Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002653.1 Hibiscus syriacus cultivar Beakdansim tig00005425_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: 58512
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:2784 original size:17 final size:16
Alignment explanation
Indices: 2758--2825 Score: 68
Period size: 17 Copynumber: 4.1 Consensus size: 16
2748 ATTTTTGTTC
*
2758 TTTCTTTTTTTCTTTTG
1 TTTCTTTTCTT-TTTTG
2775 TTTCTCTTT-TTTCTTTG
1 TTTCT-TTTCTTT-TTTG
2792 TTT-TTTTCTTCTTTTG
1 TTTCTTTTCTT-TTTTG
*
2808 CTTCTTTTCTTTTTTG
1 TTTCTTTTCTTTTTTG
2824 TT
1 TT
2826 CTTGATTGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
15 3 0.07
16 16 0.36
17 22 0.50
18 3 0.07
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (16 bp):
TTTCTTTTCTTTTTTG
Found at i:2787 original size:9 final size:8
Alignment explanation
Indices: 2758--2828 Score: 56
Period size: 8 Copynumber: 8.8 Consensus size: 8
2748 ATTTTTGTTC
2758 TTTCTTTT
1 TTTCTTTT
2766 TTTCTTTT
1 TTTCTTTT
2774 GTTTCTCTTT
1 -TTTCT-TTT
*
2784 TTTCTTTG
1 TTTCTTTT
2792 TTT-TTTT
1 TTTCTTTT
*
2799 CTTCTTTT
1 TTTCTTTT
*
2807 GCTTCTTTT
1 -TTTCTTTT
*
2816 CTT-TTTT
1 TTTCTTTT
*
2823 GTTCTT
1 TTTCTT
2829 GATTGGATCT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
7 11 0.20
8 22 0.41
9 18 0.33
10 3 0.06
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (8 bp):
TTTCTTTT
Found at i:2804 original size:33 final size:31
Alignment explanation
Indices: 2762--2825 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 31
2752 TTGTTCTTTC
*
2762 TTTTTTTCTTTTGTTTCTCTTT-TTTCTTTGTT
1 TTTTTTTCTTTTGCTTCT-TTTCTTT-TTTGTT
2794 TTTTTCTTCTTTTGCTTCTTTTCTTTTTTGTT
1 TTTTT-TTCTTTTGCTTCTTTTCTTTTTTGTT
2826 CTTGATTGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (31 bp):
TTTTTTTCTTTTGCTTCTTTTCTTTTTTGTT
Found at i:2827 original size:24 final size:23
Alignment explanation
Indices: 2749--2828 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 23
2739 TTCTTTTTGA
*
2749 TTTTTGTTC-TTTCTTTTTTTCT
1 TTTTTGTTCTTTTCTTCTTTTCT
2771 TTTGTT-TCTCTTTT-TTCTTTGT-T
1 TTT-TTGT-TCTTTTCTTCTTT-TCT
*
2794 TTTTTCTTCTTTTGCTTCTTTTCT
1 TTTTTGTTCTTTT-CTTCTTTTCT
2818 TTTTTGTTCTT
1 TTTTTGTTCTT
2829 GATTGGATCT
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
22 12 0.25
23 15 0.31
24 21 0.44
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (23 bp):
TTTTTGTTCTTTTCTTCTTTTCT
Found at i:7289 original size:19 final size:19
Alignment explanation
Indices: 7253--7288 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
7243 CATAACAATA
*
7253 ATAATAGTAATATGAAAAT
1 ATAATAGTAATATAAAAAT
7272 ATAATA-TAATATAAAAA
1 ATAATAGTAATATAAAAA
7289 AACCAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (19 bp):
ATAATAGTAATATAAAAAT
Found at i:7522 original size:20 final size:21
Alignment explanation
Indices: 7485--7584 Score: 73
Period size: 20 Copynumber: 4.8 Consensus size: 21
7475 AAAAAAGTAT
* *
7485 ATATATATATATAAATAATAA
1 ATATATATAAAAAAATAATAA
*
7506 ATATAT-TAAAAAAATAACCAA
1 ATATATATAAAAAAATAA-TAA
*
7527 ATGA-ATATAAATAAATAA-AA
1 AT-ATATATAAAAAAATAATAA
* * *
7547 ATATATGT-ATATAATAATAA
1 ATATATATAAAAAAATAATAA
7567 TATATAGTATAAAAAAAT
1 -ATATA-TATAAAAAAAT
7585 CAATTGAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
19 7 0.12
20 18 0.30
21 17 0.28
22 13 0.22
23 5 0.08
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (21 bp):
ATATATATAAAAAAATAATAA
Found at i:8122 original size:37 final size:37
Alignment explanation
Indices: 8029--8130 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
8019 GTGCTTGTGG
* * * * *
8029 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
8066 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
8103 ATCCTATTTTTAGGAGTTTGAATTCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
8131 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:21084 original size:42 final size:41
