Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 78
Found at i:3080 original size:114 final size:114
Alignment explanation
Indices: 2863--3229 Score: 426
Period size: 114 Copynumber: 3.2 Consensus size: 114
2853 CCCTATTCGA
* * *
2863 AAATCCATAC-CATTAGTATGAATT-CATTACCATTTTAGCACACGAAGTGCCCTATGTGAAAAT
1 AAATCCATACAC-TCAGTATG-ATTCCTTTACCATTTTAGCATA--AAGTGCCCTATGTGAAAAT
* *
2926 CCATACCCTTAGTATGATTTCCTATCCTTGTAGCACCCTTAGTGCTTTATCTGG
62 CCATA-CCTTAGTATGATTTCTTATCATTGTAGCACCCTTAGTGCTTTATCTGG
* *
2980 AAATCCATACACTCAGTTTGATTCCTTTACCATTTTAGCATAAAATGCCCTATGTGAAAATCCAT
1 AAATCCATACACTCAGTATGATTCCTTTACCATTTTAGCATAAAGTGCCCTATGTGAAAATCCAT
*
3045 ACCTTAGTATGATTTCTTATCATTGTAGCACCCTTAGTGCTTTATCTAG
66 ACCTTAGTATGATTTCTTATCATTGTAGCACCCTTAGTGCTTTATCTGG
* **
3094 AAATCCAT--ACTCAGTATGATTTCTTTACCATTTTAGCACATAAAGTGCCCTAT-CCAGAAATC
1 AAATCCATACACTCAGTATGATTCCTTTACCATTTTAG--CATAAAGTGCCCTATGTGA-AAATC
* * * * ** *
3156 CATA--TTCATTATGATCTCCTTATCATT-TAGCACACTCAGTGCTCCATATGG
63 CATACCTT-AGTATGAT-TTCTTATCATTGTAGCACCCTTAGTGCTTTATCTGG
3207 AAATCCATACACTCAGTATGATT
1 AAATCCATACACTCAGTATGATT
3230 TCCTGATCCT
Statistics
Matches: 220, Mismatches: 21, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
112 28 0.13
113 34 0.15
114 86 0.39
115 36 0.16
116 3 0.01
117 32 0.15
118 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (114 bp):
AAATCCATACACTCAGTATGATTCCTTTACCATTTTAGCATAAAGTGCCCTATGTGAAAATCCAT
ACCTTAGTATGATTTCTTATCATTGTAGCACCCTTAGTGCTTTATCTGG
Found at i:3098 original size:57 final size:57
Alignment explanation
Indices: 2760--3231 Score: 256
Period size: 59 Copynumber: 8.2 Consensus size: 57
2750 CATATAATTT
* * * * * * **
2760 GTATAATTTCCTTACAATATTAGCACTCTCAGTGCTTTATCTGAAAGAT-CATACACTTA
1 GTATGATTTCTTTACCATTTTAGCACCCTAAGTGCCCTATCTG-AA-ATCCATAC-CTTA
* * *
2819 GTATGATTTCTCTT-TCATTTTAGTA-CATGAAGTGCCCTAT-TCGAAAATCCATACCATTA
1 GTATGATTTCT-TTACCATTTTAGCACCCT-AAGTGCCCTATCT-G-AAATCCATACC-TTA
* * * * *
2878 GTATGAATTCATTACCATTTTAGCACACGAAGTGCCCTATGTGAAAATCCATACCCTTA
1 GTATGATTTCTTTACCATTTTAGCACCCTAAGTGCCCTATCTG-AAATCCATA-CCTTA
* * * ** *
2937 GTATGATTTC-CTATCC-TTGTAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTCA
1 GTATGATTTCTTTA-CCATTTTAGCACCCTAAGTGCCCTATCT-GAAATCCATAC-CTTA
* * * *
2995 GTTTGATTCCTTTACCATTTTAGCA---TAAAATGCCCTATGTGAAAATCCATACCTTA
1 GTATGATTTCTTTACCATTTTAGCACCCT-AAGTGCCCTATCTG-AAATCCATACCTTA
* * * ** *
3051 GTATGATTTC-TTATCATTGTAGCACCCTTAGTGCTTTATCTAGAAATCCATA-CTCA
1 GTATGATTTCTTTACCATTTTAGCACCCTAAGTGCCCTATCT-GAAATCCATACCTTA
* *
3107 GTATGATTTCTTTACCATTTTAGCA-CATAAAGTGCCCTATCCAGAAATCCATA--TTCA
1 GTATGATTTCTTTACCATTTTAGCACCCT-AAGTGCCCTAT-CTGAAATCCATACCTT-A
* * * * * * * *
3164 TTATGATCTCCTTATCA-TTTAGCACACTCAGTGCTCCATAT-GGAAATCCATACACTCA
1 GTATGATTTCTTTACCATTTTAGCACCCTAAGTGC-CC-TATCTGAAATCCATAC-CTTA
3222 GTATGATTTC
1 GTATGATTTC
3232 CTGATCCTTT
Statistics
Matches: 316, Mismatches: 67, Indels: 61
0.71 0.15 0.14
Matches are distributed among these distances:
55 12 0.04
56 51 0.16
57 83 0.26
58 64 0.20
59 101 0.32
60 5 0.02
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (57 bp):
GTATGATTTCTTTACCATTTTAGCACCCTAAGTGCCCTATCTGAAATCCATACCTTA
Found at i:9840 original size:14 final size:14
Alignment explanation
Indices: 9817--9851 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
9807 TCACGTAATT
9817 TGTTTT-CGGAAAA
1 TGTTTTCCGGAAAA
9830 TGTTTTCCGGAAAA
1 TGTTTTCCGGAAAA
9844 TGTTTTCC
1 TGTTTTCC
9852 CATGTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (14 bp):
TGTTTTCCGGAAAA
Found at i:10126 original size:17 final size:17
Alignment explanation
Indices: 10106--10138 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10096 TTATATTTTA
10106 AATTATATAAAATAATC
1 AATTATATAAAATAATC
*
10123 AATTATATATAATAAT
1 AATTATATAAAATAAT
10139 ATGATATGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTATATAAAATAATC
Found at i:10162 original size:27 final size:27
Alignment explanation
Indices: 10125--10230 Score: 94
Period size: 27 Copynumber: 3.9 Consensus size: 27
10115 AAATAATCAA
*
10125 TTATATATAATAATATGAT-ATGATAT-TT
1 TTATATTTAATAATAT-ATAAT-A-ATGTT
10153 TTAT-TTTAATAATATATAATAATGTT
1 TTATATTTAATAATATATAATAATGTT
* *
10179 TTATATTTAATAATGA-ATAATATTATT
1 TTATATTTAATAAT-ATATAATAATGTT
*
10206 TATATATTTAAATAATATTTAATAA
1 T-TATATTT-AATAATATATAATAA
10231 AGATATTTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
25 2 0.03
26 9 0.14
27 31 0.47
28 13 0.20
29 11 0.17
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (27 bp):
TTATATTTAATAATATATAATAATGTT
Found at i:10201 original size:17 final size:17
Alignment explanation
Indices: 10160--10202 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
10150 TTTTTATTTT
*
10160 AATAATATATAATAATG
1 AATAATATTTAATAATG
** *
10177 TTTTATATTTAATAATG
1 AATAATATTTAATAATG
10194 AATAATATT
1 AATAATATT
10203 ATTTATATAT
Statistics
Matches: 19, Mismatches: 7, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
AATAATATTTAATAATG
Found at i:10220 original size:56 final size:55
Alignment explanation
Indices: 10096--10230 Score: 134
Period size: 54 Copynumber: 2.5 Consensus size: 55
10086 TAACATAATA
* * *
10096 TTATAT-TTTAAATTATATAAAATAATCAATTATATATAATAATATGATATGATAT
1 TTATATATTTAAATAATATATAATAATCAATTATATATAATAATATAATAT-ATAT
* *** *
10151 TT-T-TATTTTAATAATATATAATAATGTTTTATATTTAATAATGAATAATAT-TAT
1 TTATATATTTAAATAATATATAATAATCAATTATATATAATAAT--ATAATATATAT
*
10205 TTATATATTTAAATAATATTTAATAA
1 TTATATATTTAAATAATATATAATAA
10231 AGATATTTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
53 1 0.02
54 36 0.55
55 3 0.05
56 25 0.38
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.50
Consensus pattern (55 bp):
TTATATATTTAAATAATATATAATAATCAATTATATATAATAATATAATATATAT
Found at i:10647 original size:21 final size:21
Alignment explanation
Indices: 10623--10665 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
10613 AGAATTCAAA
**
10623 TTCCACTAATTCATTTTCCAG
1 TTCCACTAATTCAAATTCCAG
*
10644 TTCCAGTAATTCAAATTCCAG
1 TTCCACTAATTCAAATTCCAG
10665 T
1 T
10666 AATTTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.40
Consensus pattern (21 bp):
TTCCACTAATTCAAATTCCAG
Found at i:10898 original size:59 final size:57
Alignment explanation
Indices: 10708--10998 Score: 218
Period size: 58 Copynumber: 5.0 Consensus size: 57
10698 ACAAACAGAC
* * *
10708 CCTTAGTATGATTTCTCTTT--CA-TTTAGTACATGAAGTGCCCTATGTGAAAATCCATA
1 CCTTAGTATGA-TTC-CTTTACCATTTTAGCACAT-AAGTGCCTTATCTGAAAATCCATA
* * * * * *
10765 CCCTTAGTATGATTCC-TTATCC-TTGTAGCACCCTTAGTGCTTTATCTGGAAATTCATA
1 -CCTTAGTATGATTCCTTTA-CCATTTTAGCA-CATAAGTGCCTTATCTGAAAATCCATA
* * *
10823 CACTCAGTATGATTCCTTTACCATTTTAGCACATAAAGTTCCTTATGTGAAAATCCATA
1 C-CTTAGTATGATTCCTTTACCATTTTAGCACAT-AAGTGCCTTATCTGAAAATCCATA
* * * * * *
10882 CCTTAGTATGATTTCC-TTATCC-TTGTAGCACCCTTATTGCTTTATCTGGAAATCCATA
1 CCTTAGTATGA-TTCCTTTA-CCATTTTAGCA-CATAAGTGCCTTATCTGAAAATCCATA
* * * *
10940 CACTCAGTATGATTCCTTTACCATTTTAGCACATAAAGTGCCATATCCGGAAATCCATA
1 C-CTTAGTATGATTCCTTTACCATTTTAGCACAT-AAGTGCCTTATCTGAAAATCCATA
10999 TATTGAATAT
Statistics
Matches: 182, Mismatches: 35, Indels: 31
0.73 0.14 0.12
Matches are distributed among these distances:
55 2 0.01
56 1 0.01
57 4 0.02
58 98 0.54
59 77 0.42
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.37
Consensus pattern (57 bp):
CCTTAGTATGATTCCTTTACCATTTTAGCACATAAGTGCCTTATCTGAAAATCCATA
Found at i:10917 original size:117 final size:117
Alignment explanation
Indices: 10730--11067 Score: 436
Period size: 117 Copynumber: 2.9 Consensus size: 117
10720 TTCTCTTTCA
* *
10730 TTTAGTACATGAAGTGCCCTATGTGAAAATCCATACCCTTAGTATGATTCCTTATCCTTGTAGCA
1 TTTAGCACATAAAGTGCCCTATGTGAAAATCCATACCCTTAGTATGATTCCTTATCCTTGTAGCA
*
10795 CCCTTAGTGCTTTATCTGGAAATTCATACACTCAGTATGATTCCTTTACCAT
66 CCCTTAGTGCTTTATCTGGAAATCCATACACTCAGTATGATTCCTTTACCAT
* *
10847 TTTAGCACATAAAGTTCCTTATGTGAAAATCCATA-CCTTAGTATGATTTCCTTATCCTTGTAGC
1 TTTAGCACATAAAGTGCCCTATGTGAAAATCCATACCCTTAGTATGA-TTCCTTATCCTTGTAGC
*
10911 ACCCTTATTGCTTTATCTGGAAATCCATACACTCAGTATGATTCCTTTACCAT
65 ACCCTTAGTGCTTTATCTGGAAATCCATACACTCAGTATGATTCCTTTACCAT
* ** * ** * *
10964 TTTAGCACATAAAGTGCCATATCCGGAAATCCATA-TATTGAATAT-ATCTCC-T-TCATT-TAG
1 TTTAGCACATAAAGTGCCCTATGTGAAAATCCATACCCTT-AGTATGAT-TCCTTATCCTTGTAG
* * ** *
11024 CACACTTAGTTCTCCATATGGAAATCCATACACTCAGTATGATT
64 CACCCTTAGTGCTTTATCTGGAAATCCATACACTCAGTATGATT
11068 TTAATCCTTA
Statistics
Matches: 197, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
114 41 0.21
115 4 0.02
116 13 0.07
117 135 0.69
118 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (117 bp):
TTTAGCACATAAAGTGCCCTATGTGAAAATCCATACCCTTAGTATGATTCCTTATCCTTGTAGCA
CCCTTAGTGCTTTATCTGGAAATCCATACACTCAGTATGATTCCTTTACCAT
Found at i:12788 original size:21 final size:21
Alignment explanation
Indices: 12762--12803 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
12752 TCAATAAGTG
12762 TCAATGATATTCATGTCTCTA
1 TCAATGATATTCATGTCTCTA
12783 TCAATGATATTCATGTCTCTA
1 TCAATGATATTCATGTCTCTA
12804 GAGTGTCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (21 bp):
TCAATGATATTCATGTCTCTA
Found at i:13664 original size:17 final size:17
Alignment explanation
Indices: 13645--13703 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
13635 ATTAAGTTAG
*
13645 TTCATTAATCAAACTAG
1 TTCATTAATCAAACTAA
* *
13662 TTCATTCATTAAACTAA
1 TTCATTAATCAAACTAA
* *
13679 TGCATTAATCGAACTAA
1 TTCATTAATCAAACTAA
13696 TT-ATTAAT
1 TTCATTAAT
13704 TGTTTCATGC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
16 6 0.18
17 28 0.82
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (17 bp):
TTCATTAATCAAACTAA
Found at i:15468 original size:13 final size:13
Alignment explanation
Indices: 15450--15479 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
15440 GTTTAAGTAG
15450 TTTAGGAATTATC
1 TTTAGGAATTATC
*
15463 TTTAGGATTTATC
1 TTTAGGAATTATC
15476 TTTA
1 TTTA
15480 TTTTAGGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (13 bp):
TTTAGGAATTATC
Found at i:24686 original size:36 final size:36
Alignment explanation
Indices: 24646--24733 Score: 169
Period size: 36 Copynumber: 2.5 Consensus size: 36
24636 GTATAGTTAT
24646 TCATGCTTTTGTTGATAGAGATAAACTTAATATGCA
1 TCATGCTTTTGTTGATAGAGATAAACTTAATATGCA
24682 TCATGCTTTTGTTGATAGAGATAAACTTAATATGCA
1 TCATGCTTTTGTTGATAGAGATAAACTTAATATGCA
24718 TCATGCTTTTG-TGATA
1 TCATGCTTTTGTTGATA
24734 TAAACCTTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 5 0.10
36 47 0.90
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (36 bp):
TCATGCTTTTGTTGATAGAGATAAACTTAATATGCA
Found at i:26052 original size:38 final size:38
Alignment explanation
Indices: 26009--26118 Score: 88
Period size: 34 Copynumber: 3.0 Consensus size: 38
25999 AGTTTTTAGG
