Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000641.1 Hibiscus syriacus cultivar Beakdansim tig00001241_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: 64918
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:7503 original size:9 final size:9
Alignment explanation
Indices: 7489--7519 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
7479 TCAATTAAAT
7489 CGATTGAAC
1 CGATTGAAC
7498 CGATTGAAC
1 CGATTGAAC
7507 CGATTGAAC
1 CGATTGAAC
7516 CGAT
1 CGAT
7520 AGATCCGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (9 bp):
CGATTGAAC
Found at i:7527 original size:18 final size:18
Alignment explanation
Indices: 7489--7528 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
7479 TCAATTAAAT
*
7489 CGATTGAACCGATTGAAC
1 CGATTGAACCGATAGAAC
*
7507 CGATTGAACCGATAGATC
1 CGATTGAACCGATAGAAC
7525 CGAT
1 CGAT
7529 CCGATTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.23
Consensus pattern (18 bp):
CGATTGAACCGATAGAAC
Found at i:10068 original size:56 final size:57
Alignment explanation
Indices: 10002--10115 Score: 169
Period size: 57 Copynumber: 2.0 Consensus size: 57
9992 TATTGTAGGG
*
10002 TGCTACTGCTTTTACCTTTACCG-TTTTTCATTAATTTTCAT-GAATTTCAGCAAGCA
1 TGCTACTGCTTTTACATTTACCGCTTTTTCATTAATTTTCATAG-ATTTCAGCAAGCA
* * *
10058 TGCTACTGCTTTTACATTTACTGCTTTTTGATTAATTTTCATAGATTTCTGCAAGCA
1 TGCTACTGCTTTTACATTTACCGCTTTTTCATTAATTTTCATAGATTTCAGCAAGCA
10115 T
1 T
10116 ATAAATGAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 21 0.40
57 30 0.58
58 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.46
Consensus pattern (57 bp):
TGCTACTGCTTTTACATTTACCGCTTTTTCATTAATTTTCATAGATTTCAGCAAGCA
Found at i:10918 original size:23 final size:23
Alignment explanation
Indices: 10891--10935 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
10881 GCGTAGAATT
*
10891 TGTCCCGAAGGACCACATAGAAA
1 TGTCCCGAAAGACCACATAGAAA
10914 TGTCCCGAAAGACCACATAGAA
1 TGTCCCGAAAGACCACATAGAA
10936 CACATATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.27, G:0.20, T:0.13
Consensus pattern (23 bp):
TGTCCCGAAAGACCACATAGAAA
Found at i:11376 original size:30 final size:30
Alignment explanation
Indices: 11320--11377 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
11310 TTCATTATAT
* *
11320 CACATAAATTATATCATATATTCATATAGA
1 CACATAAATCATATCATATATACATATAGA
11350 CACATAAATCATCATCATATA-ACATATA
1 CACATAAATCAT-ATCATATATACATATA
11378 TATAGCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33
Consensus pattern (30 bp):
CACATAAATCATATCATATATACATATAGA
Found at i:11412 original size:21 final size:21
Alignment explanation
Indices: 11386--11437 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
11376 TATATAGCAT
11386 ATACATATCACATCACATATA
1 ATACATATCACATCACATATA
11407 ATACATATCACATCACATATA
1 ATACATATCACATCACATATA
11428 ATACATATCA
1 ATACATATCA
11438 GGCACATTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (21 bp):
ATACATATCACATCACATATA
Found at i:11798 original size:21 final size:23
Alignment explanation
Indices: 11774--11816 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
11764 TATCGGTACC
*
11774 CCCT-GTAG-GGTATTGATACTT
1 CCCTAGTAGTGGTATCGATACTT
*
11795 CCCTAGTTGTGGTATCGATACT
1 CCCTAGTAGTGGTATCGATACT
11817 AAGCCTGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 3 0.17
23 11 0.61
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (23 bp):
CCCTAGTAGTGGTATCGATACTT
Found at i:15218 original size:21 final size:22
Alignment explanation
Indices: 15194--15244 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
15184 GCTTTACTAT
*
15194 TGATTGGA-TTGGTATTAATGC
1 TGATTGGACTTGGTATGAATGC
*
15215 TGATTGGACTTGGTCTGAATGC
1 TGATTGGACTTGGTATGAATGC
*
15237 TCATTGGA
1 TGATTGGA
15245 ATTCGTTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.22, C:0.10, G:0.29, T:0.39
Consensus pattern (22 bp):
TGATTGGACTTGGTATGAATGC
Found at i:15255 original size:22 final size:22
Alignment explanation
Indices: 15210--15255 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
15200 GATTGGTATT
* * *
15210 AATGCTGATTGGACTTGGTCTG
1 AATGCTCATTGGAATTCGTCTG
*
15232 AATGCTCATTGGAATTCGTTTG
1 AATGCTCATTGGAATTCGTCTG
15254 AA
1 AA
15256 AACTGATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (22 bp):
AATGCTCATTGGAATTCGTCTG
Found at i:24994 original size:15 final size:16
Alignment explanation
Indices: 24967--24998 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
24957 AGAAGGAAAA
24967 ATATATAAAAAATGTT
1 ATATATAAAAAATGTT
24983 ATATAT-AAAAATGTT
1 ATATATAAAAAATGTT
24998 A
1 A
24999 AAAGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
ATATATAAAAAATGTT
Found at i:25091 original size:38 final size:38
Alignment explanation
Indices: 25033--25151 Score: 111
Period size: 38 Copynumber: 3.0 Consensus size: 38
25023 TGTTAAATTT
25033 AAGAGAAAAAAATAAAATAAATAAATAAAT-AAAATGTTAA
1 AAGAGAAAAAAAT--AATAAATAAA-AAATAAAAATGTTAA
*
25073 AAGAGAAAAAAATAATAAA-ACAAAAATGAAAAA-GTGAA
1 AAGAGAAAAAAATAATAAATA-AAAAAT-AAAAATGTTAA
* *
25111 AA-AGTGAAAAAATAAAAAATAAAAAAATAAAAAATGTTAA
1 AAGAG-AAAAAAATAATAAAT-AAAAAAT-AAAAATGTTAA
25151 A
1 A
25152 TTTTAAAGAA
Statistics
Matches: 67, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
37 7 0.10
38 26 0.39
39 15 0.22
40 19 0.28
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.16
Consensus pattern (38 bp):
AAGAGAAAAAAATAATAAATAAAAAATAAAAATGTTAA
Found at i:25105 original size:8 final size:8
Alignment explanation
Indices: 25094--25146 Score: 65
Period size: 8 Copynumber: 6.9 Consensus size: 8
25084 ATAATAAAAC
25094 AAAAATGA
1 AAAAATGA
*
25102 AAAAGTGA
1 AAAAATGA
*
25110 AAAAGTGA
1 AAAAATGA
25118 AAAAAT-A
1 AAAAATGA
*
25125 AAAAATAA
1 AAAAATGA
25133 AAAAAT-A
1 AAAAATGA
25140 AAAAATG
1 AAAAATG
25147 TTAAATTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
7 14 0.34
8 27 0.66
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.13
Consensus pattern (8 bp):
AAAAATGA
Found at i:25112 original size:15 final size:15
Alignment explanation
Indices: 25094--25146 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
25084 ATAATAAAAC
*
25094 AAAAATGAAAAAGTGA
1 AAAAATGAAAAAAT-A
*
25110 AAAAGTGAAAAAATA
1 AAAAATGAAAAAATA
*
25125 AAAAATAAAAAAATA
1 AAAAATGAAAAAATA
25140 AAAAATG
1 AAAAATG
25147 TTAAATTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 20 0.62
16 12 0.38
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.13
Consensus pattern (15 bp):
AAAAATGAAAAAATA
Found at i:25134 original size:6 final size:7
Alignment explanation
Indices: 25039--25145 Score: 56
Period size: 8 Copynumber: 14.0 Consensus size: 7
25029 ATTTAAGAGA
25039 AAAAAAT
1 AAAAAAT
25046 AAAATAAAT
1 -AAA-AAAT
25055 AAATAAAT
1 AAA-AAAT
**
25063 AAAATGTT
1 AAAA-AAT
