Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000030.1 Hibiscus syriacus cultivar Beakdansim tig00000050_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: 118436
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2894 original size:58 final size:57
Alignment explanation
Indices: 2794--2904 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 57
2784 ATAATCATCT
** *
2794 GCAAAATTATAAGAAATTATATCAGCTCAGATCAAGATATTTACCCAAAATCTAAAC
1 GCAAAATTATAAGAAATTATATCAGCTCAGAAAAAGACATTTACCCAAAATCTAAAC
* *
2851 GCAAAATTATTAGAGAAA-TATATCAGCTCTATAAAAAG-CATTTACCCAGAATCT
1 GCAAAATTA-TA-AGAAATTATATCAGCTC-AGAAAAAGACATTTACCCAAAATCT
2905 GAACTTTAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
57 9 0.20
58 27 0.59
59 10 0.22
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (57 bp):
GCAAAATTATAAGAAATTATATCAGCTCAGAAAAAGACATTTACCCAAAATCTAAAC
Found at i:12575 original size:16 final size:17
Alignment explanation
Indices: 12556--12605 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
12546 AGGGATCGAG
*
12556 AAAAATTATTATTTTA-
1 AAAAATTATTAATTTAT
*
12572 AAAAAATATTAATTTAT
1 AAAAATTATTAATTTAT
*
12589 AAAAATT-TTACTTTAT
1 AAAAATTATTAATTTAT
12605 A
1 A
12606 TCACAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 23 0.79
17 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
AAAAATTATTAATTTAT
Found at i:13145 original size:60 final size:60
Alignment explanation
Indices: 13071--13191 Score: 143
Period size: 60 Copynumber: 2.0 Consensus size: 60
13061 ATCATTCGAT
* ** * *
13071 TATAAGGTAATATTTTATTTTGTCCCTCAACTATTAAAAATTATAAAATAATCCCTCAAC
1 TATAAAGTAATATTTTATTGAGTCCCTCAACTATTAAAAATTACAAAATAATCACTCAAC
* * * * * *
13131 TATAAAGTATTATTTTGTTGAGTCTCTCAACTATTGAAAGTTACAAAATAGTCACTCAAC
1 TATAAAGTAATATTTTATTGAGTCCCTCAACTATTAAAAATTACAAAATAATCACTCAAC
13191 T
1 T
13192 GCTCATATAT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (60 bp):
TATAAAGTAATATTTTATTGAGTCCCTCAACTATTAAAAATTACAAAATAATCACTCAAC
Found at i:14269 original size:31 final size:31
Alignment explanation
Indices: 14234--14292 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
14224 AACATTTAAA
*
14234 TTTTATTTTATATTTAAT-TTTGAATTTACTT
1 TTTTAATTTA-ATTTAATATTTGAATTTACTT
**
14265 TTTTAATTTAATTTGGTATTTGAATTTA
1 TTTTAATTTAATTTAATATTTGAATTTA
14293 TAAAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (31 bp):
TTTTAATTTAATTTAATATTTGAATTTACTT
Found at i:15861 original size:21 final size:21
Alignment explanation
Indices: 15835--15888 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
15825 TTCATCTTGT
15835 ACAAACTTCAAGAAATATGGG
1 ACAAACTTCAAGAAATATGGG
15856 ACAAACTTCAAGAAATATGGG
1 ACAAACTTCAAGAAATATGGG
15877 ACAAACTTCAAG
1 ACAAACTTCAAG
15889 TCACTCATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.19
Consensus pattern (21 bp):
ACAAACTTCAAGAAATATGGG
Found at i:20591 original size:19 final size:19
Alignment explanation
Indices: 20563--20604 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
20553 CCCCCTTTGA
*
20563 AGGGGAATCGATTCCCCCT
1 AGGGGAATCGATACCCCCT
*
20582 AGGGGGATCGATACCCCCT
1 AGGGGAATCGATACCCCCT
20601 -GGGG
1 AGGGG
20605 TTCTGGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.19, C:0.29, G:0.36, T:0.17
Consensus pattern (19 bp):
AGGGGAATCGATACCCCCT
Found at i:28022 original size:65 final size:65
Alignment explanation
Indices: 27946--28076 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
27936 TTTGCCCGGA
27946 TGACTTCCATTAACCAATTATTAAAACGTTTGCTACATTTTCCTTTGACACTTTGCCAGTTTCTT
1 TGACTTCCATTAACCAATTATTAAAACGTTTGCTACATTTTCCTTTGACACTTTGCCAGTTTCTT
28011 TGACTTCCATTAACCAATTATTAAAACGTTTGCTACATTTTCCTTTGACACTTTGCCAGTTTCTT
1 TGACTTCCATTAACCAATTATTAAAACGTTTGCTACATTTTCCTTTGACACTTTGCCAGTTTCTT
28076 T
1 T
28077 CAGTTATTCC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (65 bp):
TGACTTCCATTAACCAATTATTAAAACGTTTGCTACATTTTCCTTTGACACTTTGCCAGTTTCTT
Found at i:34440 original size:13 final size:12