Alignment explanation
Indices: 20977--21084 Score: 144
Period size: 42 Copynumber: 2.6 Consensus size: 41
20967 AGGTCTTATG
* *
20977 GATGACCCAAAGGACTTATCATCTTGCTCGAAAGACTTACA
1 GATGACCCGAAGGACTTATCATCATGCTCGAAAGACTTACA
* * *
21018 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGACTT-ATCATCATGCTCGAAAGACTTACA
*
21060 GATGGCCCGAAGGACTTACTCATCA
1 GATGACCCGAAGGACTTA-TCATCA
21085 AGAAACACTT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 16 0.28
42 41 0.72
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (41 bp):
GATGACCCGAAGGACTTATCATCATGCTCGAAAGACTTACA
Found at i:21090 original size:239 final size:238
Alignment explanation
Indices: 20547--21079 Score: 757
Period size: 239 Copynumber: 2.2 Consensus size: 238
20537 TGGACGGCCT
* * * *
20547 GAAAGATTTAATCATCATGTTCGAAAGACTTACT-AGTGACCCGAGGGACTTACTAAGTAAGAAA
1 GAAAGATTTAAGCATCATGCTCGAAAGACTTACTGA-TGGCCCGAAGGACTTACTAAGTAAGAAA
*
20611 ATTTGGAAATCATTTTCTTACTTTTCAAGAAAAATAAACTTTTAGAAAAGATTTAATGAGAAACT
65 CTTTGGAAATCATTTTCTTACTTTTC-A-AAAAATAAACTTTTAGAAAAGATTTAATGAGAAACT
* * * * *
20676 TTGGAAATCGCTTTCTCATTTTTCGAAAGTCATATGAAAACATCCTGCCCAAAGGTCTTATGGAT
128 TTGGAAATCGATTTCTCATTTTTAGAAAATCATATGAAAACATCCGGACCAAAGGTCTTATGGAT
** * ***
20741 GACCTGAAGCACTTATCATCTTGCTCGAAAGACTTATAGATGAGTT
193 GACCCAAAGCACTTATCATCTTGCTCGAAAGACTTACAGATGACCC
* *
20787 GAAAGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGAATTACTAAGTAAGAAAC
1 GAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAAGTAAGAAAC
* *
20852 TTTGGAAATCATTTTCTTAGTTTTC-AAAAATCAA-TTTTCAGAAAAGATTTAAATGAGAAACTT
66 TTTGGAAATCATTTTCTTACTTTTCAAAAAATAAACTTTT-AGAAAAGATTT-AATGAGAAACTT
* * **
20915 TGGAAATTGATTTCTTATTTTTTAGAAAATCATATGAAAACATCCGGACTTAAGGTCTTATGGAT
129 TGGAAATCGATTTCTCA-TTTTTAGAAAATCATATGAAAACATCCGGACCAAAGGTCTTATGGAT
*
20980 GACCCAAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCC
193 GACCCAAAGCACTTATCATCTTGCTCGAAAGACTTACAGATGACCC
*
21026 GAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACT
1 GAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACT
21080 CATCAAGAAA
Statistics
Matches: 261, Mismatches: 28, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
236 4 0.02
237 19 0.07
238 26 0.10
239 131 0.50
240 80 0.31
241 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (238 bp):
GAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAAGTAAGAAAC
TTTGGAAATCATTTTCTTACTTTTCAAAAAATAAACTTTTAGAAAAGATTTAATGAGAAACTTTG
GAAATCGATTTCTCATTTTTAGAAAATCATATGAAAACATCCGGACCAAAGGTCTTATGGATGAC
CCAAAGCACTTATCATCTTGCTCGAAAGACTTACAGATGACCC
Found at i:21251 original size:53 final size:53
Alignment explanation
Indices: 21138--21393 Score: 368
Period size: 53 Copynumber: 4.8 Consensus size: 53
21128 TTACAATTAT
* *
21138 CATCAAGAAACCCCTAAAAATTAGGATTAGCTTCTTTAAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTT-CAAATTCATTTGAAAA
* * * *
21192 CATCAAGAAACCCATGAAAATTAGGCTTATCTTCCTTCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
*
21245 CATCAAGAAACCCCTAAAAATTAGGCTTTGCTTCTTTCAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* * *
21298 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAATTCATTTCAACA
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
* * * * *
21351 TATCAAGAAACTCCTGAAAATCAGGCTTAACTTCTTTCAAATT
1 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATT
21394 TATTATGTCA
Statistics
Matches: 181, Mismatches: 21, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
53 149 0.82
54 32 0.18
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (53 bp):
CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAA
Found at i:21457 original size:49 final size:48
Alignment explanation
Indices: 21344--21477 Score: 153
Period size: 49 Copynumber: 2.8 Consensus size: 48
21334 TAAAATTCAT
* * * * *
21344 TTCAACATATCAAGAAA-CTCCTGAAAATCAGGCTTAACTTCTTTCAAA
