Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004339.1 Hibiscus syriacus cultivar Beakdansim tig00009509_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: 82359
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:4808 original size:13 final size:13
Alignment explanation
Indices: 4790--4873 Score: 72
Period size: 13 Copynumber: 6.8 Consensus size: 13
4780 ACTGTAAAAA
*
4790 AAATAAAATAATT
1 AAATAAAATAACT
4803 AAATAAAAT-ACT
1 AAATAAAATAACT
4815 AAA-AAAATTAACT
1 AAATAAAA-TAACT
* *
4828 -AATTAAATAATT
1 AAATAAAATAACT
4840 AAATAAAAT-ACT
1 AAATAAAATAACT
*
4852 -AATAAAAT-ATT
1 AAATAAAATAACT
*
4863 AAATAGAATAA
1 AAATAAAATAA
4874 AATACCTTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
11 14 0.24
12 21 0.36
13 23 0.40
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.29
Consensus pattern (13 bp):
AAATAAAATAACT
Found at i:4846 original size:29 final size:29
Alignment explanation
Indices: 4786--4873 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
4776 TATAACTGTA
*
4786 AAAAAAATAAAATAATTAAATAAAATACT
1 AAAAAAATAAAATAATTAAATAAAATAAT
* * *
4815 AAAAAAATTAACTAATTAAAT-AATTAAAT
1 AAAAAAATAAAATAATTAAATAAAAT-AAT
*
4844 AAAATACTAATAAAAT-ATTAAATAGAATAA
1 AAAA-A--AATAAAATAATTAAATAAAATAA
4874 AATACCTTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
28 3 0.07
29 25 0.54
30 1 0.02
31 9 0.20
32 8 0.17
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.27
Consensus pattern (29 bp):
AAAAAAATAAAATAATTAAATAAAATAAT
Found at i:8076 original size:36 final size:36
Alignment explanation
Indices: 8025--8103 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
8015 CGTATTCATT
8025 GAAACATTATCGGCATTTAATAGATTATATTTTGGA
1 GAAACATTATCGGCATTTAATAGATTATATTTTGGA
*
8061 GAAACATTATTGGCATTTAATAGATTATATTTTGGA
1 GAAACATTATCGGCATTTAATAGATTATATTTTGGA
8097 GAAACAT
1 GAAACAT
8104 CGCAATGATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (36 bp):
GAAACATTATCGGCATTTAATAGATTATATTTTGGA
Found at i:11639 original size:22 final size:22
Alignment explanation
Indices: 11613--11656 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
11603 TCTCTCTCTA
* *
11613 TTTCTCTGGTTTTTTTAGATTT
1 TTTCTCTAGTTTTATTAGATTT
*
11635 TTTCTCTAGTTTTATTATATTT
1 TTTCTCTAGTTTTATTAGATTT
11657 CAAAATCACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.68
Consensus pattern (22 bp):
TTTCTCTAGTTTTATTAGATTT
Found at i:15102 original size:21 final size:20
Alignment explanation
Indices: 15056--15112 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
15046 TTTTCTGGCT
*
15056 CAAAGGATCGATCCGTTAGA
1 CAAAGGATCGATCCCTTAGA
*
15076 -AAAGGATCGATCCCTTTGA
1 CAAAGGATCGATCCCTTAGA
15095 CCAAAGGATCGATCCCTT
1 -CAAAGGATCGATCCCTT
15113 GGATAATAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (20 bp):
CAAAGGATCGATCCCTTAGA
Found at i:17489 original size:20 final size:18
Alignment explanation
Indices: 17454--17494 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
17444 GAAAAAATAT
17454 AAATAAAAAAAGGTCAAA
1 AAATAAAAAAAGGTCAAA
*
17472 AAATAGAAAAACATGTCAAA
1 AAATA-AAAAA-AGGTCAAA
17492 AAA
1 AAA
17495 CATAAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 5 0.25
20 10 0.50
ACGTcount: A:0.71, C:0.07, G:0.10, T:0.12
Consensus pattern (18 bp):
AAATAAAAAAAGGTCAAA
Found at i:17504 original size:22 final size:23
Alignment explanation
Indices: 17479--17528 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
17469 AAAAAATAGA
*
17479 AAAACATGTCA-AAAAACATAAG
1 AAAACATGACATAAAAACATAAG
* * *
17501 AAAACGTGACATAAAGACATATG
1 AAAACATGACATAAAAACATAAG
17524 AAAAC
1 AAAAC
17529 TTGCAACACA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.60, C:0.14, G:0.12, T:0.14
Consensus pattern (23 bp):
AAAACATGACATAAAAACATAAG
Found at i:18267 original size:16 final size:16
Alignment explanation
Indices: 18246--18302 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
18236 CAAAAGTCTC
18246 TGAATCATTCAACATT
1 TGAATCATTCAACATT
* *
18262 TGAATCATTTAGCATT
1 TGAATCATTCAACATT
*
18278 TGAATCATTCAACACT
1 TGAATCATTCAACATT
18294 T-AATCATTC
1 TGAATCATTC
18303 TAAAGTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 8 0.22
16 28 0.78
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (16 bp):
TGAATCATTCAACATT
Found at i:19579 original size:20 final size:19
Alignment explanation