Alignment explanation
Indices: 34415--34449 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
34405 TTTATGTATA
34415 AACAAAAATTTT
1 AACAAAAATTTT
34427 AACAAAAATATTT
1 AACAAAAAT-TTT
*
34440 ATCAAAAATT
1 AACAAAAATT
34450 CAATAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (12 bp):
AACAAAAATTTT
Found at i:35802 original size:23 final size:20
Alignment explanation
Indices: 35751--35802 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
35741 TTATTCTTGT
*
35751 AAATTATTAATTAAATAATA
1 AAATTATTTATTAAATAATA
*
35771 ATATT-TTTATTAAAATAACTA
1 AAATTATTTATT-AAATAA-TA
35792 ACAATTATTTA
1 A-AATTATTTA
35803 GTATAGTGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 5 0.20
20 10 0.40
21 3 0.12
22 3 0.12
23 4 0.16
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTATTTATTAAATAATA
Found at i:37698 original size:35 final size:35
Alignment explanation
Indices: 37625--37700 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 35
37615 AACATAACCC
* * *
37625 TTAATTTTATTCTAAACCCTAAATTCCAAATTAAT
1 TTAATTATATTCTAAACCCTAAATTACAAAATAAT
* * *
37660 TTAATTATATTTTAAACCCTAAATTATAAAATACT
1 TTAATTATATTCTAAACCCTAAATTACAAAATAAT
37695 TTAATT
1 TTAATT
37701 TAGGATTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (35 bp):
TTAATTATATTCTAAACCCTAAATTACAAAATAAT
Found at i:38412 original size:21 final size:21
Alignment explanation
Indices: 38386--38436 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
38376 AGACGTTGTA
38386 AAACATATAGGACACTGCAAC
1 AAACATATAGGACACTGCAAC
38407 AAACATATAGGACACTGCAAC
1 AAACATATAGGACACTGCAAC
38428 AAACATATA
1 AAACATATA
38437 TATGGCAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.51, C:0.22, G:0.12, T:0.16
Consensus pattern (21 bp):
AAACATATAGGACACTGCAAC
Found at i:39409 original size:22 final size:20
Alignment explanation
Indices: 39381--39425 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
39371 GATATATTGG
39381 TACCATGGTATAGTAGTATCGA
1 TACCATGGTA-AG-AGTATCGA
* *
39403 TACCATGTTAAGGGTATCGA
1 TACCATGGTAAGAGTATCGA
39423 TAC
1 TAC
39426 TAGACAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 2 0.10
22 9 0.43
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (20 bp):
TACCATGGTAAGAGTATCGA
Found at i:40061 original size:30 final size:30
Alignment explanation
Indices: 39970--40053 Score: 89
Period size: 32 Copynumber: 2.8 Consensus size: 30
39960 AATGATCTGA
* * * *
39970 ACATGTGATATATGAACATAAGAGATTAAGTG
1 ACATGAGATATATGATCATATGAGAAT-A-TG
*
40002 ACATGAGTTATATGATCATATGAGAATATG
1 ACATGAGATATATGATCATATGAGAATATG
*
40032 ACATGAGATATGTGAT-ATATGA
1 ACATGAGATATATGATCATATGA
40054 ATTATATGGA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
29 6 0.13
30 16 0.36
31 1 0.02
32 22 0.49
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (30 bp):
ACATGAGATATATGATCATATGAGAATATG
Found at i:41732 original size:149 final size:150
Alignment explanation
Indices: 41543--41858 Score: 555
Period size: 150 Copynumber: 2.1 Consensus size: 150
41533 GGGTAGAGGG
* *
41543 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* * *
41607 TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAATATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
41672 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
41692 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
41757 TACTTGATCCCTAATATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAATATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
41822 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
41842 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
41859 TGCATTTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
149 52 0.33
150 107 0.67
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAATATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:41870 original size:23 final size:23
Alignment explanation
Indices: 41826--41870 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
