Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006822.1 Hibiscus syriacus cultivar Beakdansim tig00017333_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: 111091
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:3247 original size:31 final size:31
Alignment explanation
Indices: 3198--3284 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 31
3188 AAATTACACG
* *
3198 TTTAGTACCTAAATTATCAATTTTAATCCGT
1 TTTAATACCTAAACTATCAATTTTAATCCGT
* * ** *
3229 TTTAATACTTAAACTATCAGTTTTGGTCTGT
1 TTTAATACCTAAACTATCAATTTTAATCCGT
* *
3260 TTTAATGCCTAAACTTTCATATTTT
1 TTTAATACCTAAACTATCA-ATTTT
3285 CCCCCCAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
31 40 0.91
32 4 0.09
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (31 bp):
TTTAATACCTAAACTATCAATTTTAATCCGT
Found at i:3489 original size:17 final size:17
Alignment explanation
Indices: 3467--3519 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
3457 TAAGCTTTTT
3467 CGTCACATCTTTTTGAC
1 CGTCACATCTTTTTGAC
*
3484 CGTCACA--TATTTGAAC
1 CGTCACATCTTTTTG-AC
*
3500 TGTCACATC-TTTTGAC
1 CGTCACATCTTTTTGAC
3516 CGTC
1 CGTC
3520 CGATAGGCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 5 0.17
16 13 0.45
17 11 0.38
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (17 bp):
CGTCACATCTTTTTGAC
Found at i:5407 original size:20 final size:20
Alignment explanation
Indices: 5384--5421 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5374 CCATACTCTT
*
5384 TAGGTAGCATCGATACTATC
1 TAGGTAGCATCAATACTATC
5404 TAGGTAGCATCAATACTA
1 TAGGTAGCATCAATACTA
5422 CCAGATGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (20 bp):
TAGGTAGCATCAATACTATC
Found at i:6774 original size:21 final size:21
Alignment explanation
Indices: 6748--6817 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
6738 CATAAAATAC
6748 GAAAGAATTCTTTTGAAAAGA
1 GAAAGAATTCTTTTGAAAAGA
* *
6769 GAAAGAA----TTTGAATTATA
1 GAAAGAATTCTTTTGAA-AAGA
6787 CGAAAGAATTCTTTTGAAAAGA
1 -GAAAGAATTCTTTTGAAAAGA
6809 GAAAGAATT
1 GAAAGAATT
6818 TGAATTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
17 6 0.15
18 2 0.05
19 7 0.18
21 16 0.41
22 2 0.05
23 6 0.15
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.29
Consensus pattern (21 bp):
GAAAGAATTCTTTTGAAAAGA
Found at i:6779 original size:17 final size:17
Alignment explanation
Indices: 6759--6821 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
6749 AAAGAATTCT
6759 TTTGAAAAGAGAAAGAA
1 TTTGAAAAGAGAAAGAA
* *
6776 TTTGAATTATACGAAAGAA
1 TTTGAA-AAGA-GAAAGAA
6795 TTCTTTTGAAAAGAGAAAGAA
1 ----TTTGAAAAGAGAAAGAA
6816 TTTGAA
1 TTTGAA
6822 TTTAAAACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
17 12 0.33
18 2 0.06
19 7 0.19
21 7 0.19
22 2 0.06
23 6 0.17
ACGTcount: A:0.49, C:0.03, G:0.19, T:0.29
Consensus pattern (17 bp):
TTTGAAAAGAGAAAGAA
Found at i:6799 original size:40 final size:40
Alignment explanation
Indices: 6744--6823 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
6734 TCTCCATAAA
6744 ATACGAAAGAATTCTTTTGAAAAGAGAAAGAATTTGAATT
1 ATACGAAAGAATTCTTTTGAAAAGAGAAAGAATTTGAATT
6784 ATACGAAAGAATTCTTTTGAAAAGAGAAAGAATTTGAATT
1 ATACGAAAGAATTCTTTTGAAAAGAGAAAGAATTTGAATT
6824 TAAAACATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.30
Consensus pattern (40 bp):
ATACGAAAGAATTCTTTTGAAAAGAGAAAGAATTTGAATT
Found at i:7910 original size:42 final size:42
Alignment explanation
Indices: 7863--7947 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
7853 AAGTTGGATC
* *
7863 CACTTATTGTTTCATATAATTATTTTTAAAATTATTATTTAT
1 CACTTATCGTTTCATATAATTATTTTTAAAATTAATATTTAT
