Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006605.1 Hibiscus syriacus cultivar Beakdansim tig00016203_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: 167702
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3477 original size:27 final size:27
Alignment explanation
Indices: 3407--3468 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
3397 GCCCTTAGAC
* *
3407 CCAAAATAACTAAAATAACCTCTAGCA
1 CCAAAATGACTAAAATAACCTCGAGCA
*
3434 CCAAAATGACTAAAATAACCTCGAGTA
1 CCAAAATGACTAAAATAACCTCGAGCA
*
3461 CTAAAATG
1 CCAAAATG
3469 GCCTAAATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.50, C:0.23, G:0.08, T:0.19
Consensus pattern (27 bp):
CCAAAATGACTAAAATAACCTCGAGCA
Found at i:3796 original size:21 final size:18
Alignment explanation
Indices: 3772--3812 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 18
3762 GTTTAGTTTG
3772 ATTTGACTATAAATCTTGAGA
1 ATTTGA-TATAAAT-TT-AGA
3793 ATTTGATATAAATTTAGA
1 ATTTGATATAAATTTAGA
3811 AT
1 AT
3813 ATTGCAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 2 0.10
20 7 0.35
21 6 0.30
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (18 bp):
ATTTGATATAAATTTAGA
Found at i:11557 original size:15 final size:15
Alignment explanation
Indices: 11539--11572 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
11529 GGTGTGATAC
*
11539 TTTCCTTTATTTGTT
1 TTTCCTTTATATGTT
11554 TTTCCTTTATATGTT
1 TTTCCTTTATATGTT
11569 TTTC
1 TTTC
11573 TTAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.15, G:0.06, T:0.71
Consensus pattern (15 bp):
TTTCCTTTATATGTT
Found at i:13629 original size:43 final size:43
Alignment explanation
Indices: 13510--13746 Score: 215
Period size: 43 Copynumber: 5.5 Consensus size: 43
13500 AGTTAGCAGA
* * * *
13510 GTTTTTGGAACAAATGTCGCAAAAAGGTCGATATCTATAGCGAC
1 GTTTTTGGAACAAACGCCGC-AAAAGGTTGATATCTATAGCGGC
* * * * ** *
13554 ATTTTTTGAATAAACGTCGCAAAAGGGAGATATATATAGCGGC
1 GTTTTTGGAACAAACGCCGCAAAAGGTTGATATCTATAGCGGC
* * *
13597 GTTTCTGGAACAAACGCCGCAAAAGGTTGATATCTATAGAGGT
1 GTTTTTGGAACAAACGCCGCAAAAGGTTGATATCTATAGCGGC
* * * * *
13640 GTTTTTGGGATAAACACCACAAAAGGTTGATATATATAGCGGC
1 GTTTTTGGAACAAACGCCGCAAAAGGTTGATATCTATAGCGGC
** * *
13683 GTTTTTGGACACAAAAACCGCAAAAGG-TCAGATCTATAGCGGC
1 GTTTTTGGA-ACAAACGCCGCAAAAGGTTGATATCTATAGCGGC
**
13726 GTTTTTTTATACAAACGCCGC
1 GTTTTTGGA-ACAAACGCCGC
13747 TAATTACCTT
Statistics
Matches: 154, Mismatches: 38, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
43 124 0.81
44 30 0.19
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (43 bp):
GTTTTTGGAACAAACGCCGCAAAAGGTTGATATCTATAGCGGC
Found at i:13633 original size:86 final size:86
Alignment explanation
Indices: 13510--13732 Score: 250
Period size: 86 Copynumber: 2.6 Consensus size: 86
13500 AGTTAGCAGA
* * * * * ** *
13510 GTTTTTGGAACAAATGTCGCAAAAAGGTCGATATCTATAGCGACATTTTTTGAATAAACGTCGCA
1 GTTTTTGGAACAAAAGCCGC-AAAAGGTTGATATCTATAGCGGCGTTTTTTGAATAAACACCACA
13575 AAAGGGAGATATATATAGCGGC
65 AAAGGGAGATATATATAGCGGC
* * * * * *
13597 GTTTCTGGAACAAACGCCGCAAAAGGTTGATATCTATAGAGGTGTTTTTGGGATAAACACCACAA
1 GTTTTTGGAACAAAAGCCGCAAAAGGTTGATATCTATAGCGGCGTTTTTTGAATAAACACCACAA
**
13662 AAGGTTGATATATATAGCGGC
66 AAGGGAGATATATATAGCGGC
* * *
13683 GTTTTTGGACACAAAAACCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTT
1 GTTTTTGGA-ACAAAAGCCGCAAAAGGTTGATATCTATAGCGGCGTTTTTT
13733 TATACAAACG
Statistics
Matches: 112, Mismatches: 23, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
86 80 0.71
87 32 0.29
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (86 bp):
GTTTTTGGAACAAAAGCCGCAAAAGGTTGATATCTATAGCGGCGTTTTTTGAATAAACACCACAA
AAGGGAGATATATATAGCGGC
Found at i:15120 original size:17 final size:18
Alignment explanation
Indices: 15087--15120 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
15077 TATTCTTATA
15087 TTTAATCTCCAAGGAATC
1 TTTAATCTCCAAGGAATC
*
15105 TTTAAT-TCCAATGAAT
1 TTTAATCTCCAAGGAAT
15121 ATACTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (18 bp):
TTTAATCTCCAAGGAATC
Found at i:15410 original size:59 final size:57
Alignment explanation
Indices: 15283--15585 Score: 188
Period size: 59 Copynumber: 5.2 Consensus size: 57
15273 CTTACTCTTT
** * * * **
15283 CATTTTAGCACACGAAGTACCCTATTCAAAAATCCATACCATTAGTATGATTTTGTTAC
1 CATTTTAGCACATAAAATGCCCTATT-GAAAATCCATA-CATTAGTATGATTTCCTTAC
*
15342 CATTTTAGCACATAAAATGCCCTATGTGAAAATCCATACCATTATTATGATTTCCTTATC
1 CATTTTAGCACATAAAATGCCCTAT-TGAAAATCCATA-CATTAGTATGATTTCCTTA-C
* * * * ** * * * *
15402 C-TTATAGCACCCT-TAGTGCTTTATATGGAAATTCATACACTCAGTATGATTCCCTTAC
1 CATTTTAGCA-CATAAAATGCCCTAT-TGAAAATCCATACA-TTAGTATGATTTCCTTAC
* ** * *
15460 CATTTTAGCACATAAAATGCCCTATTGGAAATCCATATTTTCAATATGATTTCCTTAT
1 CATTTTAGCACATAAAATGCCCTATTGAAAATCCATACATT-AGTATGATTTCCTTAC
* * * * *
15518 CA-TTTAGCACACT-CAGTGCTCC-ATATGGAAAT--ATACACTCAGTATGATTTCCTTAT
1 CATTTTAGCACA-TAAAATGC-CCTAT-TGAAAATCCATACA-TTAGTATGATTTCCTTAC
15574 CATTTTAGCACA
1 CATTTTAGCACA
15586 CAAAGTGACA
Statistics
Matches: 193, Mismatches: 39, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
56 20 0.10
57 26 0.13
58 42 0.22
59 100 0.52
60 5 0.03
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (57 bp):
CATTTTAGCACATAAAATGCCCTATTGAAAATCCATACATTAGTATGATTTCCTTAC
Found at i:15466 original size:118 final size:114
Alignment explanation
Indices: 15338--15585 Score: 345
Period size: 114 Copynumber: 2.1 Consensus size: 114
15328 TATGATTTTG
*
15338 TTACCATTTTAGCACATAAAATGCCCTATGTGAAAATCCATACCATT-ATTATGATTTCCTTATC
1 TTACCATTTTAGCACATAAAATGCCCTAT-TGAAAATCCATA-CATTCAATATGATTTCCTTATC
* * * **
15402 CTTATAGCACCCTTAGTGCTTTATATGGAAATTCATACACTCAGTATGATTCCC
64 ATT-TAGCACACTCAGTGCTCCATATGGAAA-T-ATACACTCAGTATGATTCCC
* **
15456 TTACCATTTTAGCACATAAAATGCCCTATTGGAAATCCATATTTTCAATATGATTTCCTTATCAT
1 TTACCATTTTAGCACATAAAATGCCCTATTGAAAATCCATACATTCAATATGATTTCCTTATCAT