1 TTCAACATGTCAAGAAACCT-CTGAAAATCAGACTTAGCTTATTTAAAA
* ** *
21392 TTTATTATGTCAAGAAACCTCTGAAAATCAAACTTAGCTTATTTAAAAA
1 TTCAACATGTCAAGAAACCTCTGAAAATCAGACTTAGCTTATTT-AAAA
*
21441 TTCAACATGTCAAGAAACCTCTAAAAATCAGACTTAG
1 TTCAACATGTCAAGAAACCTCTGAAAATCAGACTTAG
21478 TTTCTTTGAA
Statistics
Matches: 70, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
48 33 0.47
49 37 0.53
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (48 bp):
TTCAACATGTCAAGAAACCTCTGAAAATCAGACTTAGCTTATTTAAAA
Found at i:21594 original size:54 final size:54
Alignment explanation
Indices: 21449--21709 Score: 266
Period size: 55 Copynumber: 4.8 Consensus size: 54
21439 AATTCAACAT
* * * *
21449 GTCAAGAAACCTCT-AAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATA
1 GTCAAGAAACTTATGAAAAAT-AGACTTAGTTTCTTT-AAAACTCATTTAAAAATC
* * * * *
21504 AT-AAAAAACTT-TCAAAAATCAGACTTAGCTTCTTTAAACACTCATTTAAAAATT
1 GTCAAGAAACTTATGAAAAAT-AGACTTAGTTTCTTTAAA-ACTCATTTAAAAATC
* * * *
21558 GTCAAGAAACTTCTGAAAACTAGACTTAGTTT-TTT--AACTTATTTGAAAATC
1 GTCAAGAAACTTATGAAAAATAGACTTAGTTTCTTTAAAACTCATTTAAAAATC
21609 GTCAAGAAACTTATG-AAAATATGACTTAGTTTCTTTAAAAACTCATTTAAAAATC
1 GTCAAGAAACTTATGAAAAATA-GACTTAGTTTCTTT-AAAACTCATTTAAAAATC
* * *
21664 ATCAAGAAACTTATGAAAATTAGACTTAATTTCTTTAAAAGCTCAT
1 GTCAAGAAACTTATGAAAAATAGACTTAGTTTCTTTAAAA-CTCAT
21710 CATGTAAAGA
Statistics
Matches: 174, Mismatches: 21, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
50 5 0.03
51 36 0.21
52 4 0.02
53 4 0.02
54 49 0.28
55 65 0.37
56 11 0.06
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (54 bp):
GTCAAGAAACTTATGAAAAATAGACTTAGTTTCTTTAAAACTCATTTAAAAATC
Found at i:21674 original size:55 final size:56
Alignment explanation
Indices: 21470--21779 Score: 258
Period size: 55 Copynumber: 5.8 Consensus size: 56
21460 TCTAAAAATC
* * * * *
21470 AGACTTAGTTTCTTTGAAAGCTCATTTAAAAATAAT-AAAAAACTT-TCAAAA-AT
1 AGACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTATGAAAATAT
* * ** * *
21523 CAGACTTAGCTTCTTTAAACACTCATTTAAAAATTGTCAAGAAACTTCTGAAAA-CT
1 -AGACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTATGAAAATAT
* * *
21579 AGACTTAGTTT-TTT---AACTTATTTGAAAATCGTCAAGAAACTTATGAAAATAT
1 AGACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTATGAAAATAT
21631 -GACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTATGAAAAT-T
1 AGACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTATGAAAATAT
* * * * * ***
21685 AGACTTAATTTCTTTAAAAGCTCA--T---CAT-GTAAAGAAACCCCTGAAAATA-
1 AGACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTATGAAAATAT
** * *
21734 AGACTTAGTTTCTTTAAAAGTTCATTTAAAAATCATTATGAAACTT
1 AGACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTT
21780 CCAAAAATCA
Statistics
Matches: 206, Mismatches: 35, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
49 37 0.18
50 2 0.01
51 41 0.20
52 4 0.02
53 1 0.00
54 36 0.17
55 79 0.38
56 6 0.03
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (56 bp):
AGACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTATGAAAATAT
Found at i:23099 original size:28 final size:28
Alignment explanation
Indices: 23061--23135 Score: 123
Period size: 28 Copynumber: 2.6 Consensus size: 28
23051 AGGATGCCTT
*
23061 GGGAAGGTAATGTATTTCAAGTTAATTTG
1 GGGAA-GTAATGTGTTTCAAGTTAATTTG
23090 GGGAAGTAATGTGTTTCAAGTTAATTTG
1 GGGAAGTAATGTGTTTCAAGTTAATTTG
*
23118 GGGAGGTAATGTGTTTCA
1 GGGAAGTAATGTGTTTCA
23136 GGTTGGCTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 39 0.89
29 5 0.11
ACGTcount: A:0.28, C:0.04, G:0.31, T:0.37
Consensus pattern (28 bp):
GGGAAGTAATGTGTTTCAAGTTAATTTG
Found at i:23885 original size:6 final size:6
Alignment explanation
Indices: 23876--23936 Score: 60
Period size: 6 Copynumber: 10.8 Consensus size: 6
23866 TTTTCTTTTC
*
23876 TCTCTT TCTCTT TCTCTT TCTC-- TCTCTC TCTCTT TCTCTT T-T-TT
1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT
*
23920 CTTTCTT TCT-TT TCTCT
1 -TCTCTT TCTCTT TCTCT
23937 CTTTTCTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
4 6 0.13
5 7 0.15
6 32 0.68
7 2 0.04
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
TCTCTT
Found at i:23885 original size:8 final size:8
Alignment explanation
Indices: 23872--23940 Score: 62
Period size: 8 Copynumber: 9.4 Consensus size: 8
23862 GTATTTTTCT
23872 TTTCTCTC
1 TTTCTCTC
23880 -TT-TCTC
1 TTTCTCTC
23886 -TT-TCTC
1 TTTCTCTC
23892 TTTCTCTC
1 TTTCTCTC
*
23900 TCTCTCTC
1 TTTCTCTC
23908 TTTCTCT-
1 TTTCTCTC
23915 TTT-T-TC
1 TTTCTCTC
*
23921 TTTCTTTC
1 TTTCTCTC
23929 TTTTCTCTC
1 -TTTCTCTC
23938 TTT
1 TTT
23941 TCTTTTATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
5 1 0.02
6 14 0.27
7 8 0.15
8 22 0.42
9 7 0.13
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTCTCTC
Found at i:23902 original size:22 final size:22
Alignment explanation
Indices: 23865--23916 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
23855 TCTTAAAGTA
23865 TTTTTCTTT-TCTCTCTTTCTC
1 TTTTTCTTTCTCTCTCTTTCTC
* *
23886 TTTCTCTTTCTCTCTCTCTCTC
1 TTTTTCTTTCTCTCTCTTTCTC
*
23908 TTTCTCTTT
1 TTTTTCTTT
23917 TTTCTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTTCTTTCTCTCTCTTTCTC
Found at i:23964 original size:25 final size:25
Alignment explanation
Indices: 23926--23990 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
23916 TTTTCTTTCT
* * * *
23926 TTCTTTTCTCTCTTTTCTTTTATTTT
1 TTCTTTT-TTTCTTTTCTTATATCTA
* *
23952 TTTTTTTTTTCTTTTGTTATATCTA
1 TTCTTTTTTTCTTTTCTTATATCTA
23977 TTCTTTTTTTCTTT
1 TTCTTTTTTTCTTT
23991 ATGTGTTGTC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 26 0.81
26 6 0.19
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.78
Consensus pattern (25 bp):
TTCTTTTTTTCTTTTCTTATATCTA
Found at i:23966 original size:13 final size:13
Alignment explanation
Indices: 23906--23990 Score: 68
Period size: 13 Copynumber: 6.4 Consensus size: 13
23896 TCTCTCTCTC
*
23906 TCTTTCTCTTTTT
1 TCTTTCTTTTTTT
*
23919 TCTTTCTTTCTTT
1 TCTTTCTTTTTTT
*
23932 TCTCTCTTTTCTTT
1 TCTTTCTTTT-TTT
*
23946 TATTT-TTTTTTT
1 TCTTTCTTTTTTT
23958 T-TTTCTTTTGTTAT
1 TCTTTCTTTT-TT-T
23972 ATCTATTC-TTTTTT
1 -TCT-TTCTTTTTTT
23986 TCTTT
1 TCTTT
23991 ATGTGTTGTC
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
11 3 0.05
12 10 0.17
13 28 0.47
14 8 0.14
15 3 0.05
16 4 0.07
17 3 0.05
ACGTcount: A:0.05, C:0.16, G:0.01, T:0.78
Consensus pattern (13 bp):
TCTTTCTTTTTTT
Found at i:24220 original size:2 final size:2
Alignment explanation
Indices: 24213--24273 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
24203 GGACAACAAG
24213 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
24255 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
24274 AAGGATAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25869 original size:46 final size:46
Alignment explanation
Indices: 25802--25975 Score: 278
Period size: 46 Copynumber: 3.8 Consensus size: 46
25792 CAATTATGTA
* *
25802 ATTTT-ATTTGTGGCATACTTTCATGTAAATTATGCACTGATATAC
1 ATTTTCATTTGTGACATCCTTTCATGTAAATTATGCACTGATATAC
*
25847 ATTTTCAGTTGTGACATCCTTTCATGTAAATTATGCACTGATATAC
1 ATTTTCATTTGTGACATCCTTTCATGTAAATTATGCACTGATATAC
25893 ATTTTCATTTGTGACATCCTTTCATGTAAATTATGCACTGATATAC
1 ATTTTCATTTGTGACATCCTTTCATGTAAATTATGCACTGATATAC
** **
25939 ATTTTCATTTGTGGTATCCTTTCATGCCAATTATGCA
1 ATTTTCATTTGTGACATCCTTTCATGTAAATTATGCA
25976 TTGTTCTTCA
Statistics
Matches: 120, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
45 5 0.04
46 115 0.96
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.44
Consensus pattern (46 bp):
ATTTTCATTTGTGACATCCTTTCATGTAAATTATGCACTGATATAC
Found at i:26372 original size:54 final size:54
Alignment explanation
Indices: 26271--26813 Score: 842
Period size: 54 Copynumber: 10.1 Consensus size: 54
26261 TAGTGCCAAT
* * *