25071 AAAAGAGA-
1 AAAA-A-AT
25079 AAAAAAT
1 AAAAAAT
25086 AATAAAA-
1 AA-AAAAT
*
25093 CAAAAAT
1 AAAAAAT
*
25100 GAAAAAGT
1 -AAAAAAT
*
25108 GAAAAAGT
1 -AAAAAAT
25116 GAAAAAAT
1 -AAAAAAT
25124 AAAAAAT
1 AAAAAAT
25131 AAAAAAAT
1 -AAAAAAT
25139 AAAAAAT
1 AAAAAAT
25146 GTTAAATTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
6 5 0.06
7 19 0.23
8 54 0.66
9 4 0.05
ACGTcount: A:0.76, C:0.01, G:0.07, T:0.16
Consensus pattern (7 bp):
AAAAAAT
Found at i:25180 original size:28 final size:25
Alignment explanation
Indices: 25130--25181 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
25120 AAATAAAAAA
*
25130 TAAAAAAATAAAAAATGTTAAATTT
1 TAAAAAAATAAAAAATGTCAAATTT
25155 TAAAGAAAATATAAAAATGATCAAATT
1 TAAA-AAAATA-AAAAATG-TCAAATT
25182 GAAATGAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 6 0.26
27 7 0.30
28 6 0.26
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (25 bp):
TAAAAAAATAAAAAATGTCAAATTT
Found at i:26664 original size:18 final size:19
Alignment explanation
Indices: 26649--26693 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
26639 TTAAATAAGT
26649 AATAAT-ATAAAAATAATA
1 AATAATAATAAAAATAATA
*
26667 AATAATAATAAATA-AATA
1 AATAATAATAAAAATAATA
26685 AATAA-AATA
1 AATAATAATA
26694 TATATAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 4 0.16
18 15 0.60
19 6 0.24
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AATAATAATAAAAATAATA
Found at i:26672 original size:21 final size:22
Alignment explanation
Indices: 26640--26690 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
26630 AAAACAAAAT
*
26640 TAAATAAGTAATAATATAA-AAA
1 TAAATAAATAATAATA-AATAAA
26662 T-AATAAATAATAATAAATAAA
1 TAAATAAATAATAATAAATAAA
26683 TAAATAAA
1 TAAATAAA
26691 ATATATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 17 0.65
22 7 0.27
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (22 bp):
TAAATAAATAATAATAAATAAA
Found at i:26794 original size:37 final size:36
Alignment explanation
Indices: 26743--27123 Score: 162
Period size: 36 Copynumber: 10.7 Consensus size: 36
26733 GCTATATATC
26743 ATATGTTTTCAAAAACTATATTATATATACTTTTTAAAA
1 ATAT-TTTT-AAAAACTATATTATATATA-TTTTTAAAA
26782 ATATTTTTAAAAACTATA-TATTATATATTTTTCAAAAA
1 ATATTTTTAAAAACTATATTA-TATATATTTTT--AAAA
*
26820 ATATTTTCAAAATTA-TATATTATATATATTTTT-AAA
1 ATATTTTTAAAA--ACTATATTATATATATTTTTAAAA
* *
26856 AT-GTTTTCAAAACTATA-TAT-TATA----T----
1 ATATTTTTAAAAACTATATTATATATATTTTTAAAA
* *
26881 ATATTTTCAAAACTA-TATATTATATATA-TTTTCAAA
1 ATATTTTTAAAA--ACTATATTATATATATTTTTAAAA
* *
26917 ATGTTTTGAAAACTA-TATATTATATATATTTTTTCAAAA
1 ATATTTTTAAAA--ACTATATTATATATA-TTTTT-AAAA
*** * * *
26956 ATCA--TTGGGAAACTATAATATATATATATTCAAAA
1 AT-ATTTTTAAAAACTATATTATATATATTTTTAAAA
* * *
26991 GTCA-TTTTCAAAACTATATAATATATATTTTTAAAA
1 AT-ATTTTTAAAAACTATATTATATATATTTTTAAAA
* * * * *
27027 ACCGATTTTTAAACAGTATA-T-TATATGTTTTCAAAA
1 A--TATTTTTAAAAACTATATTATATATATTTTTAAAA
** *
27063 ACCGTTTTCTAAAAATTATA-TAT-TATATTTTTCAAAA
1 A-TATTTT-TAAAAACTATATTATATATATTTTT-AAAA
* * *
27100 ATATTTTCAAAAATTATACTATAT
1 ATATTTTTAAAAACTATATTATAT
27124 TAATATATAT
Statistics
Matches: 268, Mismatches: 41, Indels: 68
0.71 0.11 0.18
Matches are distributed among these distances:
25 2 0.01
26 6 0.02
27 4 0.01
28 5 0.02
29 4 0.01
32 5 0.02
33 4 0.01
34 4 0.01
35 28 0.10
36 104 0.39
37 36 0.13
38 39 0.15
39 24 0.09
40 3 0.01
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (36 bp):
ATATTTTTAAAAACTATATTATATATATTTTTAAAA
Found at i:26837 original size:14 final size:13
Alignment explanation
Indices: 26804--26918 Score: 57
Period size: 11 Copynumber: 9.2 Consensus size: 13
26794 ACTATATATT
26804 ATATATTTTTCAAA
1 ATATA-TTTTCAAA
*
26818 AAATATTTTCAAA
1 ATATATTTTCAAA
* *
26831 ATTATATATT--AT
1 A-TATATTTTCAAA
*
26843 ATATATTTT-TAA
1 ATATATTTTCAAA
*
26855 A-ATGTTTTCAAA
1 ATATATTTTCAAA
* *
26867 ACTATATATT--AT
1 A-TATATTTTCAAA
26879 ATATATTTTCAAA
1 ATATATTTTCAAA
* *
26892 ACTATATATT--AT
1 A-TATATTTTCAAA
26904 ATATATTTTCAAA
1 ATATATTTTCAAA
26917 AT
1 AT
26919 GTTTTGAAAA
Statistics
Matches: 74, Mismatches: 17, Indels: 21
0.66 0.15 0.19
Matches are distributed among these distances:
11 27 0.36
12 11 0.15
13 14 0.19
14 22 0.30
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (13 bp):
ATATATTTTCAAA
Found at i:26864 original size:36 final size:36
Alignment explanation
Indices: 26745--27026 Score: 204
Period size: 36 Copynumber: 8.0 Consensus size: 36
26735 TATATATCAT
26745 ATGTTTTCAAAA--ACTATATTATATATACTTTTTAAAA
1 ATGTTTTCAAAACTA-TATATTATATATA-TTTTT-AAA
* * *
26782 ATATTTTTAAAAACTATATATTATATAT-TTTTCAAAAA
1 AT-GTTTTCAAAACTATATATTATATATATTTT--TAAA
* *
26820 ATATTTTCAAAATTATATATTATATATATTTTTAAA
1 ATGTTTTCAAAACTATATATTATATATATTTTTAAA
26856 ATGTTTTCAAAACTATATA-T-TATATA----T---
1 ATGTTTTCAAAACTATATATTATATATATTTTTAAA
*
26883 A--TTTTCAAAACTATATATTATATATATTTTCAAA
1 ATGTTTTCAAAACTATATATTATATATATTTTTAAA
*
26917 ATGTTTTGAAAACTATATATTATATATATTTTTTCAAAA
1 ATGTTTTCAAAACTATATATTATATATA-TTTTT--AAA
** *** * *
26956 ATCATTGGGAAACTATA-A-TATATATATATTCAAA
1 ATGTTTTCAAAACTATATATTATATATATTTTTAAA
*
26990 AGTCATTTTCAAAACTATATA--ATATATATTTTTAAA
1 A-T-GTTTTCAAAACTATATATTATATATATTTTTAAA
27026 A
1 A
27027 ACCGATTTTT
Statistics
Matches: 197, Mismatches: 25, Indels: 47
0.73 0.09 0.17
Matches are distributed among these distances:
25 16 0.08
26 1 0.01
27 7 0.04
30 1 0.01
34 11 0.06
35 2 0.01
36 71 0.36
37 41 0.21
38 18 0.09
39 28 0.14
40 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (36 bp):
ATGTTTTCAAAACTATATATTATATATATTTTTAAA
Found at i:26872 original size:25 final size:26
Alignment explanation
Indices: 26844--26917 Score: 91
Period size: 25 Copynumber: 3.0 Consensus size: 26
26834 ATATATTATA
* *
26844 TATATTTTTA-AAATGTTTTCAAAAC
1 TATATTATTATAAATATTTTCAAAAC
*
26869 TATA-TATTATATATATTTTCAAAAC
1 TATATTATTATAAATATTTTCAAAAC
*
26894 TATA-TATTATATATATTTTCAAAA
1 TATATTATTATAAATATTTTCAAAA
26918 TGTTTTGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
24 4 0.09
25 41 0.91
ACGTcount: A:0.43, C:0.07, G:0.01, T:0.49
Consensus pattern (26 bp):
TATATTATTATAAATATTTTCAAAAC
Found at i:26892 original size:61 final size:61
Alignment explanation
Indices: 26820--26948 Score: 231
Period size: 61 Copynumber: 2.1 Consensus size: 61
26810 TTTTCAAAAA
* *
26820 ATATTTTCAAAATTATATATTATATATATTTTTAAAATGTTTTCAAAACTATATATTATAT
1 ATATTTTCAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAACTATATATTATAT
*
26881 ATATTTTCAAAACTATATATTATATATATTTTCAAAATGTTTTGAAAACTATATATTATAT
1 ATATTTTCAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAACTATATATTATAT
26942 ATATTTT
1 ATATTTT
26949 TTCAAAAATC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.50
Consensus pattern (61 bp):
ATATTTTCAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAACTATATATTATAT
Found at i:26899 original size:27 final size:25
Alignment explanation
Indices: 26859--26917 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
26849 TTTTAAAATG
26859 TTTTCAAAACTATATATTATATATA
1 TTTTCAAAACTATATATTATATATA
26884 TTTTCAAAACTATATATTATATATA
1 TTTTCAAAACTATATATTATATATA
26909 TTTTCAAAA
1 TTTTCAAAA
26918 TGTTTTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (25 bp):
TTTTCAAAACTATATATTATATATA
Found at i:27491 original size:16 final size:17
Alignment explanation
Indices: 27466--27514 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 17
27456 TGAATCCAAT
27466 TATT-TTATAAA-AATA
1 TATTATTATAAATAATA
27481 TATTATTATAAATAATA
1 TATTATTATAAATAATA
*
27498 T-TTA-TA-AATTAATA
1 TATTATTATAAATAATA
27512 TAT
1 TAT
27515 CCTAATTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 8 0.27
15 7 0.23
16 10 0.33
17 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTATTATAAATAATA
Found at i:29416 original size:2 final size:2
Alignment explanation
Indices: 29409--29438 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29399 ACTTCATCTG
29409 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
29439 TTAAATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29698 original size:15 final size:15
Alignment explanation
Indices: 29659--29715 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
29649 TACAGAGCCT
*
29659 CTTAATCATTCAACA
1 CTTAATCATTCAACG
* *
29674 TTTGAATCATTCAATG
1 CTT-AATCATTCAACG
*
29690 CTTAATCATTCAGCG
1 CTTAATCATTCAACG
*
29705 CTTAATAATTC
1 CTTAATCATTC
29716 TTTAGTAAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 22 0.65
16 12 0.35
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (15 bp):
CTTAATCATTCAACG
Found at i:29891 original size:23 final size:23
Alignment explanation
Indices: 29865--29936 Score: 135
Period size: 23 Copynumber: 3.1 Consensus size: 23
29855 AATAAATGTG
29865 CATATAACGTTCATAGAGTGTTA
1 CATATAACGTTCATAGAGTGTTA
*
29888 CATATAAAGTTCATAGAGTGTTA
1 CATATAACGTTCATAGAGTGTTA
29911 CATATAACGTTCATAGAGTGTTA
1 CATATAACGTTCATAGAGTGTTA
29934 CAT
1 CAT
29937 GCTTTTCTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (23 bp):
CATATAACGTTCATAGAGTGTTA
Found at i:30217 original size:60 final size:60
Alignment explanation
Indices: 30105--30236 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 60
30095 TTTAATATTC
* * *
30105 CAATTCCATCCCTAAAATATGACCCTCATTCTAAATTAGTTCTCAAAATTTTGAGGATTT
1 CAATTCCATCCCTAAAATATGACCCTAATTCTAAATTAGTCCTCAAAATTTTGAGCATTT
* * *
30165 CAATTTCATACCC-AAAATATGACCTTAATTCTAAATT-GATCCATC-AACTTTTGAGCATTT
1 CAATTCCAT-CCCTAAAATATGACCCTAATTCTAAATTAG-TCC-TCAAAATTTTGAGCATTT
* *
30225 TAGTTCCATCCC
1 CAATTCCATCCC
30237 AAACTATAGG
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
59 4 0.07
60 51 0.85
61 5 0.08
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (60 bp):
CAATTCCATCCCTAAAATATGACCCTAATTCTAAATTAGTCCTCAAAATTTTGAGCATTT
Found at i:30434 original size:60 final size:60
Alignment explanation
Indices: 30367--30526 Score: 200
Period size: 60 Copynumber: 2.7 Consensus size: 60
30357 ATTTGGATGG
* *
30367 AATTGGAAGATTCAAAAGTTT-AGGGACCAATCTAGAATTATGGCCAT-AGTTTGGGGAAGA
1 AATTGGAAGATTCAAAAGTTTGA-GGACCAATTTAGAATGATGGCCATGA-TTTGGGGAAGA
* * * *
30427 AATTGGAATATTCAAAAGTTTGAGGATCAATTTAGAATGATGGTCATGATTTGGGGATGA
1 AATTGGAAGATTCAAAAGTTTGAGGACCAATTTAGAATGATGGCCATGATTTGGGGAAGA
* *
30487 AATTGGAATG-TTTAAAAGTTTGAGGACTAATTTAGAATGA
1 AATTGGAA-GATTCAAAAGTTTGAGGACCAATTTAGAATGA
30527 AATTTATATT
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
60 85 0.98
61 2 0.02
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (60 bp):
AATTGGAAGATTCAAAAGTTTGAGGACCAATTTAGAATGATGGCCATGATTTGGGGAAGA
Found at i:30654 original size:20 final size:20
Alignment explanation
Indices: 30626--30663 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
30616 ATACTAAAAT
30626 AATAATAAAATATCATTTCA
1 AATAATAAAATATCATTTCA
*
30646 AATATTAAAATATCATTT
1 AATAATAAAATATCATTT
30664 AACCCTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (20 bp):
AATAATAAAATATCATTTCA
Found at i:37670 original size:13 final size:13
Alignment explanation
Indices: 37650--37732 Score: 78
Period size: 13 Copynumber: 6.5 Consensus size: 13
37640 CAACATGATT
37650 CAAA-AACAGCTC
1 CAAACAACAGCTC
*
37662 CAAACAACACCTC
1 CAAACAACAGCTC
* * *
37675 CAAATAGCAACTC
1 CAAACAACAGCTC
** *
37688 CAAACAGTAACTC
1 CAAACAACAGCTC
*
37701 CAAACAATAGCTC
1 CAAACAACAGCTC
*
37714 CAAACATCAGCTC
1 CAAACAACAGCTC
37727 CAAACA
1 CAAACA
37733 GTAACATGAT
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
12 4 0.07
13 56 0.93
ACGTcount: A:0.47, C:0.35, G:0.06, T:0.12
Consensus pattern (13 bp):
CAAACAACAGCTC
Found at i:37703 original size:39 final size:39
Alignment explanation
Indices: 37659--37737 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
37649 TCAAAAACAG
*
37659 CTCCAAACAACACCTCCAAATAGCAACTCCAAACAGTAA
1 CTCCAAACAACACCTCCAAACAGCAACTCCAAACAGTAA
* * * *
37698 CTCCAAACAATAGCTCCAAACATCAGCTCCAAACAGTAA
1 CTCCAAACAACACCTCCAAACAGCAACTCCAAACAGTAA
37737 C
1 C
37738 ATGATCCCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.44, C:0.35, G:0.06, T:0.14
Consensus pattern (39 bp):
CTCCAAACAACACCTCCAAACAGCAACTCCAAACAGTAA
Found at i:44096 original size:75 final size:74
Alignment explanation
Indices: 44004--44198 Score: 246
Period size: 75 Copynumber: 2.6 Consensus size: 74
43994 TTGGGTTTAA
* * *
44004 TACTTTTCTAGACTTAATATTCTGGTTTGAGTCTTAAGATTTGACACTTTAATATTATGATTTGA
1 TACTATTCTAGACTTAATATTGTGGTTTGAGTCTTAA-ATTTGACACTTTAATATTATGAGTTGA
44069 TTATGAATTT
65 TTATGAATTT
* * * * * * *
44079 TATTATTCTAGAGTTAATATTGTGGTTTGAATCTTGAAATTTGACATTTTAATATTGTGGGTTGT
1 TACTATTCTAGACTTAATATTGTGGTTTGAGTCTT-AAATTTGACACTTTAATATTATGAGTTGA
44144 TTATGAATTT
65 TTATGAATTT
* * *
44154 TACTGTTCTAAACTTAATATTGTGGTTTGAGTCTTGATATTTGAC
1 TACTATTCTAGACTTAATATTGTGGTTTGAGTCTT-AAATTTGAC
44199 TTTATTTCTG
Statistics
Matches: 103, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
75 101 0.98
76 2 0.02
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49
Consensus pattern (74 bp):
TACTATTCTAGACTTAATATTGTGGTTTGAGTCTTAAATTTGACACTTTAATATTATGAGTTGAT
TATGAATTT
Found at i:45930 original size:20 final size:20
Alignment explanation
Indices: 45907--45977 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
45897 AAAAGAAAGG
45907 AGAAAAAATAAAATAAAATA
1 AGAAAAAATAAAATAAAATA
45927 AGAAATAAAT-AAAT-AAATCAA
1 AGAAA-AAATAAAATAAAAT--A
*
45948 AGGAAAAATAAAATAAGAA-A
1 AGAAAAAATAAAATAA-AATA
45968 AGGAAAAAAT
1 A-GAAAAAAT
45978 GATGATAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
19 4 0.10
20 15 0.36
21 20 0.48