Indices: 19534--19588 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
19524 TTGATAATAT
* *
19534 GAGTTTATTTATTTTTATC
1 GAGTTTATTCATTTTTAAC
* *
19553 AATTTTATCTCATTTTTAAC
1 GAGTTTAT-TCATTTTTAAC
19573 GAGTTTAATTCATTTT
1 GAGTTT-ATTCATTTT
19589 ACTACAAAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 6 0.21
20 20 0.71
21 2 0.07
ACGTcount: A:0.25, C:0.09, G:0.07, T:0.58
Consensus pattern (19 bp):
GAGTTTATTCATTTTTAAC
Found at i:19608 original size:3 final size:3
Alignment explanation
Indices: 19600--19666 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
19590 CTACAAAAGA
19600 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19648 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
19667 CAGTCCACGC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:31141 original size:23 final size:23
Alignment explanation
Indices: 31115--31180 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
31105 CACCACAGCT
31115 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
31138 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
31161 CATAGAATTGCACCGTAGTG
1 CATATAATTGCACCGAAGTG
31181 TCATATAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:31370 original size:103 final size:103
Alignment explanation
Indices: 31199--31416 Score: 393
Period size: 103 Copynumber: 2.1 Consensus size: 103
31189 TAATGTCCAT
*
31199 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
31264 GACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
*
31302 AAGGACCACATATCATTCCTTAAGAATCATATACATAT-GTCAAGGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACT-AAGGATCAAGTATGTGTCTCACC
*
31366 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
31405 AAGGACCACATA
1 AAGGACCACATA
31417 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
102 1 0.01
103 110 0.99
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
GACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
Found at i:32803 original size:22 final size:22
Alignment explanation
Indices: 32778--32834 Score: 82
Period size: 20 Copynumber: 2.7 Consensus size: 22
32768 TTTGCTTGAG
*
32778 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCCATTGAAT
*
32800 GGGTACCGATT--CCTTTGAAT
1 GGGTACCGATTCCCCATTGAAT
32820 GGGTACCGATTCCCC
1 GGGTACCGATTCCCC
32835 TTGCCCAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 19 0.61
22 12 0.39
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (22 bp):
GGGTACCGATTCCCCATTGAAT
Found at i:33754 original size:16 final size:16
Alignment explanation
Indices: 33715--33757 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
33705 ATCATCAGTT
*
33715 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
33731 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
33748 CTTATCAATC
1 CTTATCAATC
33758 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:36421 original size:23 final size:23
Alignment explanation
Indices: 36395--36472 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
36385 CACCACAGCT
36395 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
36418 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
36441 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
36464 TATAATAAT
1 CAT-ATAAT
36473 GTCCATAAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 43 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:36660 original size:104 final size:103
Alignment explanation
Indices: 36479--36697 Score: 368
Period size: 104 Copynumber: 2.1 Consensus size: 103
36469 TAATGTCCAT
* *
36479 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGCTTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGCTTCTCACCA
*
36544 GACTTTAAACATGTTCCAAAGAATACATATATGTCCCCG
66 GACTTCAAACATGTTCCAAAGAATACATATATGT-CCCG
*
36583 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATG-TGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGCT-TCTCACC
*
36647 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
36686 AAGGACCACATA
1 AAGGACCACATA
36698 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
103 17 0.16
104 92 0.84
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGCTTCTCACCA
GACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
Found at i:38096 original size:22 final size:21
Alignment explanation