26271 AATTCATAAACTTATTATAAATTACGTGT-GGTTGCACACACAGTGCCAATACAGA
1 AATTCATAAACTCATTATGAATTTC-T-TAGGTTGCACACACAGTGCCAATACAGA
* *
26326 AATTCATAAACTCATTATGAATTTCTTAGGTTGTACACATAGTGCCAATACAGA
1 AATTCATAAACTCATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACAGA
26380 AATTCATAAACTCATTATGAATTTCTTAGGTTGCACACACAGTGCCAATAC-GAA
1 AATTCATAAACTCATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACAG-A
* *
26434 AATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGA
1 AATTCATAAACTCATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACAGA
* * * *
26488 AATTCATAAACTCATAATGACTTTCTTAGGTTGCACACATAGTGCCAATATAGA
1 AATTCATAAACTCATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACAGA
* *
26542 AATTCATAAACTCGTTATGAATTTCTTAGGTTGCACACACAGTGCCAATACATA
1 AATTCATAAACTCATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACAGA
*
26596 AATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACAGA
1 AATTCATAAACTCATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACAGA
* *
26650 AATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGGA
1 AATTCATAAACTCATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACAGA
*
26704 AATTCATAAACTCATTATGAATTTCTTAGGTTGCACACACAATGCCAATAC-GAA
1 AATTCATAAACTCATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACAG-A
* * *
26758 AATTCATAAACTCATTATAAATTTCTTAGGTTGCACACATAGTGCC-ATTCAGA
1 AATTCATAAACTCATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACAGA
26811 AAT
1 AAT
26814 CACAATAAAT
Statistics
Matches: 453, Mismatches: 30, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
53 10 0.02
54 420 0.93
55 23 0.05
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (54 bp):
AATTCATAAACTCATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACAGA
Found at i:29779 original size:10 final size:11
Alignment explanation
Indices: 29766--29797 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
29756 ATACAAGGAT
29766 ATAA-AATAAA
1 ATAATAATAAA
29776 ATAATAAT-AA
1 ATAATAATAAA
29786 ATAATAATAAA
1 ATAATAATAAA
29797 A
1 A
29798 GAATGAGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 14 0.70
11 6 0.30
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
ATAATAATAAA
Found at i:31337 original size:16 final size:16
Alignment explanation
Indices: 31314--31349 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
31304 AAATAGAAAG
*
31314 TAAA-GTGAATAAATT
1 TAAATGTGAATAAAAT
31329 TAAATGTGAATAAAAT
1 TAAATGTGAATAAAAT
31345 TAAAT
1 TAAAT
31350 AATAAACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (16 bp):
TAAATGTGAATAAAAT
Found at i:45074 original size:22 final size:22
Alignment explanation
Indices: 45049--45134 Score: 93
Period size: 22 Copynumber: 3.9 Consensus size: 22
45039 ACTAGAACCC
*
45049 CAAGGGGGTATCGATTCCCCTA
1 CAAGGGGGAATCGATTCCCCTA
* *
45071 CAAGGGGAAATCGGTTCCCCTTTA
1 CAAGGGGGAATCGATTCCCC--TA
* *
45095 -AAGGGGGAATCGGTTCCCCTT
1 CAAGGGGGAATCGATTCCCCTA
*
45116 CAAGGGGGTATCGATTCCC
1 CAAGGGGGAATCGATTCCC
45135 TCTGCACTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
21 1 0.02
22 33 0.61
23 18 0.33
24 2 0.04
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.23
Consensus pattern (22 bp):
CAAGGGGGAATCGATTCCCCTA
Found at i:50660 original size:109 final size:110
Alignment explanation
Indices: 50473--50808 Score: 330
Period size: 109 Copynumber: 3.1 Consensus size: 110
50463 ACTTAAATAA
* * * * ** *
50473 GGGGACTAAACAACAAATTTTCCAATAAACATATAATATACAAG-AAAAAAAATGGTAAATAACA
1 GGGGACTAAACAACAAA-TTCCCAAAAAAAATAT-ATA-ACATGCATGAAAAAGGGTAAATAACA
* *
50537 A-TGGTGGTCC-TCACAGTTGACCAACATGCAAAAACATGCTAAACTATG
63 ACT-TTAGTCCATCACAG-TGACCAACATGCAAAAACATGCTAAACTATG
* *
50585 GGGGACTAAACAACAAATATCTCC-AAAACAA-ATATAACATGCATG-AAAAGGGTAAATAGCAA
1 GGGGACTAAACAACAAAT-TC-CCAAAAAAAATATATAACATGCATGAAAAAGGGTAAATAACAA
* * *
50647 CTTTAGT-CATCACAGGTAACCAACATGCAAAAACACGCTAAACTATA