41816 ATCATTATAT
*
41826 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
41849 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
41871 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:47964 original size:21 final size:21
Alignment explanation
Indices: 47922--47964 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
47912 TTTTTGGGCT
* * *
47922 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
47943 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
47964 A
1 A
47965 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:48696 original size:149 final size:150
Alignment explanation
Indices: 48506--48821 Score: 546
Period size: 150 Copynumber: 2.1 Consensus size: 150
48496 GGGTAGAGGG
* *
48506 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTAGAAAGACACA
* *
48570 TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATCCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATCATATGTGGTCCTTATGGACATCATT
48635 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
* *
48655 TCTACGTGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTAGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTAGAAAGACACA
*
48720 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATCATATGTGGTCCTTATGGACATCATT
48785 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
48805 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
48822 TGCATTTATA
Statistics
Matches: 157, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
149 51 0.32
150 106 0.68
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTAGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATCATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:48833 original size:23 final size:23
Alignment explanation
Indices: 48789--48833 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
48779 ATCATTATAT
*
48789 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
48812 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
48834 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:52270 original size:20 final size:22
Alignment explanation
Indices: 52224--52276 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
52214 AATGAGGAGA
52224 TATCGATACCATAGTATAGTAG
1 TATCGATACCATAGTATAGTAG
* *
52246 TATCGATACCATATTA-AG-GG
1 TATCGATACCATAGTATAGTAG
52266 TATCGATACCA
1 TATCGATACCA
52277 GGCAACATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.41
21 2 0.07
22 15 0.52
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (22 bp):
TATCGATACCATAGTATAGTAG
Found at i:54807 original size:35 final size:35
Alignment explanation
Indices: 54766--54840 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
54756 TTTAAACCCT
* *
54766 AAATTAAAGTATTTTAGAATTTAGGGTTTAAAATA
1 AAATTAAAGTAATTTAAAATTTAGGGTTTAAAATA
* * * *
54801 TAATTAAATTAATTTAAAATTTGGGGTTTAGAATA
1 AAATTAAAGTAATTTAAAATTTAGGGTTTAAAATA
54836 AAATT
1 AAATT
54841 GAGAGTTGTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.41
Consensus pattern (35 bp):
AAATTAAAGTAATTTAAAATTTAGGGTTTAAAATA
Found at i:56881 original size:80 final size:80
Alignment explanation
Indices: 56797--56946 Score: 205
Period size: 80 Copynumber: 1.9 Consensus size: 80
56787 GTTATAAATT
* * *
56797 CATAAGGTATTAGAATTACCATGGAAATAAAAATGTATG-TAT-TATTAAAGTTGTATTTATAAT
1 CATAAGGCATTAGAAGTACCATGGAAATAAAAATGTA-GAT-TCTATTAAAATTGTATTTATAAT
*
56860 TTTATGATATATAAAGA
64 TTCATGATATATAAAGA
* * *
56877 CATAATGCATTAGAAGTATCATGGAAATAAAAGTGTAGATTCTATTAAAATTGTATTTATAATTT
1 CATAAGGCATTAGAAGTACCATGGAAATAAAAATGTAGATTCTATTAAAATTGTATTTATAATTT
56942 CATGA
66 CATGA
56947 GGGGTAGAGT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
79 2 0.03
80 59 0.97
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (80 bp):
CATAAGGCATTAGAAGTACCATGGAAATAAAAATGTAGATTCTATTAAAATTGTATTTATAATTT
CATGATATATAAAGA
Found at i:70412 original size:23 final size:23
Alignment explanation
