGC-GAAT
* * *
103662 TAGTAAACACACGCAGTGC-AAT
1 CAGTAAGCACACACAGTGCGAAT
*
103684 CCAGTAAGCACATACAGTGCGAAT
1 -CAGTAAGCACACACAGTGCGAAT
103708 CAGTAAGCAC
1 CAGTAAGCAC
103718 TTACAGTGTT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
22 2 0.03
23 61 0.92
24 3 0.05
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCGAAT
Found at i:103725 original size:46 final size:46
Alignment explanation
Indices: 103616--103713 Score: 137
Period size: 46 Copynumber: 2.1 Consensus size: 46
103606 TGTTGGGCAA
103616 CAGTAAACACACACAGTGCTAATCAGTAAGCACACACAGTGCTGAT
1 CAGTAAACACACACAGTGCTAATCAGTAAGCACACACAGTGCTGAT
* * *
103662 TAGTAAACACACGCAGTGC-AATCCAGTAAGCACATACAGTGC-GAAT
1 CAGTAAACACACACAGTGCTAAT-CAGTAAGCACACACAGTGCTG-AT
103708 CAGTAA
1 CAGTAA
103714 GCACTTACAG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
45 4 0.09
46 42 0.91
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.17
Consensus pattern (46 bp):
CAGTAAACACACACAGTGCTAATCAGTAAGCACACACAGTGCTGAT
Found at i:108605 original size:23 final size:23
Alignment explanation
Indices: 108578--108631 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
108568 AATATCCTAG
*
108578 GAATAATTAGAGTTTAGCTGGGAA
1 GAATAATTAGAGTTTAACT-GGAA
* *
108602 -AATATAGTATAGTTTAACTGGAA
1 GAATA-ATTAGAGTTTAACTGGAA
108625 GAATAAT
1 GAATAAT
108632 ACGAGGCACA
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.31
Consensus pattern (23 bp):
GAATAATTAGAGTTTAACTGGAA
Found at i:113820 original size:27 final size:30
Alignment explanation
Indices: 113758--113829 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
113748 ATCATAATTT
* * *
113758 TAAAAAAATTCAAAAATATATATAAATACA
1 TAAATAAATTTAAATATATATATAAATACA
* *
113788 TAAAT-ATTTTAAATATATATATATATA-A
1 TAAATAAATTTAAATATATATATAAATACA
113816 T-AATAAATTTAAAT
1 TAAATAAATTTAAAT
113830 TTTGTATTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 3 0.09
28 10 0.29
29 18 0.51
30 4 0.11
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (30 bp):
TAAATAAATTTAAATATATATATAAATACA
Found at i:114416 original size:26 final size:25
Alignment explanation
Indices: 114386--114443 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
114376 TTGGGAAACA
*
114386 TTTATTGAAATTTTTTTAGTGTATT
1 TTTATTGAAATTTTTTTAATGTATT
* * *
114411 TGTTATATTATATTTTTTTAATTTATT
1 T-TTAT-TGAAATTTTTTTAATGTATT
114438 TTTATT
1 TTTATT
114444 TAAAAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
25 2 0.07
26 8 0.30
27 17 0.63
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (25 bp):
TTTATTGAAATTTTTTTAATGTATT
Found at i:121429 original size:3 final size:3
Alignment explanation
Indices: 121421--121451 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
121411 CCAACAAGTT
121421 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
121452 ATTTTTCCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:123547 original size:38 final size:38
Alignment explanation
Indices: 123502--123578 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
123492 CCATCAACTA
123502 AACACAACATTGACTAAAATAACTCACGTATAGCTCTT
1 AACACAACATTGACTAAAATAACTCACGTATAGCTCTT
123540 AACACAACATTGACTAAAATAACTCACGTATAGCTCTT
1 AACACAACATTGACTAAAATAACTCACGTATAGCTCTT
123578 A
1 A
123579 GAACTGGTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26