64 CTTTAGTCCATCACA-GTGACCAACATGCAAAAACATGCTAAACTATG
* * *
50694 GGGGACTAAACAACAAATTCCCAAAAAAAATATATAACTTGCATGAAAAAGGGTAAATAATAATT
1 GGGGACTAAACAACAAATTCCCAAAAAAAATATATAACATGCATGAAAAAGGGTAAATAACAACT
* * **
50759 TTGGTCCTTGCA-AGTGACCAACATATAAAAA-ATGCTAAACTATG
66 TTAGTCCAT-CACAGTGACCAACATGCAAAAACATGCTAAACTATG
*
50803 GTGGAC
1 GGGGAC
50809 CTATGCGATA
Statistics
Matches: 186, Mismatches: 27, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
107 2 0.01
108 9 0.05
109 102 0.55
110 41 0.22
111 6 0.03
112 24 0.13
113 2 0.01
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (110 bp):
GGGGACTAAACAACAAATTCCCAAAAAAAATATATAACATGCATGAAAAAGGGTAAATAACAACT
TTAGTCCATCACAGTGACCAACATGCAAAAACATGCTAAACTATG
Found at i:51780 original size:6 final size:6
Alignment explanation
Indices: 51769--51798 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
51759 ATATTAAAAT
*
51769 TTTATA TTTATA TTTATA TTTAAA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA
51799 ATTAGATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TTTATA
Found at i:51786 original size:12 final size:12
Alignment explanation
Indices: 51759--51798 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
51749 AAAATTTAAA
*
51759 ATATTAAAATTTT
1 ATATTTAAA-TTT
*
51772 ATATTTATATTT
1 ATATTTAAATTT
51784 ATATTTAAATTT
1 ATATTTAAATTT
51796 ATA
1 ATA
51799 ATTAGATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATATTTAAATTT
Found at i:52199 original size:134 final size:134
Alignment explanation
Indices: 52010--52498 Score: 513
Period size: 133 Copynumber: 3.6 Consensus size: 134
52000 ATCGAATCTG
* * *
52010 AAAAGGGG-TCTGCTTCGCTAC-TCTTCAGGGTAGATCATATCTGGAAATGTTGATTCATTCCAC
1 AAAAGGGGATCTACTCCGCTACTTCTTCAGGGTAGATCAGATCTGGAAATGTTGATTCATTCCAC
* * * * * *
52073 TATTCTTCAGGGAAGATAT-AATTGAGGAAGATTTGTTCCACTGCTACTTCATGGAAGATCAAAT
66 TATTCTTCAGGGAAGAT-TGAATCGAGGTAGACTTGTTTCACTGCTTCTTCAGGGAAGATCAAAT
52137 ATGGA
130 ATGGA
* * * * * *
52142 AAAAGGGGATATACTCCGCTGCTTCTTCAGGGTAGATTAGATCTGAAAATATTGATTCATTCCAT
1 AAAAGGGGATCTACTCCGCTACTTCTTCAGGGTAGATCAGATCTGGAAATGTTGATTCATTCCAC
* * * * * * *
52207 TGTTCTTCATGGAATATTGAATCGATGTAGACTTGTTTCATTTCTTCTTCAGGGAAGTTCAAATA
66 TATTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTTCACTGCTTCTTCAGGGAAGATCAAATA
52272 TGG-
131 TGGA
* * ** * *
52275 AAAAGGGGATCTACCCCACTACTTCTTCAGGGTAGATCTTATTTGGAAATGGTGATTCATTCCAC
1 AAAAGGGGATCTACTCCGCTACTTCTTCAGGGTAGATCAGATCTGGAAATGTTGATTCATTCCAC
* * * * * *
52340 TGTTCTTCAAGGAATATTGAATCGAGGTAGACTTGTTTCAGTGCTTCTTCAGGGAGGATCAAATC
66 TATTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTTCACTGCTTCTTCAGGGAAGATCAAATA
52405 TGGAAAA
131 TGG---A
* * * * * * *
52412 AGAAAGGGGATCTTCTCCGCTTCTTTTTCAAGGTAAATCAGATC-CGAAACGTTGATTCATTCCA
1 A-AAAGGGGATCTACTCCGCTACTTCTTCAGGGTAGATCAGATCTGGAAATGTTGATTCATTCCA
52476 C-AGTTCTTCAGGGAAGATTGAAT
65 CTA-TTCTTCAGGGAAGATTGAAT
52499 GGAGTTCAAT
Statistics
Matches: 291, Mismatches: 57, Indels: 13
0.81 0.16 0.04
Matches are distributed among these distances:
132 8 0.03
133 124 0.43
134 90 0.31
137 37 0.13
138 32 0.11
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (134 bp):
AAAAGGGGATCTACTCCGCTACTTCTTCAGGGTAGATCAGATCTGGAAATGTTGATTCATTCCAC
TATTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTTCACTGCTTCTTCAGGGAAGATCAAATA
TGGA
Found at i:53966 original size:641 final size:644
Alignment explanation
Indices: 52726--53991 Score: 1902
Period size: 641 Copynumber: 2.0 Consensus size: 644
52716 TGGGACTTTG
* *
52726 AATTGGTTACTTTTATATTGGGTCCCGACATCTTCAACCTTTCCCTTTAGAAAACTTGTAAGTAC
1 AATTGGTTACTTTTATATTGGATCCCGACATCTTCAACCTTTCCCTTTAGAAAACCTGTAAGTAC
* * * *
52791 TCAATTACAACTATCATCATCATGCATTTTATGAATATCATGATCTTATTTATACTTAATATGTG
66 TCAATTACAACTATCATCATCATGCATTTCATGAATATCACGATCTTATTTATACCTAAAATGTG
* * * * * *
52856 CGCAATTATGTAATTTTAGGGTATTTTCTTTTTCAAATGATAACTCTCTTTTGTCGACCCCTTGT
