Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006380.1 Hibiscus syriacus cultivar Beakdansim tig00015353_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: 74040
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:736 original size:37 final size:36
Alignment explanation
Indices: 636--774 Score: 155
Period size: 34 Copynumber: 4.0 Consensus size: 36
626 AACTAAGACG
* * * *
636 ATGATACGTGTGAG-ATGGGACGAAGTTAGGATCAAT
1 ATGATATGTGTGAGCAT-CGACGGAGCTAGGATCAAT
672 -T-ATATGTGTGAGCAT-GACGGAGCTAGGATCAAT
1 ATGATATGTGTGAGCATCGACGGAGCTAGGATCAAT
*
705 CATGATATGTGCGAGCATCGACGGAGCTAGGATC-A-
1 -ATGATATGTGTGAGCATCGACGGAGCTAGGATCAAT
* *
740 ATGATATGCGTGAGCATCGACAGAGCTAGGATCAA
1 ATGATATGTGTGAGCATCGACGGAGCTAGGATCAA
775 ATTTAGGAGA
Statistics
Matches: 90, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
33 16 0.18
34 40 0.44
35 5 0.06
36 14 0.16
37 15 0.17
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.23
Consensus pattern (36 bp):
ATGATATGTGTGAGCATCGACGGAGCTAGGATCAAT
Found at i:8147 original size:59 final size:60
Alignment explanation
Indices: 8038--8184 Score: 142
Period size: 59 Copynumber: 2.4 Consensus size: 60
8028 TATCATGTCC
* * * *
8038 CCAAACTATGACTTTCATTTTAAATTGATCTTTAAATTTTTTTGATATTCCAA-TTCCATCAT
1 CCAAACTATGAC-TTCATTCTAAATTGATCCTTAAATATTTTTGACATTCCAACTT-CATC-T
8100 -CAAACTATGAC-TCATTCTAAATT-AGTCCTTAAA-ATTTTTGAACATTCCAACTTCATCT
1 CCAAACTATGACTTCATTCTAAATTGA-TCCTTAAATATTTTTG-ACATTCCAACTTCATCT
* * *
8158 CCAAACTATAACCCTCATTTTAAATTG
1 CCAAACTATGA-CTTCATTCTAAATTG
8185 GTCCCCAAAC
Statistics
Matches: 72, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
58 8 0.11
59 39 0.54
60 3 0.04
61 22 0.31
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (60 bp):
CCAAACTATGACTTCATTCTAAATTGATCCTTAAATATTTTTGACATTCCAACTTCATCT
Found at i:8436 original size:60 final size:60
Alignment explanation
Indices: 8343--8458 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
8333 AGTATATACA
* **
8343 CATAGTTTGAGATTAAATTGAAATGTTTAAAAAGTTTGGGGACTAATTTAGAATGAAGGT
1 CATAGTTTGAGATGAAATTGAAATGTTTAAAAAGTTTAAGGACTAATTTAGAATGAAGGT
* * *
8403 CATAGTTTGGTGATGAAATTGAAATG-TTCAAAAGTTTAAGGACTAATTTATAATGA
1 CATAGTTT-GAGATGAAATTGAAATGTTTAAAAAGTTTAAGGACTAATTTAGAATGA
8459 GGTACAATGC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 34 0.69
61 15 0.31
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (60 bp):
CATAGTTTGAGATGAAATTGAAATGTTTAAAAAGTTTAAGGACTAATTTAGAATGAAGGT
Found at i:10242 original size:2 final size:2
Alignment explanation
Indices: 10237--10273 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
10227 TCTCTCTCTT
*
10237 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10274 CATCTTCTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12211 original size:33 final size:33
Alignment explanation
Indices: 12161--12238 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
12151 CATATTAAAT
* *
12161 ATTTCCGAATG-AACATATCAATATTATCAAGA
1 ATTTCCAAATGCAACATATCAATATAATCAAGA
* *
12193 ATTTCCAAATGCAACATATCAATATAATTAAGT
1 ATTTCCAAATGCAACATATCAATATAATCAAGA