Consensus pattern (38 bp):
AACACAACATTGACTAAAATAACTCACGTATAGCTCTT
Found at i:123844 original size:20 final size:20
Alignment explanation
Indices: 123815--123852 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
123805 GTTTTTCGAA
*
123815 AAAAAATCAATGGTCAACCT
1 AAAAAATCAATGATCAACCT
*
123835 AAAAAGTCAATGATCAAC
1 AAAAAATCAATGATCAAC
123853 GATCAACTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.18, G:0.11, T:0.18
Consensus pattern (20 bp):
AAAAAATCAATGATCAACCT
Found at i:123891 original size:21 final size:21
Alignment explanation
Indices: 123821--123892 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
123811 CGAAAAAAAA
* * *
123821 TCAATGGTCAAC-CTAAAAAG
1 TCAATGGTCAACGATCAACAG
* *
123841 TCAATGATCAACGATCAACTG
1 TCAATGGTCAACGATCAACAG
* *
123862 TTAATGGTCAACGGTCAACAG
1 TCAATGGTCAACGATCAACAG
*
123883 TCAACGGTCA
1 TCAATGGTCA
123893 GGTTCGATCA
Statistics
Matches: 40, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 11 0.28
21 29 0.73
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (21 bp):
TCAATGGTCAACGATCAACAG
Found at i:127857 original size:18 final size:18
Alignment explanation
Indices: 127836--127875 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
127826 TCAAAATTCA
127836 AAAATATTATAAAAT-TAT
1 AAAATATTA-AAAATATAT
*
127854 AAAATTTTAAAAATATAT
1 AAAATATTAAAAATATAT
127872 AAAA
1 AAAA
127876 AAATTAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATATTAAAAATATAT
Found at i:127966 original size:30 final size:30
Alignment explanation
Indices: 127932--127990 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
127922 TAAAAATGTA
*
127932 ACTTTTTAAAAAGGTTG-AGAATCAAAATTT
1 ACTTTTTAAAAAGATTGAAG-ATCAAAATTT
127962 ACTTTTTAAAAAGATTGAAGATCAAAATT
1 ACTTTTTAAAAAGATTGAAGATCAAAATT
127991 AATAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.36
Consensus pattern (30 bp):
ACTTTTTAAAAAGATTGAAGATCAAAATTT
Found at i:129167 original size:146 final size:147
Alignment explanation
Indices: 128903--129190 Score: 368
Period size: 146 Copynumber: 2.0 Consensus size: 147
128893 ATTTGAACTT
* *
128903 AACAAGTGGTTCCAGTAGAAAAGAATAGATTGTTCATCCTAGAGATCACAGGTTCGAGTACCTGT
1 AACAAGTGGCTCCAGTAGAAAAGAATAGATTGTTCATCCTAGAGATCACAGGTTCGAGCACCTGT
* * * * *
128968 GTGTGTAAGGTGTGTGTGCCTTATCAAAGAATTAAGAAAGTGTGAACAGATACTACAATGTAAT-
66 GCGTGCAAGATGTGTGTGCCTTATCAAAAAATTAAGAAAGTATGAACAGATACTACAATGTAATA
129032 CACTAATATATGAACCC
131 CACTAATATATGAACCC
* * *
129049 AACAAGTGGCTCCAGTAGAAAAGAGA-ATG-TTGTTCATTCTAGAGATTA-AGGGTTTGAGCACC
1 AACAAGTGGCTCCAGTAGAAAAGA-ATA-GATTGTTCATCCTAGAGATCACA-GGTTCGAGCACC
* * * * **
129111 TGTGCGTGCAAGATGTGTGTGCGTTGTCAAAAAATTAAGAAAGTATGAATATATACTATTATGTA
63 TGTGCGTGCAAGATGTGTGTGCCTTATCAAAAAATTAAGAAAGTATGAACAGATACTACAATGTA
129176 ATCACACTAATATAT
128 AT-ACACTAATATAT
129191 TCAAAAAAAA
Statistics
Matches: 121, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
145 1 0.01
146 107 0.88
147 2 0.02
148 11 0.09
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.29
Consensus pattern (147 bp):
AACAAGTGGCTCCAGTAGAAAAGAATAGATTGTTCATCCTAGAGATCACAGGTTCGAGCACCTGT
GCGTGCAAGATGTGTGTGCCTTATCAAAAAATTAAGAAAGTATGAACAGATACTACAATGTAATA
CACTAATATATGAACCC
Found at i:132909 original size:16 final size:16
Alignment explanation