26009 ATTTTAGTTTAATTAATTCAAGAATTATCTTTAAGATT
1 ATTTTAGTTTAATTAATTCAAGAATTATCTTTAAGATT
* * **
26047 ATTTTA--TT-ATT-ATTCCATG-TTTATCTTTAA-AAG
1 ATTTTAGTTTAATTAATT-CAAGAATTATCTTTAAGATT
* * * *
26080 AGTTTTAGTTTAAGTAGTTTAGGAATTATCTTTAAGATT
1 A-TTTTAGTTTAATTAATTCAAGAATTATCTTTAAGATT
26119 TATCTCTTTA
Statistics
Matches: 53, Mismatches: 11, Indels: 15
0.67 0.14 0.19
Matches are distributed among these distances:
33 2 0.04
34 18 0.34
35 6 0.11
36 4 0.08
37 4 0.08
38 18 0.34
39 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (38 bp):
ATTTTAGTTTAATTAATTCAAGAATTATCTTTAAGATT
Found at i:27709 original size:20 final size:21
Alignment explanation
Indices: 27681--27719 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
27671 AGTTTAGGAA
*
27681 TTATCTTTAGGATTTATCTCT
1 TTATCTTTAGGAATTATCTCT
27702 TTAT-TTTAGGAATTATCT
1 TTATCTTTAGGAATTATCT
27720 TTTCCTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.56
Consensus pattern (21 bp):
TTATCTTTAGGAATTATCTCT
Found at i:29954 original size:37 final size:37
Alignment explanation
Indices: 29901--29975 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
29891 TGAAAAAGCA
29901 TGATAAAAGATATGAAGAAAGGGAGATCTTAGAGGTG
1 TGATAAAAGATATGAAGAAAGGGAGATCTTAGAGGTG
*
29938 TGATAAAAGATCTGAAGAAAGGGAGATCTTAGAGGTG
1 TGATAAAAGATATGAAGAAAGGGAGATCTTAGAGGTG
29975 T
1 T
29976 TCCAAAAAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.04, G:0.32, T:0.23
Consensus pattern (37 bp):
TGATAAAAGATATGAAGAAAGGGAGATCTTAGAGGTG
Found at i:34760 original size:36 final size:36
Alignment explanation
Indices: 34713--34801 Score: 169
Period size: 36 Copynumber: 2.5 Consensus size: 36
34703 TATAGTTATT
34713 TCATGCTTTTGTTGATAGAGATAAACTTAATATGCA
1 TCATGCTTTTGTTGATAGAGATAAACTTAATATGCA
*
34749 TCATGCTTTTGTTGATAGAGATAAACTTAATATGTA
1 TCATGCTTTTGTTGATAGAGATAAACTTAATATGCA
34785 TCATGCTTTTGTTGATA
1 TCATGCTTTTGTTGATA
34802 TAAACCTTTC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (36 bp):
TCATGCTTTTGTTGATAGAGATAAACTTAATATGCA
Found at i:38627 original size:17 final size:17
Alignment explanation
Indices: 38602--38654 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
38592 TGAATTAAGT
*
38602 TAGTTCATTAATCAAAC
1 TAGTCCATTAATCAAAC
* *
38619 TAGTCCATTCATTAAAC
1 TAGTCCATTAATCAAAC
* *
38636 TAGTGCATTAATCGAAC
1 TAGTCCATTAATCAAAC
38653 TA
1 TA
38655 ATTCTGAATT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (17 bp):
TAGTCCATTAATCAAAC
Found at i:39644 original size:78 final size:78
Alignment explanation
Indices: 39552--39707 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
39542 GTGGGTCACA
*
39552 TTCCACCCTCTTCCACTTTAAATTCATTTATTTATATTGTTGATTCCTAGCTCTTATAACTAGTG
1 TTCCACCCTCTTCCACTTTAAATCCATTTATTTATATTGTTGATTCCTAGCTCTTATAACTAGTG
39617 GATCACAATCCAT
66 GATCACAATCCAT
39630 TTCCACCCTCTTCCACTTTAAATCCATTTATTTATATTGTTGATTCCTAGCTCTTATAACTAGTG
1 TTCCACCCTCTTCCACTTTAAATCCATTTATTTATATTGTTGATTCCTAGCTCTTATAACTAGTG
39695 GATCACAATCCAT
66 GATCACAATCCAT
39708 AGTCCTTTAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.26, C:0.25, G:0.08, T:0.42
Consensus pattern (78 bp):
TTCCACCCTCTTCCACTTTAAATCCATTTATTTATATTGTTGATTCCTAGCTCTTATAACTAGTG
GATCACAATCCAT
Found at i:52510 original size:22 final size:22
Alignment explanation
Indices: 52474--52532 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
52464 AAGTTCCTTA
* *
52474 GCACTAATACTAAAGTGC-CTC
1 GCACTGATACAAAAGTGCACTC
* *
52495 AGCACTGGTACAAAAGTGCATTC
1 -GCACTGATACAAAAGTGCACTC
52518 GCACTGATACAAAAG
1 GCACTGATACAAAAG
52533 GGTCATAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 29 0.94
23 2 0.06
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (22 bp):
GCACTGATACAAAAGTGCACTC
Found at i:58763 original size:2 final size:2
Alignment explanation
Indices: 58756--58790 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
58746 AACTGTTTAA
58756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58791 AACTATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:62522 original size:27 final size:27
Alignment explanation
Indices: 62466--62516 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
62456 TGAATAATAT
62466 AATGAACAAAATACCCTTGAAACTTAA
1 AATGAACAAAATACCCTTGAAACTTAA
62493 AATG-ACAATAATACCCTT-AAACTT
1 AATGAACAA-AATACCCTTGAAACTT
62517 TGAAATTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.25
Consensus pattern (27 bp):
AATGAACAAAATACCCTTGAAACTTAA
Found at i:66380 original size:137 final size:137
Alignment explanation
Indices: 66139--66405 Score: 360
Period size: 137 Copynumber: 1.9 Consensus size: 137
66129 TTCTATATAC
* * *
66139 ATTTGTATATAAAGGTTATATATCGATTTTGTTTAATGCATATTTTGCATTTTCGTATCAATACT
1 ATTTGTATATAAAGGTTATAGATCGATTTTGTTTAATCCATATGTTGCATTTTCGTATCAATACT
* * * *
66204 ATGTGCACTTTCGACACTAGATGTGCAACCATAGTATTCATAATGAGTTTGTGAATTAT-CATTT
66 ATATGCACTTTCGACACTAGATGTGCAACCATAGAATTCATAATAAGTTTATGAATT-TCCATTT
66268 CAACATAT
130 CAACATAT
* * * *
66276 ATTTGTGTATAAAGGTTATCGATCGATTTTGTTTAATCCATATGTTGTATTTTCGTATCATTACT
1 ATTTGTATATAAAGGTTATAGATCGATTTTGTTTAATCCATATGTTGCATTTTCGTATCAATACT
* * *
66341 ATATGTACTTTC-AGCACTATG-TGTGCATCCATGGAATTCATAATAAGTTTATGAATTTCCATT
66 ATATGCACTTTCGA-CACTA-GATGTGCAACCATAGAATTCATAATAAGTTTATGAATTTCCATT
66404 TC
129 TC
66406 GACACTTAGT
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
136 2 0.02
137 110 0.97
138 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.43
Consensus pattern (137 bp):
ATTTGTATATAAAGGTTATAGATCGATTTTGTTTAATCCATATGTTGCATTTTCGTATCAATACT
ATATGCACTTTCGACACTAGATGTGCAACCATAGAATTCATAATAAGTTTATGAATTTCCATTTC
AACATAT
Found at i:68224 original size:18 final size:18
Alignment explanation
Indices: 68201--68256 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
68191 AGAGTTTAGG
68201 AATTTAGGGTTCAAATCT
1 AATTTAGGGTTCAAATCT
* *
68219 AATTTA-GGTT-TAA--G
1 AATTTAGGGTTCAAATCT
68233 AATTTAGGGTTCAAATCT
1 AATTTAGGGTTCAAATCT
68251 AATTTA
1 AATTTA
68257 AGTTTAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 6 0.20
15 4 0.13
16 4 0.13
17 4 0.13
18 12 0.40
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (18 bp):
AATTTAGGGTTCAAATCT
Found at i:68236 original size:32 final size:32
Alignment explanation
Indices: 68193--68284 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 32
68183 ATAACCCTAG
*
68193 AGTTTAGGAATTTAGGGTTCAAATCTAATTTA
1 AGTTTAAGAATTTAGGGTTCAAATCTAATTTA
*
68225 GGTTTAAGAATTTAGGGTTCAAATCTAATTTA
1 AGTTTAAGAATTTAGGGTTCAAATCTAATTTA
*
68257 AGTTTAAGAATTTAGGGTTTTAAATCTA
1 AGTTTAAGAATTTAGGG-TTCAAATCTA
68285 CTTTGGTGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
32 46 0.84
33 9 0.16
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.41
Consensus pattern (32 bp):
AGTTTAAGAATTTAGGGTTCAAATCTAATTTA
Found at i:72063 original size:21 final size:19
Alignment explanation
Indices: 72013--72064 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
72003 TTAAATTTTA
72013 ATATTTTCTAAAAGATTAT
1 ATATTTTCTAAAAGATTAT
* * *
72032 CTATATT-TAAAATATATAT
1 ATATTTTCTAAAAGAT-TAT
72051 ATGATTTTCTAAAA
1 AT-ATTTTCTAAAA
72065 AATGATTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 7 0.28
19 9 0.36
20 4 0.16
21 5 0.20
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (19 bp):
ATATTTTCTAAAAGATTAT
Found at i:73274 original size:2 final size:2
Alignment explanation
Indices: 73269--73306 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
73259 TATAAAACAA
73269 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
73307 TATTTTGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74720 original size:30 final size:30
Alignment explanation
Indices: 74685--74765 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 30
74675 CATATTCGAT
* *
74685 TTAAAGAACCAAAATAGCAAAAACAAAAAC
1 TTAAAGGACTAAAATAGCAAAAACAAAAAC
* * *
74715 TTAAAGGACTAAAATAGCAAAAATATAAAT
1 TTAAAGGACTAAAATAGCAAAAACAAAAAC
74745 TTAAAGGACTAAAATAG-AAAA
1 TTAAAGGACTAAAATAGCAAAA
74766 TAGAAATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 4 0.09
30 42 0.91
ACGTcount: A:0.63, C:0.10, G:0.10, T:0.17
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGCAAAAACAAAAAC
Found at i:75115 original size:20 final size:21
Alignment explanation
Indices: 75074--75115 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
75064 GGAATTACGT
*
75074 AACATATAATAACAAGACTAA
1 AACATATAATAACAAAACTAA
75095 AACATA-AAT-ACAAAACATAA
1 AACATATAATAACAAAAC-TAA
75115 A
1 A
75116 TTAAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 6 0.32
20 7 0.37
21 6 0.32
ACGTcount: A:0.67, C:0.14, G:0.02, T:0.17
Consensus pattern (21 bp):
AACATATAATAACAAAACTAA
Found at i:76655 original size:130 final size:130
Alignment explanation
Indices: 76468--76720 Score: 382
Period size: 130 Copynumber: 1.9 Consensus size: 130
76458 GTGATAACAC
* * *
76468 GGTTCCTACGAGATGAGGATGACTGGTTATCTAGGGGTGACACGGCTCCTACTTGATGAGGAGGT
1 GGTTCCTACGAGATGAGGATGACTGATTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGT
* ** *
76533 ATGGT-TGGTGGATGACACGGTTCCTCCGTGATGAGGATGGCAAGCCATCTTTAGGGATATAATA
66 ATGGTCGGGT-GATGACACAATTCCTACGTGATGAGGATGGCAAGCCATCTTTAGGGATATAATA
76597 T
130 T
* *
76598 GGTTCCTACGTGATGAGGATGACTGATTATCTAGGGTTGACACGACTCCTACGTGATGAGGAGGT
1 GGTTCCTACGAGATGAGGATGACTGATTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGT
***
76663 ATGGTCGGGTGATGACACAATTCCTACGTGATGAGGATGGTTGGCCATCTTTAGGGAT
66 ATGGTCGGGTGATGACACAATTCCTACGTGATGAGGATGGCAAGCCATCTTTAGGGAT
76721 TTGTTTCAAG
Statistics
Matches: 110, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
130 107 0.97
131 3 0.03
ACGTcount: A:0.23, C:0.16, G:0.33, T:0.28
Consensus pattern (130 bp):
GGTTCCTACGAGATGAGGATGACTGATTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGT
ATGGTCGGGTGATGACACAATTCCTACGTGATGAGGATGGCAAGCCATCTTTAGGGATATAATAT
Found at i:78242 original size:8 final size:8
Alignment explanation
Indices: 78218--78265 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
78208 TTTTTGTCCT
78218 TTTTTTTC
1 TTTTTTTC
**
78226 TTTGCTTC
1 TTTTTTTC
78234 TTTTTTTC
1 TTTTTTTC
78242 TTTTTTT-
1 TTTTTTTC
* *
78249 TTTCTTTG
1 TTTTTTTC
78257 TTTTTTTC
1 TTTTTTTC
78265 T
1 T
78266 CTTTGCTTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
7 6 0.19
8 26 0.81
ACGTcount: A:0.00, C:0.12, G:0.04, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:80285 original size:57 final size:57
Alignment explanation
Indices: 80224--80336 Score: 217
Period size: 57 Copynumber: 2.0 Consensus size: 57
80214 TAATTTAAAA
*
80224 ATTTGTTGATTTTGGATTAATTAGAATTAAATTGAAAAGGAGTCGCCATTGACCTTG
1 ATTTGTTGATTTTGGATTAATTAGAATTAAATTGAAAAGGAGTCGCCATCGACCTTG
80281 ATTTGTTGATTTTGGATTAATTAGAATTAAATTGAAAAGGAGTCGCCATCGACCTT
1 ATTTGTTGATTTTGGATTAATTAGAATTAAATTGAAAAGGAGTCGCCATCGACCTT
80337 TGGGTTAGGT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (57 bp):