22 1 0.02
23 2 0.05
ACGTcount: A:0.75, C:0.01, G:0.10, T:0.14
Consensus pattern (20 bp):
AGAAAAAATAAAATAAAATA
Found at i:47421 original size:16 final size:15
Alignment explanation
Indices: 47375--47428 Score: 72
Period size: 16 Copynumber: 3.5 Consensus size: 15
47365 CTAGACAATT
47375 AAAATAAAAATAAAA
1 AAAATAAAAATAAAA
**
47390 TTAATAAAAGATAAAA
1 AAAATAAAA-ATAAAA
47406 AAAATAAAAATAAAA
1 AAAATAAAAATAAAA
47421 AATAATAA
1 AA-AATAA
47429 CAACGATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 15 0.45
16 18 0.55
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.19
Consensus pattern (15 bp):
AAAATAAAAATAAAA
Found at i:47428 original size:25 final size:25
Alignment explanation
Indices: 47380--47428 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
47370 CAATTAAAAT
* *
47380 AAAAATAAAATTAATAAAAGATAAA
1 AAAAATAAAAATAATAAAAAATAAA
47405 AAAAATAAAAATAA-AAAATAATAA
1 AAAAATAAAAATAATAAAA-AATAA
47429 CAACGATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (25 bp):
AAAAATAAAAATAATAAAAAATAAA
Found at i:47481 original size:23 final size:24
Alignment explanation
Indices: 47455--47499 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
47445 ATTATTATTA
47455 TATATAA-A-ATATTTTCCAAAAAC
1 TATATAATATATATTTT-CAAAAAC
47478 TATATAATATATATTTTCAAAA
1 TATATAATATATATTTTCAAAA
47500 GTATTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 6 0.30
25 7 0.35
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (24 bp):
TATATAATATATATTTTCAAAAAC
Found at i:47525 original size:36 final size:35
Alignment explanation
Indices: 47473--47840 Score: 255
Period size: 36 Copynumber: 10.5 Consensus size: 35
47463 ATATTTTCCA
47473 AAAACTATATA--ATATATATTTTCAAAAGTATTTT
1 AAAACTATATATTATATATATTTTCAAAAGT-TTTT
* *
47507 AAAATTATATATTATATAT-TTTTTAAAA-TGTTTT
1 AAAACTATATATTATATATATTTTCAAAAGT-TTTT
* *
47541 ----C-A-AAATTATATA-GTTTTCAAAAATGTTTTT
1 AAAACTATATATTATATATATTTTC-AAAA-GTTTTT
* * *
47571 AAAACTATATATTATA-A-GTTTTCAAAATGATTTC
1 AAAACTATATATTATATATATTTTCAAAA-GTTTTT
*
47605 AAAACTATATAATATATATATGTTTTTCAAAATGTTTTT
1 AAAACTATAT-AT-TATATAT-ATTTTCAAAA-GTTTTT
*** * * * *
47644 --TTTTAAAAACTATATATATTTTCAAAA-TGTTTA
1 AAAACTATATATTATATATATTTTCAAAAGT-TTTT
* *
47677 AAAACTATATAATATATATATTTTCAAAAATGTTTTA
1 AAAACTATATATTATATATATTTTC-AAAA-GTTTTT
* * *
47714 AAAACTATATATTATATTTATTTCCAAAATGTTTTA
1 AAAACTATATATTATATATATTTTCAAAA-GTTTTT
* *
47750 AAAACTATATAATATATATATTTTCAAAAATGTTTTA
1 AAAACTATATATTATATATATTTTC-AAAA-GTTTTT
* *
47787 AAAACTATATATTATATTTATTTTCAAAATGTTTTA
1 AAAACTATATATTATATATATTTTCAAAA-GTTTTT
*
47823 AAAACTATATAATATATA
1 AAAACTATATATTATATA
47841 AATGTTTTCA
Statistics
Matches: 274, Mismatches: 36, Indels: 46
0.77 0.10 0.13
Matches are distributed among these distances:
28 13 0.05
29 5 0.02
30 4 0.01
31 1 0.00
32 1 0.00
33 3 0.01
34 44 0.16
35 42 0.15
36 82 0.30
37 64 0.23
38 1 0.00
39 14 0.05
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (35 bp):
AAAACTATATATTATATATATTTTCAAAAGTTTTT
Found at i:47567 original size:29 final size:28
Alignment explanation
Indices: 47517--47583 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 28
47507 AAAATTATAT
**
47517 ATTATATATTTTTTAAAATGTTTTCAAA
1 ATTATATATTTTCAAAAATGTTTTCAAA
*
47545 ATTATATAGTTTTCAAAAATGTTTTTAAA
1 ATTATATA-TTTTCAAAAATGTTTTCAAA
*
47574 ACTATATATT
1 ATTATATATT
47584 ATAAGTTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 10 0.29
29 24 0.71
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (28 bp):
ATTATATATTTTCAAAAATGTTTTCAAA
Found at i:47606 original size:63 final size:62
Alignment explanation
Indices: 47485--47615 Score: 176
Period size: 63 Copynumber: 2.1 Consensus size: 62
47475 AACTATATAA
* * * * *
47485 TATATATTTTCAAAAGTATTTTAAAATTATATATTATATATTTTTTAAAATGTTTTCAAAAT
1 TATATATTTTCAAAAGTATTTTAAAACTATATATTATATAGTTTTCAAAATGATTTCAAAAC
47547 TATATAGTTTTCAAAAATGT-TTTTAAAACTATATATTATA-AGTTTTCAAAATGATTTCAAAAC
1 TATATA-TTTTC-AAAA-GTATTTTAAAACTATATATTATATAGTTTTCAAAATGATTTCAAAAC
47610 TATATA
1 TATATA
47616 ATATATATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
62 6 0.10
63 30 0.49
64 23 0.38
65 2 0.03
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (62 bp):
TATATATTTTCAAAAGTATTTTAAAACTATATATTATATAGTTTTCAAAATGATTTCAAAAC
Found at i:47641 original size:73 final size:71
Alignment explanation
Indices: 47547--47853 Score: 378
Period size: 73 Copynumber: 4.2 Consensus size: 71
47537 TTTTCAAAAT
* * *
47547 TATATAGTTTTCAAAAATGTTTTTAAAACTATATATTATAAGTTTTCAAAATGATTTCAAAACTA
1 TATATAGTTTTCAAAAATGTTTTAAAAACTATATATTATAA-TTTTCAAAATGTTTTAAAAACTA
47612 TATAATA
65 TATAATA
47619 TATATATGTTTTTC-AAAATGTTTTTTTTTAAAAAC--TATA-TAT-ATTTTCAAAATG-TTTAA
1 TATATA-G-TTTTCAAAAATG-----TTTTAAAAACTATATATTATAATTTTCAAAATGTTTTAA
47678 AAACTATATAATA
59 AAACTATATAATA
*
47691 TATATA-TTTTCAAAAATGTTTTAAAAACTATATATTATATTTATTTCCAAAATGTTTTAAAAAC
1 TATATAGTTTTCAAAAATGTTTTAAAAACTATATATTATA---ATTTTCAAAATGTTTTAAAAAC
47755 TATATAATA
63 TATATAATA
47764 TATATA-TTTTCAAAAATGTTTTAAAAACTATATATTATATTTATTTTCAAAATGTTTTAAAAAC
1 TATATAGTTTTCAAAAATGTTTTAAAAACTATATATTATA---ATTTTCAAAATGTTTTAAAAAC
47828 TATATAATA
63 TATATAATA
*
47837 TATAAATGTTTTCAAAA
1 TATATA-GTTTTCAAAA
47854 CTCTATATTA
Statistics
Matches: 212, Mismatches: 5, Indels: 33
0.85 0.02 0.13
Matches are distributed among these distances:
65 10 0.05
67 4 0.02
68 3 0.01
69 5 0.02
70 6 0.03
72 40 0.19
73 113 0.53
74 6 0.03
75 12 0.06
76 4 0.02
78 9 0.04
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (71 bp):
TATATAGTTTTCAAAAATGTTTTAAAAACTATATATTATAATTTTCAAAATGTTTTAAAAACTAT
ATAATA
Found at i:47695 original size:37 final size:37
Alignment explanation
Indices: 47547--47853 Score: 323
Period size: 37 Copynumber: 8.4 Consensus size: 37
47537 TTTTCAAAAT
*
47547 TATATAGTTTTCAAAAATGTTTTTAAAACTATATAT-TA
1 TATATA-TTTTC-AAAATGTTTTAAAAACTATATATATA
* * *
47585 TA-A-GTTTTCAAAATGATTTCAAAACTATATAATATA
1 TATATATTTTCAAAATGTTTTAAAAACTATAT-ATATA
* ** * * *
47621 TATATGTTTTTCAAAATGTTTT----TTTTTAAAAACTA
1 TATAT-ATTTTCAAAATGTTTTAAAAACTATATATA-TA
47656 TATATATTTTCAAAATG-TTTAAAAACTATATA-ATA
1 TATATATTTTCAAAATGTTTTAAAAACTATATATATA
47691 TATATATTTTCAAAAATGTTTTAAAAACTATATAT-TA
1 TATATATTTTC-AAAATGTTTTAAAAACTATATATATA
* *
47728 TATTTATTTCCAAAATGTTTTAAAAACTATATA-ATA
1 TATATATTTTCAAAATGTTTTAAAAACTATATATATA
47764 TATATATTTTCAAAAATGTTTTAAAAACTATATAT-TA
1 TATATATTTTC-AAAATGTTTTAAAAACTATATATATA
*
47801 TATTTATTTTCAAAATGTTTTAAAAACTATATAATATA
1 TATATATTTTCAAAATGTTTTAAAAACTATAT-ATATA
* *
47839 TAAATGTTTTCAAAA
1 TATATATTTTCAAAA
47854 CTCTATATTA
Statistics
Matches: 228, Mismatches: 23, Indels: 36
0.79 0.08 0.13
Matches are distributed among these distances:
33 3 0.01
34 32 0.14
35 30 0.13