*
15521 TTAGCACACTCAGTGCTCCATATGGAAATATACACTCAGTATGATTTCC
66 TTAGCACACTCAGTGCTCCATATGGAAATATACACTCAGTATGATTCCC
*
15570 TTATCATTTTAGCACA
1 TTACCATTTTAGCACA
15586 CAAAGTGACA
Statistics
Matches: 118, Mismatches: 11, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
114 34 0.29
115 1 0.01
116 25 0.21
117 29 0.25
118 29 0.25
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (114 bp):
TTACCATTTTAGCACATAAAATGCCCTATTGAAAATCCATACATTCAATATGATTTCCTTATCAT
TTAGCACACTCAGTGCTCCATATGGAAATATACACTCAGTATGATTCCC
Found at i:15547 original size:58 final size:58
Alignment explanation
Indices: 15387--15592 Score: 206
Period size: 58 Copynumber: 3.6 Consensus size: 58
15377 ATACCATTAT
* * * * **
15387 TATGATTTCCTTATCCTTATAGCACCCTTAGTGCTTTATATGGAAATTCATACACTCAG
1 TATGATTTCCTTATCATTTTAGCACACTAAGTGCTCCATATGGAAA-TCATACACTCAG
* * * *** *
15446 TATGATTCCCTTACCATTTTAGCACA-TAAAATGC-CC-TATTGGAAATCCATATTTTCAA
1 TATGATTTCCTTATCATTTTAGCACACT-AAGTGCTCCATA-TGGAAAT-CATACACTCAG
*
15504 TATGATTTCCTTATCA-TTTAGCACACTCAGTGCTCCATATGGAAAT-ATACACTCAG
1 TATGATTTCCTTATCATTTTAGCACACTAAGTGCTCCATATGGAAATCATACACTCAG
*
15560 TATGATTTCCTTATCATTTTAGCACACAAAGTG
1 TATGATTTCCTTATCATTTTAGCACACTAAGTG
15593 ACATTCGGTA
Statistics
Matches: 117, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
56 22 0.19
57 30 0.26
58 38 0.32
59 27 0.23
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (58 bp):
TATGATTTCCTTATCATTTTAGCACACTAAGTGCTCCATATGGAAATCATACACTCAG
Found at i:22191 original size:17 final size:18
Alignment explanation
Indices: 22158--22191 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
22148 TATTATGATA
22158 TTTAATCTCCAAGGAATC
1 TTTAATCTCCAAGGAATC
*
22176 TTTAAT-TCCAATGAAT
1 TTTAATCTCCAAGGAAT
22192 ATATTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (18 bp):
TTTAATCTCCAAGGAATC
Found at i:22556 original size:59 final size:59
Alignment explanation
Indices: 22329--22567 Score: 174
Period size: 59 Copynumber: 4.1 Consensus size: 59
22319 TCTGGAAGAT
* * * *
22329 CATACACTTAGTAT-ACTTCCCCTT-TCATTTTAGCACACGAAGTGCCCTAT-TCA-AAATC
1 CATACACTTAGTATGA-TT-CTCTTACCATTTTAGCACATGAAATGCCCTATCT-AGAAATC
* * *
22387 CATATCA-TTAGTATGCTTCTGTTACCATTTTAGCACATGAAATGCCCTATGT-GAAAATC
1 CATA-CACTTAGTATGATTCTCTTACCATTTTAGCACATGAAATGCCCTATCTAG-AAATC
* * * * * * **
22446 CATAC-CATTAGTGTGATT-TCCTTATCC-TTGTAGTACCCT-TAGTGCTTTATCTAGAAATC
1 CATACAC-TTAGTATGATTCT-CTTA-CCATTTTAGCA-CATGAAATGCCCTATCTAGAAATC
* *
22505 CATACACTCAGTATGATTCTCTTACCATTTTAGCACATAAAATGCCCTATCTAGAAATC
1 CATACACTTAGTATGATTCTCTTACCATTTTAGCACATGAAATGCCCTATCTAGAAATC
22564 CATA
1 CATA
22568 TTTTCAATAT
Statistics
Matches: 139, Mismatches: 26, Indels: 31
0.71 0.13 0.16
Matches are distributed among these distances:
57 3 0.02
58 42 0.30
59 87 0.63
60 7 0.05
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (59 bp):
CATACACTTAGTATGATTCTCTTACCATTTTAGCACATGAAATGCCCTATCTAGAAATC
Found at i:25874 original size:41 final size:41
Alignment explanation
Indices: 25829--25912 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
25819 AACCATCTTA
* *
25829 CGGCATTTGTATAAAAATGCCGCTAAAGTATTACTCTATTG
1 CGGCATTTGTATAAAAACGCCGCTAAAGTACTACTCTATTG
* * *
25870 CGGCATTTGTATATAAACGTCGCTAACGTACTACTCTATTG
1 CGGCATTTGTATAAAAACGCCGCTAAAGTACTACTCTATTG
25911 CG
1 CG
25913 ACGTTTGTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (41 bp):
CGGCATTTGTATAAAAACGCCGCTAAAGTACTACTCTATTG
Found at i:28393 original size:20 final size:21
Alignment explanation
Indices: 28368--28407 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28358 TTATTGGTAA
*
28368 AAAAATA-ATATTTTAGGTCC
1 AAAAATAGAAATTTTAGGTCC
28388 AAAAATAGAAATTTTAGGTC
1 AAAAATAGAAATTTTAGGTC
28408 AGTTATAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (21 bp):
AAAAATAGAAATTTTAGGTCC
Found at i:29677 original size:40 final size:40
Alignment explanation
Indices: 29633--29725 Score: 159
Period size: 40 Copynumber: 2.3 Consensus size: 40
29623 GGTTATACTA
29633 AAAATATTATAAAGAATGTAACATTTTCGATTTTTAAATG
1 AAAATATTATAAAGAATGTAACATTTTCGATTTTTAAATG
* *
29673 AAAATATTATAAATAATGTAATATTTTCGATTTTTAAATG
1 AAAATATTATAAAGAATGTAACATTTTCGATTTTTAAATG
*
29713 AAAATTTTATAAA
1 AAAATATTATAAA
29726 AAATATACAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (40 bp):
AAAATATTATAAAGAATGTAACATTTTCGATTTTTAAATG
Found at i:30135 original size:15 final size:15
Alignment explanation
Indices: 30115--30143 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
30105 ATTATTATAT
30115 ATTTTAGATTTTTAG
1 ATTTTAGATTTTTAG
30130 ATTTTAGATTTTTA
1 ATTTTAGATTTTTA
30144 TTTTTATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (15 bp):
ATTTTAGATTTTTAG
Found at i:30449 original size:20 final size:20
Alignment explanation
Indices: 30424--30461 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30414 TTCTAAATTT
30424 TCTTTCAAAGAA-TCAAAAGA
1 TCTTTCAAA-AATTCAAAAGA
30444 TCTTTCAAAAATTCAAAA
1 TCTTTCAAAAATTCAAAA
30462 TATATGATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.50, C:0.16, G:0.05, T:0.29
Consensus pattern (20 bp):
TCTTTCAAAAATTCAAAAGA
Found at i:38047 original size:18 final size:18
Alignment explanation
Indices: 38014--38051 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
38004 AAAATGAACT
38014 AAATGTAAACAACATGCAA
1 AAATGTAAACAACATG-AA
*
38033 AAATTTAAA-AACATGAA
1 AAATGTAAACAACATGAA
38050 AA
1 AA
38052 TATGACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 6 0.33
19 8 0.44
ACGTcount: A:0.63, C:0.11, G:0.08, T:0.18
Consensus pattern (18 bp):
AAATGTAAACAACATGAA
Found at i:38812 original size:14 final size:14
Alignment explanation
Indices: 38781--38817 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
38771 TTTGCTTCGA
38781 AAATAAAT--AAAT
1 AAATAAATAGAAAT
38793 -AATAAATAGAAAT
1 AAATAAATAGAAAT
38806 AAATAAATAGAA