ATTTGTTGATTTTGGATTAATTAGAATTAAATTGAAAAGGAGTCGCCATCGACCTTG
Found at i:80400 original size:18 final size:18
Alignment explanation
Indices: 80373--80412 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
80363 AACGTCATTT
80373 AAAACAATTTTAAGA-AA
1 AAAACAATTTTAAGACAA
*
80390 AAAATCAATTTTTAGACAA
1 AAAA-CAATTTTAAGACAA
80409 AAAA
1 AAAA
80413 GTTGGTCTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 10 0.50
19 6 0.30
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (18 bp):
AAAACAATTTTAAGACAA
Found at i:81222 original size:30 final size:30
Alignment explanation
Indices: 81157--81240 Score: 125
Period size: 30 Copynumber: 2.8 Consensus size: 30
81147 ATCATATTCG
* *
81157 ATTTAAAGGACCAAAATAG-CAAAATAGAA
1 ATTTAAAGGACTAAAATAGAAAAAATAGAA
* *
81186 ACTTAAAGGACTAAAATAGAAAAAATATAA
1 ATTTAAAGGACTAAAATAGAAAAAATAGAA
81216 ATTTAAAGGACTAAAATAGAAAAAA
1 ATTTAAAGGACTAAAATAGAAAAAA
81241 CAAAAAGTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 17 0.35
30 32 0.65
ACGTcount: A:0.62, C:0.07, G:0.12, T:0.19
Consensus pattern (30 bp):
ATTTAAAGGACTAAAATAGAAAAAATAGAA
Found at i:81260 original size:30 final size:30
Alignment explanation
Indices: 81159--81260 Score: 107
Period size: 30 Copynumber: 3.4 Consensus size: 30
81149 CATATTCGAT
* * * * *
81159 TTAAAGGACCAAAATAG-CAAAATAGAAAC
1 TTAAAGGACTAAAATAGAAAAAACAAAAAG
* * *
81188 TTAAAGGACTAAAATAGAAAAAATATAAAT
1 TTAAAGGACTAAAATAGAAAAAACAAAAAG
81218 TTAAAGGACTAAAATAGAAAAAACAAAAAG
1 TTAAAGGACTAAAATAGAAAAAACAAAAAG
* *
81248 TTAGAGGGCTAAA
1 TTAAAGGACTAAA
81261 CCACAATATA
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
29 16 0.25
30 47 0.75
ACGTcount: A:0.60, C:0.08, G:0.15, T:0.18
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGAAAAAACAAAAAG
Found at i:82759 original size:293 final size:292
Alignment explanation
Indices: 82193--82771 Score: 981
Period size: 293 Copynumber: 2.0 Consensus size: 292
82183 CTCTATCTTT
*
82193 TGCTTGCTTTATGGTCTCCTCCTGCTTTGTTTGGTGAGATGATGATATCTCTGGGGTAGGGTTAT
1 TGCTTGCTTTATGGTCTCCTCCTGCTTTGTTTGGTGAGATGATGATATCTCGGGGGTAGGGTTAT
*
82258 GAGACTTACTGACATGCTAAGTAATCCCCTTTTTTTGGGATTATGTTATTTTAAAATAGGGTTTT
66 GAGACTTACTGACATGCTAAGTAATCCCCTTTTTTTGGGATTATATTATTTTAAAATAGGGTTTT
82323 GATTTTGGTTGATTTATTGATGATTTGATTGTTTTTTCATCGTGGCCTTTGTTGATGACGCGACT
131 GATTTTGGTTGATTTATTGATGATTTGATTGTTTTTTCATCGTGGCCTTTGTTGATGACGCGACT
* *
82388 GCTCGGGAGTGCTCAATATCGGCTCACGCGCGAGGAGATGGACGATGAAGCTCACGCGCCGGTGG
196 GCTCGGAAGTGCTCAACATCGGCTCACGCGCGAGGAGATGGACGATGAAGCTCAC-CGCCGGTGG
*
82453 GAGTGAGGAGTTTGGCGGCGACAACTGTTAAGC
260 GAGTGAAGAGTTTGGCGGCGACAACTGTTAAGC
82486 TGCTTGCTTTATGGTCTCCTCCTGCTTTGTTTGGTGAGATGATGATATCT-GGGGGTAGGGTTAT
1 TGCTTGCTTTATGGTCTCCTCCTGCTTTGTTTGGTGAGATGATGATATCTCGGGGGTAGGGTTAT
82550 GAGACTTACTGACATGCTAAGTAATCCCCTTTTTTTGGGATTATATGTATTTTAAAATAGGGTTT
66 GAGACTTACTGACATGCTAAGTAATCCCCTTTTTTTGGGATTATAT-TATTTTAAAATAGGGTTT
82615 TGA-TTTGGTTGATTTATTGATGATTTGATTGTTTTTTTCATCGTGTGGCC-TTGTTGATGACGC
130 TGATTTTGGTTGATTTATTGATGATTTGATTG-TTTTTTCATC--GTGGCCTTTGTTGATGACG-
* *
82678 CGACTGCTCGGAAGTGCTCAACGTC-GCTCACGCGCGAGGAGATGGGCGATGAAGCTCA-CG-CG
191 CGACTGCTCGGAAGTGCTCAACATCGGCTCACGCGCGAGGAGATGGACGATGAAGCTCACCGCCG
82740 GTGGGAGGTTGAAGAGTTTGGCGGCGACAACT
256 GTGGGA-G-TGAAGAGTTTGGCGGCGACAACT
82772 ATTAGCTTTA
Statistics
Matches: 272, Mismatches: 7, Indels: 14
0.93 0.02 0.05
Matches are distributed among these distances:
291 8 0.03
292 89 0.33
293 103 0.38
294 44 0.16
295 28 0.10
ACGTcount: A:0.19, C:0.16, G:0.29, T:0.36
Consensus pattern (292 bp):
TGCTTGCTTTATGGTCTCCTCCTGCTTTGTTTGGTGAGATGATGATATCTCGGGGGTAGGGTTAT
GAGACTTACTGACATGCTAAGTAATCCCCTTTTTTTGGGATTATATTATTTTAAAATAGGGTTTT
GATTTTGGTTGATTTATTGATGATTTGATTGTTTTTTCATCGTGGCCTTTGTTGATGACGCGACT
GCTCGGAAGTGCTCAACATCGGCTCACGCGCGAGGAGATGGACGATGAAGCTCACCGCCGGTGGG
AGTGAAGAGTTTGGCGGCGACAACTGTTAAGC
Found at i:82971 original size:3 final size:3
Alignment explanation
Indices: 82963--82990 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
82953 TGTAAATTAA
82963 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
82991 TTTTTTAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:84438 original size:37 final size:38
Alignment explanation
Indices: 84388--84466 Score: 151
Period size: 37 Copynumber: 2.1 Consensus size: 38
84378 TTGTTATGCT
84388 ATTTAAAGCTTGTAATTATTCTTTGGATCAGCA-GGTC
1 ATTTAAAGCTTGTAATTATTCTTTGGATCAGCAGGGTC
84425 ATTTAAAGCTTGTAATTATTCTTTGGATCAGCAGGGTC
1 ATTTAAAGCTTGTAATTATTCTTTGGATCAGCAGGGTC
84463 ATTT
1 ATTT
84467 CTTATGCTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 33 0.80
38 8 0.20
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.42
Consensus pattern (38 bp):
ATTTAAAGCTTGTAATTATTCTTTGGATCAGCAGGGTC
Found at i:86228 original size:21 final size:21
Alignment explanation
Indices: 86202--86257 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
86192 CGAGTTACCT
*
86202 GCGACGGCCGCAATAGCGTCC
1 GCGACGGCCGCAATAGCGCCC
*
86223 GCGACGACCGCAATAGCGCCC
1 GCGACGGCCGCAATAGCGCCC
*
86244 GCGACTGCCGCAAT
1 GCGACGGCCGCAAT
86258 CACGGTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.39, G:0.30, T:0.09
Consensus pattern (21 bp):
GCGACGGCCGCAATAGCGCCC
Found at i:88129 original size:16 final size:16
Alignment explanation
Indices: 88110--88147 Score: 62
Period size: 14 Copynumber: 2.5 Consensus size: 16
88100 TAATAACCAA
88110 GAGAGAGAATAAGTGC
1 GAGAGAGAATAAGTGC
88126 --GAGAGAATAAGTGC
1 GAGAGAGAATAAGTGC
88140 GAGAGAGA
1 GAGAGAGA
88148 GAGAATTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 14 0.70
16 6 0.30
ACGTcount: A:0.45, C:0.05, G:0.39, T:0.11
Consensus pattern (16 bp):
GAGAGAGAATAAGTGC
Found at i:88131 original size:14 final size:14
Alignment explanation
Indices: 88112--88145 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
88102 ATAACCAAGA
88112 GAGAGAATAAGTGC
1 GAGAGAATAAGTGC
88126 GAGAGAATAAGTGC
1 GAGAGAATAAGTGC
88140 GAGAGA
1 GAGAGA
88146 GAGAGAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.38, T:0.12
Consensus pattern (14 bp):
GAGAGAATAAGTGC
Found at i:98090 original size:27 final size:26
Alignment explanation
Indices: 98036--98094 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
98026 TTTTCTTCGA
*
98036 TATTGAAAAATAAATATTAAAATAATT
1 TATT-AAAAATAAATATAAAAATAATT
* *
98063 TATTAAAAATATATATAAATAATTATT
1 TATTAAAAATAAATATAAA-AATAATT
98090 TATTA
1 TATTA
98095 TATATATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
TATTAAAAATAAATATAAAAATAATT
Found at i:99400 original size:3 final size:3
Alignment explanation
Indices: 99382--99465 Score: 107
Period size: 3 Copynumber: 27.7 Consensus size: 3
99372 TTGTAATATA
* * *
99382 AAT AAT ATAT ATAT AAT AAT AAT AAT AAT TAT TAT TAT AAT AAT AAT
1 AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
99429 AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
99466 AAAAAAATGA
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.03
3 66 0.88
4 7 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:99719 original size:17 final size:17
Alignment explanation
Indices: 99697--99752 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
99687 TTGAATAAGC
99697 TCTTCTTATTATGAACT
1 TCTTCTTATTATGAACT
* *
99714 TCTTCTTCTCCTGATG-AGT
1 TCTTCTTAT--T-ATGAACT
*
99733 TCTTCTCATTATGAACT
1 TCTTCTTATTATGAACT
99750 TCT
1 TCT
99753 CTGGGAAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
16 3 0.10
17 14 0.47
19 10 0.33
20 3 0.10
ACGTcount: A:0.18, C:0.23, G:0.09, T:0.50
Consensus pattern (17 bp):
TCTTCTTATTATGAACT
Found at i:100150 original size:112 final size:112
Alignment explanation
Indices: 99680--100238 Score: 702
Period size: 112 Copynumber: 5.0 Consensus size: 112
99670 TAGAGTCATT
* ** * * *
99680 CAAAAGGTTGAATAAGCTCTTCTTATTATGAACTTC-T--T-CTTCTCCTGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* * * *
99741 TTATGAACTTCTCTGGGAAAA-CTGACCCATCAAGTGATGGATTTGAG
66 TTATGAACTTCACT-GGAAAAGATAATCCATCAAGTGATGGATTTGAG
** * * *
99788 CAAAAAATTGAACAAAGTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* * *
99853 TTATGAAC-TCGAACTGGAAAAGATAGTCCATCAAGTGATAGATTTGAA
66 TTATGAACTTC--ACTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
*
99901 CAAAAGGTTGAACAAATTCTTCTCGTTATGAACTTCTTCATCCTTCTTCAAGTAATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTC-AG--ATGAGTTCTTC
*** *
99966 TCATTATGAACTAT-ACCTGGAAATTTTAATCCATCAAGTGATAGATTTGAG
63 TCATTATGAACT-TCA-CTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
100017 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* * * *
100082 TTATGAACTTCTCTGGAAAAGCTGACCCATCAAGTGATGGATTTGAG
66 TTATGAACTTCACTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
*
100129 CAAAAGGTTGAACAAATTCTTCTCATTTTGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* *
100194 TTACGAAC-TCGAACTGGAAAAGATAATCCATCAAGTGATGAATTT
66 TTATGAACTTC--ACTGGAAAAGATAATCCATCAAGTGATGGATTT
100239 AAATCTTTGC
Statistics
Matches: 393, Mismatches: 42, Indels: 27
0.85 0.09 0.06
Matches are distributed among these distances:
108 30 0.08
109 1 0.00
111 5 0.01
112 135 0.34
113 116 0.30
114 2 0.01
115 3 0.01
116 100 0.25
118 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35
Consensus pattern (112 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTCACTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
Found at i:101125 original size:115 final size:115
Alignment explanation
Indices: 100919--101214 Score: 479
Period size: 115 Copynumber: 2.6 Consensus size: 115
100909 GATCATGCAG
* * * * *
100919 TTCATCTTTTAATTCCAATGATTGGTTCTGTAG-TTCCTACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACTAAACCAGATCAGATAACTCAAAG
*
100983 AACACTTCCAGAAGATGCTATTTAGTCTCCTTATTTCTACTATGAGAAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGAAAA
*
101033 TTTATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACTAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACTAAACCAGATCAGATAACTCAAAG
*
101098 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGAAAA
* *
101148 TTCATCTTTCAAATTCAATGATTGGTTCTGTGGTTTCATA-TCAAACCAAATCAGATAACTCAAA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACT-AAACCAGATCAGATAACTCAAA
101212 GAA
65 GAA
101215 GATGCTATTA
Statistics
Matches: 169, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
114 30 0.18
115 139 0.82
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (115 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACTAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGAAAA
Found at i:101319 original size:83 final size:83
Alignment explanation
Indices: 101213--101396 Score: 341
Period size: 83 Copynumber: 2.2 Consensus size: 83
101203 TAACTCAAAG
*
101213 AAGATGCTATTAGCACATTTATCTTTCAAATTCAATGATTGGTTTTACCAAACCGGATCAGATAA