Indices: 38071--38130 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
38061 TTCGCTTGAG
*
38071 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
38093 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
38113 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
38131 CCCAGAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 17 0.47
21 9 0.25
22 10 0.28
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:39058 original size:16 final size:16
Alignment explanation
Indices: 39019--39061 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
39009 AGCATCAGTT
*
39019 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
39035 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
39052 CTTATCAATC
1 CTTATCAATC
39062 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:41711 original size:23 final size:23
Alignment explanation
Indices: 41685--41750 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
41675 CACCACAGCT
41685 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
41708 CATATAATTGCACAGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
41731 CATAGAATTGCACCGTAGTG
1 CATATAATTGCACCGAAGTG
41751 TCATATAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:41940 original size:103 final size:103
Alignment explanation
Indices: 41769--41986 Score: 393
Period size: 103 Copynumber: 2.1 Consensus size: 103
41759 TAATGTCCAT
*
41769 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
41834 GACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
*
41872 AAGGACCACATATCATTCCTTAAGAATCATATACATAT-GTCAAGGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACT-AAGGATCAAGTATGTGTCTCACC
*
41936 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
41975 AAGGACCACATA
1 AAGGACCACATA
41987 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
102 1 0.01
103 110 0.99
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTCACCA
GACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
Found at i:43393 original size:22 final size:21
Alignment explanation
Indices: 43362--43420 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
43352 TTCGCTTGAG
43362 GGGTATCGATTCCCCATTAAAT
1 GGGTATCGATTCCCC-TTAAAT
* *
43384 GGGTACCGATT-CCCTTGAAT
1 GGGTATCGATTCCCCTTAAAT
*
43404 GGGTATTGATTCCCCTT
1 GGGTATCGATTCCCCTT
43421 GCCCAGAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 14 0.44
21 8 0.25
22 10 0.31
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (21 bp):
GGGTATCGATTCCCCTTAAAT
Found at i:44514 original size:55 final size:55
Alignment explanation
Indices: 44398--44585 Score: 227
Period size: 56 Copynumber: 3.4 Consensus size: 55
44388 CTATACGGAA
* * * * *
44398 ATTCATCAACTCATGATGAATTATGTGG-GTTACACACATATTG-TCTGTACGGTG
1 ATTCATCAACCCATGATGAATTCTGTGGATTTGCACACAAATTGCT-TGTACGGTG
* * * *
44452 ATTCATCAACTCATAATGAATTCTGTGGATTTGCACACAAAGTGCTTGTACGATG
1 ATTCATCAACCCATGATGAATTCTGTGGATTTGCACACAAATTGCTTGTACGGTG
* * * *
44507 ATTCATCAACCCCATGATGAATTCTGTGAATATGCACACAAATTGCATGTATGGTG
1 ATTCATCAA-CCCATGATGAATTCTGTGGATTTGCACACAAATTGCTTGTACGGTG
44563 ATTCATCAACCCATGATGAATTC
1 ATTCATCAACCCATGATGAATTC
44586 CGTTGATGAA
Statistics
Matches: 116, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
54 26 0.22
55 42 0.36
56 48 0.41
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (55 bp):
ATTCATCAACCCATGATGAATTCTGTGGATTTGCACACAAATTGCTTGTACGGTG
Found at i:44594 original size:13 final size:13
Alignment explanation
Indices: 44576--44601 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44566 CATCAACCCA
44576 TGATGAATTCCGT
1 TGATGAATTCCGT
44589 TGATGAATTCCGT
1 TGATGAATTCCGT
44602 GAATATGTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (13 bp):
TGATGAATTCCGT
Found at i:44604 original size:68 final size:68
Alignment explanation
Indices: 44521--44653 Score: 212
Period size: 68 Copynumber: 2.0 Consensus size: 68
44511 ATCAACCCCA
* * *
44521 TGATGAATTCTGTGAATATGCACACAAATTGCATGTATGGTGATTCATCAACCCATGATGAATTC
1 TGATGAATTCCGTGAATATGCACACAAAGTGCATGTACGGTGATTCATCAACCCATGATGAATTC
44586 CGT
66 CGT
* * *
44589 TGATGAATTCCGTGAATATGTACACAAAGTGCCTGTACGGTGATTTATCAACCCATGATGAATTC
1 TGATGAATTCCGTGAATATGCACACAAAGTGCATGTACGGTGATTCATCAACCCATGATGAATTC
44654 TGTGAATATG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (68 bp):