1 AAATAAATAGAA
38818 TACCTCTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 7 0.32
13 4 0.18
14 11 0.50
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (14 bp):
AAATAAATAGAAAT
Found at i:39324 original size:25 final size:26
Alignment explanation
Indices: 39279--39347 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
39269 TATTTGTAAC
*
39279 ATGAATCTATTAATAAA-ATAATAAT-
1 ATGAAT-TAATAATAAATATAATAATA
39304 ATGAATTAATAATAAATATAATAATA
1 ATGAATTAATAATAAATATAATAATA
* *
39330 ATAACATTAATATTAAAT
1 ATGA-ATTAATAATAAAT
39348 GGGACGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 9 0.24
25 14 0.37
26 3 0.08
27 12 0.32
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (26 bp):
ATGAATTAATAATAAATATAATAATA
Found at i:52180 original size:113 final size:114
Alignment explanation
Indices: 51868--52270 Score: 614
Period size: 114 Copynumber: 3.5 Consensus size: 114
51858 ACATGTCCCA
* * *
51868 CTTACTCTTAAGGGAATATCAGATCTGGAGGGAGTTGATCCATTGAATCGGGGCATACTTGTTCG
1 CTTACTCTGAAGGGAATATCAGATCTGGAGGGAGTTGATCCATTGAATCGGGGTAGACTTGTTC-
* * * *
51933 C-TTTATTCTAAAGGGAATATCCAATCTTGGAAAAGAGAGACATGTTTCG
65 CACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTTCG
*
51982 CTTACTCTGAAGGGAATATCAGATATGGAGGGAGTTGATCCATTGAATCGGGGTAGACTTGTTCC
1 CTTACTCTGAAGGGAATATCAGATCTGGAGGGAGTTGATCCATTGAATCGGGGTAGACTTGTTCC
*
52047 ACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACTTGTTTCG
66 ACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTTCG
* * * * *
52096 CTTACTCTGACGGGAATATCGGTTTTGG-GGGAGTTGATCCATTGAATCGAGGTAGACTTGTTCC
1 CTTACTCTGAAGGGAATATCAGATCTGGAGGGAGTTGATCCATTGAATCGGGGTAGACTTGTTCC
*
52160 ACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACCTG-TTCTG
66 ACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTTC-G
*
52209 CTTACTCTGAAGGGAATATCAGATCTGGAGGGAGTTGATCCATTGAATCGTGGTCAGACTTG
1 CTTACTCTGAAGGGAATATCAGATCTGGAGGGAGTTGATCCATTGAATCGGGGT-AGACTTG
52271 AGAATTAAAC
Statistics
Matches: 265, Mismatches: 20, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
112 3 0.01
113 104 0.39
114 151 0.57
115 7 0.03
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (114 bp):
CTTACTCTGAAGGGAATATCAGATCTGGAGGGAGTTGATCCATTGAATCGGGGTAGACTTGTTCC
ACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTTCG
Found at i:60228 original size:14 final size:14
Alignment explanation
Indices: 60209--60246 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
60199 AATCTTTTTA
*
60209 TTAATATTGGTGTT
1 TTAATAATGGTGTT
60223 TTAATAATGGTGTT
1 TTAATAATGGTGTT
60237 TTAATAATGG
1 TTAATAATGG
60247 GGTGTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
TTAATAATGGTGTT
Found at i:60230 original size:17 final size:16
Alignment explanation
Indices: 60204--60244 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
60194 CGCATAATCT
*
60204 TTTTATTAATATTGGTG
1 TTTTAATAATA-TGGTG
60221 TTTTAAT-A-ATGGTG
1 TTTTAATAATATGGTG
60235 TTTTAATAAT
1 TTTTAATAAT
60245 GGGGTGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
14 12 0.57
15 2 0.10
16 1 0.05
17 6 0.29
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (16 bp):
TTTTAATAATATGGTG
Found at i:64562 original size:18 final size:18
Alignment explanation
Indices: 64529--64566 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
64519 AAAATGAACT
64529 AAATGTAAACAACATGCAA
1 AAATGTAAACAACATG-AA
*
64548 AAATTTAAA-AACATGAA
1 AAATGTAAACAACATGAA
64565 AA
1 AA
64567 TAGGACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 6 0.33
19 8 0.44
ACGTcount: A:0.63, C:0.11, G:0.08, T:0.18
Consensus pattern (18 bp):
AAATGTAAACAACATGAA
Found at i:64766 original size:16 final size:15
Alignment explanation
Indices: 64741--64770 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
64731 ACATATGTTC
64741 ATACTCAAAATATAA
1 ATACTCAAAATATAA
64756 ATACATCAAAATATA
1 ATAC-TCAAAATATA
64771 GAGGGTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (15 bp):
ATACTCAAAATATAA
Found at i:71410 original size:37 final size:37
Alignment explanation
Indices: 71360--71433 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
71350 TAACAAGCCA
*
71360 ACATAAACTTTCATTTTATTTTTAA-TGATATAGTTGT
1 ACATAAACTTTCATTTCA-TTTTAACTGATATAGTTGT
71397 ACATAAACTTTCATTTCATTTTAACTGATATAGTTGT
1 ACATAAACTTTCATTTCATTTTAACTGATATAGTTGT
71434 TAGAATGTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 6 0.17
37 29 0.83
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (37 bp):
ACATAAACTTTCATTTCATTTTAACTGATATAGTTGT
Found at i:76062 original size:3 final size:3
Alignment explanation
Indices: 76054--76088 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
76044 TGAAAATGAA
76054 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
76089 AAACATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:76176 original size:17 final size:18
Alignment explanation
Indices: 76154--76224 Score: 57
Period size: 17 Copynumber: 4.2 Consensus size: 18
76144 TTTTATATTA
76154 TATATTTATTTTC-AAAC
1 TATATTTATTTTCAAAAC
* *
76171 TATA-TTA-TAT-ATATA-
1 TATATTTATTTTCA-AAAC
76186 TATATATT-TTT-CAAAAC
1 TATAT-TTATTTTCAAAAC
76203 TATATTTATTTTCAAAAC
1 TATATTTATTTTCAAAAC
76221 TATA
1 TATA
76225 CTATATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 17
0.66 0.06 0.27
Matches are distributed among these distances:
15 6 0.15
16 9 0.22
17 16 0.39
18 10 0.24
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATTTATTTTCAAAAC
Found at i:76177 original size:46 final size:48
Alignment explanation
Indices: 76125--76278 Score: 178
Period size: 46 Copynumber: 3.2 Consensus size: 48
76115 AAACATAAAT
*
76125 TATATTATATATTTATATTTTTT-ATATTA-TATATTTATTTTC-AAAC
1 TATATTATATATTTATATTTTTTCATA-AACTATATTTATTTTCAAAAC
76171 TATATTATATATATATATATATTTTTCA-AAACTATATTTATTTTCAAAAC
1 TATATTATATAT-T-TATAT-TTTTTCATAAACTATATTTATTTTCAAAAC
* * *