7905 CACTTATCGTTTCATATAATTATTTTTAAAATTAATATTTAT
1 CACTTATCGTTTCATATAATTATTTTTAAAATTAATATTTAT
7947 C
1 C
7948 GCATTTGGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.54
Consensus pattern (42 bp):
CACTTATCGTTTCATATAATTATTTTTAAAATTAATATTTAT
Found at i:20210 original size:251 final size:250
Alignment explanation
Indices: 19764--20306 Score: 867
Period size: 251 Copynumber: 2.2 Consensus size: 250
19754 ATATATATAT
* * *
19764 ATATCAATCCCAAAACTTAATTCTTTATAGAGGAATACAAAATCTAGCATCATTTACTAAACCTT
1 ATATCAATCCCAAAACTTAATTCCTTATAGAGGATTACAAAATCTAACATCATTTACTAAACCTT
*
19829 CAGGAACCAATTAAATCCAGAGGTTCACCCAAGAACAATGCACAAGTAATTTTCCTAAAGTTTAC
66 CAGGAACCAATTAAAGCCAGAGGTTCACCCAAGAACAATGCACAAGTAATTTTCCTAAAGTTTAC
* * * *
19894 GAGAACCTGGTTCACAAAAGGAAACAAAGCCTGCTTTTTTACATCAGGTTTAAAAACCTAAAATC
131 GAGAACCTAGTTCACAAAAGGAAACAAAGCATGCTATTTTACATCAGGTTTAAAAACCCAAAATC
* *
19959 TCATCCAAAAAGAGGATCAAACAACATCAAAACGCCTCAAGAAACAATTGAACTC
196 TCAGCCAAAAAGAGGATCAAACAACATCAAAACACCTCAAGAAACAATTGAACTC
*
20014 ATACATCAATCCCAAAACTTAATTCCTTATAGAGGATTACAAAAT-TAACATCATTTACTGAACC
1 AT--ATCAATCCCAAAACTTAATTCCTTATAGAGGATTACAAAATCTAACATCATTTACTAAACC
* *
20078 TTCAGGCACCAA-TAAAGCCAGAGGTTCACCCCAAGAACAATGCACAAGTAATTTTCCTGAAGTT
64 TTCAGGAACCAATTAAAGCCAGAGGTTCA-CCCAAGAACAATGCACAAGTAATTTTCCTAAAGTT
* * * *
20142 TATGAGAACCTAGTTCACAAAAGGCAACAAAGCATGCTATTTTACATCATGTTTATAAACCCAAA
128 TACGAGAACCTAGTTCACAAAAGGAAACAAAGCATGCTATTTTACATCAGGTTTAAAAACCCAAA
* *
20207 ATCTCAGCCAAAAAGAGGATCAAACAACATCAGAACACCTCAATAAACAATTGAACTC
193 ATCTCAGCCAAAAAGAGGATCAAACAACATCAAAACACCTCAAGAAACAATTGAACTC
20265 ATATCAA-CCCAAAACTTAATTCCTTATAGAGGATTACAAAAT
1 ATATCAATCCCAAAACTTAATTCCTTATAGAGGATTACAAAAT
20307 GTAGCAAGCA
Statistics
Matches: 271, Mismatches: 19, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
248 35 0.13
249 5 0.02
250 17 0.06
251 175 0.65
252 39 0.14
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.24
Consensus pattern (250 bp):
ATATCAATCCCAAAACTTAATTCCTTATAGAGGATTACAAAATCTAACATCATTTACTAAACCTT
CAGGAACCAATTAAAGCCAGAGGTTCACCCAAGAACAATGCACAAGTAATTTTCCTAAAGTTTAC
GAGAACCTAGTTCACAAAAGGAAACAAAGCATGCTATTTTACATCAGGTTTAAAAACCCAAAATC
TCAGCCAAAAAGAGGATCAAACAACATCAAAACACCTCAAGAAACAATTGAACTC
Found at i:27670 original size:24 final size:24
Alignment explanation
Indices: 27626--27672 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
27616 ATAAAGAACC
*
27626 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
27650 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
27673 CAACCAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:30994 original size:19 final size:20
Alignment explanation
Indices: 30972--31015 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
30962 GAGAAAAGGT
30972 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
30991 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
31011 AAAAG
1 AAAAG
31016 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:37206 original size:17 final size:16
Alignment explanation
Indices: 37184--37217 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
37174 TAAAAACAGT
37184 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
37201 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
37217 A
1 A
37218 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:37736 original size:24 final size:24
Alignment explanation
Indices: 37692--37738 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
37682 ATAAAGAACC
*
37692 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
37716 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