1 AAGATGCTATTAGCACATTTATCTTTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAA
101278 CTCAAAGAACACTTCCAA
66 CTCAAAGAACACTTCCAA
101296 AAGATGCTATTAGCACATTTATCTTTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAA
1 AAGATGCTATTAGCACATTTATCTTTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAA
*
101361 CTCAAAGAACACTTCCAG
66 CTCAAAGAACACTTCCAA
*
101379 AAGATGCTATGAGCACAT
1 AAGATGCTATTAGCACAT
101397 GGCATTTGTT
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 98 1.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (83 bp):
AAGATGCTATTAGCACATTTATCTTTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAA
CTCAAAGAACACTTCCAA
Found at i:102551 original size:10 final size:10
Alignment explanation
Indices: 102536--102590 Score: 65
Period size: 11 Copynumber: 5.2 Consensus size: 10
102526 TCTTGACTCC
102536 CTTTTTTCTT
1 CTTTTTTCTT
102546 CTTTTTTCTT
1 CTTTTTTCTT
*
102556 CTTTTTTTTTT
1 C-TTTTTTCTT
102567 CTCTTTTTCTCT
1 CT-TTTTTCT-T
*
102579 CTTTTTTTTT
1 CTTTTTTCTT
102589 CT
1 CT
102591 CTTGAAGCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
10 15 0.38
11 21 0.54
12 3 0.08
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
CTTTTTTCTT
Found at i:102566 original size:24 final size:24
Alignment explanation
Indices: 102537--102593 Score: 82
Period size: 23 Copynumber: 2.4 Consensus size: 24
102527 CTTGACTCCC
102537 TTTTTTCTTCTTTTT-TCTTCTTTT
1 TTTTTTCTTCTTTTTCTC-TCTTTT
102561 TTTTTTC-TCTTTTTCTCTCTTTT
1 TTTTTTCTTCTTTTTCTCTCTTTT
102584 TTTTTCTCTT
1 TTTTT-TCTT
102594 GAAGCATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 18 0.60
24 11 0.37
25 1 0.03
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTTTTCTTCTTTTTCTCTCTTTT
Found at i:102573 original size:22 final size:22
Alignment explanation
Indices: 102536--102593 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
102526 TCTTGACTCC
*
102536 CTTTTTTCTTCT-TTTTTCT-T
1 CTTTTTTTTTCTCTTTTTCTCT
102556 CTTTTTTTTTTCTCTTTTTCTCT
1 C-TTTTTTTTTCTCTTTTTCTCT
102579 CTTTTTTTTTCTCTT
1 CTTTTTTTTTCTCTT
102594 GAAGCATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 1 0.03
21 10 0.29
22 21 0.62
23 2 0.06
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (22 bp):
CTTTTTTTTTCTCTTTTTCTCT
Found at i:109934 original size:15 final size:15
Alignment explanation
Indices: 109911--109942 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
109901 TGAAATGAAT
109911 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
109926 AATGCATGTATGCAA
1 AATGAATGTATGCAA
109941 AA
1 AA
109943 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:113277 original size:22 final size:22
Alignment explanation
Indices: 113233--113280 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
113223 ATGAAATATT
113233 AATAATATATATAAATACTAAAA
1 AATAATATATATAAATAC-AAAA
*
113256 AATAATAGTATATATATA-AAAA
1 AATAATA-TATATAAATACAAAA
113278 AAT
1 AAT
113281 TATAATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 7 0.30
24 9 0.39
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
AATAATATATATAAATACAAAA
Found at i:113326 original size:26 final size:27
Alignment explanation
Indices: 113280--113333 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
113270 TATAAAAAAA
*
113280 TTATAATTAATATATGAAATTT-TAAT
1 TTATAATTAATAGATGAAATTTATAAT
113306 TTATAATTAATAGA-GACAATTTATAAT
1 TTATAATTAATAGATGA-AATTTATAAT
113333 T
1 T
113334 GATTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 2 0.08
26 18 0.72
27 5 0.20
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (27 bp):
TTATAATTAATAGATGAAATTTATAAT
Found at i:113949 original size:23 final size:23
Alignment explanation
Indices: 113904--113987 Score: 71
Period size: 23 Copynumber: 3.5 Consensus size: 23
113894 TTTTCTTCGA
*
113904 TATTGAAAAATAAATATTAAAATAAT
1 TATT-AAAAATATATA-T-AAATAAT
113930 TATTAAAAATATATATAAATAAT
1 TATTAAAAATATATATAAATAAT
* ** *
113953 TATTTATTATATATTTAAAT-AT
1 TATTAAAAATATATATAAATAAT
*
113975 ATAATAAAAATAT
1 -TATTAAAAATAT
113988 TAAATATGTA
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
22 2 0.04
23 31 0.65
24 1 0.02
25 10 0.21
26 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (23 bp):
TATTAAAAATATATATAAATAAT
Found at i:117507 original size:21 final size:21
Alignment explanation
Indices: 117483--117569 Score: 54
Period size: 21 Copynumber: 4.0 Consensus size: 21
117473 TCCCTAATAT
117483 CATGGTACCAAATTCACTTAC
1 CATGGTACCAAATTCACTTAC
117504 CAT-GTACTCAATATAGTTGCAC--AC
1 CATGGTAC-C-A-A-A-TT-CACTTAC
* * * *
117528 AATAGTACCAAACTCACTTAA
1 CATGGTACCAAATTCACTTAC
*
117549 CATGGTAACAAATTCACTTAC
1 CATGGTACCAAATTCACTTAC
117570 TGTAGTTATG
Statistics
Matches: 49, Mismatches: 8, Indels: 18
0.65 0.11 0.24
Matches are distributed among these distances:
19 3 0.06
20 5 0.10
21 22 0.45
22 2 0.04
23 2 0.04
24 6 0.12
25 6 0.12
26 3 0.06
ACGTcount: A:0.38, C:0.25, G:0.09, T:0.28
Consensus pattern (21 bp):
CATGGTACCAAATTCACTTAC
Found at i:121192 original size:32 final size:32
Alignment explanation
Indices: 120984--121206 Score: 187
Period size: 32 Copynumber: 7.0 Consensus size: 32
120974 GTATTGTTTA
* * * *
120984 AATGCAATACTGACGCTCCTTTGCATTATCTG
1 AATGCAACACTGACTCTGCTATGCATTATCTG
* * *
121016 GATGCAACACTAACT-TCGCTATGCATTATTTG
1 AATGCAACACTGACTCT-GCTATGCATTATCTG
* * * * *
121048 AACGCAACACTAACTTTTCTATGCATTATCTA
1 AATGCAACACTGACTCTGCTATGCATTATCTG
** * * *
121080 AATATAATAGTGACTTTGCTATGCATTATCTG
1 AATGCAACACTGACTCTGCTATGCATTATCTG
* * * *
121112 AATGCAATATTGACTCTTCTATACATTATCTG
1 AATGCAACACTGACTCTGCTATGCATTATCTG
* * *
121144 AATGAAACACTCACTCTGCTATGTATTATCTG
1 AATGCAACACTGACTCTGCTATGCATTATCTG
** *
121176 AATGCAACACTGACTCTTTTGTGCATTATCT
1 AATGCAACACTGACTCTGCTATGCATTATCT
121207 AAATACGAAA
Statistics
Matches: 150, Mismatches: 39, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
31 1 0.01
32 148 0.99
33 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.37
Consensus pattern (32 bp):
AATGCAACACTGACTCTGCTATGCATTATCTG
Found at i:124942 original size:2 final size:2
Alignment explanation
Indices: 124937--124992 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
124927 TTCGGTCATT
124937 TA TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA
124979 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
124993 CATAATTATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:129247 original size:26 final size:24
Alignment explanation
Indices: 129193--129248 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
129183 AAAAGGGCAC
*
129193 TTTTTTCAAAATTTTTGATTGAAA
1 TTTTTTCAAAATTTTTAATTGAAA
* *
129217 ATTTTTCAAAATTCTTTTAATTG-AT
1 TTTTTTCAAAA-T-TTTTAATTGAAA
129242 TTTTTTC
1 TTTTTTC
129249 CAATTTTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 10 0.38
25 8 0.31
26 8 0.31
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (24 bp):
TTTTTTCAAAATTTTTAATTGAAA
Found at i:132267 original size:104 final size:103
Alignment explanation
Indices: 132032--132260 Score: 280
Period size: 104 Copynumber: 2.2 Consensus size: 103
132022 TATTGAACAT
* * * ***
132032 ACTTCCTCAACGAGAAGAAATAACGTCATATGAAATAGGTAGAACTCTTCAGTTTGGATCAACAG
1 ACTTCCTCAACAAGAAGGAATAACGTCATAGGAAATAGGTAGAACTCTTCAACATGGATCAACAG
* * * *
132097 TGTCGTCTTCAACACCATATTATCTTTGGATTGACCCG
66 TATCGTCTTCAACACCATATTATCTCTAGATTGACCCA
* * * * *
132135 ATTTCCTCAACAAGAAAGAACAACGTCATAGGAAA-ACGGTCAGAACTCTTCAACATGGATGAGC
1 ACTTCCTCAACAAGAAGGAATAACGTCATAGGAAATA-GGT-AGAACTCTTCAACATGGATCAAC
* *
132199 AGTATCGTCTTCGACACCATATTATCTCTAGATTGACTCA
64 AGTATCGTCTTCAACACCATATTATCTCTAGATTGACCCA
132239 ACTTCCTCAACAAGAAGGAATA
1 ACTTCCTCAACAAGAAGGAATA
132261 GTGTCATCTT
Statistics
Matches: 104, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
102 1 0.01
103 32 0.31
104 71 0.68
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (103 bp):
ACTTCCTCAACAAGAAGGAATAACGTCATAGGAAATAGGTAGAACTCTTCAACATGGATCAACAG
TATCGTCTTCAACACCATATTATCTCTAGATTGACCCA
Found at i:134088 original size:2 final size:2
Alignment explanation
Indices: 134081--134118 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
134071 TTCGGTCATT
134081 TA TA TA TA TA TA TA 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 TA TA TA TA
134119 CATAATTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:134128 original size:12 final size:14
Alignment explanation
Indices: 134081--134135 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
134071 TTCGGTCATT
*
134081 TATATATATATATA
1 TATATATATACATA
*
134095 TATATATATATATA
1 TATATATATACATA
134109 TATATATATACATA
1 TATATATATACATA
*
134123 -AT-TATACACATA
1 TATATATATACATA
134135 T
1 T
134136 GGGTGATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
12 9 0.24
13 2 0.05
14 27 0.71
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATATATACATA
Found at i:134335 original size:17 final size:16
Alignment explanation
Indices: 134295--134337 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
134285 ATAATCATAC
*
134295 ATATATTTTGTTTCGA
1 ATATATTTTATTTCGA
* *
134311 ATAAATTTTATTTGCTA
1 ATATATTTTATTT-CGA
134328 ATATATTTTA
1 ATATATTTTA
134338 ATATGTTACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.56
Consensus pattern (16 bp):
ATATATTTTATTTCGA
Found at i:142533 original size:3 final size:3
Alignment explanation
Indices: 142525--142665 Score: 250
Period size: 3 Copynumber: 47.3 Consensus size: 3
142515 GCCTGCAAGC
142525 ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
142572 ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
*
142617 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
142665 A
1 A
142666 AGGGGAAAAA
Statistics
Matches: 133, Mismatches: 2, Indels: 6
0.94 0.01 0.04
Matches are distributed among these distances:
2 4 0.03
3 126 0.95
4 3 0.02
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:143343 original size:135 final size:135
Alignment explanation
Indices: 142881--143466 Score: 585
Period size: 135 Copynumber: 4.4 Consensus size: 135
142871 TTCAGGGTAG
* ** * * * *
142881 ATCAGATCTGGATACATTGATTTATTCCACTATTCTTCAGGGAAGATTGAATCGAGGAAAAC---
1 ATCAGATCTGGAAATGTTGATTCATTCCACTATTCTTCAAGGAAGATTGAATCGAGGCAGACTTG
* * *
142943 -T----TGTTCCT-ATGGAAGATCAAATCT--AAAAAA-ACGGGATCTATTCTGTTGCTTCTTGA
66 TTCCACTGTTCCTCATGGAAGATCAAATCTGGAAAAAAGA-GGGATCTATTATGCTGCTTCTTAA
*
142999 GGAAAA
130 GGGAAA
* * * * *
143005 ATCATATTTGAAAATGTTGATTCATTCCACTGTTCTT-ATGGAAGATTGAATCGAGGCAGACTTG
1 ATCAGATCTGGAAATGTTGATTCATTCCACTATTCTTCAAGGAAGATTGAATCGAGGCAGACTTG
* * * * * * *
143069 TTCAACTGTTCTTCAAGAAAGATCAAATCTAGAAAAAAGAGGGATATGTTCCAT--TGCTTCTTA
66 TTCCACTGTTCCTCATGGAAGATCAAATCTGGAAAAAAGAGGGATCTATT--ATGCTGCTTCTTA
143132 AGGGAAAA
129 AGGG-AAA
* * * *
143140 ATCAGATCTAGAAATGTTCATTCATTCCACTATTCTTCAGGGAAGATTGAATCAAGGCAGACTTG
1 ATCAGATCTGGAAATGTTGATTCATTCCACTATTCTTCAAGGAAGATTGAATCGAGGCAGACTTG