76221 TATACTATAT-TTT-T-TTTTTTCTTAAAACTATATTTATTTTCTAAAC
1 TATATTATATATTTATATTTTTTCAT-AAACTATATTTATTTTCAAAAC
76267 TATATTATATAT
1 TATATTATATAT
76279 AACCAAAATA
Statistics
Matches: 94, Mismatches: 5, Indels: 17
0.81 0.04 0.15
Matches are distributed among these distances:
44 6 0.06
45 1 0.01
46 43 0.46
47 3 0.03
48 7 0.07
49 20 0.21
50 14 0.15
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.56
Consensus pattern (48 bp):
TATATTATATATTTATATTTTTTCATAAACTATATTTATTTTCAAAAC
Found at i:76188 original size:30 final size:31
Alignment explanation
Indices: 76146--76212 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 31
76136 TTTATATTTT
*
76146 TTATATTATATATTTA-TTTTC-AAACTATA
1 TTATATTATATATATATTTTTCAAAACTATA
76175 TTATATATATATATATATTTTTCAAAACTATA
1 TTATAT-TATATATATATTTTTCAAAACTATA
76207 TT-TATT
1 TTATATT
76213 TTCAAAACTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 6 0.18
30 10 0.29
31 8 0.24
32 10 0.29
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (31 bp):
TTATATTATATATATATTTTTCAAAACTATA
Found at i:76212 original size:19 final size:19
Alignment explanation
Indices: 76184--76234 Score: 77
Period size: 18 Copynumber: 2.7 Consensus size: 19
76174 ATTATATATA
76184 TATATATATTTTTCAAAAC
1 TATATATATTTTTCAAAAC
*
76203 TATATTTA-TTTTCAAAAC
1 TATATATATTTTTCAAAAC
76221 TATACTATATTTTT
1 TATA-TATATTTTT
76235 TTTTTTCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 14 0.50
19 10 0.36
20 4 0.14
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATATATTTTTCAAAAC
Found at i:76897 original size:181 final size:180
Alignment explanation
Indices: 76506--77056 Score: 780
Period size: 181 Copynumber: 3.0 Consensus size: 180
76496 GTCAAATCTG
* ** * *
76506 AAAAATTGTGATTTACTTCACTTCTCTTCAGGGAAGATTAAATCAAGATTGATTTGCTTCACTGC
1 AAAAATTTTGATCAACTTCACTACTCTTCAGGGAAGATTGAATCAAGATTGATTTGCTTCACTGC
* * * *
76571 TCTTCAGGAAGACCAAATCTGGAAAATGATGATATGCTCTGCTACTCTTTAGGACATATCAGATC
66 TCTTCAGGAAGATCAAATATGGAAAATGATGATATGCTCTGCTACTCTTTAGGAGAGATCAGATC
* * *
76636 TAAGGGAAGAGGGGGTTTGCTCCACTATTCTTTAGGGGAGATCAGATTCGAT
131 TAAGGGAAGA-CGGGTCTGCTCCACTACTCTTTA-GGGAGATCAGATTCGAT
* * * *
76688 AAAAA-ATTGATCAATTTCGCTACTCTTCAGGGAAGATTGAATCAAGATTGATTTGCTTCACTAC
1 AAAAATTTTGATCAACTTCACTACTCTTCAGGGAAGATTGAATCAAGATTGATTTGCTTCACTGC
* * * *
76752 TCCTCAGGAAGATCAAATATGGAAAATGACGATCTGCTCTCCTACTCTTTAGGAGAGATCAGATC
66 TCTTCAGGAAGATCAAATATGGAAAATGATGATATGCTCTGCTACTCTTTAGGAGAGATCAGATC
76817 TAAGGGAAGACGGGTCTGCTCCACTACTCTTTAGAGGAGATCAGATTCGAT
131 TAAGGGAAGACGGGTCTGCTCCACTACTCTTTAG-GGAGATCAGATTCGAT
* * *
76868 AAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCAAGATTGATTTACTTCACTGC
1 AAAAATTTTGATCAACTTCACTACTCTTCAGGGAAGATTGAATCAAGATTGATTTGCTTCACTGC
* *
76933 TCTTCAGGAAGATCAAATATGGAAAATGATGATATGCTCAGCTACTCTTTAGGAGAGATCAAATC
66 TCTTCAGGAAGATCAAATATGGAAAATGATGATATGCTCTGCTACTCTTTAGGAGAGATCAGATC
* * * * * *
76998 TAAGGGAATATGAGTCTGCTCCACTACTCTTTAGGGAAGATCATACTCGAG
131 TAAGGGAAGACGGGTCTGCTCCACTACTCTTTAGGG-AGATCAGATTCGAT
77049 AAAAATTT
1 AAAAATTT
77057 AAACATATCT
Statistics
Matches: 327, Mismatches: 39, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
179 1 0.00
180 43 0.13
181 278 0.85
182 5 0.02
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (180 bp):
AAAAATTTTGATCAACTTCACTACTCTTCAGGGAAGATTGAATCAAGATTGATTTGCTTCACTGC
TCTTCAGGAAGATCAAATATGGAAAATGATGATATGCTCTGCTACTCTTTAGGAGAGATCAGATC
TAAGGGAAGACGGGTCTGCTCCACTACTCTTTAGGGAGATCAGATTCGAT
Found at i:76906 original size:43 final size:40
Alignment explanation
Indices: 76866--76945 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 40
76856 ATCAGATTCG
76866 ATAAAAATTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGA
1 ATAAAAA--TTGATCCACTTCACTGCTCTTCA-GGAAGATTGA
* * **
76909 ATCAAGATTGATTTACTTCACTGCTCTTCAGGAAGAT
1 ATAAAAATTGATCCACTTCACTGCTCTTCAGGAAGAT
76946 CAAATATGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 7 0.21
41 21 0.64
43 5 0.15
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (40 bp):
ATAAAAATTGATCCACTTCACTGCTCTTCAGGAAGATTGA
Found at i:78132 original size:8 final size:8
Alignment explanation
Indices: 78119--78148 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
78109 TTTATTTATT
78119 TTTTTTTC
1 TTTTTTTC
78127 TTTTTTTC
1 TTTTTTTC
*
78135 TTTTTTCC
1 TTTTTTTC
78143 TTTTTT
1 TTTTTT
78149 CAGGTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTC
Found at i:78140 original size:15 final size:15
Alignment explanation
Indices: 78120--78149 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
78110 TTATTTATTT
*
78120 TTTTTTCTTTTTTTC
1 TTTTTTCCTTTTTTC
78135 TTTTTTCCTTTTTTC
1 TTTTTTCCTTTTTTC
78150 AGGTAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTCCTTTTTTC
Found at i:78888 original size:15 final size:16
Alignment explanation
Indices: 78868--78897 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
78858 AAAAGAAAAT
78868 GATTAAAT-AAATGAA
1 GATTAAATGAAATGAA
78883 GATTAAATGAAATGA
1 GATTAAATGAAATGA
78898 TAAAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.27
Consensus pattern (16 bp):
GATTAAATGAAATGAA
Found at i:79322 original size:19 final size:19
Alignment explanation
Indices: 79298--79342 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
79288 GCCGAATGGT
79298 TACATGGTTGTTCGGTTGA
1 TACATGGTTGTTCGGTTGA
79317 TACATGGTTGTTCGGTTGA
1 TACATGGTTGTTCGGTTGA
79336 TACATGG
1 TACATGG
79343 CTTTTGATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.18, C:0.11, G:0.31, T:0.40
Consensus pattern (19 bp):
TACATGGTTGTTCGGTTGA
Found at i:81227 original size:24 final size:24
Alignment explanation
Indices: 81191--81251 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
81181 GTGCAATGCA
81191 CTTGGAA-TGTCAA-CGAAAACAACT
1 CTTGGAACT-TCAAGCG-AAACAACT
* **
81215 CTTGGAACTTCAAGCGATACTTCT
1 CTTGGAACTTCAAGCGAAACAACT