12226 ATTTCCAAATGCA
1 ATTTCCAAATGCA
12239 CATCATACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 10 0.24
33 31 0.76
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.32
Consensus pattern (33 bp):
ATTTCCAAATGCAACATATCAATATAATCAAGA
Found at i:14517 original size:36 final size:36
Alignment explanation
Indices: 14470--14713 Score: 382
Period size: 36 Copynumber: 6.8 Consensus size: 36
14460 ATCAAAAGTT
* * *
14470 CACTTCTGATTCAAGTAGAACGGAAGAAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
14506 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
*
14542 CACTTCCGATTCAAGTCGAACGGAGGGAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
*
14578 CACTTCCGATTCAAGTCGAACGGAGGGAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
* * *
14614 CACTTCTGATTCAAGTCGAACGGAAAGAAGCATCGA
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
**
14650 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCAA
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
14686 CACTTCCGATTCATA-TCGAACGGAAGGA
1 CACTTCCGATTCA-AGTCGAACGGAAGGA
14714 TGTGTCTTAC
Statistics
Matches: 196, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
36 195 0.99
37 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (36 bp):
CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
Found at i:16926 original size:20 final size:20
Alignment explanation
Indices: 16888--16927 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16878 TGTATACAAT
*
16888 AGTAATAAACATTGATTAAG
1 AGTAATAAACATAGATTAAG
*
16908 AGTAATAAACATAGTTTAAG
1 AGTAATAAACATAGATTAAG
16928 TAGATCTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (20 bp):
AGTAATAAACATAGATTAAG
Found at i:20821 original size:36 final size:36
Alignment explanation
Indices: 20766--20836 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
20756 GATTATAGGT
* *
20766 TTTATTCTTGTGAAGTAAGAAACTAAAATTAAGGAC
1 TTTATTCTTGTAAAATAAGAAACTAAAATTAAGGAC
** *
20802 TTTATTCTTGTAAAATAAGATGCTGAAATTAAGGA
1 TTTATTCTTGTAAAATAAGAAACTAAAATTAAGGA
20837 TTTTTAATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (36 bp):
TTTATTCTTGTAAAATAAGAAACTAAAATTAAGGAC
Found at i:29343 original size:21 final size:20
Alignment explanation
Indices: 29319--29373 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 20
29309 CTCAGAGGGA
29319 ACCGATTCCCCCCAAGGGGGT
1 ACCGATTCCCCCC-AGGGGGT
29340 ACCGATTCCCCCTCAGGGGGT
1 ACCGATTCCCCC-CAGGGGGT
29361 ACCGATTCCCCCC
1 ACCGATTCCCCCC
29374 TTGTATAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.16, C:0.44, G:0.24, T:0.16
Consensus pattern (20 bp):
ACCGATTCCCCCCAGGGGGT
Found at i:36235 original size:17 final size:18
Alignment explanation
Indices: 36197--36235 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
36187 TTTTAACATT
*
36197 TTGAATATTTTGGAATGT
1 TTGAATATTTTGGAATGA
*
36215 TTGAAT-TTTTGGATTGA
1 TTGAATATTTTGGAATGA
36232 TTGA
1 TTGA
36236 CTTTGAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (18 bp):
TTGAATATTTTGGAATGA
Found at i:44780 original size:89 final size:89
Alignment explanation