131 CGAAATGATGCAATTTTAGGGTATTTTCATTTTCAAATGAGAACTCTCTTTTGTCGAACCCTTGT
* * *
52921 AATTCAATCAAATCTTGGGAATAAAATCACCAACAGTTCACCCTAACTAACAATCCTGATCAGTC
196 AATTCAATCAAATCATGGGAATAAAATCACCAACAGTTCACCCCAACTAACAATCCTGATCAGAC
52986 ACTCTTTGGTTAGACATGACTTTGATTCTCTTTAATCTTGAACCCAGGCATTATTCATGACCAAC
261 ACTCTTTGGTTAGACATGACTTTGATTCTCTTTAATCTTGAACCCAGGCATTATTCATGACCAAC
* * *
53051 TACTTGATCAGCGATAAATATCTTGGATTATCCCAACTTGCTGAGCTTTTATATGTAGCCCAAGG
326 TACTTGATCAACGACAAATATATTGGATTATCCCAACTTGCTGAGCTTTTATATGTAGCCCAAGG
* * * * *
53116 TTTTAATTTTCTATAACCCATCTTCATGTAAGCATCATGCTAAAACCATTTCATCTTCGGAACAC
391 TTTTAATTTTCCATAACCCATCATCATGTAAACATCATGCTAAAACCATTTCAGCTTCAGAACAC
* *
53181 TTACACTTTTCCAAAACTTTTTGTACAATAATACACACTGATCTCATATTTCCCAAGTTAATCTA
456 ATACACTTTTCCAAAACCTTTTGTACAATAATACACACTGATCTCATATTTCCCAAGTTAATCTA
* *
53246 CATGTTTTTATCTTCAAATTAGGATGCTTTCAATATGGTTTTAATAAGAAAAATCACTCATATTA
521 CATGTTTTTATCTTCAAATTAGGATGCTTTCAACATGGTTTTAACAAGAAAAATCACTCATATTA
53311 TTTATATAAATGTAAAGAGTTTTTTTGGGTAAATACATGGAAAAATATTAATTTAACTC
586 TTTATATAAATGTAAAGAGTTTTTTTGGGTAAATACATGGAAAAATATTAATTTAACTC
* *
53370 AATTGGTTACTTTTATATTGGATCTCGACATCTTCAACCTTT-CCTTTCGAAAAACCTGTAAGTA
1 AATTGGTTACTTTTATATTGGATCCCGACATCTTCAACCTTTCCCTTTAG-AAAACCTGTAAGTA
* * * *
53434 CTCAATTGCATCTATCATCATCATGCATTTCATGAATGTCACGAT-TCTATTTATGCCTAAAATG
65 CTCAATTACAACTATCATCATCATGCATTTCATGAATATCACGATCT-TATTTATACCTAAAATG
*
53498 TGTGAAATGATGCAATTTTAGGGTATTTTCATTTTCAAATGAGAACT-TACTTTTGTC-AACCCT
129 TGCGAAATGATGCAATTTTAGGGTATTTTCATTTTCAAATGAGAACTCT-CTTTTGTCGAACCCT
* ** * *
53561 TGTAATTCAGTCAAAT-ATGGGACATAAAAT-ACCAGTAGTTCACCCCAGCTGACAATCCTGATC
193 TGTAATTCAATCAAATCATGGGA-ATAAAATCACCAACAGTTCACCCCAACTAACAATCCTGATC
* * * *
53624 AGAGACTCTTTGGTTTGACATGACTTTGATTCTCTTTATTCTTGAACCCATGCATTATTCATGAC
257 AGACACTCTTTGGTTAGACATGACTTTGATTCTCTTTAATCTTGAACCCAGGCATTATTCATGAC
* *
53689 CAGCTACTTGATCAATGACAAATATATTGGATTATCCCAACTTGCTGAGC-TTT-TATGTAGCCC
322 CAACTACTTGATCAACGACAAATATATTGGATTATCCCAACTTGCTGAGCTTTTATATGTAGCCC
* * * * *
53752 AAGTTTTTGATTTTCCGTAGCCCATCATCATGTAAACCTCATGCTAAAACCATTTTCAGCTTCAG
387 AAGGTTTTAATTTTCCATAACCCATCATCATGTAAACATCATGCTAAAACCA-TTTCAGCTTCAG
* * *
53817 AACGCATGCACTTTTCCAAAACCTTTTGTACAATAATACACACTGATCTCATGTTTCCCAAGTTA
451 AACACATACACTTTTCCAAAACCTTTTGTACAATAATACACACTGATCTCATATTTCCCAAGTTA
*
53882 ATCTACATGTTTTTATCTTCAAATTAGGATG-TTTGCAACATGGTTTTAACAAGAAAAATGACTC
516 ATCTACATGTTTTTATCTTCAAATTAGGATGCTTT-CAACATGGTTTTAACAAGAAAAATCACTC
* * *
53946 GTTTTATTTTTATAAATGTAAAGAGTTTTTTTGGGTAAATACATGG
580 ATATTATTTATATAAATGTAAAGAGTTTTTTTGGGTAAATACATGG
53992 TAAACTTTTA
Statistics
Matches: 559, Mismatches: 57, Indels: 15
0.89 0.09 0.02
Matches are distributed among these distances:
640 57 0.10
641 173 0.31
642 138 0.25
643 35 0.06
644 156 0.28
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (644 bp):
AATTGGTTACTTTTATATTGGATCCCGACATCTTCAACCTTTCCCTTTAGAAAACCTGTAAGTAC
TCAATTACAACTATCATCATCATGCATTTCATGAATATCACGATCTTATTTATACCTAAAATGTG
CGAAATGATGCAATTTTAGGGTATTTTCATTTTCAAATGAGAACTCTCTTTTGTCGAACCCTTGT
AATTCAATCAAATCATGGGAATAAAATCACCAACAGTTCACCCCAACTAACAATCCTGATCAGAC
ACTCTTTGGTTAGACATGACTTTGATTCTCTTTAATCTTGAACCCAGGCATTATTCATGACCAAC
TACTTGATCAACGACAAATATATTGGATTATCCCAACTTGCTGAGCTTTTATATGTAGCCCAAGG
TTTTAATTTTCCATAACCCATCATCATGTAAACATCATGCTAAAACCATTTCAGCTTCAGAACAC
ATACACTTTTCCAAAACCTTTTGTACAATAATACACACTGATCTCATATTTCCCAAGTTAATCTA
CATGTTTTTATCTTCAAATTAGGATGCTTTCAACATGGTTTTAACAAGAAAAATCACTCATATTA
TTTATATAAATGTAAAGAGTTTTTTTGGGTAAATACATGGAAAAATATTAATTTAACTC
Found at i:54460 original size:19 final size:20
Alignment explanation
Indices: 54438--54478 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
54428 CTTTTATTTA
54438 TTTTCTTT-TCTTTTTTATT
1 TTTTCTTTATCTTTTTTATT
*
54457 TTTTCTTTATTTTTTTTATT
1 TTTTCTTTATCTTTTTTATT
54477 TT
1 TT