36 65 0.29
37 68 0.30
38 16 0.07
39 14 0.06
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (37 bp):
TATATATTTTCAAAATGTTTTAAAAACTATATATATA
Found at i:47844 original size:27 final size:27
Alignment explanation
Indices: 47813--47880 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
47803 TTTATTTTCA
47813 AAATGTTTTAAAAACTATATAATATAT
1 AAATGTTTTAAAAACTATATAATATAT
* * *
47840 AAATGTTTTCAAAACTCTATATTATAT
1 AAATGTTTTAAAAACTATATAATATAT
*
47867 ACATGTTTTAAAAA
1 AAATGTTTTAAAAA
47881 TGTTTTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.41
Consensus pattern (27 bp):
AAATGTTTTAAAAACTATATAATATAT
Found at i:47912 original size:2 final size:2
Alignment explanation
Indices: 47907--47953 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
47897 TATATATATA
47907 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
47949 TG TG T
1 TG TG T
47954 ATAAAAAGGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:48682 original size:84 final size:84
Alignment explanation
Indices: 48516--49380 Score: 656
Period size: 84 Copynumber: 10.5 Consensus size: 84
48506 GCTATACTAT
* * *
48516 AAATGATGT-GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG--TTTTTT-GCAGACAACCCTTC
1 AAATGATATAGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTTTGGCAGATAACCCTTC
* * * *
48577 TAGCCTTGAGTTATACCGC
66 TAGACTTAAGTTATGCTGC
* * * *
48596 AAATGATATATCGTT-GAGCTGAGTGTAATCGAACTCAAAGGTCTTTGTTTGGCAGATAACCCTT
1 AAATGATATAGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT-TTTGGCAGATAACCCTT
*
48660 CTCGACTTAAGTTATGCTGC
65 CTAGACTTAAGTTATGCTGC
* * *
48680 AAATAATAT-GCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC--TTTTGGTCACTGATAACCC
1 AAATGATATAGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTTTGG-CA--GATAACCC
* * * *
48742 TTCTAGCCTTGAGTTATGTTGT
63 TTCTAGACTTAAGTTATGCTGC
* * * * * * * * *
48764 AAATTATGT-GCCCTCGAAGCTGAGTGTAATCGAACTCAAGGGTC---TTTGGCGGATAGCCCTT
1 AAATGATATAG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTTTGGCAGATAACCCTT
* *
48825 CTTGACTTAAGCTATGCTGC
65 CTAGACTTAAGTTATGCTGC
* * * * *
48845 AAATGATAT-GCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGACAACCCTT
1 AAATGATATAGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT-TTTGGCAGATAACCCTT
*
48909 CTCGACTTAAGTTATGCTGC
65 CTAGACTTAAGTTATGCTGC
* * * **
48929 AAATAATAT-GCCTTGGAGCTGAGCGTAGTCGAACTCTAAGGTCTTTTGGTCACAGATAACCCTT
1 AAATGATATAGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTT-TTGGCAGATAACCCTT
* * * *
48993 CTAGCCTTGAGTTATACTGT
65 CTAGACTTAAGTTATGCTGC
* * * * * * * * * * *
49013 AAATAATGTACCCTTGAAGCTGAGTGTAATCGAACTC-GAGG--GTATTTGGCTGATAGCCCTTC
1 AAATGATATAGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTTTGGCAGATAACCCTTC
* **
49075 TCGACTTAAACTATGCTGC
66 TAGACTTAAGTTATGCTGC
* * * * * *
49094 AAATGATGT-GCCTTGGAGTTGAGGGTAGTCAAACTCAAAGGTCTTTGGTTGGTAGATAACCCTT
1 AAATGATATAGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT-TTTGGCAGATAACCCTT
* *
49158 CTCGACTTAAGTTATGCTAC
65 CTAGACTTAAGTTATGCTGC
** **
49178 AAATGATAT-GCCTTGGAGCTGAGCGTAGTCGAACTCGAAA-GTCTTTGGTGATAGATAACCCTT
1 AAATGATATAGCCTTGGAGCTGAGCGTAGTCGAACTC-AAAGGTCTTTTTTGGCAGATAACCCTT
* * * *
49241 CTAGCCTTGAGTTATGTTGT
65 CTAGACTTAAGTTATGCTGC
* * * *** * *
49261 AAATGATGT-GCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTAGCTGACAGACAACCC-T-
1 AAATGATATAGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTTTGGCAGATAACCCTTC
* *
49323 T-G-----AGTTATGTTGT
66 TAGACTTAAGTTATGCTGC
* *
49336 AAATGATGTA-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
1 AAATGATATAGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTT
49381 GGCTGACAGA
Statistics
Matches: 636, Mismatches: 126, Indels: 51
0.78 0.15 0.06
Matches are distributed among these distances:
75 54 0.08
80 80 0.13
81 75 0.12
82 11 0.02
83 88 0.14
84 276 0.43
85 52 0.08
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (84 bp):
AAATGATATAGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTTTGGCAGATAACCCTTC
TAGACTTAAGTTATGCTGC
Found at i:48856 original size:165 final size:165
Alignment explanation
Indices: 48516--49380 Score: 773
Period size: 165 Copynumber: 5.3 Consensus size: 165
48506 GCTATACTAT
* * * *
48516 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTG-CA--GACAACCCTTCT
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCACTGATAACCCTTCT
* * * * *
48578 AGCCTTGAGTTATACCGCAAATGATATATCGTT-GAGCTGAGTGTAATCGAACTCAAAGGTCTTT
66 AGCCTTGAGTTATGCTGCAAATGATGT-GCCTTGGAGCTGAGTGTAATCGAACTCAAAGGTC--T
48642 GTTTGG-CAGATAACCCTTCTCGACTTAAGTTATGCTGC
128 -TTTGGTCAGATAACCCTTCTCGACTTAAGTTATGCTGC
* *
48680 AAATAATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTCACTGATAACCCTTC
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTCACTGATAACCCTTC
* * * * * *
48745 TAGCCTTGAGTTATGTTGTAAATTATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAGGGTC-T
65 TAGCCTTGAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGTGTAATCGAACTCAAAGGTCTT
* * * *
48809 TTGG-CGGATAGCCCTTCTTGACTTAAGCTATGCTGC
129 TTGGTCAGATAACCCTTCTCGACTTAAGTTATGCTGC
* * ** * *
48845 AAATGATATGCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGACAACCCTTC
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TCACTGATAACCCTTC
* * * * * * * *
48910 TCGACTTAAGTTATGCTGCAAATAATATGCCTTGGAGCTGAGCGTAGTCGAACTCTAAGGTCTTT
65 TAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCAAAGGTCTTT
* * * * *
48975 TGGTCACAGATAACCCTTCTAGCCTTGAGTTATACTGT
130 TGGT--CAGATAACCCTTCTCGACTTAAGTTATGCTGC
* * * * * * * * *
49013 AAATAATGTACCCTTGAAGCTGAGTGTAATCGAACTCGAGGGTATTTGG---CTGATAGCCCTTC
1 AAATGATAT-GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCACTGATAACCCTTC
* * * ** * * * *
49075 TCGACTTAAACTATGCTGCAAATGATGTGCCTTGGAGTTGAGGGTAGTCAAACTCAAAGGTCTTT
65 TAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCAAAGGTC-TT
*
49140 GGTTGGT-AGATAACCCTTCTCGACTTAAGTTATGCTAC
129 --TTGGTCAGATAACCCTTCTCGACTTAAGTTATGCTGC
* *
49178 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAAGTCTTTGGTGA-TAGATAACCCTTC
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCACT-GATAACCCTTC
* * * * * *
49242 TAGCCTTGAGTTATGTTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC-TT
65 TAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCAAAGGTCTTT
* * * * *
49306 AGCTGACAGACAACCC-T-T-G-----AGTTATGTTGT
130 TG--GTCAGATAACCCTTCTCGACTTAAGTTATGCTGC
* *
49336 AAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
49381 GGCTGACAGA
Statistics
Matches: 577, Mismatches: 102, Indels: 50
0.79 0.14 0.07
Matches are distributed among these distances:
158 50 0.09
163 3 0.01
164 104 0.18
165 216 0.37
166 13 0.02
167 62 0.11
168 70 0.12
169 59 0.10