Indices: 70363--70425 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
70353 TAGTGTTATT
* **
70363 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
70386 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
70409 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
70426 AATAATATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:70506 original size:22 final size:21
Alignment explanation
Indices: 70481--70556 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 21
70471 TTAAAATAAA
70481 AATATAATATCTTATATTATAT
1 AATATAATAT-TTATATTATAT
*
70503 AATATAAT-TGATTATTTTATAT
1 AATATAATAT--TTATATTATAT
* *
70525 AATATTAAAATATATATTATTAT
1 AATA-TAATATTTATATTA-TAT
70548 AATATAATA
1 AATATAATA
70557 AATAAATAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
21 1 0.02
22 32 0.73
23 10 0.23
24 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (21 bp):
AATATAATATTTATATTATAT
Found at i:70538 original size:15 final size:15
Alignment explanation
Indices: 70520--70573 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
70510 TTGATTATTT
70520 TATATAATATTAAAA
1 TATATAATATTAAAA
* *
70535 TATATATTATTATAA
1 TATATAATATTAAAA
70550 TATAATAA-A-T-AAA
1 TAT-ATAATATTAAAA
*
70563 TAAATAATATT
1 TATATAATATT
70574 TTGATGAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
12 4 0.13
13 5 0.16
14 2 0.06
15 17 0.55
16 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATATAATATTAAAA
Found at i:70790 original size:42 final size:42
Alignment explanation
Indices: 70732--70851 Score: 186
Period size: 42 Copynumber: 2.9 Consensus size: 42
70722 ATGAATTACA
* * *
70732 TTCCGGAAAACCAATTACGTTAAACAAACATGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
70774 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
70816 TTCTGGAAAACGAATTACGAGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
70852 TTCGGGGAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.46, C:0.17, G:0.18, T:0.18
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:71801 original size:22 final size:22
Alignment explanation
Indices: 71747--71802 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
71737 TTCCATTTCG
*
71747 CGTTGCGATAATCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
71769 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
71791 CGTTGCGATAGT
1 CGTTGCGATAGT
71803 TAAAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.36
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:72417 original size:6 final size:6
Alignment explanation
Indices: 72406--72432 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
72396 TCTCGTCTCG
72406 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
72433 AATGGTAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:72438 original size:6 final size:6
Alignment explanation
Indices: 72429--72477 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
72419 GTCGTGGTCG
** * *
72429 TGGTAA TGGTAA TGGTAA TGGTAA TGGTCG TGATAA TGGTAA TGATAA
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA
72477 T
1 T
72478 ATATGTCTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.35
Consensus pattern (6 bp):
TGGTAA
Found at i:72438 original size:18 final size:18
Alignment explanation
Indices: 72406--72460 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
72396 TCTCGTCTCG
**
72406 GGTCGTGGTCGTGGTCGT
1 GGTCGTGGTAATGGTCGT
**
72424 GGTCGTGGTAATGGTAAT
1 GGTCGTGGTAATGGTCGT
**
72442 GGTAATGGTAATGGTCGT
1 GGTCGTGGTAATGGTCGT
72460 G
1 G
72461 ATAATGGTAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.15, C:0.09, G:0.44, T:0.33
Consensus pattern (18 bp):
GGTCGTGGTAATGGTCGT
Found at i:74591 original size:17 final size:17
Alignment explanation
Indices: 74569--74666 Score: 58
Period size: 18 Copynumber: 5.6 Consensus size: 17
74559 CTTTTTTGTA
74569 TTATTTTATTC-TTATTT
1 TTATTTTATTCATT-TTT
**
74586 TTATTTTTAACCATTTTT
1 TTA-TTTTATTCATTTTT
*
74604 TTATTTTATTCATTTGACT
1 TTATTTTATTCATTT--TT