54479 CCTCTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTCTTTATCTTTTTTATT
Found at i:54466 original size:32 final size:32
Alignment explanation
Indices: 54430--54544 Score: 85
Period size: 32 Copynumber: 3.5 Consensus size: 32
54420 TGAAGCCCCT
54430 TTTATTTATTTTCTTTTCTTTTTTATTTTTTC
1 TTTATTTATTTTCTTTTCTTTTTTATTTTTTC
* *
54462 TTTATTTTTTTTATTTTCCTCTTTTTTCATTTTTTC
1 TTTATTTATTTT-CTTT--TCTTTTTT-ATTTTTTC
* * * *
54498 --CATTT-TTCTCATTTTCATTTTTA-TTCTTC
1 TTTATTTATTTTC-TTTTCTTTTTTATTTTTTC
54527 TTTCATTTCATTTTCTTT
1 TTT-ATTT-ATTTTCTTT
54545 CTTCAGGCGA
Statistics
Matches: 64, Mismatches: 9, Indels: 19
0.70 0.10 0.21
Matches are distributed among these distances:
29 5 0.08
30 1 0.02
31 7 0.11
32 15 0.23
33 12 0.19
34 8 0.12
35 8 0.12
36 8 0.12
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (32 bp):
TTTATTTATTTTCTTTTCTTTTTTATTTTTTC
Found at i:54469 original size:18 final size:17
Alignment explanation
Indices: 54429--54497 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 17
54419 TTGAAGCCCC
*
54429 TTTTATTTATTTTCTT-T
1 TTTTTTTTATTTT-TTCT
*
54446 TCTTTTTTATTTTTTCT
1 TTTTTTTTATTTTTTCT
54463 TTATTTTTT-TTATTTTCCT
1 TT-TTTTTTATT-TTTT-CT
* *
54482 CTTTTTTCATTTTTTC
1 TTTTTTTTATTTTTTC
54498 CATTTTTCTC
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
16 2 0.05
17 16 0.38
18 19 0.45
19 5 0.12
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTTTTATTTTTTCT
Found at i:54486 original size:28 final size:28
Alignment explanation
Indices: 54429--54497 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
54419 TTGAAGCCCC
* * *
54429 TTTTATTTATTTTCTTTTCTTTTTTATT
1 TTTTCTTTATTTTCTTTTATTTTCTATT
*
54457 TTTTCTTTATTTT-TTTTATTTTCCTCTT
1 TTTTCTTTATTTTCTTTTATTTT-CTATT
*
54485 TTTTCATT-TTTTC
1 TTTTCTTTATTTTC
54498 CATTTTTCTC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 12 0.35
28 22 0.65
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.80
Consensus pattern (28 bp):
TTTTCTTTATTTTCTTTTATTTTCTATT
Found at i:54488 original size:19 final size:18
Alignment explanation
Indices: 54429--54488 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 18
54419 TTGAAGCCCC
*
54429 TTTTATTTATTTTCT-TT
1 TTTTTTTTATTTTCTCTT
* *
54446 TCTTTTTTATTTTTTCTTT
1 TTTTTTTTATTTTCTC-TT
54465 ATTTTTTTTATTTTCCTCTT
1 -TTTTTTTTATTTT-CTCTT
54485 TTTT
1 TTTT
54489 CATTTTTTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 12 0.35
19 6 0.18
20 14 0.41
21 2 0.06
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTTTATTTTCTCTT
Found at i:54493 original size:25 final size:24
Alignment explanation
Indices: 54465--54519 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
54455 TTTTTTCTTT
** *
54465 ATTTTTTTTATTTTCCTCTTTTTTC
1 ATTTTTTCCATTTTCCTC-ATTTTC
*
54490 ATTTTTTCCATTTTTCTCATTTTC
1 ATTTTTTCCATTTTCCTCATTTTC
54514 ATTTTT
1 ATTTTT
54520 ATTCTTCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (24 bp):
ATTTTTTCCATTTTCCTCATTTTC
Found at i:54498 original size:18 final size:17
Alignment explanation
Indices: 54448--54512 Score: 53
Period size: 18 Copynumber: 3.7 Consensus size: 17
54438 TTTTCTTTTC
54448 TTTTTT-ATTTTTT-CT
1 TTTTTTCATTTTTTCCT
**
54463 TTATTTTTTTTATTTTCCT
1 TT-TTTTCATT-TTTTCCT
54482 CTTTTTTCATTTTTTCCAT
1 -TTTTTTCATTTTTTCC-T
*
54501 TTTTCTCATTTT
1 TTTTTTCATTTT
54513 CATTTTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
15 2 0.05
16 4 0.10
17 2 0.05
18 21 0.52
19 9 0.22
20 2 0.05
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTTCATTTTTTCCT
Found at i:58042 original size:20 final size:19
Alignment explanation
Indices: 58006--58045 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
57996 CATTGCAGGA
* *
58006 ATTTATGGCTTCGACAAAG
1 ATTTATGGCCTCAACAAAG
58025 ATTTCATGGCCTCAACAAAG
1 ATTT-ATGGCCTCAACAAAG
58045 A
1 A
58046 CCTTGATGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (19 bp):
ATTTATGGCCTCAACAAAG
Done.