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (165 bp):
AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCACTGATAACCCTTCT
AGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCAAAGGTCTTTT
GGTCAGATAACCCTTCTCGACTTAAGTTATGCTGC
Found at i:48972 original size:249 final size:249
Alignment explanation
Indices: 48594--49272 Score: 1058
Period size: 249 Copynumber: 2.7 Consensus size: 249
48584 GAGTTATACC
* * * * *
48594 GCAAATGATATATCGTT-GAGCTGAGTGTAATCGAACTCAAAGGTCTTTGTTTGGCAGATAACCC
1 GCAAATGATAT-GCCTTGGAGCTGAGTGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGATAACCC
*
48658 TTCTCGACTTAAGTTATGCTGCAAATAATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC
65 TTCTCGACTTAAGTTATGCTGCAAATAATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
*
48723 TTTTGGTCACTGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATTATGTGCCCTCGAAGCTGAG
130 TTTTGGTCACTGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATAATGTGCCCTCGAAGCTGAG
* * *
48788 TGTAATCGAACTCAAGGGTCTTTGGCGGATAGCCCTTCTTGACTTAAGCTATGCT
195 TGTAATCGAACTCAAGGGTATTTGGCGGATAGCCCTTCTCGACTTAAACTATGCT
* *
48843 GCAAATGATATGCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGACAACCCT
1 GCAAATGATATGCCTTGGAGCTGAGTGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGATAACCCT
*
48908 TCTCGACTTAAGTTATGCTGCAAATAATATGCCTTGGAGCTGAGCGTAGTCGAACTCTAAGGTCT
66 TCTCGACTTAAGTTATGCTGCAAATAATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
* ** * *
48973 TTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATAATGTACCCTTGAAGCTGAGT
131 TTTGGTCACTGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATAATGTGCCCTCGAAGCTGAGT
* *
49038 GTAATCGAACTCGAGGGTATTTGGCTGATAGCCCTTCTCGACTTAAACTATGCT
196 GTAATCGAACTCAAGGGTATTTGGCGGATAGCCCTTCTCGACTTAAACTATGCT
* * * *
49092 GCAAATGATGTGCCTTGGAGTTGAGGGTAGTCAAACTCAAAGGTCTTTGGTTGGTAGATAACCCT
1 GCAAATGATATGCCTTGGAGCTGAGTGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGATAACCCT
* * *
49157 TCTCGACTTAAGTTATGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAAGTC-
66 TCTCGACTTAAGTTATGCTGCAAATAATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
* *
49221 TTTGGTGA-TAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCC
131 TTTGGTCACT-GATAACCCTTCTAGCCTTGAGTTATGTTGTAAATAATGTGCC
49273 TTGGAGCTGA
Statistics
Matches: 392, Mismatches: 36, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
248 48 0.12
249 344 0.88
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (249 bp):
GCAAATGATATGCCTTGGAGCTGAGTGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGATAACCCT
TCTCGACTTAAGTTATGCTGCAAATAATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
TTTGGTCACTGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATAATGTGCCCTCGAAGCTGAGT
GTAATCGAACTCAAGGGTATTTGGCGGATAGCCCTTCTCGACTTAAACTATGCT
Found at i:49371 original size:75 final size:75
Alignment explanation
Indices: 49245--49406 Score: 288
Period size: 75 Copynumber: 2.2 Consensus size: 75
49235 ACCCTTCTAG
*
49245 CCTTGAGTTATGTTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTAGCT
1 CCTTGAGTTATGTTGTAAATGATGTACCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTAGCT
*
49310 GACAGACAAC
66 GACAGAAAAC
* *
49320 CCTTGAGTTATGTTGTAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGCT
1 CCTTGAGTTATGTTGTAAATGATGTACCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTAGCT
49385 GACAGAAAAC
66 GACAGAAAAC
49395 CCTTGAGTTATG
1 CCTTGAGTTATG
49407 ATGCCGATAG
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 83 1.00
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (75 bp):
CCTTGAGTTATGTTGTAAATGATGTACCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTAGCT
GACAGAAAAC
Found at i:49696 original size:21 final size:21
Alignment explanation
Indices: 49632--49696 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
49622 ATTTAAACGA
* *
49632 GGATCCCTATCGGGTAATCGA
1 GGATCCCCATCGGGTAATCGG
*** * * *
49653 GGAAAACCGT-GGGTAAACAG
1 GGATCCCCATCGGGTAATCGG
49673 GGATCCCCATCGGGTAATCGG
1 GGATCCCCATCGGGTAATCGG
49694 GGA
1 GGA
49697 AAATCGCGGG
Statistics
Matches: 29, Mismatches: 14, Indels: 2
0.64 0.31 0.04
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.28, C:0.22, G:0.34, T:0.17
Consensus pattern (21 bp):
GGATCCCCATCGGGTAATCGG
Found at i:49720 original size:41 final size:40
Alignment explanation
Indices: 49626--49723 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 40
49616 GCGGGGATTT
* * *
49626 AAACGAGGATCCCTATCGGGTAATCGAGGAAAACCGTGGGT
1 AAACG-GGATCCCCATCGGGTAATCGAGGAAAACCGCGGGG
* *
49667 AAACAGGGATCCCCATCGGGTAATCGGGGAAAATCGCGGGG
1 AAAC-GGGATCCCCATCGGGTAATCGAGGAAAACCGCGGGG
49708 AAACGGGTATCCCCAT
1 AAACGGG-ATCCCCAT
49724 TTAGCATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 3 0.06
41 46 0.92
42 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.32, T:0.15
Consensus pattern (40 bp):
AAACGGGATCCCCATCGGGTAATCGAGGAAAACCGCGGGG
Found at i:49972 original size:36 final size:36
Alignment explanation
Indices: 49925--49997 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
49915 ACCAAACTCA
49925 TCCCCGTTTAGCATAAATGATTTTTCCCCATCCCCG
1 TCCCCGTTTAGCATAAATGATTTTTCCCCATCCCCG
*
49961 TCCCCGTTTAGCATAAATGATTTTTCCCCGTCCCCG
1 TCCCCGTTTAGCATAAATGATTTTTCCCCATCCCCG
49997 T
1 T
49998 TTAATTAGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.18, C:0.36, G:0.12, T:0.34
Consensus pattern (36 bp):
TCCCCGTTTAGCATAAATGATTTTTCCCCATCCCCG
Found at i:51117 original size:83 final size:87
Alignment explanation
Indices: 51020--51246 Score: 284
Period size: 95 Copynumber: 2.6 Consensus size: 87
51010 GGCTAGCTGA
*
51020 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAA-TAT-GTA-AAT-ACC
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATAGTATAATCACC
* *
51081 TTTATCAGGTTAGTTGAATATT
66 TTTATCAGGCTAGCTGAATATT
*
51103 ATCCATAAAGCCGGGGCATTTAACCAATTG-TCTTAGAGGGACAACTCAAGCTTTATTGTATAGT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTC-TAGAGGGACAACTC-A-----A-T-TATAGT
51167 ATAATCACCTTTATCAGGCTAGCTGAATATT
57 ATAATCACCTTTATCAGGCTAGCTGAATATT
* *
51198 ATCCATAAAGCTGGAGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA
51247 GCTTTATTGT
Statistics
Matches: 123, Mismatches: 7, Indels: 22
0.81 0.05 0.14
Matches are distributed among these distances:
82 2 0.02
83 42 0.34
84 1 0.01
89 2 0.02
92 3 0.02
93 3 0.02
94 4 0.03
95 64 0.52
96 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (87 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATAGTATAATCACC
TTTATCAGGCTAGCTGAATATT
Found at i:51241 original size:95 final size:94
Alignment explanation
Indices: 51078--51263 Score: 302
Period size: 95 Copynumber: 2.0 Consensus size: 94
51068 ATATGTAAAT
* * *
51078 ACCTTTATCAGGTTAGTTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTGTCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGAGCATTTAACCAATTGTCTTAGAGGG
51143 ACAACTCAAGCTTTATTGTATAGTATAATC
66 ACAACTCAAGCTTTATTGTATA-TATAATC
* *
51173 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCTGGAGCGTTTAACCAATTG-CTCTAGAGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGAGCATTTAACCAATTGTCT-TAGAGG
51237 GACAACTCAAGCTTTATTGTATATATA
65 GACAACTCAAGCTTTATTGTATATATA
51264 TAATATTATA
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
94 6 0.07
95 79 0.93
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (94 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGAGCATTTAACCAATTGTCTTAGAGGG
ACAACTCAAGCTTTATTGTATATATAATC
Found at i:51793 original size:30 final size:29
Alignment explanation
Indices: 51738--51794 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
51728 AAATATCCAA
*
51738 AGAAAGTTCAAAAACAAGTTCCAAACATG
1 AGAAAGTTCAAAAACAAATTCCAAACATG
51767 AGAAAGTTCAAAAAAACAAATT-CAAACA
1 AGAAAGTTC--AAAAACAAATTCCAAACA
51795 AGACACCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 9 0.36
30 6 0.24
31 10 0.40
ACGTcount: A:0.58, C:0.16, G:0.11, T:0.16
Consensus pattern (29 bp):
AGAAAGTTCAAAAACAAATTCCAAACATG
Found at i:54747 original size:20 final size:20
Alignment explanation
Indices: 54724--54793 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 20
54714 AAAGAAAGGG
54724 GAAAAAATAAAATAAAATAA
1 GAAAAAATAAAATAAAATAA
54744 GAAATAAAT-AAAT-AAATCAAA
1 GAAA-AAATAAAATAAAAT--AA
*
54765 GGAAAAATAAAATAAGAA-AA
1 GAAAAAATAAAATAA-AATAA
54785 GGAAAAAAT
1 -GAAAAAAT
54794 GATGATAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
19 4 0.10
20 14 0.34
21 20 0.49
22 1 0.02
23 2 0.05
ACGTcount: A:0.74, C:0.01, G:0.10, T:0.14
Consensus pattern (20 bp):
GAAAAAATAAAATAAAATAA
Found at i:54878 original size:2 final size:2
Alignment explanation
Indices: 54871--54896 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54861 TAATAAATAA
54871 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
54897 GAAAAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55117 original size:30 final size:27
Alignment explanation
Indices: 55055--55123 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 27
55045 ATATGAATGT
* *
55055 AAATAAAAAAAGTATTAAATAAAAAAA
1 AAATAAAAAAAGTAATAAAGAAAAAAA
*
55082 TAATAATAACAAAGTAATAAAGAAAATAAA
1 AAATAA-AA-AAAGTAATAAAGAAAA-AAA
55112 AAATAAGAAAAA
1 AAATAA-AAAAA
55124 ACAATAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 5 0.15
28 2 0.06
29 17 0.50
30 10 0.29
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.17
Consensus pattern (27 bp):
AAATAAAAAAAGTAATAAAGAAAAAAA
Found at i:55132 original size:16 final size:16
Alignment explanation
Indices: 55071--55147 Score: 50
Period size: 17 Copynumber: 4.7 Consensus size: 16
55061 AAAAAGTATT
* *
55071 AAATAAAAAAATAATA
1 AAATAAAATAATAAGA
* *
55087 ATAACAAAGTAATAAAGA
1 A-AATAAAATAAT-AAGA
55105 AAATAAAA-AATAAGA
1 AAATAAAATAATAAGA
*
55120 AAA-AACAATAATAATA
1 AAATAA-AATAATAAGA
*
55136 TAATAATAATAA
1 AAATAA-AATAA
55148 AATATGCATG
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
14 2 0.04
15 9 0.19
16 12 0.26
17 20 0.43
18 4 0.09
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.19
Consensus pattern (16 bp):
AAATAAAATAATAAGA
Found at i:55140 original size:11 final size:11
Alignment explanation
Indices: 55072--55151 Score: 56
Period size: 11 Copynumber: 7.1 Consensus size: 11
55062 AAAAGTATTA
*
55072 AATAAAAAAAT
1 AATAATAAAAT
55083 AATAATAACAA-
1 AATAATAA-AAT
* *
55094 AGTAATAAAGAA
1 AATAATAAA-AT
55106 AATAA-AAAAT
1 AATAATAAAAT
* *
55116 AAGAAAAAACAAT
1 AA-TAATAA-AAT
*
55129 AATAATATAAT
1 AATAATAAAAT
55140 AATAATAAAAT
1 AATAATAAAAT
55151 A
1 A
55152 TGCATGAGTG
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
10 4 0.07
11 34 0.63
12 11 0.20
13 5 0.09
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.20
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:56134 original size:16 final size:15
Alignment explanation
Indices: 56108--56138 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
56098 ATGTGTGACC
56108 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
56123 GGTCAGTCCCGGGATG
1 GGTCA-TCCCGGGATG
56139 TCGGCAGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.13, C:0.26, G:0.42, T:0.19
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:56451 original size:25 final size:24
Alignment explanation
Indices: 56423--56470 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
56413 ATAATATTAT
56423 TATAT-ATAAAATATTTTCCAAAAAC
1 TATATAAT-AAATATTTT-CAAAAAC
*
56448 TATATAATATATATTTTCAAAAA
1 TATATAATAAATATTTTCAAAAA
56471 TATTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 13 0.62
26 2 0.10
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (24 bp):
TATATAATAAATATTTTCAAAAAC
Found at i:56452 original size:23 final size:24
Alignment explanation
Indices: 56425--56470 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
56415 AATATTATTA
56425 TATATAA-A-ATATTTTCCAAAAAC
1 TATATAATATATATTTT-CAAAAAC
56448 TATATAATATATATTTTCAAAAA
1 TATATAATATATATTTTCAAAAA
56471 TATTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 7 0.33
25 7 0.33
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (24 bp):
TATATAATATATATTTTCAAAAAC
Found at i:56486 original size:34 final size:35
Alignment explanation
Indices: 56443--56843 Score: 152
Period size: 36 Copynumber: 11.5 Consensus size: 35
56433 ATATTTTCCA
56443 AAAACTATATAATATATATTTTCAAAAAT-ATTTT
1 AAAACTATATAATATATATTTTCAAAAATGATTTT
* * **
56477 AAAATTATATATTATATAATTTTTTTGAAAATG-TTTT
1 AAAACTATATA--ATAT-ATATTTTCAAAAATGATTTT
* * *
56514 CAAA--AT-T-ATATA-GTTTTCAAAAATGTTTTT
1 AAAACTATATAATATATATTTTCAAAAATGATTTT
* *
56544 AAAACTATATATTATA-AGTTTTC-AAAATGATTTC
1 AAAACTATATAATATATA-TTTTCAAAAATGATTTT
* * *
56578 AAAACTATATATAATATATATATATAT-ATATATGTTTTT
1 AAAAC--TATATAATATATAT-T-T-TCAAAAATGATTTT
* * * *
56617 CAAA--ATGT--T-T-T-TTTT-AAAAA--ACTAT
1 AAAACTATATAATATATATTTTCAAAAATGATTTT
* *
56642 ATATA-TATATATATATATATATTCAAAAATG-TTTT
1 A-AAACTATATA-ATATATATTTTCAAAAATGATTTT
* * *
56677 AAAAACTATATATTATATTTATTTCCAAAATG-TTTT
1 -AAAACTATATAATATATAT-TTTCAAAAATGATTTT
56713 AAAAACTATATAATATATATATATTCAAAAATG-TTTT
1 -AAAACTATATAATATATAT-T-TTCAAAAATGATTTT
* * *
56750 AAAAACTATATATTTTATTTAATTTC-AAAATG-TTTT
1 -AAAACTATATA--ATATATATTTTCAAAAATGATTTT
* * * *
56786 AAAAACTATATTATATACATGTTTTAAAAATGTTTTT
1 -AAAACTATATAATATATAT-TTTCAAAAATGATTTT
*
56823 TAAACTATAATATATATATAT
1 AAAACTAT-ATA-ATATATAT
56844 ATATATATAT
Statistics
Matches: 277, Mismatches: 51, Indels: 74
0.69 0.13 0.18
Matches are distributed among these distances:
25 2 0.01
26 2 0.01
27 7 0.03
28 1 0.00