Indices: 44680--44859 Score: 360
Period size: 89 Copynumber: 2.0 Consensus size: 89
44670 TCGTTCAAAA
44680 ATAAACAAACAAATGAGAAAACAACTTTATTTATTCAAGTCTAATTCATTTATACTCCTACATAA
1 ATAAACAAACAAATGAGAAAACAACTTTATTTATTCAAGTCTAATTCATTTATACTCCTACATAA
44745 AACGAAAAACTCATAAAAGTATTT
66 AACGAAAAACTCATAAAAGTATTT
44769 ATAAACAAACAAATGAGAAAACAACTTTATTTATTCAAGTCTAATTCATTTATACTCCTACATAA
1 ATAAACAAACAAATGAGAAAACAACTTTATTTATTCAAGTCTAATTCATTTATACTCCTACATAA
44834 AACGAAAAACTCATAAAAGTATTT
66 AACGAAAAACTCATAAAAGTATTT
44858 AT
1 AT
44860 TTAAATTTAG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 91 1.00
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.31
Consensus pattern (89 bp):
ATAAACAAACAAATGAGAAAACAACTTTATTTATTCAAGTCTAATTCATTTATACTCCTACATAA
AACGAAAAACTCATAAAAGTATTT
Found at i:44993 original size:61 final size:62
Alignment explanation
Indices: 44923--45086 Score: 206
Period size: 62 Copynumber: 2.6 Consensus size: 62
44913 ATTGACATAC
44923 AAATTGTATTTATGTTTGTTTGTTTATTTTTAAAGGTGTTTATATTCGTTCGTGTTCATTT-
1 AAATTGTATTTATGTTTGTTTGTTTATTTTTAAAGGTGTTTATATTCGTTCGTGTTCATTTA
* * * * *
44984 AAATTGTATTTATGTTTGTTTGTTTGTTTTTTTAATGTATTTATGTTCGTTCGTGTTCATTTA
1 AAATTGTATTTATGTTTGTTTGTTT-ATTTTTAAAGGTGTTTATATTCGTTCGTGTTCATTTA
** *
45047 AAATT-TCAATATCGTGTTTGTTTGTTTATTTTTGAAGGTG
1 AAATTGT--AT-TTATGTTTGTTTGTTTATTTTTAAAGGTG
45087 CTCGTGTTCA
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
61 25 0.29
62 32 0.37
63 5 0.06
64 11 0.13
65 14 0.16
ACGTcount: A:0.20, C:0.05, G:0.17, T:0.59
Consensus pattern (62 bp):
AAATTGTATTTATGTTTGTTTGTTTATTTTTAAAGGTGTTTATATTCGTTCGTGTTCATTTA
Found at i:45023 original size:31 final size:31
Alignment explanation
Indices: 44927--45030 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
44917 ACATACAAAT
*
44927 TGTATTTATGTTTGTTTGTTT-ATTTTTAAA
1 TGTATTTATGTTTGTTTGTTTGTTTTTTAAA
* * * * * *
44957 GGTGTTTATATTCGTTCG--TGTTCATTTAAA
1 TGTATTTATGTTTGTTTGTTTGTT-TTTTAAA
*
44987 TTGTATTTATGTTTGTTTGTTTGTTTTTTTAA
1 -TGTATTTATGTTTGTTTGTTTGTTTTTTAAA
45019 TGTATTTATGTT
1 TGTATTTATGTT
45031 CGTTCGTGTT
Statistics
Matches: 55, Mismatches: 14, Indels: 9
0.71 0.18 0.12
Matches are distributed among these distances:
28 1 0.02
29 1 0.02
30 19 0.35
31 25 0.45
32 5 0.09
33 4 0.07
ACGTcount: A:0.17, C:0.03, G:0.16, T:0.63
Consensus pattern (31 bp):
TGTATTTATGTTTGTTTGTTTGTTTTTTAAA
Found at i:45394 original size:24 final size:24
Alignment explanation
Indices: 45367--45420 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
45357 AACCTTGTTT
*
45367 GCTTATAAACAAGTCGATAAACGA
1 GCTTATAAACAAGTCAATAAACGA
45391 GCTTATAAACAAGTCAATAAACGA
1 GCTTATAAACAAGTCAATAAACGA
*
45415 GTTTAT
1 GCTTAT
45421 TTGTGAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (24 bp):
GCTTATAAACAAGTCAATAAACGA
Found at i:46672 original size:41 final size:41
Alignment explanation
Indices: 46627--46707 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
46617 TTTACCGGTT
*
46627 AAAAGAAAGCAGGTGTTCAAGCTACTATAAAGATGATGATG
1 AAAAGAAAGCAGGTGTTCAAGCTACTATAAAGACGATGATG
*