81239 CTTGGAACTTCAA
1 CTTGGAACTTCAA
81252 ATGGCATAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 29 0.91
25 3 0.09
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (24 bp):
CTTGGAACTTCAAGCGAAACAACT
Found at i:82208 original size:9 final size:9
Alignment explanation
Indices: 82194--82226 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
82184 GAAACATCGA
82194 ATGCACTTG
1 ATGCACTTG
82203 ATGCACTTG
1 ATGCACTTG
*
82212 ATGCA-TCG
1 ATGCACTTG
82220 ATGCACT
1 ATGCACT
82227 CTTAGTGCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (9 bp):
ATGCACTTG
Found at i:82224 original size:17 final size:19
Alignment explanation
Indices: 82202--82245 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
82192 GAATGCACTT
*
82202 GATGCACT-TGA-TGCATC
1 GATGCACTCTGAGTGCACC
*
82219 GATGCACTCTTAGTGCACC
1 GATGCACTCTGAGTGCACC
82238 GATGCACT
1 GATGCACT
82246 GAGAGTCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 2 0.09
19 13 0.57
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (19 bp):
GATGCACTCTGAGTGCACC
Found at i:82313 original size:21 final size:21
Alignment explanation
Indices: 82283--82359 Score: 145
Period size: 21 Copynumber: 3.7 Consensus size: 21
82273 TTTTACACTG
*
82283 ATGCACCGATGCACCTAGGGT
1 ATGCATCGATGCACCTAGGGT
82304 ATGCATCGATGCACCTAGGGT
1 ATGCATCGATGCACCTAGGGT
82325 ATGCATCGATGCACCTAGGGT
1 ATGCATCGATGCACCTAGGGT
82346 ATGCATCGATGCAC
1 ATGCATCGATGCAC
82360 TGGCGCTCCC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.25, C:0.26, G:0.27, T:0.22
Consensus pattern (21 bp):
ATGCATCGATGCACCTAGGGT
Found at i:89184 original size:21 final size:21
Alignment explanation
Indices: 89142--89185 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
89132 GCCCCGGGAG
*
89142 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
89163 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
89184 CT
1 CT
89186 CCTCCTACAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:89705 original size:2 final size:2
Alignment explanation
Indices: 89698--89726 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
89688 CAGCTTAAGC
89698 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
89727 TTAATCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:90313 original size:66 final size:63
Alignment explanation
Indices: 90234--90394 Score: 182
Period size: 66 Copynumber: 2.5 Consensus size: 63
90224 AATTAAATTG
* *
90234 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCA-CTGATGCACTGGGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCATC-GATGCACTCGGGATATTT-TG
90297 AAA
63 --A
* * * *
90300 AACATCGAATGCATTTGATGCATTGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCATCGATGCACTCGGGATATTTTGA
* *
90364 AAGATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
90395 TCTTAGTGTA
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
63 1 0.01
64 28 0.34
66 48 0.58
67 6 0.07
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCATCGATGCACTCGGGATATTTTGA
Found at i:91950 original size:29 final size:29
Alignment explanation
Indices: 91918--91973 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
91908 GTAGAGCACT
91918 TTTTCCTTGTC-TTGCTTTCTCTTTTTAAA
1 TTTTCCTTGTCTTTGCTTT-TCTTTTTAAA
* * *
91947 TTTTTCTTTTCTTTTCTTTTCTTTTTA
1 TTTTCCTTGTCTTTGCTTTTCTTTTTA
91974 TCTGATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 17 0.74
30 6 0.26
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (29 bp):
TTTTCCTTGTCTTTGCTTTTCTTTTTAAA
Found at i:92701 original size:19 final size:19
Alignment explanation
Indices: 92677--92721 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
92667 GCTGAATGGT
92677 TACATGGTTGTTCGGTTGA
1 TACATGGTTGTTCGGTTGA
92696 TACATGGTTGTTCGGTTGA
1 TACATGGTTGTTCGGTTGA
92715 TACATGG
1 TACATGG
92722 CTTTTGATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.18, C:0.11, G:0.31, T:0.40
Consensus pattern (19 bp):
TACATGGTTGTTCGGTTGA
Found at i:98064 original size:3 final size:3
Alignment explanation
Indices: 98056--98088 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
98046 TGCAATTAAA
98056 AAT AAT AAT AAT GAA- AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
98089 TAAAACGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.86
4 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:98074 original size:15 final size:15
Alignment explanation
Indices: 98054--98082 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
98044 CCTGCAATTA
98054 AAAATAATAATAATG
1 AAAATAATAATAATG
98069 AAAATAATAATAAT
1 AAAATAATAATAAT
98083 AATAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AAAATAATAATAATG
Found at i:98101 original size:21 final size:20
Alignment explanation
Indices: 98054--98093 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
98044 CCTGCAATTA
98054 AAAATAATAATAATGAAAAT
1 AAAATAATAATAATGAAAAT
*
98074 AATAATAATAATAATTAAAA
1 AA-AATAATAATAATGAAAA
98094 CGTAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (20 bp):
AAAATAATAATAATGAAAAT
Found at i:98209 original size:42 final size:42
Alignment explanation
Indices: 98156--98310 Score: 174
Period size: 42 Copynumber: 3.6 Consensus size: 42
98146 AATATATATT
*
98156 TATTTTC-AAACTATATTATATATATATTTTC-AAAGTTATA
1 TATTTTCAAAACTATACTATATATATATTTTCAAAAGTTATA
* *
98196 TATTTTCTAAAACTATACTATATATATATATATTTTCAAAACTATATT
1 TATTTTC-AAAACTATAC----TATATATATATTTTCAAAAGT-TATA
*
98244 TATTTTCAAAACTATACTATATATAT-TTTCCAAAAG-TATA
1 TATTTTCAAAACTATACTATATATATATTTTCAAAAGTTATA
98284 CTTATTTTCAAAACTATACTATATATA
1 --TATTTTCAAAACTATACTATATATA
98311 ACAAAATAAA
Statistics
Matches: 99, Mismatches: 6, Indels: 18
0.80 0.05 0.15
Matches are distributed among these distances:
40 10 0.10
42 41 0.41
43 9 0.09
46 15 0.15
47 14 0.14
48 10 0.10
ACGTcount: A:0.41, C:0.11, G:0.01, T:0.46
Consensus pattern (42 bp):