Indices: 132885--132918 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
132875 TTCTAATAAT
*
132885 AAATATATAGATATTA
1 AAATATATAAATATTA
*
132901 AAATTTATAAATATTA
1 AAATATATAAATATTA
132917 AA
1 AA
132919 TAAAAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAATATATAAATATTA
Found at i:138022 original size:5 final size:5
Alignment explanation
Indices: 138012--138038 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
138002 CCCAAATAAC
138012 CCTCT CCTCT CCTCT CCTCT CCTCT CC
1 CCTCT CCTCT CCTCT CCTCT CCTCT CC
138039 ACCAGCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (5 bp):
CCTCT
Found at i:143896 original size:20 final size:20
Alignment explanation
Indices: 143872--143910 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
143862 ATTTTTATCT
143872 TAAAAAAATT-AAATTTAAA
1 TAAAAAAATTAAAATTTAAA
*
143891 TAAAAATATTAAAATTTAAA
1 TAAAAAAATTAAAATTTAAA
143911 ATTAAATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAAAAATTAAAATTTAAA
Found at i:146956 original size:31 final size:31
Alignment explanation
Indices: 146918--146988 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
146908 TTGGTAGAGG
146918 TGAAAAATGGAAGGAAAGAAAATAAAACATT
1 TGAAAAATGGAAGGAAAGAAAATAAAACATT
146949 TGAAAAATGGAAGGAAAGAAAATAAAACATT
1 TGAAAAATGGAAGGAAAGAAAATAAAACATT
146980 TGAAAAATG
1 TGAAAAATG
146989 CATAATTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.61, C:0.03, G:0.20, T:0.17
Consensus pattern (31 bp):
TGAAAAATGGAAGGAAAGAAAATAAAACATT
Found at i:151186 original size:29 final size:29
Alignment explanation
Indices: 151149--151204 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
151139 ATTTTCAAAA
* * *
151149 TTAACAAAGATTAAATTAATTCAATTTTT
1 TTAAAAAAGATCAAATTAACTCAATTTTT
*
151178 TTAAAAAAGATCAAATTTACTCAATTT
1 TTAAAAAAGATCAAATTAACTCAATTT
151205 CAAAAATAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (29 bp):
TTAAAAAAGATCAAATTAACTCAATTTTT
Found at i:153926 original size:175 final size:175
Alignment explanation
Indices: 153634--154300 Score: 1043
Period size: 175 Copynumber: 3.8 Consensus size: 175
153624 AATTTGCATA
* ** * * *
153634 TTTGTTGCTGTGATGATTATATTAAAATTTATGAAAATTTTGTGAATCATCGGCAACTATGTCGA
1 TTTGTTGCTGTGATGATTATATTAGAATTTATGAAAATTTAATGAAACATCGACAACCATGTCGA
* * *
153699 TCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCTATCTCTTTGTTGATTTATTACATTG
66 TCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATTG
* * ** * * *
153764 TTTTAGTTGTCTTACAATTA-ATCTTATTGTATGTGAATCTGCGGT
131 CTTTAGTCGTCTTATGA-TACATCTTATTGTATGTGAATTTGTGAT
153809 TTTGTTGCTGTGATGATTATATTAGAATTTATGAAAAATTT-ATGAAACATCGACAACCATGTCG
1 TTTGTTGCTGTGATGATTATATTAGAATTTATG-AAAATTTAATGAAACATCGACAACCATGTCG
*
153873 ATCTGAGCGGTTACCTGAGCAACAAGATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATT
65 ATCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATT
153938 GCTTTAGTCGTCTTATGATACATCTTATTGTATGTGAATTTGTGAT
130 GCTTTAGTCGTCTTATGATACATCTTATTGTATGTGAATTTGTGAT
*
153984 TTTGTTGCTGTGATGATTATATTAGAATTTAT-CAAATTTAATGAAACATCGACAACCATGTCGA
1 TTTGTTGCTGTGATGATTATATTAGAATTTATGAAAATTTAATGAAACATCGACAACCATGTCGA
* *
154048 TCTGAGCGGTTGCCTGAGCAACAAAATTTGTTCAAATTCAATTTTCTTGTTGATTTATTACATTG
66 TCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATTG
154113 CTTTAGTCGTCTTATGATACATCTTATTGTATGTGAATTTGTGAT