* * * * *
143205 TTCCACTGTTCCTCATGGAAGATCAAATTTGGATAAAAGAGGGATTTGTTATGCTGCTTCTTGAG
66 TTCCACTGTTCCTCATGGAAGATCAAATCTGGAAAAAAGAGGGATCTATTATGCTGCTTCTTAAG
143270 GGAAA
131 GGAAA
* * * * * *
143275 GTCAGATCTGGAAATATTGATTTATTCCACTGTTCTTCAAGGAAGATTGAATCCAGGTAGACTTG
1 ATCAGATCTGGAAATGTTGATTCATTCCACTATTCTTCAAGGAAGATTGAATCGAGGCAGACTTG
* * * *
143340 TTCCACTGTTCCTCAGGGAAGATTAAATTTGGAAAAAAGAGAGATCTATT-TCGCTGCTTCTTAA
66 TTCCACTGTTCCTCATGGAAGATCAAATCTGGAAAAAAGAGGGATCTATTAT-GCTGCTTCTTAA
143404 GGGAAA
130 GGGAAA
* * * *
143410 ATCATATATGGAAATGTTGATTCATTCCACTTTTCTT-AAGGGAATATTGAATCGAGG
1 ATCAGATCTGGAAATGTTGATTCATTCCACTATTCTTCAA-GGAAGATTGAATCGAGG
143467 TAGATTTTTT
Statistics
Matches: 382, Mismatches: 60, Indels: 29
0.81 0.13 0.06
Matches are distributed among these distances:
123 21 0.05
124 29 0.08
127 1 0.00
131 6 0.02
132 14 0.04
134 30 0.08
135 201 0.53
136 80 0.21
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (135 bp):
ATCAGATCTGGAAATGTTGATTCATTCCACTATTCTTCAAGGAAGATTGAATCGAGGCAGACTTG
TTCCACTGTTCCTCATGGAAGATCAAATCTGGAAAAAAGAGGGATCTATTATGCTGCTTCTTAAG
GGAAA
Found at i:144735 original size:5 final size:5
Alignment explanation
Indices: 144706--144782 Score: 51
Period size: 5 Copynumber: 16.0 Consensus size: 5
144696 TTATTTATTC
* *
144706 TCTTT TCTTT ATC-TT TCCTT T-TTT TCTTT T-ATT T-TTT TCATTT T-TTT
1 TCTTT TCTTT -TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TC-TTT TCTTT
144753 TC-TT TCTTT TCTTT TCCTTT T-TATT TCTTT
1 TCTTT TCTTT TCTTT T-CTTT TCT-TT TCTTT
144783 AGAAGAAACT
Statistics
Matches: 59, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
4 20 0.34
5 27 0.46
6 12 0.20
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:144743 original size:14 final size:13
Alignment explanation
Indices: 144724--144767 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
144714 TTATCTTTCC
*
144724 TTTTTTTCTTTTA
1 TTTTTTTCTTTTT
144737 TTTTTTTCATTTTT
1 TTTTTTTC-TTTTT
*
144751 TTTCTTTCTTTTCT
1 TTTTTTTCTTTT-T
144765 TTT
1 TTT
144768 CCTTTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 12 0.44
14 15 0.56
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTCTTTTT
Found at i:144762 original size:9 final size:9
Alignment explanation
Indices: 144709--144766 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
144699 TTTATTCTCT
144709 TTTCTTTATC
1 TTTCTTT-TC
144719 TTTCCTTTT-
1 TTT-CTTTTC
*
144728 TTTCTTTTA
1 TTTCTTTTC
144737 TTT-TTTTC
1 TTTCTTTTC
*
144745 ATTTTTTTTC
1 -TTTCTTTTC
144755 TTTCTTTTC
1 TTTCTTTTC
144764 TTT
1 TTT
144767 TCCTTTTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
8 9 0.21
9 20 0.48
10 9 0.21
11 4 0.10
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:152728 original size:18 final size:18
Alignment explanation
Indices: 152705--152748 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
152695 TCATTAATTC
152705 CATAAACCCTATTGTGAA
1 CATAAACCCTATTGTGAA
152723 CATAAACCCTATTGTGAA
1 CATAAACCCTATTGTGAA
152741 CATAAACC
1 CATAAACC
152749 TTAAAATCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.25
Consensus pattern (18 bp):
CATAAACCCTATTGTGAA
Found at i:155321 original size:13 final size:13
Alignment explanation
Indices: 155289--155321 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
155279 TATAAAATAT
155289 ATAAAATAGTTCA
1 ATAAAATAGTTCA
155302 A-AAAATAGTTCA
1 ATAAAATAGTTCA
155314 ATAAAATA
1 ATAAAATA
155322 CTATAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (13 bp):
ATAAAATAGTTCA
Found at i:160056 original size:15 final size:15
Alignment explanation
Indices: 160036--160106 Score: 56
Period size: 15 Copynumber: 4.9 Consensus size: 15
160026 CTGACTGGTC
160036 TGAGTTGACTCAACA
1 TGAGTTGACTCAACA
* **
160051 TGAGTTAACTCATTA
1 TGAGTTGACTCAACA
*
160066 CGAGTTGACTCAAC-
1 TGAGTTGACTCAACA
* * **
160080 -GGGTTAACTCATTA
1 TGAGTTGACTCAACA
160094 TGAGTTGACTCAA
1 TGAGTTGACTCAA
160107 TTTTAGAAGA
Statistics
Matches: 40, Mismatches: 14, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
13 9 0.22
15 31 0.77
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (15 bp):
TGAGTTGACTCAACA
Found at i:160098 original size:28 final size:29
Alignment explanation
Indices: 160036--160106 Score: 108
Period size: 28 Copynumber: 2.4 Consensus size: 29
160026 CTGACTGGTC
160036 TGAGTTGACTCAACATGAGTTAACTCATTA
1 TGAGTTGACTCAACA-GAGTTAACTCATTA
* *
160066 CGAGTTGACTCAAC-GGGTTAACTCATTA
1 TGAGTTGACTCAACAGAGTTAACTCATTA
160094 TGAGTTGACTCAA
1 TGAGTTGACTCAA
160107 TTTTAGAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 25 0.66
30 13 0.34
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (29 bp):
TGAGTTGACTCAACAGAGTTAACTCATTA
Found at i:162589 original size:15 final size:16
Alignment explanation
Indices: 162565--162610 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
162555 ACAAATGAAG
162565 AAAATAATAAATAGTA
1 AAAATAATAAATAGTA
162581 AAAAT-ATAAA-AG--
1 AAAATAATAAATAGTA
*
162593 AAAATAATAAATATTA
1 AAAATAATAAATAGTA
162609 AA
1 AA
162611 TGATGGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
12 5 0.20
13 5 0.20
14 3 0.12
15 5 0.20
16 7 0.28
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (16 bp):
AAAATAATAAATAGTA
Found at i:162761 original size:15 final size:15
Alignment explanation
Indices: 162743--162791 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
162733 AAAGAAAATA
162743 ATAAATAGTAAAAGT
1 ATAAATAGTAAAAGT
*
162758 ATAAA-AGGAAAA-T
1 ATAAATAGTAAAAGT
162771 AATAAATAGTAAAAGT
1 -ATAAATAGTAAAAGT
162787 ATAAA
1 ATAAA
162792 AGGTAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 1 0.03
14 11 0.38
15 16 0.55
16 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.22
Consensus pattern (15 bp):
ATAAATAGTAAAAGT
Found at i:162777 original size:29 final size:29
Alignment explanation
Indices: 162706--162807 Score: 136
Period size: 29 Copynumber: 3.4 Consensus size: 29
162696 AAAATTACCA
*
162706 AAAATAATAAATA-TAAAA-TACAAAATGAAAG
1 AAAATAATAAATAGTAAAAGTATAAAA-G---G
162737 AAAATAATAAATAGTAAAAGTATAAAAGG
1 AAAATAATAAATAGTAAAAGTATAAAAGG
162766 AAAATAATAAATAGTAAAAGTATAAAAGG
1 AAAATAATAAATAGTAAAAGTATAAAAGG
*
162795 TAAATAATAAATA
1 AAAATAATAAATA
162808 ATGATACATT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
29 42 0.63
31 13 0.19
32 6 0.09
33 6 0.09
ACGTcount: A:0.68, C:0.01, G:0.10, T:0.22
Consensus pattern (29 bp):
AAAATAATAAATAGTAAAAGTATAAAAGG
Found at i:162797 original size:15 final size:15
Alignment explanation
Indices: 162750--162798 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
162740 ATAATAAATA
162750 GTAAAAGTATAAAAG
1 GTAAAAGTATAAAAG
162765 G-AAAA-TAATAAATA-
1 GTAAAAGT-ATAAA-AG
162779 GTAAAAGTATAAAAG
1 GTAAAAGTATAAAAG
162794 GTAAA
1 GTAAA
162799 TAATAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 1 0.03
14 11 0.38
15 16 0.55
16 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.16, T:0.20
Consensus pattern (15 bp):
GTAAAAGTATAAAAG
Found at i:163012 original size:28 final size:27
Alignment explanation
Indices: 162960--163024 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
162950 ATTTTATATC
*
162960 AATAATATAAATAATGTTAATAAAATA
1 AATAATATAAATAATGTTAAAAAAATA
*
162987 AATATATATATATAATG-TAGAAAAAATTAA
1 AATA-ATATAAATAATGTTA-AAAAAA-T-A
163017 AATAATAT
1 AATAATAT
163025 GGATAAGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 6 0.19
28 16 0.50
29 5 0.16
30 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.34
Consensus pattern (27 bp):
AATAATATAAATAATGTTAAAAAAATA
Found at i:164999 original size:14 final size:13
Alignment explanation
Indices: 164980--165041 Score: 53
Period size: 12 Copynumber: 5.0 Consensus size: 13
164970 ATATTTTCAA
*
164980 ATATAATATGTATT
1 ATATAATATATA-T
164994 ATATAATATATAT
1 ATATAATATATAT
165007 A-ATAATAT-T-T
1 ATATAATATATAT
*
165017 AGA-AACTATATAT
1 ATATAA-TATATAT
165030 ATAT-ATATATAT
1 ATATAATATATAT
165042 GTGTGTGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
10 4 0.10
11 5 0.12
12 15 0.37
13 6 0.15
14 11 0.27
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:165805 original size:125 final size:125
Alignment explanation
Indices: 165575--165818 Score: 303
Period size: 125 Copynumber: 2.0 Consensus size: 125
165565 CATCCTTTAC
* * *
165575 AGGATTCTAAGTCGAAGGACGATCTTACTTCTTCCTTTAAAGGATGCTAAGTCGTAATCGATGGG
1 AGGATTCTAAGTCGAAAGACGATCTTACTCCTTCCTCTAAAGGATGCTAAGTCGTAATCGATGGG
* *** *
165640 TGATCCTTACCTCTTTCTGAAAGATGTTGAATCTCAGGATGATCTTACTCCTTCATTTGA
66 TGATCCCTACCTCTTTCTGAAAGATGCAAAATATCAGGATGATCTTACTCCTTCATTTGA
* ** * * *
165700 AGGATTCTAAGTCGAAAGTCTCTCTTACTCCTTCGTCTAAAGGATGTTAAGTCGTGATCGATGGG
1 AGGATTCTAAGTCGAAAGACGATCTTACTCCTTCCTCTAAAGGATGCTAAGTCGTAATCGATGGG
* **
165765 TGATCCACT-CCTTTTTCT-AAATGATGCAAAATATGGGGATGATCTTACTCCTTC
66 TGATCC-CTACCTCTTTCTGAAA-GATGCAAAATATCAGGATGATCTTACTCCTTC
165819 CGCTAAAGGA
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
124 3 0.03
125 96 0.96
126 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (125 bp):
AGGATTCTAAGTCGAAAGACGATCTTACTCCTTCCTCTAAAGGATGCTAAGTCGTAATCGATGGG
TGATCCCTACCTCTTTCTGAAAGATGCAAAATATCAGGATGATCTTACTCCTTCATTTGA
Found at i:168112 original size:58 final size:59
Alignment explanation
Indices: 168001--168121 Score: 163
Period size: 58 Copynumber: 2.1 Consensus size: 59
167991 AGTGGTAGCT
* * * * * *
168001 CGAATATGACATATAAGGTCGTGCCCACCATATGCACTAGTTATCCTTTAGTGCAGTCC
1 CGAACATGACACATAAGGTCGTGACCACCATATGCACTAGGTACCCTTTAGTGCAATCC
* *
168060 CGAACATGACACATAAGGTCGT-ACCATCATATGTACTAGGTACCCTTTAGTGCAATCC
1 CGAACATGACACATAAGGTCGTGACCACCATATGCACTAGGTACCCTTTAGTGCAATCC
168118 CGAA
1 CGAA
168122 TATGTAGTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
58 34 0.63
59 20 0.37
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (59 bp):
CGAACATGACACATAAGGTCGTGACCACCATATGCACTAGGTACCCTTTAGTGCAATCC
Found at i:170148 original size:40 final size:40
Alignment explanation
Indices: 170104--170183 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
170094 ATTGAATCTA
* * *
170104 GGGACGATCTTACACTTTCCTCTAAATGAAGCTAAATCAT
1 GGGACAATCTTACACCTTCCTCTAAAGGAAGCTAAATCAT
* * *
170144 GGGACAATCTTACTCCTTCCTCTAAAGGATGCTAAGTCAT
1 GGGACAATCTTACACCTTCCTCTAAAGGAAGCTAAATCAT
170184 AATAGTTAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (40 bp):
GGGACAATCTTACACCTTCCTCTAAAGGAAGCTAAATCAT
Found at i:171435 original size:36 final size:34
Alignment explanation
Indices: 171299--171437 Score: 93
Period size: 36 Copynumber: 3.9 Consensus size: 34
171289 CCTTACATCC
* *
171299 ATAAGTATTACCAGCTGATCGGTA-CTGAACCTAT
1 ATAAGAATTACCATCTGATCGG-AGCTGAACCTAT
* * ** *
171333 ATAAGAAATTACCAAAC-GATCGGTGCTGAATATGT
1 ATAAG-AATTACC-ATCTGATCGGAGCTGAACCTAT
* * ** *
171368 ATAAGGAATTTCCATCTTAATATGAGTTGAACCTAT