* * *
74623 TTCTTTTA-CCATTTTA
1 TTATTTTATTCATTTTT
*
74639 TTATTTTATT-GTTTCTGT
1 TTATTTTATTCATTT-T-T
74657 TTATTTTATT
1 TTATTTTATT
74667 TTTTACTAAC
Statistics
Matches: 61, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
16 10 0.16
17 14 0.23
18 27 0.44
19 10 0.16
ACGTcount: A:0.18, C:0.09, G:0.03, T:0.69
Consensus pattern (17 bp):
TTATTTTATTCATTTTT
Found at i:75666 original size:10 final size:10
Alignment explanation
Indices: 75651--75684 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
75641 TTCATTTACC
75651 ATTTATTTTT
1 ATTTATTTTT
75661 ATTTATTTTT
1 ATTTATTTTT
* *
75671 ATCTATTTCT
1 ATTTATTTTT
75681 ATTT
1 ATTT
75685 TACTAACGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:85176 original size:56 final size:58
Alignment explanation
Indices: 85076--85186 Score: 147
Period size: 56 Copynumber: 1.9 Consensus size: 58
85066 AATACTTCGC
* ** *
85076 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGGAAAAAAAAAAA-A-AAAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGGAAAAAAAAAAAGAGAAAAAACGT
*
85132 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATT-GAAAAAGAAAAAAGAGAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGGAAAAA-AAAAAAGAGAAAAAA
85187 GAAGAGAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
55 6 0.13
56 34 0.72
57 1 0.02
58 6 0.13
ACGTcount: A:0.52, C:0.13, G:0.23, T:0.13
Consensus pattern (58 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGGAAAAAAAAAAAGAGAAAAAACGT
Found at i:86105 original size:105 final size:105
Alignment explanation
Indices: 85923--86803 Score: 1536
Period size: 105 Copynumber: 8.4 Consensus size: 105
85913 AGGTTTTACC
*
85923 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
85988 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
86028 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
86093 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAA-TT
*
86134 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCGCG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
86199 ACGAAGGGACCGCTGGTTGTCAACAAACATTTC-CCAATCT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT-T
* * *
86239 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGATTCCAGACAATGCAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
86304 ACGAAGGGACCGCTGCTTGTCAAC-AACAACTTTC-C-AATCT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-A-TTTCTCAAAT-T
*
86344 CAGAGCCAATTCCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
86409 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
86449 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
86514 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCTAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
86554 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
86619 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
86659 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
86724 ACGAAGGGACCGCTGGTTGTCAACAAACATGTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* ** *
86764 CAGAACCAATTTCAACTTCACGGCGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
86804 GGAACAATAC
Statistics
Matches: 745, Mismatches: 24, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
104 8 0.01
105 628 0.84
106 109 0.15
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:88667 original size:17 final size:17
Alignment explanation
Indices: 88645--88742 Score: 58
Period size: 18 Copynumber: 5.6 Consensus size: 17
88635 CTTTTTTGTA
88645 TTATTTTATTC-TTATTT
1 TTATTTTATTCATT-TTT
**
88662 TTATTTTTAACCATTTTT
1 TTA-TTTTATTCATTTTT
*
88680 TTATTTTATTCATTTGACT
1 TTATTTTATTCATTT--TT
* * *
88699 TTCTTTTA-CCATTTTA
1 TTATTTTATTCATTTTT
*
88715 TTATTTTATT-GTTTCTGT
1 TTATTTTATTCATTT-T-T
88733 TTATTTTATT
1 TTATTTTATT
88743 TTTTACTAAC
Statistics
Matches: 61, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
16 10 0.16
17 14 0.23
18 27 0.44
19 10 0.16
ACGTcount: A:0.18, C:0.09, G:0.03, T:0.69