TATTTTCAAAACTATACTATATATATATTTTCAAAAGTTATA
Found at i:98265 original size:23 final size:23
Alignment explanation
Indices: 98236--98307 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
98226 TATTTTCAAA
98236 ACTATATTTATTTTCAAAACTAT
1 ACTATATTTATTTTCAAAACTAT
* *
98259 ACTATATATATTTTCCAAAAGTAT
1 ACTATATTTATTTT-CAAAACTAT
98283 AC-----TTATTTTCAAAACTAT
1 ACTATATTTATTTTCAAAACTAT
98301 ACTATAT
1 ACTATAT
98308 ATAACAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
18 10 0.26
19 6 0.15
23 13 0.33
24 10 0.26
ACGTcount: A:0.40, C:0.14, G:0.01, T:0.44
Consensus pattern (23 bp):
ACTATATTTATTTTCAAAACTAT
Found at i:98297 original size:89 final size:90
Alignment explanation
Indices: 98127--98310 Score: 254
Period size: 89 Copynumber: 2.1 Consensus size: 90
98117 AAACATAAAT
* * *
98127 TATAT-TATATATTTTTAATAATATATATTTATTTTCAAACTATATTATATATATATTTTCAAAG
1 TATATATATATATTTTCAATAATATATATTTATTTTCAAACTATACTATATATATATTTCCAAAG
98191 TTATATATTTTCTAAAACTATACTA
66 TTATATATTTTCTAAAACTATACTA
*
98216 TATATATATATATTTTCAA-AA-CTATATTTATTTTCAAAACTATACTATATATAT-TTTCCAAA
1 TATATATATATATTTTCAATAATATATATTTATTTTC-AAACTATACTATATATATATTTCC-AA
98278 AG-TATACTTATTTTC-AAAACTATACTA
64 AGTTATA--TATTTTCTAAAACTATACTA
98305 TATATA
1 TATATA
98311 ACAAAATAAA
Statistics
Matches: 86, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
88 21 0.24
89 46 0.53
90 19 0.22
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.48
Consensus pattern (90 bp):
TATATATATATATTTTCAATAATATATATTTATTTTCAAACTATACTATATATATATTTCCAAAG
TTATATATTTTCTAAAACTATACTA
Found at i:98302 original size:18 final size:18
Alignment explanation
Indices: 98226--98303 Score: 84
Period size: 18 Copynumber: 4.0 Consensus size: 18
98216 TATATATATA
*
98226 TATTTTCAAAACTATATT
1 TATTTTCAAAACTATACT
98244 TATTTTCAAAACTATACTATAT
1 TATTTTCAAAACTATAC----T
*
98266 ATATTTTCCAAAAGTATACT
1 -TATTTT-CAAAACTATACT
98286 TATTTTCAAAACTATACT
1 TATTTTCAAAACTATACT
98304 ATATATAACA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
18 27 0.53
19 6 0.12
20 1 0.02
22 1 0.02
23 6 0.12
24 10 0.20
ACGTcount: A:0.40, C:0.14, G:0.01, T:0.45
Consensus pattern (18 bp):
TATTTTCAAAACTATACT
Found at i:98353 original size:15 final size:15
Alignment explanation
Indices: 98310--98353 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
98300 TACTATATAT
* *
98310 AACAAAATAAAACCA
1 AACAAAATGAAACTA
98325 AACAAAAATG-AACTA
1 AAC-AAAATGAAACTA
98340 AACAAAATGAAACT
1 AACAAAATGAAACT
98354 CTAGGATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 6 0.24
15 14 0.56
16 5 0.20
ACGTcount: A:0.68, C:0.16, G:0.05, T:0.11
Consensus pattern (15 bp):
AACAAAATGAAACTA
Found at i:108482 original size:11 final size:12
Alignment explanation
Indices: 108468--108559 Score: 52
Period size: 11 Copynumber: 7.9 Consensus size: 12
108458 ATTTTTTTTC
108468 TTCTT-TTCTTT
1 TTCTTATTCTTT
108479 TTCTATAATT-TTT
1 TTCT-T-ATTCTTT
* *
108492 TTCTTCTTATTT
1 TTCTTATTCTTT
108504 TTCTTATT-TTT
1 TTCTTATTCTTT
* *
108515 ATTTTTATTTTTT
1 -TTCTTATTCTTT
* *
108528 TTCTTCTT-TTC
1 TTCTTATTCTTT
*
108539 TTCTT-TTCTTC
1 TTCTTATTCTTT
108550 TTCTT-TTCTT
1 TTCTTATTCTT
108560 CTTTTTTCCT
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
10 2 0.03
11 29 0.43
12 25 0.37
13 10 0.15
14 2 0.03
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (12 bp):
TTCTTATTCTTT
Found at i:108560 original size:11 final size:11
Alignment explanation
Indices: 108536--108567 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
108526 TTTTCTTCTT
108536 TTCTTCTTTTC
1 TTCTTCTTTTC
108547 TTCTTCTTTTC
1 TTCTTCTTTTC
108558 TTCTT-TTTTC
1 TTCTTCTTTTC
108568 CTTTTTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (11 bp):
TTCTTCTTTTC
Found at i:108564 original size:8 final size:8
Alignment explanation
Indices: 108526--108551 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
108516 TTTTTATTTT
108526 TTTTCTTC
1 TTTTCTTC
108534 TTTTCTTC
1 TTTTCTTC
108542 TTTTCTTC
1 TTTTCTTC
108550 TT
1 TT
108552 CTTTTCTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTCTTC
Found at i:108583 original size:19 final size:18
Alignment explanation
Indices: 108487--108584 Score: 78
Period size: 19 Copynumber: 5.3 Consensus size: 18
108477 TTTTCTATAA
108487 TTTTTTTCTTCTTATT-TT
1 TTTTTTTCTTCTT-TTCTT
* *
108505 TCTTATTT-TTATTTT-TAT
1 T-TTTTTTCTTCTTTTCT-T
108523 TTTTTTTCTTCTTTTCTT
1 TTTTTTTCTTCTTTTCTT
*
108541 CTTTTCTTCTTCTTTTCTT
1 -TTTTTTTCTTCTTTTCTT
*
108560 CTTTTTTCCTT-TTTTCCTT
1 -TTTTTTTCTTCTTTT-CTT
108579 TTTTTT
1 TTTTTT
108585 GACTCTTATG
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
17 8 0.12
18 24 0.36
19 35 0.52
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTTCTTCTTTTCTT
Found at i:108583 original size:63 final size:63
Alignment explanation
Indices: 108458--108574 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 63
108448 GCATCTCTCA
* *
108458 ATTTTTTTTCTTCTTTTCTTTTTCTATAATTTTTTTCTTCTTATTTTTCTTATTTTTATTTTT
1 ATTTTTTTTCTTCTTTTCTTTTTCTATAATTCTTTTCTTCTTATTTTCCTTATTTTTATTTTT
*
108521 ATTTTTTTTCTTCTTTTCTTCTTTTCT-T-CTTCTTTTCTTCTT-TTTTCCTT-TTTT
1 ATTTTTTTTCTTCTTTTC-T-TTTTCTATAATTCTTTTCTTCTTATTTTCCTTATTTT
108575 CCTTTTTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
61 4 0.08
62 7 0.14
63 30 0.61
64 2 0.04
65 6 0.12
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (63 bp):
ATTTTTTTTCTTCTTTTCTTTTTCTATAATTCTTTTCTTCTTATTTTCCTTATTTTTATTTTT
Found at i:111891 original size:24 final size:24
Alignment explanation
Indices: 111858--111906 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
111848 AGTCTTCCTT
111858 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
*
111882 ATGATTTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
111906 A
1 A
111907 ATGTCATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:114874 original size:41 final size:42