1 ATAA-GAATTACCATC-TGATCGGAGCTGAACCTAT
171404 ATAATGAATTACCATCTTGATCGGAGCTGAACCT
1 ATAA-GAATTACCATC-TGATCGGAGCTGAACCT
171438 GCAGAGACTT
Statistics
Matches: 77, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
34 7 0.09
35 29 0.38
36 41 0.53
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (34 bp):
ATAAGAATTACCATCTGATCGGAGCTGAACCTAT
Found at i:175441 original size:36 final size:36
Alignment explanation
Indices: 175353--175465 Score: 113
Period size: 36 Copynumber: 3.2 Consensus size: 36
175343 CTGATCGGTA
* * * *
175353 CTGAACCTATACAAAGAATTACCAAC-CGA-TTGACG
1 CTGAACCTATATAAGGAATTACCAACTTGACTAGA-G
* * * *
175388 CTAAACTTGTATAAGGAATTACCAGCTTGACTAGAG
1 CTGAACCTATATAAGGAATTACCAACTTGACTAGAG
* *
175424 TTGAACCTATATAAGGAATTACCAACTTGATTAGAG
1 CTGAACCTATATAAGGAATTACCAACTTGACTAGAG
175460 CTGAAC
1 CTGAAC
175466 ATGCAGAGAT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
35 20 0.33
36 38 0.62
37 3 0.05
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (36 bp):
CTGAACCTATATAAGGAATTACCAACTTGACTAGAG
Found at i:181113 original size:18 final size:19
Alignment explanation
Indices: 181090--181131 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
181080 GTAAGAAAAT
*
181090 ATTAAAATAA-TAAAAGCG
1 ATTAAAATAAGTAAAAGCA
181108 ATT-AAATAAGTAAAAGCA
1 ATTAAAATAAGTAAAAGCA
181126 ATTAAA
1 ATTAAA
181132 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (19 bp):
ATTAAAATAAGTAAAAGCA
Found at i:182155 original size:17 final size:18
Alignment explanation
Indices: 182126--182164 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
182116 TTTTGGTAAG
182126 AAAGTATTAAAATAA-TA
1 AAAGTATTAAAATAAGTA
182143 AAAGTGATT-AAATAAGTA
1 AAAGT-ATTAAAATAAGTA
182161 AAAG
1 AAAG
182165 CAATTAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.26
Consensus pattern (18 bp):
AAAGTATTAAAATAAGTA
Found at i:183445 original size:12 final size:14
Alignment explanation
Indices: 183428--183460 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
183418 ATCCATTCAT
183428 TCAATGCTAA-T-C
1 TCAATGCTAATTAC
183440 TCAATGCTAATTAC
1 TCAATGCTAATTAC
183454 TCAATGC
1 TCAATGC
183461 CTTACTGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 1 0.05
14 8 0.42
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.33
Consensus pattern (14 bp):
TCAATGCTAATTAC
Found at i:198053 original size:36 final size:36
Alignment explanation
Indices: 197975--198083 Score: 130
Period size: 36 Copynumber: 3.1 Consensus size: 36
197965 ATACATAACA
* * *
197975 TATATAAGGAATTACCAAC-CGATCAGTGCTGAACC
1 TATATAAGGAATTACCAACTTGATCAGAGCTAAACC
* * *
198010 TGTATAAGGAATTACCAGCTTGATCTGAGCTAAACC
1 TATATAAGGAATTACCAACTTGATCAGAGCTAAACC
* **
198046 TATATAAGAAATTATTAACTTGATCAGAGCTAAACC
1 TATATAAGGAATTACCAACTTGATCAGAGCTAAACC
198082 TA
1 TA
198084 CAGAGACTTC
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
35 17 0.28
36 44 0.72
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.28
Consensus pattern (36 bp):
TATATAAGGAATTACCAACTTGATCAGAGCTAAACC
Found at i:198873 original size:27 final size:26
Alignment explanation
Indices: 198821--198873 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
198811 GGGGGTATCA
* *
198821 TGGTTATTTACACTTCAGGGACATTT
1 TGGTTATTTACAATTCAAGGACATTT
198847 TGGTTATTTTACAATTCAAAGGA-ATTT
1 TGGTTA-TTTACAATTC-AAGGACATTT
198874 CAGTCATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 6 0.26
27 13 0.57
28 4 0.17
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.43
Consensus pattern (26 bp):
TGGTTATTTACAATTCAAGGACATTT
Found at i:203165 original size:4 final size:4
Alignment explanation
Indices: 203156--203183 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
203146 AGTAGATTGC
203156 TCTT TCTT TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT
203184 GGTTTGTCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TCTT
Found at i:215292 original size:134 final size:135
Alignment explanation
Indices: 215102--215611 Score: 498
Period size: 134 Copynumber: 3.8 Consensus size: 135
215092 AATGTTACTT
* *
215102 AGGGAATATCTAATCTTGAAAA-AGAAGGATATGTTCCGCTTCTTCTTGAGGGAAAATCATATAT
1 AGGGAATATCAAATCTTGAAAAGAGAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCATATAT
* * * * * *
215166 GGTGATGTTGACACATTCCACTATCACTT-AGGGAAGATTGAATCGAGGAAGACATGTTCCACTA
66 GGTGACGTTGACTCATTCCACTAT-TCTTCAAGGAAGATTGAATCGAGGAAGACTTGTTCCACTG
**
215230 TTACTA
130 TTACCC
* * *
215236 AGGGAATATCAAATC-T-AAAAGAGAGGGATTTGTTCCGCTTCTTCTTGAGGGAAAAATTATATC
1 AGGGAATATCAAATCTTGAAAAGAGAGGGATATGTTCCGCTTCTTCTTGAGGG-AAAATCATATA
* * * * * * * *
215299 TGGAGACGTTGATTCATTCCATTGTTCTTCAAGAAAGATTTAATCGAGGCAGATTTGTTCCACTG
65 TGGTGACGTTGACTCATTCCACTATTCTTCAAGGAAGATTGAATCGAGGAAGACTTGTTCCACTG
215364 TTACCC
130 TTACCC
* * * * * *
215370 A-GGAATATCAAATCTTG-AAAGATAGAGATATGTTACGCTTCCTCCTGAGGGAAAATCAGATAT
1 AGGGAATATCAAATCTTGAAAAGAGAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCATATAT
* * * * *
215433 -ATGGCGTTCACTCATTCCACTATTCTTCAAGGAAGATTGAATCGAGGTAGACTTTTTCCACTGT
66 GGTGACGTTGACTCATTCCACTATTCTTCAAGGAAGATTGAATCGAGGAAGACTTGTTCCACTGT
215497 TACCC
131 TACCC
* * * * * * ** *
215502 AGTGAATAACAAAT-ATGAAAATAGAGGGATTTGTTCTGCTTCACCTTGAGGGAAAATCATATTT
1 AGGGAATATCAAATCTTGAAAAGAGAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCATATAT
* * * * * * *
215566 GGGGACATTGATTTATTCTACTGTTCTTC-AGGAAATATTGAATCGA
66 GGTGACGTTGACTCATTCCACTATTCTTCAAGG-AAGATTGAATCGA
215612 TTTCGATTTG
Statistics
Matches: 301, Mismatches: 66, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
132 64 0.21
133 102 0.34
134 135 0.45
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (135 bp):
AGGGAATATCAAATCTTGAAAAGAGAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCATATAT
GGTGACGTTGACTCATTCCACTATTCTTCAAGGAAGATTGAATCGAGGAAGACTTGTTCCACTGT
TACCC
Found at i:215650 original size:266 final size:265
Alignment explanation
Indices: 215105--215611 Score: 601
Period size: 266 Copynumber: 1.9 Consensus size: 265
215095 GTTACTTAGG
* * * * * *
215105 GAATATCTAATCTTGAAAAAGAAGGATATGTTCCGCTTCTTCTTGAGGGAAAATCATATATGGTG
1 GAATATCAAATCTTGAAAAAGAAGGATATGTTACGCTTCCTCCTGAGGGAAAATCAGATATGATG
* * * *
215170 ATGTTGACACATTCCACTATCACTTAGGGAAGATTGAATCGAGGAAGACATGTTCCACTATTACT
66 ACGTTCACACATTCCACTATCACTTAAGGAAGATTGAATCGAGGAAGACATGTTCCACTATTACC
* * ** *
215235 AAGGGAATATCAAATCTAAAAGAGAGGGATTTGTTCCGCTTCTTCTTGAGGGAAAAATTATATCT
131 AAGGGAATAACAAATATAAAAGAGAGGGATTTGTTCCGCTTCACCTTGAGGGAAAAATCATATCT
* * *
215300 GGAGACGTTGATTCATTCCATTGTTCTTCAAGAAAGATTTAATCGAGGCAGATTTGTTCCACTGT
196 GGAGACATTGATTCATTCCACTGTTCTTCAAGAAAGATTGAATCGAGGCAGATTTGTT-CACTGT
*
215365 TACCCAG
260 TA-CCAA
215372 GAATATCAAATCTTG--AAAGATAGAGATATGTTACGCTTCCTCCTGAGGGAAAATCAGATAT-A
1 GAATATCAAATCTTGAAAAAGA-AG-GATATGTTACGCTTCCTCCTGAGGGAAAATCAGATATGA
* * * * * * *
215434 TGGCGTTCACTCATTCCACTAT-TCTTCAAGGAAGATTGAATCGAGGTAGACTTTTTCCACTGTT
64 TGACGTTCACACATTCCACTATCACTT-AAGGAAGATTGAATCGAGGAAGACATGTTCCACTATT
* * * *
215498 ACCCAGTGAATAACAAATATGAAAATAGAGGGATTTGTTCTGCTTCACCTTGAGGG-AAAATCAT
128 ACCAAGGGAATAACAAATAT-AAAAGAGAGGGATTTGTTCCGCTTCACCTTGAGGGAAAAATCAT
* * * * * *
215562 ATTTGGGGACATTGATTTATTCTACTGTTCTTCAGGAAATATTGAATCGA
192 ATCTGGAGACATTGATTCATTCCACTGTTCTTCAAGAAAGATTGAATCGA
215612 TTTCGATTTG
Statistics
Matches: 201, Mismatches: 35, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
265 8 0.04
266 115 0.57
267 78 0.39
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (265 bp):
GAATATCAAATCTTGAAAAAGAAGGATATGTTACGCTTCCTCCTGAGGGAAAATCAGATATGATG
ACGTTCACACATTCCACTATCACTTAAGGAAGATTGAATCGAGGAAGACATGTTCCACTATTACC
AAGGGAATAACAAATATAAAAGAGAGGGATTTGTTCCGCTTCACCTTGAGGGAAAAATCATATCT
GGAGACATTGATTCATTCCACTGTTCTTCAAGAAAGATTGAATCGAGGCAGATTTGTTCACTGTT
ACCAA
Found at i:216360 original size:4 final size:4
Alignment explanation
Indices: 216353--216430 Score: 140
Period size: 4 Copynumber: 19.8 Consensus size: 4
216343 TCTTGAAAAA
*
216353 TATG TATG AAT- TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
216400 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
216431 TTAATGGTGT
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
3 2 0.03
4 69 0.97
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:220232 original size:14 final size:13
Alignment explanation
Indices: 220209--220324 Score: 58
Period size: 15 Copynumber: 8.4 Consensus size: 13
220199 TTATTTCCTT
220209 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
220222 TTTTTCATTTTTTC
1 TTTTTC-TTTTTTC
** *
220236 -TCCTCTTTTTATA
1 TTTTTCTTTTT-TC
* *
220249 TCATTTCTCTTTTC
1 T-TTTTCTTTTTTC
220263 TTTCATCTCTTTTTTC
1 TTT--T-TCTTTTTTC
*
220279 --CTTCTTTTTTC
1 TTTTTCTTTTTTC
*
220290 TATATTTCTCTTTTC
1 T-T-TTTCTTTTTTC
220305 TTTTTTCTTTTTTTC
1 -TTTTTC-TTTTTTC
220320 TTTTT
1 TTTTT
220325 TTCTTTCTCT
Statistics
Matches: 76, Mismatches: 14, Indels: 25
0.66 0.12 0.22
Matches are distributed among these distances:
11 9 0.12
12 6 0.08
13 11 0.14
14 18 0.24
15 23 0.30
16 9 0.12
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:220245 original size:20 final size:20
Alignment explanation
Indices: 220222--220320 Score: 51
Period size: 20 Copynumber: 4.8 Consensus size: 20
220212 TTCTTTTTTC
220222 TTTTTCATTTTTTCTCCTCT
1 TTTTTCATTTTTTCTCCTCT
**
220242 TTTTAT-ATCATTTCT-CT-T
1 TTTT-TCATTTTTTCTCCTCT
*
220260 TTCTTTCATCTCTTTTTTCCTTCT
1 TT-TTTCAT-T-TTTTCTCC-TCT
* **
220284 TTTTTCTATATTTCTCTTTTCT
1 TTTTTC-AT-TTTTTCTCCTCT
*
220306 TTTTTCTTTTTTTCT
1 TTTTTCATTTTTTCT
220321 TTTTTTCTTT
Statistics
Matches: 58, Mismatches: 12, Indels: 18
0.66 0.14 0.20
Matches are distributed among these distances:
18 4 0.07
19 6 0.10
20 17 0.29
21 6 0.10
22 10 0.17
23 9 0.16
24 6 0.10
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTCATTTTTTCTCCTCT
Found at i:220262 original size:41 final size:40
Alignment explanation
Indices: 220211--220317 Score: 119
Period size: 43 Copynumber: 2.6 Consensus size: 40
220201 ATTTCCTTTT
*
220211 TTTCTTTTTTCTTTTTCATTTTTTCTCCTC-TTTTTATATCA
1 TTTCTCTTTTCTTTTTC-TTTTTTCTCCTCTTTTTTATAT-A
* *
220252 TTTCTCTTTTCTTTCATCTCTTTTTTC-CTTCTTTTTTCTATA
1 TTTCTCTTTTCTTT--T-TCTTTTTTCTCCTCTTTTTTATATA
220294 TTTCTCTTTTCTTTTTTCTTTTTT
1 TTTCTCTTTTC-TTTTTCTTTTTT
220318 TCTTTTTTTC
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
40 8 0.14
41 14 0.24
42 15 0.26
43 19 0.33
44 2 0.03
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.73
Consensus pattern (40 bp):
TTTCTCTTTTCTTTTTCTTTTTTCTCCTCTTTTTTATATA
Found at i:220324 original size:7 final size:7
Alignment explanation
Indices: 220280--220330 Score: 57
Period size: 8 Copynumber: 6.9 Consensus size: 7
220270 TCTTTTTTCC
220280 TTCTTTT
1 TTCTTTT
*
220287 TTCTATAT
1 TTCT-TTT
*
220295 TTCTCTT
1 TTCTTTT
220302 TTCTTTT
1 TTCTTTT
220309 TTCTTTTT
1 TTC-TTTT