37739 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:39408 original size:21 final size:21
Alignment explanation
Indices: 39384--39423 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39374 GGTAAAAATT
39384 TATCAAAAACATTATTATTTC
1 TATCAAAAACATTATTATTTC
** *
39405 TATCCGAAATATTATTATT
1 TATCAAAAACATTATTATT
39424 GGGTGCTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (21 bp):
TATCAAAAACATTATTATTTC
Found at i:39553 original size:22 final size:23
Alignment explanation
Indices: 39525--39567 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
39515 CTATAAATAT
*
39525 TAAAAAA-TATTAATATTTTAAG
1 TAAAAAATTAATAATATTTTAAG
39547 TAAAAAATTAATAATATTTTA
1 TAAAAAATTAATAATATTTTA
39568 GACAACTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAAAAATTAATAATATTTTAAG
Found at i:42343 original size:13 final size:14
Alignment explanation
Indices: 42316--42374 Score: 54
Period size: 13 Copynumber: 4.4 Consensus size: 14
42306 GTGCTATTAA
*
42316 ATTAAAATT-TATT
1 ATTAATATTATATT
42329 A-TAATATTATATT
1 ATTAATATTATATT
* *
42342 ATTAA-ATTAAATAA
1 ATTAATATTATAT-T
42356 ATTAATATTATATT
1 ATTAATATTATATT
42370 -TTAAT
1 ATTAAT
42375 TATTTTGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
12 6 0.16
13 17 0.46
14 8 0.22
15 6 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTAATATTATATT
Found at i:43629 original size:31 final size:31
Alignment explanation
Indices: 43606--43664 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
43596 TACTAAATTA
43606 AAACAAAAACT-AAAGTTTAGGTACTAAAAC
1 AAACAAAAACTGAAAGTTTAGGTACTAAAAC
* * *
43636 AAACCAAAACTGATAGTTTAAGTACTAAA
1 AAACAAAAACTGAAAGTTTAGGTACTAAA
43665 CGTGTAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.54, C:0.14, G:0.10, T:0.22
Consensus pattern (31 bp):
AAACAAAAACTGAAAGTTTAGGTACTAAAAC
Found at i:51843 original size:20 final size:20
Alignment explanation
Indices: 51818--51872 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
51808 TTCACTTTTT
51818 TAAAAATCAATAAAA-TACAA
1 TAAAAATCAATAAAAGT-CAA
*
51838 TAAAAAT-AATTAAAAGTGAA
1 TAAAAATCAA-TAAAAGTCAA
*
51858 TAAAATTCAATAAAA
1 TAAAAATCAATAAAA
51873 AATTTAAAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 2 0.07
20 25 0.83
21 3 0.10
ACGTcount: A:0.67, C:0.05, G:0.04, T:0.24
Consensus pattern (20 bp):
TAAAAATCAATAAAAGTCAA
Found at i:51851 original size:30 final size:30
Alignment explanation
Indices: 51817--51873 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
51807 ATTCACTTTT
51817 TTAAAAATCAATAAAATACAATAAAAATAA
1 TTAAAAATCAATAAAATACAATAAAAATAA
* * *
51847 TTAAAAGTGAATAAAATTCAATAAAAA
1 TTAAAAATCAATAAAATACAATAAAAA
51874 ATTTAAAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.67, C:0.05, G:0.04, T:0.25
Consensus pattern (30 bp):
TTAAAAATCAATAAAATACAATAAAAATAA
Found at i:52463 original size:333 final size:326
Alignment explanation
Indices: 51958--52618 Score: 1019
Period size: 333 Copynumber: 2.0 Consensus size: 326
51948 ATATTAAATT
* *
51958 ATAATTTTATTAAAAATGAATAAACAATATTAACTGTTGTTAAAAATAATAATTAATGAATAATA
1 ATAATTTTATTAAAAATGAATAAACAATATTAAATATTGTTAAAAATAATAATTAATGAATAATA
* * *
52023 ATTCATTTAATCTCTCAATTGTAATTAAAAGATTATTTTAATATTTTTTAAACAATTAATTTTAA
66 ATTCATTTAATCCCTCAATTGTAATTAAAAGATTATTTTAATATTTTTTAAACAATTAAATTAAA
*
52088 AAGTCAATAAATGTTTTAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTATTATC
131 AAGCCAATAAATGTTTTAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATA-T-TTATC
*
52153 ATCATCATCATCATTTTGTAAAAGAAATA-TAGTTATAAAACTTTTATAAAATTATTCATATTTT
194 ATCATCATCATCATTTTATAAAAGAAATATTAGTTATAAAACTTTTATAAAATTATTCATATTTT