29 11 0.04
30 10 0.04
31 6 0.02
32 4 0.01
33 5 0.02
34 38 0.14
35 23 0.08
36 89 0.32
37 54 0.19
38 9 0.03
39 16 0.06
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.46
Consensus pattern (35 bp):
AAAACTATATAATATATATTTTCAAAAATGATTTT
Found at i:56558 original size:36 final size:36
Alignment explanation
Indices: 56520--56598 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 36
56510 TTTTCAAAAT
*
56520 TATATAGTTTTCAAAAATGTTTTTAAAACTATATAT-
1 TATATA-TTTTCAAAAATGTTTTAAAAACTATATATA
* *
56556 TATA-AGTTTTC-AAAATGATTTCAAAACTATATATAA
1 TATATA-TTTTCAAAAATGTTTTAAAAACTATATAT-A
56592 TATATAT
1 TATATAT
56599 ATATATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
34 21 0.55
35 7 0.18
36 9 0.24
37 1 0.03
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (36 bp):
TATATATTTTCAAAAATGTTTTAAAAACTATATATA
Found at i:56617 original size:51 final size:51
Alignment explanation
Indices: 56549--56663 Score: 137
Period size: 55 Copynumber: 2.2 Consensus size: 51
56539 TTTTTAAAAC
*
56549 TATATAT-TATAAGTTTTCAAAATG-ATTT-CAAAACTATATATAATATATA
1 TATATATATATAAGTTTTCAAAATGTATTTAAAAAACTATATAT-ATATATA
* *
56598 TATATATATATATGTTTTTCAAAATGTTTTTTTTAAAAAACTATATATATATATA
1 TATATATATATAAG-TTTTCAAAATG---TATTTAAAAAACTATATATATATATA
56653 TATATATATAT
1 TATATATATAT
56664 TCAAAAATGT
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
49 7 0.12
50 5 0.09
51 11 0.20
55 21 0.38
56 12 0.21
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.48
Consensus pattern (51 bp):
TATATATATATAAGTTTTCAAAATGTATTTAAAAAACTATATATATATATA
Found at i:56644 original size:2 final size:2
Alignment explanation
Indices: 56639--56663 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56629 TTTAAAAAAC
56639 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
56664 TCAAAAATGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56688 original size:36 final size:36
Alignment explanation
Indices: 56647--56845 Score: 235
Period size: 36 Copynumber: 5.5 Consensus size: 36
56637 ACTATATATA
56647 TATATATATATATATATTCAAAAATGTTTTAAAAAC
1 TATATATATATATATATTCAAAAATGTTTTAAAAAC
* *
56683 TATATAT-TATATTTATTTCCAAAATGTTTTAAAAAC
1 TATATATATATATATA-TTCAAAAATGTTTTAAAAAC
56719 TATATAATATATATATATTCAAAAATGTTTTAAAAAC
1 TATAT-ATATATATATATTCAAAAATGTTTTAAAAAC
* *
56756 TATATAT-TTTATTTAATTTC-AAAATGTTTTAAAAAC
1 TATATATATATATAT-A-TTCAAAAATGTTTTAAAAAC
* * * **
56792 TATAT-TATATACATGTTTTAAAAATGTTTTTTAAAC
1 TATATATATATATAT-ATTCAAAAATGTTTTAAAAAC
56828 TATAATATATATATATAT
1 TAT-ATATATATATATAT
56846 ATATATATAT
Statistics
Matches: 138, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
35 15 0.11
36 76 0.55
37 32 0.23
38 15 0.11
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (36 bp):
TATATATATATATATATTCAAAAATGTTTTAAAAAC
Found at i:56694 original size:49 final size:49
Alignment explanation
Indices: 56564--56694 Score: 119
Period size: 49 Copynumber: 2.6 Consensus size: 49
56554 ATTATAAGTT
* * * *
56564 TTCAAAATGATTTCAAAACTATATATAATATATATATATATATATATGTTT
1 TTCAAAATGTTTTAAAAACTATATAT--TATATATATATATATATATGATA
*
56615 TTCAAAATGTTTTTTTTAAAAA--A-CTA-TATATATATATATATATAT-ATA
1 TTCAAAATG----TTTTAAAAACTATATATTATATATATATATATATATGATA
56663 TTCAAAAATGTTTTAAAAACTATATATTATAT
1 TTC-AAAATGTTTTAAAAACTATATATTATAT
56695 TTATTTCCAA
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
45 9 0.14
47 1 0.02
48 6 0.09
49 30 0.46
51 9 0.14
52 2 0.03
53 1 0.02
55 7 0.11
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (49 bp):
TTCAAAATGTTTTAAAAACTATATATTATATATATATATATATATGATA
Found at i:56743 original size:73 final size:73
Alignment explanation
Indices: 56645--56841 Score: 281
Period size: 73 Copynumber: 2.7 Consensus size: 73
56635 AAACTATATA
56645 TATATATATATATATATATTCAAAAATGTTTTAAAAACTATATATTATATTT-ATTTCCAAAATG
1 TATATA-ATATATATATATTCAAAAATGTTTTAAAAACTATATATTATATTTAATTT-CAAAATG
56709 TTTTAAAAAC
64 TTTTAAAAAC
*
56719 TATATAATATATATATATTCAAAAATGTTTTAAAAACTATATATTTTATTTAATTTCAAAATGTT
1 TATATAATATATATATATTCAAAAATGTTTTAAAAACTATATATTATATTTAATTTCAAAATGTT
56784 TTAAAAAC
66 TTAAAAAC
* * * * **
56792 TATATTATATACATGT-TTTAAAAATGTTTTTTAAACTATAATATATATAT
1 TATATAATATATATATATTCAAAAATGTTTTAAAAACTAT-ATAT-TATAT
56842 ATATATATAT
Statistics
Matches: 112, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
72 20 0.18
73 78 0.70
74 14 0.12
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (73 bp):
TATATAATATATATATATTCAAAAATGTTTTAAAAACTATATATTATATTTAATTTCAAAATGTT
TTAAAAAC
Found at i:56837 original size:2 final size:2
Alignment explanation
Indices: 56828--56856 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
56818 TTTTTTAAAC
56828 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56857 AAATAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:59127 original size:108 final size:108
Alignment explanation
Indices: 59008--59225 Score: 391
Period size: 108 Copynumber: 2.0 Consensus size: 108
58998 TTTTTTATCG
* * * *
59008 GACACTTCTTCGGAGATTTTTTTTGTCCTATCTCCGAACTTGATCTGAAATGTTGTACCCGAACC
1 GACACTTCTTCGAAGATTTTTTTTGTCCCATCCCCGAACTCGATCTGAAATGTTGTACCCGAACC
59073 CGACCTGATCCCGAGAAAAACTGTATTTTTCATTAAAAAAATA
66 CGACCTGATCCCGAGAAAAACTGTATTTTTCATTAAAAAAATA
*
59116 GACACTTCTTCGAAGATTTTTTTTGTCCCGTCCCCGAACTCGATCTGAAATGTTGTACCCGAACC
1 GACACTTCTTCGAAGATTTTTTTTGTCCCATCCCCGAACTCGATCTGAAATGTTGTACCCGAACC
59181 CGACCTGATCCCGAGAAAAACTGTATTTTTCATTAAAAAAATA
66 CGACCTGATCCCGAGAAAAACTGTATTTTTCATTAAAAAAATA
59224 GA
1 GA
59226 AAACTACATT
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 105 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (108 bp):
GACACTTCTTCGAAGATTTTTTTTGTCCCATCCCCGAACTCGATCTGAAATGTTGTACCCGAACC
CGACCTGATCCCGAGAAAAACTGTATTTTTCATTAAAAAAATA
Found at i:59410 original size:33 final size:34
Alignment explanation
Indices: 59362--59441 Score: 126
Period size: 33 Copynumber: 2.4 Consensus size: 34
59352 AGTTTAGGGT
*
59362 TTATATTATATAATTAATATAAAAATATAAAA-TA
1 TTATA-TATATAATTAATATAAAAATAAAAAATTA
59396 TTATATATATAATTAATATAAAAATAAAAAATTA
1 TTATATATATAATTAATATAAAAATAAAAAATTA
*
59430 CTATATATATAA
1 TTATATATATAA
59442 AATCGGGGCG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
33 25 0.58
34 18 0.42
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (34 bp):
TTATATATATAATTAATATAAAAATAAAAAATTA
Found at i:60492 original size:28 final size:28
Alignment explanation
Indices: 60459--60519 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
60449 ATAAGTGATT
*
60459 AAAATGTAATATTTTAAAATTAGTAATC
1 AAAATGTAATAATTTAAAATTAGTAATC
* * *
60487 AAAATGTATTAATTTAAAGTTAGTGATC
1 AAAATGTAATAATTTAAAATTAGTAATC
60515 AAAAT
1 AAAAT
60520 AAGATAGACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (28 bp):
AAAATGTAATAATTTAAAATTAGTAATC
Done.