220317 TTCTTTTT
1 TTC-TTTT
220325 TTCTTT
1 TTCTTT
220331 CTCTCTCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 17 0.45
8 21 0.55
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (7 bp):
TTCTTTT
Found at i:220332 original size:42 final size:42
Alignment explanation
Indices: 220211--220332 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
220201 ATTTCCTTTT
* * ** * *
220211 TTTCTTTTTTC-TTTTTCATTTTTTCTCCTCTTTTTATATCA
1 TTTCTCTTTTCTTTTTTCTTTTTTTCTTTTTTTTTTCTATCA
** * *
220252 TTTCTCTTTTCTTTCATCTCTTTTTTCCTTCTTTTTTCTAT-A
1 TTTCTCTTTTCTTTTTTCT-TTTTTTCTTTTTTTTTTCTATCA
220294 TTTCTCTTTTCTTTTTTCTTTTTTTCTTTTTTTCTTTCT
1 TTTCTCTTTTCTTTTTTCTTTTTTTCTTTTTTT-TTTCT
220333 CTCTCTTTAT
Statistics
Matches: 64, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
41 22 0.34
42 27 0.42
43 15 0.23
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (42 bp):
TTTCTCTTTTCTTTTTTCTTTTTTTCTTTTTTTTTTCTATCA
Found at i:224100 original size:20 final size:20
Alignment explanation
Indices: 224062--224100 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
224052 TGAAAAAATA
* * *
224062 AATTTATAATATTATAATTT
1 AATTTAAAATATAAAAATTT
224082 AATTTAAAATATAAAAATT
1 AATTTAAAATATAAAAATT
224101 AAAGAATTAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTTAAAATATAAAAATTT
Found at i:228620 original size:55 final size:55
Alignment explanation
Indices: 228541--229061 Score: 803
Period size: 55 Copynumber: 9.5 Consensus size: 55
228531 ATTATCGAAT
* *
228541 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATTAGTTTATGAATTTCTGAATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATG
* * * * ** *
228596 GGCACTTTGTTTGCAAAATTAAGAAATTCTTAATGAGTTTATAAATTTCCATTTG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATG
* *
228651 GGCACTTTGTGTGTAAAACTAAGAAATTCATAATGAGTTTATGAATTTTTGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATG
228706 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTC-GTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATG
*
228760 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATG
*
228815 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATG
* * * *
228870 GGCACATTGTGTGCAAAACTAAGAAATTCTTAATGAGTTTATGAATTTCCGTACG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATG
** * * *
228925 ATCACTTTGTGTGCAAAACAAATAAATTCATAATGAGTTTATGAATTTCTGTACG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATG
**
228980 GGCACTTTGTGTGCAAAACTATCAAATTCATAATGAGTTTATGAA-TTCTGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATG
*
229034 GGCACCTTGTGTGCAAAACTAAGAAATT
1 GGCACTTTGTGTGCAAAACTAAGAAATT
229062 TCGTATTGGC
Statistics
Matches: 426, Mismatches: 39, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
54 87 0.20
55 339 0.80
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (55 bp):
GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATG
Found at i:228933 original size:219 final size:220
Alignment explanation
Indices: 228541--229061 Score: 821
Period size: 219 Copynumber: 2.4 Consensus size: 220
228531 ATTATCGAAT
* *
228541 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATTAGTTTATGAATTTCTGAATGGGCACTTTGT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTGT
* * * * * *
228606 TTGCAAAATTAAGAAATTCTTAATGAGTTTATAAATTTCCATTTGGGCACTTTGTGTGTAAAACT
66 GTGCAAAACTAAGAAATTCATAATGAGTTTATAAATTTCCATATGGGCACATTGTGTGCAAAACT
** * * *
228671 AAGAAATTCATAATGAGTTTATGAATTTTTGTATGGGCACTTTGTGTGCAAAACTAAGAAATTCA
131 AAGAAATTCATAATGAGTTTATGAATTTCCGTACGAGCACTTTGTGTGCAAAACAAAGAAATTCA
*
228736 TAATGAGTTTATGAATTTC-GTATG
196 TAATGAGTTTATGAATTTCTGTACG
*
228760 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTGT
* *
228825 GTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACATTGTGTGCAAAACT
66 GTGCAAAACTAAGAAATTCATAATGAGTTTATAAATTTCCATATGGGCACATTGTGTGCAAAACT
* * *
228890 AAGAAATTCTTAATGAGTTTATGAATTTCCGTACGATCACTTTGTGTGCAAAACAAATAAATTCA
131 AAGAAATTCATAATGAGTTTATGAATTTCCGTACGAGCACTTTGTGTGCAAAACAAAGAAATTCA
228955 TAATGAGTTTATGAATTTCTGTACG
196 TAATGAGTTTATGAATTTCTGTACG
** *
228980 GGCACTTTGTGTGCAAAACTATCAAATTCATAATGAGTTTATGAA-TTCTGTATGGGCACCTTGT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTGT
229044 GTGCAAAACTAAGAAATT
66 GTGCAAAACTAAGAAATT
229062 TCGTATTGGC
Statistics
Matches: 277, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
219 230 0.83
220 47 0.17
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (220 bp):
GGCACTTTGTGTGCAAAACTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTGT
GTGCAAAACTAAGAAATTCATAATGAGTTTATAAATTTCCATATGGGCACATTGTGTGCAAAACT
AAGAAATTCATAATGAGTTTATGAATTTCCGTACGAGCACTTTGTGTGCAAAACAAAGAAATTCA
TAATGAGTTTATGAATTTCTGTACG
Found at i:234561 original size:22 final size:22
Alignment explanation
Indices: 234521--234562 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
234511 AAAAGTAACT
*
234521 TTATTTTCTTTTTTCTTTTATG
1 TTATTTTCTTTCTTCTTTTATG
234543 TTATTTTCATTTCTT-TTTTA
1 TTATTTTC-TTTCTTCTTTTA
234563 AAAAAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (22 bp):
TTATTTTCTTTCTTCTTTTATG
Found at i:243324 original size:130 final size:130
Alignment explanation
Indices: 243127--243363 Score: 311
Period size: 130 Copynumber: 1.8 Consensus size: 130
243117 ATAATTTAAG
* *
243127 AGAGAAAATGATAATACCTAATAATTTCAAATCGAAAATAAATGACCTATCATGCTCTAAAGTAG
1 AGAGAAAATGATAATACCTAATAATTTCAAATCGAAAACAAATGACCTATCATGCTCTAAAGCAG
*
243192 TCATTTATTACTACAA-TCAAAAT-GAATAGATATTACTATTTTATCTTAAAATTCAATATTCAT
66 TCAATTATTACTACAACT-AAAATGGAA-AGATATTACTATTTTATCTTAAAATTCAATATTCAT
243255 TA
129 TA
* * * * *
243257 AGAGAAAATGATAATATCC-AATTATTTCTAATCGAGAACAAATGATCTCTCATGC-CTTAAAGC
1 AGAGAAAATGATAATA-CCTAATAATTTCAAATCGAAAACAAATGACCTATCATGCTC-TAAAGC
* * *
243320 AGTCAATTATTATTCCAACTGAAATGGAAAGATATTACTATTTT
64 AGTCAATTATTACTACAACTAAAATGGAAAGATATTACTATTTT
243364 CAATGTTAAT
Statistics
Matches: 92, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
129 1 0.01
130 85 0.92
131 6 0.07
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.34
Consensus pattern (130 bp):
AGAGAAAATGATAATACCTAATAATTTCAAATCGAAAACAAATGACCTATCATGCTCTAAAGCAG
TCAATTATTACTACAACTAAAATGGAAAGATATTACTATTTTATCTTAAAATTCAATATTCATTA
Found at i:246115 original size:40 final size:39
Alignment explanation
Indices: 246020--246121 Score: 109
Period size: 40 Copynumber: 2.6 Consensus size: 39
246010 TGCCCGAAGT
* * *
246020 CTTATGGATGGCCGAAGGACTTATCATCTTGCTCGAAATA
1 CTTAT-GATGGCCGAAGGACTTAGCATCATGCTCGAAAGA
* *
246060 CTTAT-ATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATGATG-GCCGAAGGACTT-AGCATCATGCTCGAAAGA
246100 C-TATGATGGCACGAAGGACTTA
1 CTTATGATGGC-CGAAGGACTTA
246122 TTAAGTAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
38 3 0.06
39 15 0.29
40 33 0.65
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (39 bp):
CTTATGATGGCCGAAGGACTTAGCATCATGCTCGAAAGA
Found at i:250616 original size:27 final size:28
Alignment explanation
Indices: 250572--250636 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 28
250562 ATTATAGAAT
250572 TACCTCTAAAGTGAAAAATGACC-AAAA
1 TACCTCTAAAGTGAAAAATGACCTAAAA
* * *
250599 TGCCTCTAAAGTGTAAAATGACCTAAAG
1 TACCTCTAAAGTGAAAAATGACCTAAAA
250627 TACCTCTAAA
1 TACCTCTAAA
250637 CCCTGGAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 21 0.64
28 12 0.36
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (28 bp):
TACCTCTAAAGTGAAAAATGACCTAAAA
Found at i:250713 original size:17 final size:17
Alignment explanation
Indices: 250685--250717 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
250675 TAGCAACCTC
250685 AATGATTAGGATTAAGTA
1 AATGATTAGGA-TAAGTA
250703 AATGA-TAGGATAAGT
1 AATGATTAGGATAAGT
250718 TTAGAAACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.30
Consensus pattern (17 bp):
AATGATTAGGATAAGTA
Found at i:260318 original size:3 final size:3
Alignment explanation
Indices: 260310--260340 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
260300 TAATAGAAAT
260310 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A
260341 TAATAATAAT
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:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:260346 original size:3 final size:3
Alignment explanation
Indices: 260340--260382 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
260330 CAACAACAAC
260340 ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
260383 GTCGAAACGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:261579 original size:16 final size:16
Alignment explanation
Indices: 261558--261588 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
261548 AGGGCTATAA
*
261558 CCATGCATGTCAAACC
1 CCATGCATATCAAACC
261574 CCATGCATATCAAAC
1 CCATGCATATCAAAC
261589 ATACGTCGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.35, G:0.10, T:0.19
Consensus pattern (16 bp):
CCATGCATATCAAACC
Found at i:263423 original size:45 final size:46
Alignment explanation
Indices: 263339--263425 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 46
263329 AATAGCCTGC
* * *
263339 GTGCATCGATGCATGGTCTTGTGCATTGATGCATCAAATGCACTAA
1 GTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTAA
263385 GTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 GTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
263426 TTCGATGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
45 21 0.55
46 17 0.45
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (46 bp):
GTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTAA
Found at i:271664 original size:45 final size:46
Alignment explanation
Indices: 271579--271666 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
271569 AAATATCCTG
* * *
271579 AGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGAATAAAATGCACTA
271625 AGTGCATCGATGCATGGT-ATGTGCATCGATGAATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGAATAAAATGCA
271667 TTCGATGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.54
46 18 0.46
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCGATGAATAAAATGCACTA
Found at i:274332 original size:450 final size:451
Alignment explanation
Indices: 273490--274334 Score: 1433
Period size: 450 Copynumber: 1.9 Consensus size: 451
273480 TAGAGTTATG
*
273490 TGTTGGGTTATGGGGTCTAGCGATCACCCTTAGGGATTCTATCGTGTATGGGCGCGATATCGGTG
1 TGTTGGGTTATGGGGTCTAGCGATCACCCTTAGGGATTATATCGTGTATGGGCGCGATATCGGTG
273555 CATGACTGCCCAACCTGCCGAGGCCCACTTGTATCTTGCGAAGCCCCTAGGCCCGCCCGCAACAC
66 CATGACTGCCCAACCTGCCGAGGCCCACTTGTATCTTGCGAAGCCCCTAGGCCCGCCCGCAACAC
* *
273620 GCTATAGATGCGGGGCTCTACAATGCCGTGGTGAACTGTGGGGGGTACCCCACAAGACTCCACCT
131 GCTACAGATGCGGGGCTCTACAATGCCGTGGTGAACTGTGGGGGGTACCCCACAAGAATCCACCT
* * *
273685 TGGCTTGGGAGAACCCAGTGATCACCCACTACAAAGATATGAGGTTAAAATGACCCACCTATTTA
196 TGGCTTGAGAGAACCCAGTGATCACCCACTACAAAGATATGAGGTTAAAATGACCCAACTACTTA