* *
52217 AAGATACTTA-CCTCAAGGTTTTCCTATACTAGATTATACATATTGTGTAATTTCATGCAAAAAT
259 AAAATACTTATCCTCAAAGTTTTCCTATACTAGATTATACATA-TGTGTAATTTCATGCAAAAAT
52281 CAAA
323 CAAA
52285 ATAATTTTATT-AAAATGAATAAA-AATTATTAAATATTGTTAAAAATAATAATTAATGAATAAT
1 ATAATTTTATTAAAAATGAATAAACAA-TATTAAATATTGTTAAAAATAATAATTAATGAATAAT
* *
52348 AATTCATTTTATCCCTCAA-TGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAAT
65 AATTCATTTAATCCCTCAATTGTAATTAAAAGATTATTTT-A-A-----TAT-TTTTTAAACAAT
52412 TAAATTAAAAAGCCAATAAAT-TTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAA
122 TAAATTAAAAAGCCAATAAATGTTTT-AAAAATATATGAAATTTATAATTTTTTAAATTATAAAA
*
52476 TATTTATCATCATCATCATTATTTTATAAAAGAAATATTAGTTATAAAACTTTTATAAAATTATT
186 TATTTATCATCATCATCATCATTTTATAAAAGAAATATTAGTTATAAAACTTTTATAAAATTATT
* ** *
52541 TATATTTTAAAATACTTATCCTCAAAGTTTTTTTATACTAGATTATACGTATGTGTAATTTCATG
251 CATATTTTAAAATACTTATCCTCAAAGTTTTCCTATACTAGATTATACATATGTGTAATTTCATG
52606 CAAAAATCAAA
316 CAAAAATCAAA
52617 AT
1 AT
52619 TTGTCTTATA
Statistics
Matches: 306, Mismatches: 16, Indels: 19
0.90 0.05 0.06
Matches are distributed among these distances:
325 21 0.07
326 65 0.21
327 12 0.04
331 32 0.10
332 78 0.25
333 98 0.32
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (326 bp):
ATAATTTTATTAAAAATGAATAAACAATATTAAATATTGTTAAAAATAATAATTAATGAATAATA
ATTCATTTAATCCCTCAATTGTAATTAAAAGATTATTTTAATATTTTTTAAACAATTAAATTAAA
AAGCCAATAAATGTTTTAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATCAT
CATCATCATCATTTTATAAAAGAAATATTAGTTATAAAACTTTTATAAAATTATTCATATTTTAA
AATACTTATCCTCAAAGTTTTCCTATACTAGATTATACATATGTGTAATTTCATGCAAAAATCAA
A
Found at i:54720 original size:21 final size:21
Alignment explanation
Indices: 54655--54721 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
54645 AATGAAATTA
*
54655 TTTTATAATTTT--TATTATT
1 TTTTATCATTTTAATATTATT
*
54674 TATTTATGGCAATTTAATA-TA-T
1 T-TTTAT--CATTTTAATATTATT
54696 TTTTATCATTTTAATATTATT
1 TTTTATCATTTTAATATTATT
54717 TTTTA
1 TTTTA
54722 ATTAGTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
19 10 0.26
20 7 0.18
21 11 0.29
22 6 0.16
23 2 0.05
24 2 0.05
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (21 bp):
TTTTATCATTTTAATATTATT
Found at i:56702 original size:13 final size:13
Alignment explanation
Indices: 56684--56710 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
56674 AAGATTGACG
56684 ACTGCTAAGACAT
1 ACTGCTAAGACAT
56697 ACTGCTAAGACAT
1 ACTGCTAAGACAT
56710 A
1 A
56711 GTTGCTGTTT
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:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (13 bp):
ACTGCTAAGACAT
Found at i:57751 original size:14 final size:14
Alignment explanation
Indices: 57722--57777 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
57712 CGTTCGTGAA
57722 CGTTCGATTATATGTT
1 CGTTC-ATT-TATGTT
57738 CGTTCATTTA---T
1 CGTTCATTTATGTT
*
57749 -GTTCATTTATGTC
1 CGTTCATTTATGTT
57762 CGTTCATTTATGTT
1 CGTTCATTTATGTT
57776 CG
1 CG
57778 AACAGAGGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
14 16 0.47
15 3 0.09
16 5 0.15
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:57765 original size:24 final size:26
Alignment explanation
Indices: 57723--57778 Score: 89
Period size: 24 Copynumber: 2.2 Consensus size: 26
57713 GTTCGTGAAC
*
57723 GTTCGATTATATGTTCGTTCATTTAT
1 GTTCGATTATATGTCCGTTCATTTAT
57749 GTTC-ATT-TATGTCCGTTCATTTAT
1 GTTCGATTATATGTCCGTTCATTTAT
57773 GTTCGA
1 GTTCGA
57779 ACAGAGGGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 20 0.71
25 4 0.14
26 4 0.14
ACGTcount: A:0.18, C:0.14, G:0.16, T:0.52