Alignment explanation
Indices: 114770--114874 Score: 151
Period size: 41 Copynumber: 2.5 Consensus size: 42
114760 TTGCAACATG
* * *
114770 TTAGGACATTTAGCGGCG-TTTTATATAAATGTCGCAAAAGG
1 TTAGGTCATTTAGCGGCGTTTTTATATAAATGCCGCAAAAGA
* *
114811 TTGGGTCATTTAGCGGCTTTTTTATATAAA-GCCGCAAAAGA
1 TTAGGTCATTTAGCGGCGTTTTTATATAAATGCCGCAAAAGA
114852 TTAGGTCATTTAGCGGCGTTTTT
1 TTAGGTCATTTAGCGGCGTTTTT
114875 GGAACAAAGA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 45 0.80
42 11 0.20
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (42 bp):
TTAGGTCATTTAGCGGCGTTTTTATATAAATGCCGCAAAAGA
Found at i:117468 original size:6 final size:6
Alignment explanation
Indices: 117457--117496 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
117447 AAATGAGACT
*
117457 TTATAA TTATAA TTATAA TTATAA TTATAA TTAAAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTAT
117497 TATATTTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTATAA
Found at i:120764 original size:72 final size:72
Alignment explanation
Indices: 120668--120806 Score: 206
Period size: 72 Copynumber: 1.9 Consensus size: 72
120658 TTGAAAGATT
* *** * *
120668 TTGTTGCTCGACTCGACTCGTTATTCGTTAAACTTGTTATAATTTTGCTTGACTCGTCTTCGTTA
1 TTGTTGCTCAACTCGACTCGTTATTCGTTAAACTCACTAAAATTTTGCTTGAATCGTCTTCGTTA
120733 AGAAAAC
66 AGAAAAC
* *
120740 TTGTTGCTCAACTTGACTCTTTATTCGTTAAACTCACTAAAATTTTGCTTGAATCGTCTTCGTTA
1 TTGTTGCTCAACTCGACTCGTTATTCGTTAAACTCACTAAAATTTTGCTTGAATCGTCTTCGTTA
120805 AG
66 AG
120807 TGCTGAATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.42
Consensus pattern (72 bp):
TTGTTGCTCAACTCGACTCGTTATTCGTTAAACTCACTAAAATTTTGCTTGAATCGTCTTCGTTA
AGAAAAC
Found at i:121292 original size:29 final size:28
Alignment explanation
Indices: 121236--121292 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
121226 GTGCTCAATG
* * * *
121236 TATTTTTTTGTTTCACTTTGGTGTCTAA
1 TATTTTTTTGTTCCAATTTGATGACTAA
121264 TATTTTTGTTGTTCCAATTTGATGACTAA
1 TATTTTT-TTGTTCCAATTTGATGACTAA
121293 CGTTTCTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.19, C:0.11, G:0.14, T:0.56
Consensus pattern (28 bp):
TATTTTTTTGTTCCAATTTGATGACTAA
Found at i:124103 original size:7 final size:7
Alignment explanation
Indices: 124091--124182 Score: 53
Period size: 7 Copynumber: 13.1 Consensus size: 7
124081 ATTAGAGTTA
124091 AGGATTT
1 AGGATTT
124098 AGGATTT
1 AGGATTT
*
124105 AAGATTT
1 AGGATTT
* *
124112 AAGCTTT
1 AGGATTT
124119 AGGATTT
1 AGGATTT
**
124126 AATATTT
1 AGGATTT
124133 ATGG-TTT
1 A-GGATTT
* *
124140 GGGGTTT
1 AGGATTT
*
124147 ATGATTT
1 AGGATTT
*
124154 AGGAATT
1 AGGATTT
124161 -GTGATTT
1 AG-GATTT
* *
124168 AGGGTTA
1 AGGATTT
124175 AGGATTT
1 AGGATTT
124182 A
1 A
124183 TAATTTAGTG
Statistics
Matches: 62, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
6 3 0.05
7 58 0.94
8 1 0.02
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (7 bp):
AGGATTT
Found at i:125630 original size:2 final size:2
Alignment explanation
Indices: 125623--125674 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
125613 CATGTTTAAT
125623 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
125665 TA TA TA TA TA
1 TA TA TA TA TA
125675 ATTTTGTGCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:125733 original size:20 final size:21
Alignment explanation
Indices: 125696--125742 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
125686 GCATCACATA
125696 TATATTTATATATGTACTTATC
1 TATATTTATATA-GTACTTATC
*
125718 TATATTTATATA-TACTTATG
1 TATATTTATATAGTACTTATC
125738 TATAT
1 TATAT
125743 ATAAACACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 12 0.50
22 12 0.50
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.55
Consensus pattern (21 bp):
TATATTTATATAGTACTTATC
Found at i:126020 original size:29 final size:28
Alignment explanation
Indices: 125984--126043 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
125974 ATGATGCATG
* *
125984 TATGATGTATTTATGATACGTGTATATA
1 TATGATGTATGTATGATACGTATATATA
*
126012 TATGCATGTATGTATGATATGTATATATA
1 TATG-ATGTATGTATGATACGTATATATA
126041 TAT
1 TAT
126044 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (28 bp):
TATGATGTATGTATGATACGTATATATA
Found at i:126118 original size:35 final size:35
Alignment explanation
Indices: 126039--126118 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 35
126029 TATGTATATA
* *
126039 TATATATATATATATGCATATATATGTTATAAAAG
1 TATATATATACATATGCATATATATGATATAAAAG
* * *
126074 TATAAATATACATATGCATA-ATTAT-ATATAATAT
1 TATATATATACATATGCATATA-TATGATATAAAAG
126108 TAATATATATA
1 T-ATATATATA
126119 TTATTTTTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
34 8 0.22
35 29 0.78
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (35 bp):
TATATATATACATATGCATATATATGATATAAAAG
Found at i:126236 original size:21 final size:20
Alignment explanation
Indices: 126183--126237 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
126173 ATATACATGC
126183 ATCATACATACATGC--ATAT
1 ATCATACATACAT-CATATAT
**
126202 AT-ATACATGTATCATATAT
1 ATCATACATACATCATATAT
126221 AATCATACATACATCAT
1 -ATCATACATACATCAT
126238 TGATCACACA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 1 0.04
18 8 0.29
19 6 0.21
20 2 0.07
21 11 0.39
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.35
Consensus pattern (20 bp):
ATCATACATACATCATATAT
Found at i:126318 original size:2 final size:2
Alignment explanation
Indices: 126311--126402 Score: 184
Period size: 2 Copynumber: 46.0 Consensus size: 2
126301 ACTTATAATC
126311 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
126353 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
126395 TA TA TA TA
1 TA TA TA TA
126403 GATAGATAGT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 90 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:127362 original size:13 final size:13