131 CTTTAGTCGTCTTATGATACATCTTATTGTATGTGAATTTGTGAT
* *
154158 TTTGTTGCTGTGATGATTATACTAGAATTTATGAAAATTTAATGAAACATTGACAACCATGTCGA
1 TTTGTTGCTGTGATGATTATATTAGAATTTATGAAAATTTAATGAAACATCGACAACCATGTCGA
* * * *
154223 TCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAGTTTCTTTGTTGATTTGTTACTTTG
66 TCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATTG
* *
154288 TTTTAGTTGTCTT
131 CTTTAGTCGTCTT
154301 GTAATATCTA
Statistics
Matches: 457, Mismatches: 31, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
173 6 0.01
174 164 0.36
175 280 0.61
176 7 0.02
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (175 bp):
TTTGTTGCTGTGATGATTATATTAGAATTTATGAAAATTTAATGAAACATCGACAACCATGTCGA
TCTGAGCGGTTACCTGAGCAACAAAATTTGTTCAAATTCAATTTCCTTGTTGATTTATTACATTG
CTTTAGTCGTCTTATGATACATCTTATTGTATGTGAATTTGTGAT
Found at i:155775 original size:20 final size:20
Alignment explanation
Indices: 155752--155813 Score: 74
Period size: 19 Copynumber: 3.2 Consensus size: 20
155742 TTTAAATATC
*
155752 AAAATATTTATAAAAATTTT
1 AAAATATTTATAAAATTTTT
* *
155772 AAAATATATAT-AACTTTTT
1 AAAATATTTATAAAATTTTT
*
155791 AAAA-AATTATAAAATTTTT
1 AAAATATTTATAAAATTTTT
155810 AAAA
1 AAAA
155814 GAAATTCTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
18 4 0.11
19 21 0.60
20 10 0.29
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATATTTATAAAATTTTT
Found at i:158423 original size:27 final size:27
Alignment explanation
Indices: 158362--158413 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
158352 TGAATGTTCA
* *
158362 TGACATTAGAATTAACGTAAAAAATAG
1 TGACATAAAAATTAACGTAAAAAATAG
158389 TGACATAAAAATTAACGTAAAAAAT
1 TGACATAAAAATTAACGTAAAAAAT
158414 TAAGGCATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.25
Consensus pattern (27 bp):
TGACATAAAAATTAACGTAAAAAATAG
Found at i:161700 original size:27 final size:27
Alignment explanation
Indices: 161662--161740 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
161652 TGACAAGAAG
*
161662 GAATAGCCTTTGTGGCGAACTTTGAAA
1 GAATAGCCTTTGTGGCGAACTCTGAAA
* * *
161689 GAATAACCTTTGTGACGACCTCTGAAA
1 GAATAGCCTTTGTGGCGAACTCTGAAA
* *
161716 GAATAGCCTTTGTGGCAAATTCTGA
1 GAATAGCCTTTGTGGCGAACTCTGA
161741 TATTATAGTC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (27 bp):
GAATAGCCTTTGTGGCGAACTCTGAAA
Found at i:167721 original size:28 final size:28
Alignment explanation
Indices: 167690--167743 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
167680 ACTCATTTTA
167690 TTATAAACATAT-ATTTTATAATTAAATT
1 TTATAAACAT-TGATTTTATAATTAAATT
*
167718 TTATAAATATTGATTTTATAATTAAA
1 TTATAAACATTGATTTTATAATTAAA
167744 ATTCTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (28 bp):
TTATAAACATTGATTTTATAATTAAATT
Found at i:168675 original size:21 final size:21
Alignment explanation
Indices: 168639--168683 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
168629 ATATATCAAC
168639 AAATTAAAAAGAGAAAA-AAA
1 AAATTAAAAAGAGAAAAGAAA
168659 AAATATAATAAAG-GAAAAGAAA
1 AAAT-TAA-AAAGAGAAAAGAAA
168681 AAA
1 AAA
168684 GAAAGAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.18
21 8 0.36
22 10 0.45
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (21 bp):
AAATTAAAAAGAGAAAAGAAA
Found at i:170964 original size:24 final size:24
Alignment explanation