Consensus pattern (26 bp):
GTTCGATTATATGTCCGTTCATTTAT
Found at i:60336 original size:41 final size:40
Alignment explanation
Indices: 60287--60479 Score: 210
Period size: 41 Copynumber: 4.8 Consensus size: 40
60277 TATTCTGACT
* * *
60287 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGT-AAATCGCAACGCGAATACGTAA
* * * * * * *
60328 TTCACAACGAC-AATACGTAAAATCGTAACGCGTATCCGTAA
1 ATCGCAACG-CGTATCCGT-AAATCGCAACGCGAATACGTAA
* *
60369 ATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGCGAATACGTAA
*
60409 ATCGCAATGCGTATCCGTAAATCGCAACGAC-AATACGTAAA
1 ATCGCAACGCGTATCCGTAAATCGCAACG-CGAATACGT-AA
60450 ATCGCAACGCGTATCCGTAAATCGCAACGC
1 ATCGCAACGCGTATCCGTAAATCGCAACGC
60480 AATTTTTAAA
Statistics
Matches: 129, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
40 54 0.42
41 75 0.58
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (40 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGCGAATACGTAA
Found at i:60372 original size:20 final size:20
Alignment explanation
Indices: 60287--60479 Score: 210
Period size: 20 Copynumber: 9.5 Consensus size: 20
60277 TATTCTGACT
*
60287 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
60308 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
60328 TTCACAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
*
60349 ATCGTAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
*
60369 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
60389 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
60409 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
60429 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
60450 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
60470 ATCGCAACGC
1 ATCGCAACGC
60480 AATTTTTAAA
Statistics
Matches: 141, Mismatches: 25, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
20 93 0.66
21 48 0.34
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:60437 original size:101 final size:102
Alignment explanation
Indices: 60265--60479 Score: 328
Period size: 101 Copynumber: 2.1 Consensus size: 102
60255 GCGAATATGA
* * * *
60265 AAATCGCAACGCTATTCTGACTATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAATT
1 AAATCGCAACGCTATTCTGACAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAAT
*
60330 CACAACGACAATACGTAAAATCGTAACGCGTATCCGT
66 CACAACGACAATACGTAAAATCGCAACGCGTATCCGT
*
60367 AAATCGCAACGCGTA-TCTGTA-AATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 AAATCGCAACGC-TATTCTG-ACAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
60429 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGT
64 ATCACAACGACAATACGTAAAATCGCAACGCGTATCCGT
60468 AAATCGCAACGC
1 AAATCGCAACGC
60480 AATTTTTAAA
Statistics
Matches: 104, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
101 69 0.66
102 32 0.31
103 3 0.03
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (102 bp):
AAATCGCAACGCTATTCTGACAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAAT
CACAACGACAATACGTAAAATCGCAACGCGTATCCGT
Found at i:60560 original size:20 final size:20
Alignment explanation
Indices: 60537--60579 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
60527 TTCCAAACAT
60537 GATTTACATATTCGCATTGC
1 GATTTACATATTCGCATTGC
60557 GATTTACATATTCGCATTGC
1 GATTTACATATTCGCATTGC
60577 GAT
1 GAT
60580 AGTCCAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.40
Consensus pattern (20 bp):
GATTTACATATTCGCATTGC
Found at i:60597 original size:21 final size:21
Alignment explanation
Indices: 60567--60641 Score: 123
Period size: 21 Copynumber: 3.6 Consensus size: 21
60557 GATTTACATA