TGATGAATTCCGTGAATATGCACACAAAGTGCATGTACGGTGATTCATCAACCCATGATGAATTC
CGT
Found at i:44659 original size:55 final size:55
Alignment explanation
Indices: 44589--44735 Score: 231
Period size: 55 Copynumber: 2.7 Consensus size: 55
44579 TGAATTCCGT
*
44589 TGATGAATTCCGTGAATATGTACACAAAGTGCCTGTACGGTGATTTATCAACCCA
1 TGATGAATTCCGTGAATATGTACACAAAGTGCCTGTACGGTGATTCATCAACCCA
* * *
44644 TGATGAATTCTGTGAATATGCACACAAAGTGCATGTACGGTGATTCATCAACCCA
1 TGATGAATTCCGTGAATATGTACACAAAGTGCCTGTACGGTGATTCATCAACCCA
* * *
44699 TGATGAATTCCGTGAATATATACACAAGGTGTCTGTA
1 TGATGAATTCCGTGAATATGTACACAAAGTGCCTGTA
44736 GTACACATAG
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 82 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (55 bp):
TGATGAATTCCGTGAATATGTACACAAAGTGCCTGTACGGTGATTCATCAACCCA
Found at i:44687 original size:123 final size:124
Alignment explanation
Indices: 44467--44711 Score: 402
Period size: 123 Copynumber: 2.0 Consensus size: 124
44457 TCAACTCATA
* * * *
44467 ATGAATTCTGTGGATTTGCACACAAAGTGCTTGTACGATGATTCATCAACCCCATGATGAATTCT
1 ATGAATTCCGTGAATATGCACACAAAGTGCCTGTACGATGATTCATCAACCCCATGATGAATTCT
* *
44532 GTGAATATGCACACAAATTGCATGTATGGTGATTCATCAACCCATGATGAATTCCGTTG
66 GTGAATATGCACACAAAGTGCATGTACGGTGATTCATCAACCCATGATGAATTCCGTTG
* * *
44591 ATGAATTCCGTGAATATGTACACAAAGTGCCTGTACGGTGATTTATCAA-CCCATGATGAATTCT
1 ATGAATTCCGTGAATATGCACACAAAGTGCCTGTACGATGATTCATCAACCCCATGATGAATTCT
44655 GTGAATATGCACACAAAGTGCATGTACGGTGATTCATCAACCCATGATGAATTCCGT
66 GTGAATATGCACACAAAGTGCATGTACGGTGATTCATCAACCCATGATGAATTCCGT
44712 GAATATATAC
Statistics
Matches: 112, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
123 70 0.62
124 42 0.38
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (124 bp):
ATGAATTCCGTGAATATGCACACAAAGTGCCTGTACGATGATTCATCAACCCCATGATGAATTCT
GTGAATATGCACACAAAGTGCATGTACGGTGATTCATCAACCCATGATGAATTCCGTTG
Found at i:45199 original size:95 final size:96
Alignment explanation
Indices: 45081--45285 Score: 286
Period size: 95 Copynumber: 2.1 Consensus size: 96
45071 ATTATTTCCC
* * * ** *
45081 TGGTACCGATACTTTTATACTATGGTATTGATACCCCCATCCGATATCGATACCAAAATTAGGTT
1 TGGTATCGATACTATCATACTATGGTACCGATACCCCCATCCGATATCGATACCAAAATTAGATT
*
45146 CGATGTTGCCTAGTATTGATA-CCCTTACCA
66 CGATGTTGCCTAGTATCGATACCCCTTACCA
* *
45176 TGGTATCGATACTATCATACTATGGTACCGATACCCCCTTCCGGTATCGATACCAAAATTAGATT
1 TGGTATCGATACTATCATACTATGGTACCGATACCCCCATCCGATATCGATACCAAAATTAGATT
* * *
45241 CGATGTTGCTTGGTATCGATACCCCTTATCA
66 CGATGTTGCCTAGTATCGATACCCCTTACCA
*
45272 TGGTATGGATACTA
1 TGGTATCGATACTA
45286 CCTCATCAGT
Statistics
Matches: 96, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
95 75 0.78
96 21 0.22
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (96 bp):
TGGTATCGATACTATCATACTATGGTACCGATACCCCCATCCGATATCGATACCAAAATTAGATT
CGATGTTGCCTAGTATCGATACCCCTTACCA
Found at i:45302 original size:20 final size:19
Alignment explanation
Indices: 45274--45332 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
45264 CCTTATCATG
*
45274 GTATGGATACTACCTCATCA
1 GTATCGATACTA-CTCATCA
* *
45294 GTATCGATACTAGTTGAATCA
1 GTATCGATACTA-CT-CATCA
45315 GTATCGATACTACTCATC
1 GTATCGATACTACTCATC
45333 TAATTTATCT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 3 0.09
20 13 0.41
21 16 0.50
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (19 bp):
GTATCGATACTACTCATCA
Found at i:48222 original size:39 final size:36
Alignment explanation
Indices: 48160--48247 Score: 97
Period size: 39 Copynumber: 2.4 Consensus size: 36
48150 TCATTTCTAG
*
48160 TTTTAAAATTATTTTACCCTAACATTCTAAATCTATATT
1 TTTTAAAATTATTTCACCCTAACATT-TAAAT-TAT-TT
* * *
48199 TTTTCAAATTGTTTCACCTTAACATTTAAATTA-TT
1 TTTTAAAATTATTTCACCCTAACATTTAAATTATTT
*
48234 TTTTAGAATTATTT
1 TTTTAAAATTATTT
48248 ATTTTAATCT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
35 13 0.31
37 2 0.05
38 5 0.12
39 22 0.52
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.52
Consensus pattern (36 bp):
TTTTAAAATTATTTCACCCTAACATTTAAATTATTT
Found at i:48304 original size:13 final size:13
Alignment explanation
Indices: 48286--48319 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
48276 GTTGTAATTG
*
48286 TATTATTTTATTT
1 TATTATTTTATAT
48299 TATTATTTTATAT
1 TATTATTTTATAT
48312 T-TTATTTT
1 TATTATTTT
48320 TAGATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTATTTTATAT
Found at i:48330 original size:20 final size:20
Alignment explanation
Indices: 48289--48330 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
48279 GTAATTGTAT
* *
48289 TATTTTATTTTATTATTTTA
1 TATTTTATTTTATGATTATA
48309 TATTTTATTTT-TAGATTATA
1 TATTTTATTTTAT-GATTATA
48329 TA
1 TA
48331 ATTTGAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TATTTTATTTTATGATTATA
Found at i:48449 original size:18 final size:19
Alignment explanation
Indices: 48416--48451 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
48406 TGGATTTTTC
*
48416 TAAAAAATTAATATAAATT
1 TAAAAAATTAAAATAAATT
48435 TAAAAAA-TAAAATAAAT
1 TAAAAAATTAAAATAAAT
48452 ATTATTCGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAAAATTAAAATAAATT
Found at i:51987 original size:29 final size:29
Alignment explanation
Indices: 51954--52049 Score: 138
Period size: 29 Copynumber: 3.3 Consensus size: 29
51944 TGAATGGAAT
** *
51954 CATTCAGCACTGAATGTTGAACCGTTCAA
1 CATTCAGCGTTGAATGTTGAACCGTTCAG
*
51983 CATTCAGCGTTGAATGTTGAATCGTTCAG
1 CATTCAGCGTTGAATGTTGAACCGTTCAG
* *
52012 CATTCAACGTTGAATGTTGAACCATTCAG
1 CATTCAGCGTTGAATGTTGAACCGTTCAG
52041 CATTCAGCG
1 CATTCAGCG
52050 CGTTTGTTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (29 bp):
CATTCAGCGTTGAATGTTGAACCGTTCAG
Found at i:52452 original size:32 final size:32
Alignment explanation
Indices: 52415--52480 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
52405 AATAAAACTT
* * *
52415 AAATAAAATGTTAGAT-ATATTTTTTTAACAAA
1 AAATAAAAT-TTAAATAACATTTTGTTAACAAA
*
52447 AAATAAAGTTTAAATAACATTTTGTTAACAAA
1 AAATAAAATTTAAATAACATTTTGTTAACAAA
52479 AA
1 AA
52481 TAATAGTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 5 0.17
32 24 0.83
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (32 bp):
AAATAAAATTTAAATAACATTTTGTTAACAAA
Found at i:53892 original size:15 final size:15
Alignment explanation
Indices: 53855--53893 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
53845 TAATAGTTGC
*
53855 ATTGCATATCATATA
1 ATTGCATATCAAATA
* *
53870 GTTTCATATCAAATA
1 ATTGCATATCAAATA
53885 ATTGCATAT
1 ATTGCATAT
53894 TATATTAGAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (15 bp):
ATTGCATATCAAATA
Found at i:54668 original size:26 final size:26
Alignment explanation
Indices: 54612--54675 Score: 112
Period size: 25 Copynumber: 2.5 Consensus size: 26
54602 CGTTTTTTAG
54612 TATATACTATATAGTTCATATGTAAAC
1 TATATA-TATATAGTTCATATGTAAAC
54639 -ATATATATATAGTTCATATGTAAAC
1 TATATATATATAGTTCATATGTAAAC
54664 TATATATATATA
1 TATATATATATA
54676 TATCAACTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
25 20 0.56
26 16 0.44
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (26 bp):
TATATATATATAGTTCATATGTAAAC
Found at i:54693 original size:26 final size:26
Alignment explanation
Indices: 54664--54732 Score: 86
Period size: 26 Copynumber: 2.6 Consensus size: 26
54654 ATATGTAAAC
*
54664 TATATATATATATATCAACTATAGTA
1 TATATATATATATATAAACTATAGTA
* *
54690 TATA-ATATAAAATATAAACTATAGTT
1 TATATATAT-ATATATAAACTATAGTA
54716 TATATATATAGTATATA
1 TATATATATA-TATATA
54733 CTATATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 4 0.11
26 23 0.64
27 9 0.25
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (26 bp):
TATATATATATATATAAACTATAGTA
Found at i:54705 original size:19 final size:19
Alignment explanation
Indices: 54654--54754 Score: 71
Period size: 19 Copynumber: 5.1 Consensus size: 19
54644 TATATAGTTC
*
54654 ATATGTAAACTATATATAT
1 ATATATAAACTATATATAT
*
54673 ATATATCAACTATAGTATAT
1 ATATATAAACTATA-TATAT
*
54693 A-ATATAAAATATAAACTATAGT
1 ATATATAAACTAT--A-TATA-T
* *
54715 TTATATATA-TAGTATATACT
1 ATATATAAACTA-TATATA-T
*
54735 ATATAAAAACTATATATAT
1 ATATATAAACTATATATAT
54754 A
1 A
54755 ATTCATATGT
Statistics
Matches: 64, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
19 23 0.36
20 23 0.36
21 8 0.12
22 3 0.05
23 7 0.11
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (19 bp):
ATATATAAACTATATATAT
Found at i:54812 original size:31 final size:31
Alignment explanation
Indices: 54747--54805 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
54737 ATAAAAACTA
54747 TATATATAATTCATATGTAAACTATATAGTT
1 TATATATAATTCATATGTAAACTATATAGTT
*
54778 TATATATAGTTCATATGTAAACTATATA
1 TATATATAATTCATATGTAAACTATATA