Indices: 170936--170989 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
170926 CCTGCCTCCG
*
170936 CCAAGAAGGAAACCAAAGAAAATC
1 CCAAGAAGGAAACCAAAGAAAAGC
170960 CCAAGAAGGAAACCAAAGAAAAGC
1 CCAAGAAGGAAACCAAAGAAAAGC
170984 CCAAGA
1 CCAAGA
170990 GGGCAAAAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.57, C:0.22, G:0.19, T:0.02
Consensus pattern (24 bp):
CCAAGAAGGAAACCAAAGAAAAGC
Found at i:171221 original size:48 final size:48
Alignment explanation
Indices: 171150--171301 Score: 243
Period size: 48 Copynumber: 3.2 Consensus size: 48
171140 CAGGATCTAT
*
171150 AGAGGAAGCCAATGAATCGAAAGCAGTAAGTTCTGTTCCGAAATCTGC
1 AGAGGAAGCCGATGAATCGAAAGCAGTAAGTTCTGTTCCGAAATCTGC
* * * *
171198 AGAGGAAACCGATGAATCGAAAGCAGCAATTTCTGTTTCGAAATCTGC
1 AGAGGAAGCCGATGAATCGAAAGCAGTAAGTTCTGTTCCGAAATCTGC
171246 AGAGGAAGCCGATGAATCGAAAGCAGTAAGCTT-TGTTCCGAAATCTGC
1 AGAGGAAGCCGATGAATCGAAAGCAGTAAG-TTCTGTTCCGAAATCTGC
171294 AGAGGAAG
1 AGAGGAAG
171302 GAAGCGTTAG
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
48 92 0.98
49 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (48 bp):
AGAGGAAGCCGATGAATCGAAAGCAGTAAGTTCTGTTCCGAAATCTGC
Found at i:171715 original size:9 final size:9
Alignment explanation
Indices: 171693--171741 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
171683 CAATTCCGGC
*
171693 AGAAGAGAA
1 AGAAGTGAA
171702 AGAAGTGAA
1 AGAAGTGAA
* *
171711 GGAAGTAAA
1 AGAAGTGAA
171720 AGAAGTGAA
1 AGAAGTGAA
* *
171729 ACAAGAGAA
1 AGAAGTGAA
171738 AGAA
1 AGAA
171742 AAGAAAGAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.61, C:0.02, G:0.31, T:0.06
Consensus pattern (9 bp):
AGAAGTGAA
Found at i:171739 original size:18 final size:18
Alignment explanation
Indices: 171695--171741 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
171685 ATTCCGGCAG
**
171695 AAGAGAAAGAAGTGAAGG
1 AAGAGAAAGAAGTGAAAC
171713 AAGTA-AAAGAAGTGAAAC
1 AAG-AGAAAGAAGTGAAAC
171731 AAGAGAAAGAA
1 AAGAGAAAGAA
171742 AAGAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 1 0.04
18 23 0.92
19 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.30, T:0.06
Consensus pattern (18 bp):
AAGAGAAAGAAGTGAAAC
Found at i:173922 original size:18 final size:18
Alignment explanation
Indices: 173901--173942 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
173891 GTTGATAACA
*
173901 AAGAGGATGTTGGGAAAG
1 AAGAGGAAGTTGGGAAAG
* *
173919 AAGAAGAAGTTGGGAATG
1 AAGAGGAAGTTGGGAAAG
173937 AAGAGG
1 AAGAGG
173943 GAGAAGGAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.14
Consensus pattern (18 bp):
AAGAGGAAGTTGGGAAAG
Found at i:177950 original size:14 final size:14
Alignment explanation
Indices: 177931--177960 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
177921 ATTTATCTGA
177931 GATATATCATTTAT
1 GATATATCATTTAT
177945 GATATATCATTTAT
1 GATATATCATTTAT
177959 GA
1 GA
177961 GAAATGATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (14 bp):
GATATATCATTTAT
Found at i:178127 original size:23 final size:23
Alignment explanation
Indices: 178096--178145 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
178086 TATGTACGCC
178096 TACT-GATTGCACTGTGTGTGCT
1 TACTGGATTGCACTGTGTGTGCT
178118 TACTGGATTGCACTGTGTGTGCT
1 TACTGGATTGCACTGTGTGTGCT
178141 TACTG
1 TACTG
178146 TTAAGTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.14, C:0.18, G:0.28, T:0.40