46668 AAAAGAAAGCAGGTGTTGAAGCTACTATAAAGACGATGAT
1 AAAAGAAAGCAGGTGTTCAAGCTACTATAAAGACGATGAT
46708 AGTAAGTGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.44, C:0.10, G:0.25, T:0.21
Consensus pattern (41 bp):
AAAAGAAAGCAGGTGTTCAAGCTACTATAAAGACGATGATG
Found at i:48485 original size:2 final size:2
Alignment explanation
Indices: 48425--48470 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
48415 ACATCATAAA
48425 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
48467 AT AT
1 AT AT
48471 TTTGCATTTA
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:52341 original size:22 final size:22
Alignment explanation
Indices: 52316--52361 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
52306 AAAGATTAAC
52316 TATCCTACTTTAAAATCCTATT
1 TATCCTACTTTAAAATCCTATT
52338 TATCCTACTTTAAAATCCTATT
1 TATCCTACTTTAAAATCCTATT
52360 TA
1 TA
52362 AAATTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.46
Consensus pattern (22 bp):
TATCCTACTTTAAAATCCTATT
Found at i:52363 original size:12 final size:13
Alignment explanation
Indices: 52317--52365 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
52307 AAGATTAACT
52317 ATCCTACTTTAAA
1 ATCCTACTTTAAA
52330 ATCCTA-TTT---
1 ATCCTACTTTAAA
52339 ATCCTACTTTAAA
1 ATCCTACTTTAAA
52352 ATCCTA-TTTAAA
1 ATCCTACTTTAAA
52364 AT
1 AT
52366 TTTAATACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
9 6 0.19
10 3 0.09
12 11 0.34
13 12 0.38
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (13 bp):
ATCCTACTTTAAA
Found at i:53359 original size:140 final size:140
Alignment explanation
Indices: 53107--53378 Score: 427
Period size: 140 Copynumber: 1.9 Consensus size: 140
53097 TATATAATAG
* * * * *
53107 AAAAGTCTGATAGATAAAATTTAGGTTAGTGCTGTTGTATTACAGTTTAACTTAGGGTTAATTTA
1 AAAAGTCTGACAGATAAAATTTAGGTTAGTACTGTTGTATCACAGTTTAACTTAAGGTTAACTTA
* *
53172 CGATAGATTTCAATTAAAGATGTTATATATTTTATAATAGTTTTAGTTATAACTAAAAATTTACA
66 CGATAGATTTCAACTAAAGATGTTATACATTTTATAATAGTTTTAGTTATAACTAAAAATTTACA
53237 CAGATAGTAA
131 CAGATAGTAA
**
53247 AAAAGTCTGACAGATAAAATTTAGGTTAGTACTGTTGTATCGTAGTTTAACTTAAGGTTAACTTA
1 AAAAGTCTGACAGATAAAATTTAGGTTAGTACTGTTGTATCACAGTTTAACTTAAGGTTAACTTA
* * * *
53312 CTATAGATTTTAACTAAAGATGTTATACATTTTATTATAGTTTTAGTTATAACTACAAATTTACA
66 CGATAGATTTCAACTAAAGATGTTATACATTTTATAATAGTTTTAGTTATAACTAAAAATTTACA
53377 CA
131 CA
53379 ATGACGGATT
Statistics
Matches: 119, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
140 119 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (140 bp):
AAAAGTCTGACAGATAAAATTTAGGTTAGTACTGTTGTATCACAGTTTAACTTAAGGTTAACTTA
CGATAGATTTCAACTAAAGATGTTATACATTTTATAATAGTTTTAGTTATAACTAAAAATTTACA
CAGATAGTAA
Found at i:54536 original size:31 final size:31
Alignment explanation
Indices: 54492--54566 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
54482 GTAATTTTCA
*
54492 ATAGTTGGAGGACTAAACA-AAGCAACGTCTT
1 ATAGTCGGAGGACTAAACAGAA-CAACGTCTT
* * * *
54523 ATAGTCGGTGGACTCAACAGAATAATGTCTT
1 ATAGTCGGAGGACTAAACAGAACAACGTCTT
*
54554 ATAGTTGGAGGAC
1 ATAGTCGGAGGAC
54567 CATTTGTGTA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (31 bp):