Consensus pattern (17 bp):
TTATTTTATTCATTTTT
Found at i:93796 original size:12 final size:12
Alignment explanation
Indices: 93779--93803 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
93769 ATTTTTATGC
93779 TATTTTATTTAA
1 TATTTTATTTAA
93791 TATTTTATTTAA
1 TATTTTATTTAA
93803 T
1 T
93804 TTCTATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTTATTTAA
Found at i:100300 original size:64 final size:64
Alignment explanation
Indices: 100226--100350 Score: 214
Period size: 64 Copynumber: 2.0 Consensus size: 64
100216 TGAGTGTCTG
*
100226 TCAACAAACAACTTTCCAATTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGTAC
1 TCAACAAACAACTTTCCAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGTAC
* * *
100290 TCAACAAACAATTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGTAGGATATTG
1 TCAACAAACAACTTTCCAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTG
100351 AACTTGAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.32
Consensus pattern (64 bp):
TCAACAAACAACTTTCCAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGTAC
Found at i:100681 original size:43 final size:43
Alignment explanation
Indices: 100562--100683 Score: 158
Period size: 43 Copynumber: 2.8 Consensus size: 43
100552 CGAAGGGGCC
* * *
100562 ATCCACAATTTCAACTCCACGACGGGGGATATCATACCCACGA
1 ATCCACAATTTCAACTCCACGACGGAGGATATCGTGCCCACGA
100605 ATCCACAATTTCAACTCCACGACGGAGGATATCGTGCCCAC-A
1 ATCCACAATTTCAACTCCACGACGGAGGATATCGTGCCCACGA
* * *
100647 TATCCA-AGATTTCAACTTCACGACGAATGATATCGTG
1 -ATCCACA-ATTTCAACTCCACGACGGAGGATATCGTG
100684 TCCATCAGCA
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
42 2 0.03
43 69 0.97
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (43 bp):
ATCCACAATTTCAACTCCACGACGGAGGATATCGTGCCCACGA
Found at i:100913 original size:37 final size:37
Alignment explanation
Indices: 100834--100923 Score: 128
Period size: 37 Copynumber: 2.5 Consensus size: 37
100824 ACTTTGAAAT
* * **
100834 CAGTTTCCCTTGAAA-AAAGTTTTGTCTCTCTTTAGA
1 CAGTTTCCCTTGAAACAAAATTTTGTCTCCCTGGAGA
100870 CAGTTTCCCTTGAAACAAAATTTTGTCTCCCTGGAGA
1 CAGTTTCCCTTGAAACAAAATTTTGTCTCCCTGGAGA
*
100907 CGGTTTCCCTTGAAACA
1 CAGTTTCCCTTGAAACA
100924 TAAAATCTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 15 0.31
37 33 0.69
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.36
Consensus pattern (37 bp):
CAGTTTCCCTTGAAACAAAATTTTGTCTCCCTGGAGA
Found at i:101252 original size:129 final size:126
Alignment explanation
Indices: 101020--101417 Score: 444
Period size: 129 Copynumber: 3.1 Consensus size: 126
101010 TCTTGAAGCT
* * * * * *
101020 GTGTCAACCCCAGATAACCAGACGTCTTCATCACGTAGAAACTGTGTTATCACCCTTAGATTGCC
1 GTGTCAACCCTAGATAACCAG-CGTCCTCATCACGTAGGAACCGTATTATCACCCTTAGATGGCC
* *
101085 TGCCGTCCTCATCACGTAGGAACCGTGTCATC-CTTCGACTAGATCTCCTTAT-CGTAAAGGAGT
65 TGCCGTCCTCATCACGTAGGAACCGTGTCATCAC-TCGACT-GATCTCCTCATACGT--AGGAGC
101148 C
126 C
* * *
101149 GTGTCAACCCTAGATAACCAGCTGTCCTCATCACGTAGGAACCATATTTTCACCCTTAGATGGCA
1 GTGTCAACCCTAGATAACCAGC-GTCCTCATCACGTAGGAACCGTATTATCACCCTTAGATGGCC
* * *
101214 TGTCGTCCTCATCACATAGGAACCGTGTCATCACTCGACCTGGTCTCCTCATCACGTAGGAGCC
65 TGCCGTCCTCATCACGTAGGAACCGTGTCATCACTCGA-CTGATCTCCTCAT-ACGTAGGAGCC
* * * *
101278 GTGTCAA-CCTCATATAACCAGCCATCCTCATCACGTTGGAACCGTGA-TATCAGCCTTAGATGG
1 GTGTCAACCCT-AGATAACCAG-CGTCCTCATCACGTAGGAACCGT-ATTATCACCCTTAGATGG
* * * *
101341 CCTGCCGCCCTCATCACGTAGGAACCGTGTCATCACCCGACCTGACCTCTTCATCACGTAGGAGC
63 CCTGCCGTCCTCATCACGTAGGAACCGTGTCATCACTCGA-CTGATCTCCTCAT-ACGTAGGAGC
*
101406 A
126 C
101407 GTGTCAACCCT
1 GTGTCAACCCT
101418 TAGACGATCC
Statistics
Matches: 231, Mismatches: 29, Indels: 17
0.83 0.10 0.06
Matches are distributed among these distances:
128 4 0.02
129 216 0.94
130 8 0.03
131 3 0.01
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (126 bp):
GTGTCAACCCTAGATAACCAGCGTCCTCATCACGTAGGAACCGTATTATCACCCTTAGATGGCCT
GCCGTCCTCATCACGTAGGAACCGTGTCATCACTCGACTGATCTCCTCATACGTAGGAGCC