54806 TATTATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (31 bp):
TATATATAATTCATATGTAAACTATATAGTT
Found at i:54877 original size:13 final size:13
Alignment explanation
Indices: 54859--55002 Score: 63
Period size: 12 Copynumber: 11.5 Consensus size: 13
54849 AAGTATAATT
* *
54859 TATATAGTTTTTA
1 TATATAATTTATA
54872 TATATAA-TT-TA
1 TATATAATTTATA
*
54883 TATATAATTCATA
1 TATATAATTTATA
*
54896 TATA-AA-CTATA
1 TATATAATTTATA
* * *
54907 TAGT-TTATGTAGTT
1 TA-TATAATTTA-TA
*
54921 TATAT-ATATATA
1 TATATAATTTATA
54933 TATAT-ATTTATA
1 TATATAATTTATA
* *
54945 TATATATATATAGA
1 TATATA-ATTTATA
* *
54959 TAGATAATTTTTA
1 TATATAATTTATA
*
54972 TATAT-TTTTATA
1 TATATAATTTATA
*
54984 TATA-AATATATA
1 TATATAATTTATA
54996 GTATATA
1 -TATATA
55003 TTATGAATAT
Statistics
Matches: 98, Mismatches: 21, Indels: 23
0.69 0.15 0.16
Matches are distributed among these distances:
11 14 0.14
12 38 0.39
13 31 0.32
14 15 0.15
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.51
Consensus pattern (13 bp):
TATATAATTTATA
Found at i:54880 original size:22 final size:22
Alignment explanation
Indices: 54834--54912 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
54824 TCAACTATAG
*
54834 TATATAGTTTATATAAAGTATAATT
1 TATATAGTTT-T-TATA-TATAATT
54859 TATATAGTTTTTATATATAATT
1 TATATAGTTTTTATATATAATT
* * **
54881 TATATA-TAATTCATATATAAAC
1 TATATAGT-TTTTATATATAATT
54903 TATATAGTTT
1 TATATAGTTT
54913 ATGTAGTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
21 1 0.02
22 30 0.65
23 4 0.09
24 1 0.02
25 10 0.22
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (22 bp):
TATATAGTTTTTATATATAATT
Found at i:54882 original size:11 final size:11
Alignment explanation
Indices: 54852--54948 Score: 66
Period size: 11 Copynumber: 9.4 Consensus size: 11
54842 TTATATAAAG
54852 TATAATTTATA
1 TATAATTTATA
*
54863 TAGT-TTTTATA
1 TA-TAATTTATA
54874 TATAATTTATA
1 TATAATTTATA
*
54885 TATAATTCATA
1 TATAATTTATA
54896 TATAA---ACTA
1 TATAATTTA-TA
*
54905 TAT-AGTT-TA
1 TATAATTTATA
* *
54914 TGTAGTTTATA
1 TATAATTTATA
*
54925 TAT-ATATATA
1 TATAATTTATA
54935 TAT-ATTTATA
1 TATAATTTATA
54945 TATA
1 TATA
54949 TATATATAGA
Statistics
Matches: 67, Mismatches: 10, Indels: 18
0.71 0.11 0.19
Matches are distributed among these distances:
8 2 0.03
9 9 0.13
10 20 0.30
11 35 0.52
12 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (11 bp):
TATAATTTATA
Found at i:54926 original size:2 final size:2
Alignment explanation
Indices: 54921--55362 Score: 132
Period size: 2 Copynumber: 222.0 Consensus size: 2
54911 TTATGTAGTT
* * *
54921 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA GA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
54963 TA -A TT TT TA TA TA TT TT TA TA TA TA AA TA TA TA GTA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * **
55004 TA TGA -A TA TA -A CTA CA TA TA -A T- TA CA TA AA T- TA -A CCC
1 TA T-A TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
55041 TA AA CCA TA TA TA TA TA TA TA TA TT TA -A TA AA CTA TA TA TA CTA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA
* * * * * *
55085 TA TA TA TA AA CTG CA TA TA TA AA CTA TA TA GTT TA TA TA CA TA
1 TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
* *
55128 -A TA TA TA TA CTT TA TA TA AA CTA TA -A TA -A GT- TA TA TA -A
1 TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA
* * *
55166 TT TA TA CA TA TA T- TA -A TA TA TA GTT TA TA TA TA TA -A TGA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA T-A TA
* * *
55206 CTA TA TA -A TA TA GTT TA TA TGA -A CTA TA TA -A TT TA TA TA GTT
1 -TA TA TA TA TA TA -TA TA TA T-A TA -TA TA TA TA TA TA TA TA -TA
* *
55248 TA TA TC TA T- TA -A TGA -A CTA TA TA TA TA TA -A TT TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA TA TA TA TA TA TA TA
*
55288 CTA -A TGA CTA TA TA GTT TA T- TA -A TA TA -A CTA TA TA TA TA TA
1 -TA TA T-A -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
55329 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
55363 ATTCATATAC
Statistics
Matches: 322, Mismatches: 62, Indels: 112
0.65 0.12 0.23
Matches are distributed among these distances:
1 29 0.09
2 265 0.82
3 27 0.08
4 1 0.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:55177 original size:25 final size:23