ATAGTCGGAGGACTAAACAGAACAACGTCTT
Found at i:56761 original size:59 final size:59
Alignment explanation
Indices: 56692--56803 Score: 215
Period size: 59 Copynumber: 1.9 Consensus size: 59
56682 GATGATTATC
*
56692 GATACTCTTAGGCTTGATATTGATATTCATATGAGGATATTGATACCATGTGGACAGTG
1 GATACTCTTAGGCTTGATATTGATACTCATATGAGGATATTGATACCATGTGGACAGTG
56751 GATACTCTTAGGCTTGATATTGATACTCATATGAGGATATTGATACCATGTGG
1 GATACTCTTAGGCTTGATATTGATACTCATATGAGGATATTGATACCATGTGG
56804 TATTAGTTTC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (59 bp):
GATACTCTTAGGCTTGATATTGATACTCATATGAGGATATTGATACCATGTGGACAGTG
Found at i:56791 original size:20 final size:20
Alignment explanation
Indices: 56707--56796 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 20
56697 TCTTAGGCTT
*
56707 GATATTGATATTCATATGAG
1 GATATTGATACTCATATGAG
*
56727 GATATTGATAC-C--ATGTG
1 GATATTGATACTCATATGAG
* * * * **
56744 GACAGTGGATACTCTTAGGCTT
1 GATA-TTGATACTCATATG-AG
56766 GATATTGATACTCATATGAG
1 GATATTGATACTCATATGAG
56786 GATATTGATAC
1 GATATTGATAC
56797 CATGTGGTAT
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
17 7 0.13
18 6 0.11
19 2 0.04
20 21 0.40
21 13 0.25
22 4 0.08
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (20 bp):
GATATTGATACTCATATGAG
Found at i:56966 original size:25 final size:25
Alignment explanation
Indices: 56938--56997 Score: 113
Period size: 24 Copynumber: 2.4 Consensus size: 25
56928 CAAAATTGGT
56938 TAAAGTTAAAATACGTTTAAAAGAG
1 TAAAGTTAAAATACGTTTAAAAGAG
56963 TAAAGTT-AAATACGTTTAAAAGAG
1 TAAAGTTAAAATACGTTTAAAAGAG
56987 TAAAGTTAAAA
1 TAAAGTTAAAA
56998 AATATCTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 24 0.71
25 10 0.29
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.28
Consensus pattern (25 bp):
TAAAGTTAAAATACGTTTAAAAGAG
Found at i:63039 original size:22 final size:24
Alignment explanation
Indices: 63013--63056 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
63003 GAAAACTGGT
63013 TGGTCAAC-G-TAAAACATTTTTC
1 TGGTCAACAGATAAAACATTTTTC
*
63035 TGGTCAACAGATAAAATATTTT
1 TGGTCAACAGATAAAACATTTT
63057 AATATCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 1 0.05
24 10 0.53
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (24 bp):
TGGTCAACAGATAAAACATTTTTC
Found at i:70844 original size:23 final size:23
Alignment explanation
Indices: 70817--70871 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
70807 TGAGATCTGT
70817 CGACGATGAGAGGCTGAGAGCTC
1 CGACGATGAGAGGCTGAGAGCTC
70840 CGACGATGAGAGGCTGAGAGCTC
1 CGACGATGAGAGGCTGAGAGCTC
70863 CGACGATGA
1 CGACGATGA
70872 AAGGTTCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.27, C:0.22, G:0.38, T:0.13
Consensus pattern (23 bp):
CGACGATGAGAGGCTGAGAGCTC
Found at i:71925 original size:2 final size:2
Alignment explanation
Indices: 71918--71966 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
71908 TAATAATTTC
*
71918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71960 AT AT AT A
1 AT AT AT A
71967 ACTCAATTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.