60567 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
60588 TTCACATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
60609 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
60630 TTCGCGTTGCGA
1 TTCGCATTGCGA
60642 ATCTGGAAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:61141 original size:23 final size:23
Alignment explanation
Indices: 61110--61182 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
61100 ATAGATAAAA
*
61110 ATATGATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGTTT
*
61133 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGTTT
61156 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGTTT
61179 ATAT
1 ATAT
61183 TGTAAAGTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGTTT
Found at i:74113 original size:22 final size:22
Alignment explanation
Indices: 74087--74129 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
74077 CGAAAAACCG
*
74087 AACCGAACCGAACCGTTAAAAA
1 AACCGAACCGAACCGATAAAAA
74109 AACCGAACCGAACCGATAAAA
1 AACCGAACCGAACCGATAAAA
74130 CCGGTTTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.28, G:0.14, T:0.07
Consensus pattern (22 bp):
AACCGAACCGAACCGATAAAAA
Found at i:79138 original size:19 final size:19
Alignment explanation
Indices: 79114--79173 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
79104 TACGGAATGT
79114 AAGATTATCAGTGGGAATA
1 AAGATTATCAGTGGGAATA
*
79133 AAGATTATCAGTAGGAATAA
1 AAGATTATCAGTGGGAAT-A
* *
79153 AAGATTACCAGTGGAAATA
1 AAGATTATCAGTGGGAATA
79172 AA
1 AA
79174 AAACCAGGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.23
Consensus pattern (19 bp):
AAGATTATCAGTGGGAATA
Found at i:87547 original size:51 final size:52
Alignment explanation
Indices: 87438--87554 Score: 166
Period size: 51 Copynumber: 2.2 Consensus size: 52
87428 AGGATTTGAT
* *
87438 TTATTATTTTATTAGGAATTAAGATAGAGTAAAAAAATATTATTTTTAGTTTA
1 TTATTATTTTATTAGAAATTAAGATA-AGTAAAAAAATATTATATTTAGTTTA
* *
87491 TTATTATTTTATTAGAAATTAGGAT-A-TAATCAAAATATTATATTTAGTTTA
1 TTATTATTTTATTAGAAATTAAGATAAGTAA-AAAAATATTATATTTAGTTTA
87542 TTATTATTTTATT
1 TTATTATTTTATT
87555 CAGCAGCTAC
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
50 3 0.05
51 33 0.56
53 23 0.39
ACGTcount: A:0.39, C:0.01, G:0.09, T:0.51
Consensus pattern (52 bp):
TTATTATTTTATTAGAAATTAAGATAAGTAAAAAAATATTATATTTAGTTTA
Found at i:88717 original size:37 final size:37
Alignment explanation
Indices: 88637--88717 Score: 85
Period size: 37 Copynumber: 2.2 Consensus size: 37
88627 AACAAGTTGG
* *
88637 AAAATATTTATATATTTTCCTTAAAAAATTTAAATTC
1 AAAAAATTTATATATTTTCCTTAAAAAATTAAAATTC
* * *
88674 ATAAAATTTATATATTTT-TTTATAAAATTGAAAATAT-
1 AAAAAATTTATATATTTTCCTTAAAAAATT-AAAAT-TC
88711 AAAAAAT
1 AAAAAAT
88718 GTTTAATGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
36 9 0.25
37 26 0.72
38 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (37 bp):
AAAAAATTTATATATTTTCCTTAAAAAATTAAAATTC
Found at i:89383 original size:15 final size:14
Alignment explanation
Indices: 89343--89374 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
89333 TCAATTATGT
89343 CATGATTTTTGTAA
1 CATGATTTTTGTAA
*
89357 CATGATTTTTGTAT
1 CATGATTTTTGTAA
89371 CATG
1 CATG
89375 TTATTTTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.50
Consensus pattern (14 bp):
CATGATTTTTGTAA
Found at i:91787 original size:32 final size:32
Alignment explanation
Indices: 91751--91818 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
91741 TTGCTTGGTG
* *
91751 TTGTATTGAGCTAACTAATTAGAATTCTACCT
1 TTGTATTGAGCTAAATAATTAGAATTCTACCA
91783 TTGTATTGAGCTAAATAATTAGAATTCTACCA