* *
273750 TCACCAATTGGTTTTAAGAAGAAATGGTGACCATTCGCTTCAGAACTTTGTGGTTAAGCATGCTT
261 TCACCAATTAGTTTTAAGAAGAAATGGTGAACATTCGCTTCAGAACTTTGTGGTTAAGCATGCTT
* *
273815 GGACTAGGGAAATCCAAGGATGGGTGACCCACTGGTAAGTTGTTCAAAAATGAATGACTCGATCC
326 GGACTAGGGAAATCAAAGGATGGGTGACCCACTGGGAAGTTGTTCAAAAATGAATGACTCGATCC
273880 TAACAACTGGTATCAGAGTAGGTTGCAGGTTCGAATCCCCAGGTGTCGCTGGGGGTGTGAT
391 TAACAACTGGTATCAGAGTAGGTTGCAGGTTCGAATCCCCAGGTGTCGCTGGGGGTGTGAT
*
273941 TGTTGGGTTATGGGGTCTAGGGATCACCCTTAGGGATTATATCGTGTATGGGCGCGATATCGGTG
1 TGTTGGGTTATGGGGTCTAGCGATCACCCTTAGGGATTATATCGTGTATGGGCGCGATATCGGTG
* * * * *
274006 CGTGACTGCCCAACCTGTCGAGGCTCA-TGTGTGTCTTGCGAAGCCCCTAGGCCCGCCCGCAGCA
66 CATGACTGCCCAACCTGCCGAGGCCCACT-TGTATCTTGCGAAGCCCCTAGGCCCGCCCGCAACA
** * *
274070 CGCTACAGATGCGGGGCTCTGTAATGCCGTGGTGAACTGT-GGGGGTGCCCCACAAGAATCTACC
130 CGCTACAGATGCGGGGCTCTACAATGCCGTGGTGAACTGTGGGGGGTACCCCACAAGAATCCACC
* *
274134 TTGGCTTGAGAGAATCCAGTGATCACCCACTATAAAGATATGAGGTTAAAATGACCCAACTACTT
195 TTGGCTTGAGAGAACCCAGTGATCACCCACTACAAAGATATGAGGTTAAAATGACCCAACTACTT
* * *
274199 ATCACCAATTAGTTTTAAGAAGGAATGGTGAATATTCGCTTCAGAACTTTGTGGTTAAGCGTGCT
260 ATCACCAATTAGTTTTAAGAAGAAATGGTGAACATTCGCTTCAGAACTTTGTGGTTAAGCATGCT
*
274264 TGGACTAGGGAAATCAAAGGATGGGTGACCCACTGGGAAGTTGTTCAGAAATGAATGACTCGATC
325 TGGACTAGGGAAATCAAAGGATGGGTGACCCACTGGGAAGTTGTTCAAAAATGAATGACTCGATC
274329 CTAACA
390 CTAACA
274335 TTATGGTTAT
Statistics
Matches: 367, Mismatches: 26, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
450 210 0.57
451 157 0.43
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (451 bp):
TGTTGGGTTATGGGGTCTAGCGATCACCCTTAGGGATTATATCGTGTATGGGCGCGATATCGGTG
CATGACTGCCCAACCTGCCGAGGCCCACTTGTATCTTGCGAAGCCCCTAGGCCCGCCCGCAACAC
GCTACAGATGCGGGGCTCTACAATGCCGTGGTGAACTGTGGGGGGTACCCCACAAGAATCCACCT
TGGCTTGAGAGAACCCAGTGATCACCCACTACAAAGATATGAGGTTAAAATGACCCAACTACTTA
TCACCAATTAGTTTTAAGAAGAAATGGTGAACATTCGCTTCAGAACTTTGTGGTTAAGCATGCTT
GGACTAGGGAAATCAAAGGATGGGTGACCCACTGGGAAGTTGTTCAAAAATGAATGACTCGATCC
TAACAACTGGTATCAGAGTAGGTTGCAGGTTCGAATCCCCAGGTGTCGCTGGGGGTGTGAT
Found at i:278226 original size:15 final size:16
Alignment explanation
Indices: 278199--278232 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
278189 AATAATCCCT
*
278199 AAATAATATTAAAGAA
1 AAATAATATTAAACAA
278215 AAATAA-ATTAAACAA
1 AAATAATATTAAACAA
278230 AAA
1 AAA
278233 ATCTAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (16 bp):
AAATAATATTAAACAA
Found at i:280809 original size:89 final size:90
Alignment explanation
Indices: 280458--280925 Score: 761
Period size: 90 Copynumber: 5.3 Consensus size: 90
280448 TATGGGTCCT
* *
280458 GAAGGACTTAAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACATCC
1 GAAGGACTT-AAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAAAACAT-C
* *
280523 A-GCACTGAAGATCTTACAGATGACCC
64 ATGCACTGAAGGTCTTACAGATGGCCC
* * *
280549 GAAGGACTTAAAAATCAAGAAAACCCCGAAGGCTTAGTTTCTTAGATCTCATTTGAAAACATCCT
1 GAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAAAACATCAT
280614 GCACTGAAGGTCTTACAGATGG-CC
66 GCACTGAAGGTCTTACAGATGGCCC
* *
280638 GAAGGACTAAAAAATCAAGAAA-CCCCGAA-G-TCAGTTT-TTAGATCTCATTTGAAAACATCCT
1 GAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAAAACATCAT
280699 GCACTGAAGGTCTTACAGATGGCCC
66 GCACTGAAGGTCTTACAGATGGCCC
280724 GAAGGACTT-AAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAAAACATCAT
1 GAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAAAACATCAT
*
280788 GCACTGAAGGTCTTACGGATGGCCC
66 GCACTGAAGGTCTTACAGATGGCCC
280813 GAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAAAACATCAT
1 GAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAAAACATCAT
**
280878 GCACTGAAGGTCTTATGGATGGCCC
66 GCACTGAAGGTCTTACAGATGGCCC
280903 GAAGGACTTAAAAATCAAGAAAC
1 GAAGGACTTAAAAATCAAGAAAC
280926 TCTTGAAAAT
Statistics
Matches: 359, Mismatches: 11, Indels: 15
0.93 0.03 0.04
Matches are distributed among these distances:
85 58 0.16
86 23 0.06
87 2 0.01
88 14 0.04
89 80 0.22
90 173 0.48
91 9 0.03
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (90 bp):
GAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAAAACATCAT
GCACTGAAGGTCTTACAGATGGCCC
Found at i:281172 original size:42 final size:42
Alignment explanation
Indices: 281022--281191 Score: 236
Period size: 42 Copynumber: 4.1 Consensus size: 42
281012 TTTAAGGAAC
281022 CCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAA
1 CCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAA
* ** * * *
281064 CCCCTACATATCACGATGATTTCTCAAG-GTGTCATCAAGGAA
1 -CCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAA
281106 CCCTAC-TATCACGATGGTCCCTCAAGCTTTTCATCAAGAAA
1 CCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAA
** *
281147 CCCTACATATCACGATGGTTTCTCAAGCTTTTCTTCAAGAAA
1 CCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAA
281189 CCC
1 CCC
281192 CTGAAAATCA
Statistics
Matches: 110, Mismatches: 15, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
40 17 0.15
41 23 0.21
42 46 0.42
43 24 0.22
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.28
Consensus pattern (42 bp):
CCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAA
Found at i:281185 original size:83 final size:84
Alignment explanation
Indices: 281010--281191 Score: 278
Period size: 83 Copynumber: 2.2 Consensus size: 84
281000 ATCAAATTTA
*
281010 TCTTTAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACATAT
1 TCTTCAAGGAA-CCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACATAT
281075 CACGATGATTTCTCAAGGTG
65 CACGATGATTTCTCAAGGTG
*
281095 TCATCAAGGAACCCTAC-TATCACGATGGTCCCTCAAGCTTTTCATCAAGAAA-CCCTACATATC
1 TCTTCAAGGAACCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACATATC
* * *
281158 ACGATGGTTTCTCAAGCTTT
66 ACGATGATTTCTCAAG-GTG
*
281178 TCTTCAAGAAACCC
1 TCTTCAAGGAACCC
281192 CTGAAAATCA
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
82 26 0.29
83 48 0.54
84 6 0.07
85 9 0.10
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (84 bp):
TCTTCAAGGAACCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACATATC
ACGATGATTTCTCAAGGTG
Found at i:281362 original size:36 final size:36
Alignment explanation
Indices: 281252--281362 Score: 159
Period size: 36 Copynumber: 3.1 Consensus size: 36
281242 CTCAAACGAG
*
281252 ACTGTCTCAAGGGTGACAAAATTTGTTTCAAGGGAA
1 ACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAA
* * * **
281288 ACCGTCTCAAGAGAGACAAAATTTGTTTCGAGAAAA
1 ACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAA
*
281324 ACTGTCTCAAGGGAGACAAAATTTTTTTCAAGGGAA
1 ACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAA
281360 ACT
1 ACT
281363 ATCTTGAGTG
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (36 bp):
ACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAA
Found at i:281705 original size:34 final size:34
Alignment explanation
Indices: 281664--281874 Score: 282
Period size: 34 Copynumber: 6.2 Consensus size: 34
281654 TCTCATAGAA
*
281664 AAATTGTCTCAAGCGAGAGGAAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
*
281698 AAATTGTCTCAAGTGAGACGAAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
*
281732 AAATGGTCTCAAGCGAGACGAAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
* ** *
281766 AAATAGTCTCAAGAAAGAAC-AAATCTGTTTTGAG
1 AAATTGTCTCAAGCGAG-ACGAAATTTGTTTTGAG
* *
281800 AAATGGTCTCAAGCGAGACCAAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
* * *
281834 AAATTGTCTCAA-CTAAGACAAAATTTATTTTGAG
1 AAATTGTCTCAAGC-GAGACGAAATTTGTTTTGAG
281868 AAATTGT
1 AAATTGT
281875 ATCGAGTGAG
Statistics
Matches: 158, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
33 3 0.02
34 153 0.97
35 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (34 bp):
AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
Found at i:281903 original size:102 final size:102
Alignment explanation
Indices: 281695--281904 Score: 226
Period size: 102 Copynumber: 2.1 Consensus size: 102
281685 AATTTGTTTT
* * * * * *
281695 GAGAAATTGTCTCAAGTGAGACGAAATTTGTTTTGAGAAATGGTCTCAAGCGAGACGAAATTTGT
1 GAGAAATGGTCTCAAGCGAGACCAAATTTGTTTTGAGAAATGGTCTCAAGCAAGACAAAATTTAT
* **** **
281760 TTTGAGAAATAGTCTCAAGAAAGAACAAATCTGTTTT
66 TTTGAGAAATAGTATCAAGAAAGAACAAAAAAATTAA
*
281797 GAGAAATGGTCTCAAGCGAGACCAAATTTGTTTTGAGAAATTGTCTCAA-CTAAGACAAAATTTA
1 GAGAAATGGTCTCAAGCGAGACCAAATTTGTTTTGAGAAATGGTCTCAAGC-AAGACAAAATTTA
* * **
281861 TTTTGAGAAATTGTATCGAGTGAG-ACAAAAAAAATTAA
65 TTTTGAGAAATAGTATCAAGAAAGAAC-AAAAAAATTAA
281899 GAGAAA
1 GAGAAA
281905 CAACATCAGA
Statistics
Matches: 88, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
101 3 0.03
102 85 0.97
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (102 bp):
GAGAAATGGTCTCAAGCGAGACCAAATTTGTTTTGAGAAATGGTCTCAAGCAAGACAAAATTTAT
TTTGAGAAATAGTATCAAGAAAGAACAAAAAAATTAA
Found at i:282083 original size:32 final size:32
Alignment explanation
Indices: 282011--282224 Score: 302
Period size: 32 Copynumber: 6.6 Consensus size: 32
282001 ATATTCAATA
282011 TTGAATCTCCAAAGATGCCCCAACATTTTGATG
1 TTGAATCTCCAAAGATGCCCCAACA-TTTGATG
* *
282044 TTAAATCTCCAAAGATGCCCCAACATTTAATG
1 TTGAATCTCCAAAGATGCCCCAACATTTGATG
* * * *
282076 TTGAATCTCCAAAGATACCCCAATATTCGATA
1 TTGAATCTCCAAAGATGCCCCAACATTTGATG
* *
282108 TTGAATATCCAAAGATACCCCAACATTTTGATG
1 TTGAATCTCCAAAGATGCCCCAACA-TTTGATG
*
282141 TTGAATCTCCAAAGATGCCTCAACATTTGATG
1 TTGAATCTCCAAAGATGCCCCAACATTTGATG
* *
282173 TTGAATCTCCAAATATGCCCCAACATTTTATG
1 TTGAATCTCCAAAGATGCCCCAACATTTGATG
*
282205 TTGAATCTTCAAAGATGCCC
1 TTGAATCTCCAAAGATGCCC
282225 TCTATTGCTT
Statistics
Matches: 160, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
32 109 0.68
33 51 0.32
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (32 bp):
TTGAATCTCCAAAGATGCCCCAACATTTGATG
Found at i:282097 original size:65 final size:64
Alignment explanation
Indices: 281993--282224 Score: 302
Period size: 65 Copynumber: 3.6 Consensus size: 64
281983 AGGATATTGA
* * * * *
281993 ATGCCACAATATTCAATATTGAATCTCCAAAGATGCCCCAACATTTTGATGTTAAATCTCCAAAG
1 ATGCCCCAACATTTAATGTTGAATCTCCAAAGATGCCCCAACA-TTTGATGTTGAATCTCCAAAG
* * * * *
282058 ATGCCCCAACATTTAATGTTGAATCTCCAAAGATACCCCAATATTCGATATTGAATATCCAAAG
1 ATGCCCCAACATTTAATGTTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAG
* * * *
282122 ATACCCCAACATTTTGATGTTGAATCTCCAAAGATGCCTCAACATTTGATGTTGAATCTCCAAAT
1 ATGCCCCAACA-TTTAATGTTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAG
* *
282187 ATGCCCCAACATTTTATGTTGAATCTTCAAAGATGCCC
1 ATGCCCCAACATTTAATGTTGAATCTCCAAAGATGCCC
282225 TCTATTGCTT
Statistics
Matches: 143, Mismatches: 23, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
64 51 0.36
65 92 0.64
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (64 bp):
ATGCCCCAACATTTAATGTTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAG
Done.