Alignment explanation
Indices: 55149--55214 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 23
55139 TTATATAAAC
55149 TATAATAAGTTATATAATTTATACA
1 TATAATAA--TATATAATTTATACA
* * *
55174 TATATTAATATATAGTTTATATA
1 TATAATAATATATAATTTATACA
55197 TATAATGAACTATATAAT
1 TATAAT-AA-TATATAAT
55215 ATAGTTTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
23 18 0.53
24 2 0.06
25 14 0.41
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (23 bp):
TATAATAATATATAATTTATACA
Found at i:55357 original size:57 final size:57
Alignment explanation
Indices: 54870--55358 Score: 171
Period size: 55 Copynumber: 8.7 Consensus size: 57
54860 ATATAGTTTT
* * * *
54870 TATATATA-ATTTATATATA-AT-TCATATATAAACTATATAGTTTATGTAGT-TTA-TA
1 TATATATATATATATATATATATAT-ATATATATA-TATATAGTTTAT-TAATATAACTA
* * * * ** *
54925 TATATATATATATATTTATATATATATATATAGATAGATAATTT-TT-ATATATTTT
1 TATATATATATATATATATATATATATATATATATATATAGTTTATTAATATAACTA
* * * * * **
54980 TATATATAAATATATAGTATATAT-TATGAATATAACTACATATAATTACATAAAT-TAACCC
1 TATATATATATATATA-TATATATATAT--ATAT-A-TATATATAGTT-TATTAATATAACTA
* * * * * * *
55041 TAAACCATATATATATATATATATTTA-ATAAACTATATATACTATA-T-ATATAAACTG
1 TATA-TATATATATATATATATATATATATATA-TATATATAGTTTATTAATAT-AACTA
* * * *
55098 CATATATA-A-ACTATATAGTTTATATACATA-ATATATATACTTTA-T-ATA-AACTA
1 TATATATATATA-TATATA-TATATATATATATATATATATAGTTTATTAATATAACTA
* *
55151 TA-ATA-AGT-TATATA-ATTTATACATATAT-TAATATATAGTTTATATATATAATGAACTA
1 TATATATA-TATATATATATATATATATATATAT-ATATATAGTTTAT-TA-AT-AT-AACTA
* * * * *
55209 TATA-ATATAGTTTATATGA-ACTATATAATTTATATAGTTTATA-TCTATTAAT-GAACTA
1 TATATATATA-TATATAT-ATA-TATAT-ATATATATA-TATATAGTTTATTAATATAACTA
* *
55267 TATATATATA-AT-T-TATATATACTA-AT-GA-CTATATAGTTTATTAATATAACTA
1 TATATATATATATATATATATATA-TATATATATATATATAGTTTATTAATATAACTA
55319 TATATATATATATATATATATATATATATATATATATATA
1 TATATATATATATATATATATATATATATATATATATATA
55359 TATAATTCAT
Statistics
Matches: 323, Mismatches: 58, Indels: 104
0.67 0.12 0.21
Matches are distributed among these distances:
50 16 0.05
51 21 0.07
52 23 0.07
53 11 0.03
54 12 0.04
55 67 0.21
56 38 0.12
57 30 0.09
58 30 0.09
59 18 0.06
60 5 0.02
61 15 0.05
62 21 0.07
63 10 0.03
64 6 0.02
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (57 bp):
TATATATATATATATATATATATATATATATATATATATAGTTTATTAATATAACTA
Found at i:57346 original size:39 final size:39
Alignment explanation
Indices: 57302--57406 Score: 115
Period size: 39 Copynumber: 2.7 Consensus size: 39
57292 TACTTTTAGA
* *
57302 AATAATTTAGATGGTTATGGTGAAATAGCTTAAGAAATT
1 AATAATTTAGATGGTTATGGTGAAATAACTTAAAAAATT
* * *
57341 AATAATTTAGAAT-GTAATGGTAAAATAATTTAAAAAATT
1 AATAATTTAG-ATGGTTATGGTGAAATAACTTAAAAAATT
* *
57380 AAGAATTTAGAAGGTTA-GAGTGAAATA
1 AATAATTTAGATGGTTATG-GTGAAATA
57407 CTTTGAAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
38 2 0.04
39 50 0.93
40 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.18, T:0.33
Consensus pattern (39 bp):
AATAATTTAGATGGTTATGGTGAAATAACTTAAAAAATT
Found at i:57443 original size:2 final size:2
Alignment explanation
Indices: 57438--57483 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
57428 AAATTTAATG
57438 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57480 AT AT
1 AT AT
57484 CGAATTAAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58075 original size:27 final size:27
Alignment explanation
Indices: 58024--58076 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
58014 TATGATATTA
*
58024 ATAATAAAATATTAAAAGAATAATTTG
1 ATAATAAAATATTAAAAGAACAATTTG
58051 ATAATAAAA-ATATAAATA-AACAATTT
1 ATAATAAAATAT-TAAA-AGAACAATTT
58077 AGAATTTACC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 2 0.09
27 20 0.87
28 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (27 bp):
ATAATAAAATATTAAAAGAACAATTTG
Found at i:58256 original size:14 final size:15
Alignment explanation
Indices: 58237--58265 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
58227 AATAATTTTG
58237 AATAATT-AAATAAT
1 AATAATTCAAATAAT
58251 AATAATTCAAATAAT
1 AATAATTCAAATAAT
58266 TACAAGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAATTCAAATAAT
Found at i:64447 original size:31 final size:31
Alignment explanation
Indices: 64405--64495 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 31