1 TTGTATTGAGCTAAATAATTAGAATTCTACCA
91815 TTGT
1 TTGT
91819 GTCTATACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (32 bp):
TTGTATTGAGCTAAATAATTAGAATTCTACCA
Found at i:99675 original size:26 final size:26
Alignment explanation
Indices: 99625--99695 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
99615 AAATTAATTT
* *
99625 TGAACATAAAAT-ATATATTTTTAAA
1 TGAAAATAAAATAAAATATTTTTAAA
99650 TGAAAATAAAATAAAATATTTTTAAA
1 TGAAAATAAAATAAAATATTTTTAAA
* **
99676 TTAAGTTAATAATAAAATAT
1 TGAAAATAA-AATAAAATAT
99696 ATTTGATAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 11 0.28
26 18 0.46
27 10 0.26
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (26 bp):
TGAAAATAAAATAAAATATTTTTAAA
Found at i:99714 original size:27 final size:25
Alignment explanation
Indices: 99654--99742 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 25
99644 TTTAAATGAA
* *
99654 AATAAAATAAAATATTTT-TAAATT
1 AATATAATAAAATATTTTATAAGTT
99678 AAGTTAATAATAAAATATATTTGATAAGTT
1 AA--T-ATAATAAAATAT-TTT-ATAAGTT
99708 AATATAA-AAAATATTGTT-TAAGTT
1 AATATAATAAAATATT-TTATAAGTT
99732 AATAT-ATAAAA
1 AATATAATAAAA
99743 AAATGTTATG
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
23 1 0.02
24 17 0.31
25 1 0.02
26 10 0.18
27 15 0.27
28 4 0.07
30 7 0.13
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (25 bp):
AATATAATAAAATATTTTATAAGTT
Found at i:99749 original size:24 final size:24
Alignment explanation
Indices: 99676--99749 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 24
99666 TATTTTTAAA
*
99676 TTAAGTTAATA-ATAAAATATAT-T
1 TTAAGTTAATATATAAAA-AAATGT
*
99699 TGATAAGTTAATATA-AAAAATATTGT
1 T--TAAGTTAATATATAAAAA-AATGT
99725 TTAAGTTAATATATAAAAAAATGT
1 TTAAGTTAATATATAAAAAAATGT
99749 T
1 T
99750 ATGAATTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
23 1 0.02
24 18 0.43
25 20 0.48
26 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (24 bp):
TTAAGTTAATATATAAAAAAATGT
Found at i:99759 original size:26 final size:26
Alignment explanation
Indices: 99676--99744 Score: 83
Period size: 24 Copynumber: 2.8 Consensus size: 26
99666 TATTTTTAAA
*
99676 TTAAGTTAATA-ATAAAATATATT-T
1 TTAAGTTAATATATAAAAAATATTGT
*
99700 GATAAGTT-A-ATATAAAAAATATTGT
1 -TTAAGTTAATATATAAAAAATATTGT
99725 TTAAGTTAATATATAAAAAA
1 TTAAGTTAATATATAAAAAA
99745 ATGTTATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
23 1 0.03
24 18 0.49
25 8 0.22
26 10 0.27
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (26 bp):
TTAAGTTAATATATAAAAAATATTGT
Found at i:100476 original size:17 final size:18
Alignment explanation
Indices: 100442--100476 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
100432 TTTTACAAAA
*
100442 TCATTAAAATCTAAACTT
1 TCATTAAAATCAAAACTT
100460 TCATTAAAAT-AAAACTT
1 TCATTAAAATCAAAACTT
100477 AGTTTAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (18 bp):
TCATTAAAATCAAAACTT
Found at i:100982 original size:35 final size:35
Alignment explanation
Indices: 100931--100997 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
100921 ATAGAATTTG
*
100931 TCCTGAAGGACCACATATATATCCCGAAGGACTAC
1 TCCTGAAGGACCACATATATATCCCAAAGGACTAC
* * * *
100966 TCCTTAAGGATCACATATTTATTCCAAAGGAC
1 TCCTGAAGGACCACATATATATCCCAAAGGAC
100998 CAAATATGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (35 bp):
TCCTGAAGGACCACATATATATCCCAAAGGACTAC
Found at i:101065 original size:21 final size:21
Alignment explanation
Indices: 100977--101066 Score: 54
Period size: 21 Copynumber: 4.3 Consensus size: 21
100967 CCTTAAGGAT
* * *
100977 CACATATTTATTCCAAAGGAC
1 CACATATATATCCCAAAGAAC