Consensus pattern (23 bp):
TACTGGATTGCACTGTGTGTGCT
Found at i:178635 original size:20 final size:21
Alignment explanation
Indices: 178597--178636 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
178587 TTTGTACTAA
**
178597 AAATCATATTTTATTTCTTTT
1 AAATCATATTTTAAGTCTTTT
178618 AAATCA-ATTTTAAGTCTTT
1 AAATCATATTTTAAGTCTTT
178637 ATTTTAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.55
Consensus pattern (21 bp):
AAATCATATTTTAAGTCTTTT
Found at i:183118 original size:17 final size:17
Alignment explanation
Indices: 183096--183134 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
183086 AAGTGGAGAA
* *
183096 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
183113 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
183130 CTTGT
1 CTTGT
183135 CAATGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:192267 original size:27 final size:27
Alignment explanation
Indices: 192237--192288 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
192227 AATCAAATCG
192237 AATTCTATTTTTATTCAA-TATATAATT
1 AATTCTATTTTT-TTCAATTATATAATT
* *
192264 AATTTTATTTTTTTTAATTATATAA
1 AATTCTATTTTTTTCAATTATATAA
192289 AAAAATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (27 bp):
AATTCTATTTTTTTCAATTATATAATT
Found at i:194834 original size:2 final size:2
Alignment explanation
Indices: 194827--194859 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
194817 GCTATTGTCT
194827 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
194860 TATTTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:209431 original size:29 final size:29
Alignment explanation
Indices: 209398--209457 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
209388 TTAAATTTTT
* * *
209398 TCTTAACAATAATTCTAAAAAATTAAAAA
1 TCTTAAAAATAAATATAAAAAATTAAAAA
**
209427 TCTTAAAAATAAATATAAATTATTAAAAA
1 TCTTAAAAATAAATATAAAAAATTAAAAA
209456 TC
1 TC
209458 ATGTTAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (29 bp):
TCTTAAAAATAAATATAAAAAATTAAAAA
Found at i:209496 original size:19 final size:18
Alignment explanation
Indices: 209462--209499 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
209452 AAAATCATGT
209462 TAAAATATTATTTAAAAA
1 TAAAATATTATTTAAAAA
209480 TAAAA-ATTATATATAAAAA
1 TAAAATATTAT-T-TAAAAA
209499 T
1 T
209500 TTCTAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 6 0.33
19 7 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATATTATTTAAAAA
Found at i:209577 original size:24 final size:24
Alignment explanation
Indices: 209528--209577 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
209518 TTTCTCATGC
* * *
209528 TTGATTGAAGCCATAAATAAATAA
1 TTGATTGAAGCAACAAATAAAAAA
209552 TTGATTGAAGCAACAACA-AAAAAA
1 TTGATTGAAGCAACAA-ATAAAAAA
209576 TT
1 TT
209578 AAAAGTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.26
Consensus pattern (24 bp):
TTGATTGAAGCAACAAATAAAAAA
Found at i:214358 original size:15 final size:15
Alignment explanation
Indices: 214338--214367 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
214328 CTTGATGTGA
214338 CAGTGTTGGTTTTGG
1 CAGTGTTGGTTTTGG
214353 CAGTGTTGGTTTTGG
1 CAGTGTTGGTTTTGG
214368 AAGGAGGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.40, T:0.47
Consensus pattern (15 bp):
CAGTGTTGGTTTTGG
Done.