Alignment explanation
Indices: 127344--127370 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
127334 TTAAAGATGC
127344 GCATATGAAGATT
1 GCATATGAAGATT
127357 GCATATGAAGATT
1 GCATATGAAGATT
127370 G
1 G
127371 TTCAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (13 bp):
GCATATGAAGATT
Found at i:133124 original size:22 final size:23
Alignment explanation
Indices: 133075--133124 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
133065 TATGTTTTAA
133075 GATTATATTTTGTTATTATGGAT
1 GATTATATTTTGTTATTATGGAT
*
133098 G-TTATATTTGTTTTATTA-GG-T
1 GATTATATTT-TGTTATTATGGAT
133119 GATTAT
1 GATTAT
133125 GTTTATTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 2 0.08
22 14 0.58
23 8 0.33
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (23 bp):
GATTATATTTTGTTATTATGGAT
Found at i:150996 original size:108 final size:109
Alignment explanation
Indices: 150800--151017 Score: 429
Period size: 108 Copynumber: 2.0 Consensus size: 109
150790 TAACCATATT
150800 GAATTGAAATAATAAGGATCTGTGTCGATCTATCAGATTATCGAGATAACTCAAACTGAACAACT
1 GAATTGAAATAATAAGGATCTGTGTCGATCTATCAGATTATCGAGATAACTCAAACTGAACAACT
150865 CCCAGAACTAATGCATGTCAACTGGTCCATTCAATGCTCTTCCA
66 CCCAGAACTAATGCATGTCAACTGGTCCATTCAATGCTCTTCCA
150909 GAATTG-AATAATAAGGATCTGTGTCGATCTATCAGATTATCGAGATAACTCAAACTGAACAACT
1 GAATTGAAATAATAAGGATCTGTGTCGATCTATCAGATTATCGAGATAACTCAAACTGAACAACT
150973 CCCAGAACTAATGCATGTCAACTGGTCCATTCAATGCTCTTCCA
66 CCCAGAACTAATGCATGTCAACTGGTCCATTCAATGCTCTTCCA
151017 G
1 G
151018 GGTATTCACT
Statistics
Matches: 109, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
108 103 0.94
109 6 0.06
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (109 bp):
GAATTGAAATAATAAGGATCTGTGTCGATCTATCAGATTATCGAGATAACTCAAACTGAACAACT
CCCAGAACTAATGCATGTCAACTGGTCCATTCAATGCTCTTCCA
Found at i:151381 original size:27 final size:26
Alignment explanation
Indices: 151351--151401 Score: 93
Period size: 27 Copynumber: 1.9 Consensus size: 26
151341 AATACTTTAA
151351 GTCATTTTACACTTTAGGGGCATTTTG
1 GTCATTTTACACTTTA-GGGCATTTTG
151378 GTCATTTTACACTTTAGGGCATTT
1 GTCATTTTACACTTTAGGGCATTT
151402 CTATAGATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.45
Consensus pattern (26 bp):
GTCATTTTACACTTTAGGGCATTTTG
Found at i:153532 original size:245 final size:245
Alignment explanation
Indices: 153092--153586 Score: 846
Period size: 245 Copynumber: 2.0 Consensus size: 245
153082 ATACAACTTT
* * *
153092 AATTATACACTTAAAATTAATAAATTCTAACCCTAAATTAGGGTGTGACAATTCTCCCCTCCTTA
1 AATTAGACACTTAAAATTAATAAATTCTAACCCTAAATTAGGGTATGACAATTCTCCCATCCTTA
*
153157 GAAGAATTTCATCCTCGAAATTCATTCAAGTCACAAGAATGCATAAATGAGGCTTCCTTCAATTC
66 AAAGAATTTCATCCTCGAAATTCATTCAAGTCACAAGAATGCATAAATGAGGCTTCCTTCAATTC
* *
153222 TTCTATATCTTCTAATAGCTTTTACAGAAGTACGAGTCCTCTACTAATCCTTAACCAACTGAGTA
131 TTCCATATCTTCTAATAGCTTTTACAAAAGTACGAGTCCTCTACTAATCCTTAACCAACTGAGTA
* ** * * *
153287 TATTTTCTTGTCAGAACACACCCTCATTCACAATAAAAGAGTTTGAACGG
196 TACTTTCTCATCAGAACACAACCTCATTCACAATAAAACAATTTGAACGG
153337 AATTAGACACTTAAAATTAATAAATTCTAACCCTAAATTAGGGTATGACAATTCTCCCATCCTTA
1 AATTAGACACTTAAAATTAATAAATTCTAACCCTAAATTAGGGTATGACAATTCTCCCATCCTTA
*
153402 AAAGAATTTCATCCTCGAAATTCATTCAAGTCACAAGAATGCATAAATGAGGCTTCCTTCAGTTC
66 AAAGAATTTCATCCTCGAAATTCATTCAAGTCACAAGAATGCATAAATGAGGCTTCCTTCAATTC
*
153467 TTCCATATCTTCTAATAGCTTTTACAAAAGTACGAGTCCTCTACTAATCCTTAACCAATTGAGTA
131 TTCCATATCTTCTAATAGCTTTTACAAAAGTACGAGTCCTCTACTAATCCTTAACCAACTGAGTA
* *
153532 TACTTTCTCATCGGAACACAACCTCATTCACAATAAAACAATTTGAATGG
196 TACTTTCTCATCAGAACACAACCTCATTCACAATAAAACAATTTGAACGG
153582 AATTA
1 AATTA
153587 TCCTTATGGA
Statistics
Matches: 234, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
245 234 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.32
Consensus pattern (245 bp):
AATTAGACACTTAAAATTAATAAATTCTAACCCTAAATTAGGGTATGACAATTCTCCCATCCTTA
AAAGAATTTCATCCTCGAAATTCATTCAAGTCACAAGAATGCATAAATGAGGCTTCCTTCAATTC
TTCCATATCTTCTAATAGCTTTTACAAAAGTACGAGTCCTCTACTAATCCTTAACCAACTGAGTA
TACTTTCTCATCAGAACACAACCTCATTCACAATAAAACAATTTGAACGG
Found at i:157066 original size:15 final size:15
Alignment explanation
Indices: 157019--157070 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 15
157009 AGTCAACGAA
*
157019 TTGACTCGGAC-GGG
1 TTGACTCAGACTGGG
*
157033 TTGACTC-GAATGGG
1 TTGACTCAGACTGGG
*
157047 TTGACTCAGACTGAG
1 TTGACTCAGACTGGG
157062 TTGACTCAG
1 TTGACTCAG
157071 TGACTGGACC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 2 0.06
14 17 0.52
15 14 0.42
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.27
Consensus pattern (15 bp):
TTGACTCAGACTGGG
Found at i:157190 original size:18 final size:18
Alignment explanation
Indices: 157167--157206 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
157157 TGGCCAAAAT
157167 CGAAATTAAAACTAATTA
1 CGAAATTAAAACTAATTA
157185 CGAAATTAAAACTAATTA
1 CGAAATTAAAACTAATTA
157203 CGAA
1 CGAA
157207 GGTGACCGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.25
Consensus pattern (18 bp):
CGAAATTAAAACTAATTA
Found at i:159808 original size:15 final size:15
Alignment explanation
Indices: 159788--159819 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
159778 AATTCTACAA
159788 TCAAAACACCATCTT
1 TCAAAACACCATCTT
159803 TCAAAACACCATCTT
1 TCAAAACACCATCTT
159818 TC
1 TC
159820 TTTAGAGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (15 bp):
TCAAAACACCATCTT
Found at i:163084 original size:22 final size:22
Alignment explanation
Indices: 163054--163096 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
163044 GAATTAACAT
*
163054 TCATAATAAACATCATATATAA
1 TCATAATAAAAATCATATATAA
* *
163076 TCATGATAAAAATCATGTATA
1 TCATAATAAAAATCATATATA
163097 TAATAACCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.33
Consensus pattern (22 bp):
TCATAATAAAAATCATATATAA
Done.