* * * **
100998 CAAATATGTGTCCTGAAGAAC
1 CACATATATATCCCAAAGAAC
* * * *
101019 CACATATATGTTCCAAAGGAT
1 CACATATATATCCCAAAGAAC
* *
101040 TACATATATATCCCTAAGAAC
1 CACATATATATCCCAAAGAAC
101061 CACATA
1 CACATA
101067 GAACCCTCGA
Statistics
Matches: 48, Mismatches: 21, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (21 bp):
CACATATATATCCCAAAGAAC
Found at i:102434 original size:2 final size:2
Alignment explanation
Indices: 102427--102454 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
102417 ATTTAAACTA
102427 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
102455 TAAAATTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:103063 original size:21 final size:20
Alignment explanation
Indices: 103037--103078 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
103027 AGATTATATT
103037 AATAATTTATTT-TTATGTAAA
1 AATAA-TTATTTATTAT-TAAA
103058 AATAATTATTTATTATTAAA
1 AATAATTATTTATTATTAAA
103078 A
1 A
103079 TTATATTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
AATAATTATTTATTATTAAA
Found at i:106551 original size:18 final size:18
Alignment explanation
Indices: 106528--106573 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
106518 GAAACTTAAG
106528 GAAGCTTAAAGACAATTA
1 GAAGCTTAAAGACAATTA
*
106546 GAAGCTTAAAGATAATTA
1 GAAGCTTAAAGACAATTA
106564 GAAGC-TAAAG
1 GAAGCTTAAAG
106574 GATTGAGGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.50, C:0.09, G:0.20, T:0.22
Consensus pattern (18 bp):
GAAGCTTAAAGACAATTA
Found at i:107696 original size:31 final size:31
Alignment explanation
Indices: 107658--107718 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
107648 CCCGAAGTAC
* *
107658 CAGTCCATATGTTCAGAAGAATATAGGTAAT
1 CAGTCCATATGTCCAGAAGAACATAGGTAAT
*
107689 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCAGAAGAACATAGGTAA
107719 CCCTCGACTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (31 bp):
CAGTCCATATGTCCAGAAGAACATAGGTAAT
Found at i:109894 original size:22 final size:20
Alignment explanation
Indices: 109866--109921 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 20
109856 ATAATAGTAC
109866 CGATACCCTGCTACAGGGGTA
1 CGATACCCTGCTACA-GGGTA
*
109887 TCGATACCCTGCTACAGTGTA
1 -CGATACCCTGCTACAGGGTA
109908 CTGATACCCTGCTA
1 C-GATACCCTGCTA
109922 TAGTAATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 1 0.03
21 16 0.50
22 15 0.47
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.25
Consensus pattern (20 bp):
CGATACCCTGCTACAGGGTA
Found at i:109915 original size:21 final size:22
Alignment explanation
Indices: 109862--109921 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
109852 TTTAATAATA
*
109862 GTACCGATACCCTGCTACAGGG
1 GTACTGATACCCTGCTACAGGG
*
109884 GTA-TCGATACCCTGCTACA-GT
1 GTACT-GATACCCTGCTACAGGG
109905 GTACTGATACCCTGCTA
1 GTACTGATACCCTGCTA
109922 TAGTAATTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 16 0.47
22 18 0.53
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (22 bp):
GTACTGATACCCTGCTACAGGG
Found at i:110478 original size:31 final size:30
Alignment explanation
Indices: 110440--110523 Score: 132
Period size: 31 Copynumber: 2.7 Consensus size: 30
110430 CCCGAAGGAC
110440 CAGTCCATATGTTCCGAAGAATATAGGTAAT
1 CAGTCCATATG-TCCGAAGAATATAGGTAAT
*
110471 CAGTCCATATGTCCTGAAGAACATAGGTAAT
1 CAGTCCATATGTCC-GAAGAATATAGGTAAT
*
110502 CAGTCTATATGTCCGAAGAATA
1 CAGTCCATATGTCCGAAGAATA
110524 AGTAACCCTC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
30 10 0.20
31 39 0.80
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (30 bp):
CAGTCCATATGTCCGAAGAATATAGGTAAT
Done.