64395 TCATACGTAA
* *
64405 CGTTTATTTTTTGTTTCATTTTAGTACCCGG
1 CGTTTACTTTTTGTTTCATTTTAGTACCCAG
* *
64436 CGTTTACTTTTTATTTCATTTTAGTACCCCAT
1 CGTTTACTTTTTGTTTCATTTTAGTA-CCCAG
* * *
64468 TGTTAACTTTTTGTCTCATTTTAGTACC
1 CGTTTACTTTTTGTTTCATTTTAGTACC
64496 TAAATTTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 26 0.51
32 25 0.49
ACGTcount: A:0.16, C:0.19, G:0.11, T:0.54
Consensus pattern (31 bp):
CGTTTACTTTTTGTTTCATTTTAGTACCCAG
Found at i:64477 original size:32 final size:32
Alignment explanation
Indices: 64412--64495 Score: 107
Period size: 32 Copynumber: 2.7 Consensus size: 32
64402 TAACGTTTAT
* *
64412 TTTTTGTTTCATTTTAGTA-CCCGGCGTTTAC
1 TTTTTGTTTCATTTTAGTACCCCAGCGTTAAC
* **
64443 TTTTTATTTCATTTTAGTACCCCATTGTTAAC
1 TTTTTGTTTCATTTTAGTACCCCAGCGTTAAC
*
64475 TTTTTGTCTCATTTTAGTACC
1 TTTTTGTTTCATTTTAGTACC
64496 TAAATTTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 18 0.40
32 27 0.60
ACGTcount: A:0.17, C:0.19, G:0.11, T:0.54
Consensus pattern (32 bp):
TTTTTGTTTCATTTTAGTACCCCAGCGTTAAC
Found at i:69844 original size:32 final size:33
Alignment explanation
Indices: 69799--69887 Score: 119
Period size: 38 Copynumber: 2.6 Consensus size: 33
69789 AAAATTTTGT
69799 TCGACTC-TTGCTCGTTAAG-AAAATTTGTTGC
1 TCGACTCGTTGCTCGTTAAGTAAAATTTGTTGC
69830 TCGACTCGTTGCTCGTTAAGGTTGTTAAAATTTGTTGC
1 TCGACTCGTTGCTCGTTAA----G-TAAAATTTGTTGC
69868 TCGACTCGTTGCTCGTTAAG
1 TCGACTCGTTGCTCGTTAAG
69888 CTTTTTGCTC
Statistics
Matches: 51, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
31 7 0.14
32 11 0.22
34 1 0.02
36 1 0.02
38 31 0.61
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (33 bp):
TCGACTCGTTGCTCGTTAAGTAAAATTTGTTGC
Found at i:70250 original size:6 final size:6
Alignment explanation
Indices: 70239--70281 Score: 77
Period size: 6 Copynumber: 7.0 Consensus size: 6
70229 GACAAAGCAA
70239 GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT GGGAGAT
1 GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT -GGAGAT
70282 TTCCCACCCA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 30 0.83
7 6 0.17
ACGTcount: A:0.33, C:0.00, G:0.51, T:0.16
Consensus pattern (6 bp):
GGAGAT
Found at i:70348 original size:12 final size:14
Alignment explanation
Indices: 70315--70344 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
70305 TCATAACACC
70315 TCCTTTCCCTCTCT
1 TCCTTTCCCTCTCT
70329 TCCTTTCCCTCTCT
1 TCCTTTCCCTCTCT
70343 TC
1 TC
70345 TTCCTTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (14 bp):
TCCTTTCCCTCTCT
Found at i:70348 original size:17 final size:15
Alignment explanation
Indices: 70315--70352 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
70305 TCATAACACC
70315 TCCTTT-CCCTCTCT
1 TCCTTTCCCCTCTCT
70329 TCCTTTCCCTCTCTTCT
1 TCCTTTCCC-CTC-TCT
70346 TCCTTTC
1 TCCTTTC
70353 TAACCCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 2 0.10
16 3 0.14
17 10 0.48
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (15 bp):
TCCTTTCCCCTCTCT
Found at i:74429 original size:16 final size:16
Alignment explanation
Indices: 74410--74448 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
74400 ATATCCTGTG
*
74410 TTTTATATCTATAATA
1 TTTTATATCTATAAAA
* *
74426 TTTTCTATCTCTAAAA
1 TTTTATATCTATAAAA
74442 TTTTATA
1 TTTTATA
74449 AGTCGCACCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTATATCTATAAAA
Found at i:77648 original size:3 final size:3
Alignment explanation
Indices: 77640--77686 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
77630 TAATCAAATG
77640 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
77687 ATTCCTAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:79892 original size:50 final size:52
Alignment explanation
Indices: 79795--79903 Score: 159
Period size: 50 Copynumber: 2.1 Consensus size: 52
79785 ATGTACTTTC
* *
79795 GACACTATGTATGCACCCATGGTATTCATATTGAGTTTGTGAATTACCATTTT
1 GACACTATG-ATGCACCCATGGAATTCATAATGAGTTTGTGAATTACCATTTT
* *
79848 GGCACTATG-TGCATCCATGGAATTCATAATGA-TTTGTGAATTACCATTTT
1 GACACTATGATGCACCCATGGAATTCATAATGAGTTTGTGAATTACCATTTT
79898 GACACT
1 GACACT
79904 TAGGTTTTGG
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
50 23 0.45
51 20 0.39
53 8 0.16
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (52 bp):
GACACTATGATGCACCCATGGAATTCATAATGAGTTTGTGAATTACCATTTT
Done.