Found at i:101574 original size:3 final size:3
Alignment explanation
Indices: 101568--101628 Score: 86
Period size: 3 Copynumber: 20.3 Consensus size: 3
101558 TCGAAAAAAA
* * * *
101568 TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAC TAT TAC CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
101616 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
101629 TAAAACCACT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:102553 original size:30 final size:30
Alignment explanation
Indices: 102498--102616 Score: 116
Period size: 30 Copynumber: 3.9 Consensus size: 30
102488 TCTGTTATTT
*
102498 TATTTTAGTCAC-TTAAGTTTATGTTTTTAC
1 TATTTTAGTC-CTTTAAGTTTTTGTTTTTAC
* *
102528 TA-TTTATGTCCTTTAAATTTTTGTTTTAAC
1 TATTTTA-GTCCTTTAAGTTTTTGTTTTTAC
* *
102558 TATTTTAGTCTTTTAAGTTTTTGTTCTTAC
1 TATTTTAGTCCTTTAAGTTTTTGTTTTTAC
* * **
102588 CATTTTTAATCCTTTAAGTTCATGTTTTT
1 TA-TTTTAGTCCTTTAAGTTTTTGTTTTT
102617 GCTAGATCTA
Statistics
Matches: 72, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
29 5 0.07
30 42 0.58
31 25 0.35
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.60
Consensus pattern (30 bp):
TATTTTAGTCCTTTAAGTTTTTGTTTTTAC
Found at i:103171 original size:8 final size:8
Alignment explanation
Indices: 103158--103188 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
103148 TATTACAAAA
103158 CAGCAACT
1 CAGCAACT
103166 CAGCAACT
1 CAGCAACT
103174 CAGCAACT
1 CAGCAACT
103182 CAGCAAC
1 CAGCAAC
103189 CAACCAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.39, G:0.13, T:0.10
Consensus pattern (8 bp):
CAGCAACT
Found at i:105568 original size:25 final size:25
Alignment explanation
Indices: 105540--105589 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
105530 AGGCTGGTGC
*
105540 GGACGTTGAATCTTGGGATAATTGT
1 GGACGTTGAATCTTGGGACAATTGT
*
105565 GGACTTTGAATCTTGGGACAATTGT
1 GGACGTTGAATCTTGGGACAATTGT
105590 CAAACTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.10, G:0.30, T:0.36
Consensus pattern (25 bp):
GGACGTTGAATCTTGGGACAATTGT
Found at i:107234 original size:13 final size:13
Alignment explanation
Indices: 107216--107260 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
107206 ATAAATAATA
*
107216 AAAAAATTACAAT
1 AAAAAACTACAAT
* *
107229 AAAAAAGTCCAAT
1 AAAAAACTACAAT
*
107242 AAACAACTACAAT
1 AAAAAACTACAAT
107255 AAAAAA
1 AAAAAA
107261 GTACTAAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.69, C:0.13, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAACTACAAT
Found at i:107777 original size:18 final size:18
Alignment explanation
Indices: 107754--107793 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
107744 AATGGAAAGG
107754 TGGTGGCGAAATCATATA
1 TGGTGGCGAAATCATATA
107772 TGGTGGCGAAATCATATA
1 TGGTGGCGAAATCATATA
107790 TGGT
1 TGGT
107794 TGCGGTATGT
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:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (18 bp):
TGGTGGCGAAATCATATA
Found at i:108978 original size:20 final size:20
Alignment explanation
Indices: 108916--109018 Score: 111
Period size: 20 Copynumber: 5.0 Consensus size: 20
108906 ATCAGATTGT
*
108916 CCAGGGGGTACAGATTCCCC
1 CCAGGGGATACAGATTCCCC
108936 CTGCAAGGGG-TACAGATTCCCC
1 C--C-AGGGGATACAGATTCCCC
* *
108958 CCAGGGGATACCGATTTCCC
1 CCAGGGGATACAGATTCCCC
108978 CCAGGGGGA-ACAGATTCCCC
1 CCA-GGGGATACAGATTCCCC
* *
108998 CCAGGGGGTACCGATTCCCC
1 CCAGGGGATACAGATTCCCC
109018 C
1 C
109019 TGTCTAACGG
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
19 9 0.13
20 38 0.54
21 5 0.07
22 14 0.20
23 5 0.07
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.16
Consensus pattern (20 bp):
CCAGGGGATACAGATTCCCC
Found at i:108991 original size:40 final size:39
Alignment explanation
Indices: 108942--109018 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 39
108932 CCCCCTGCAA
*
108942 GGGGTACAGATTCCCCCCAGGGGATACCGATTTCCCCCAG
1 GGGGAACAGATTCCCCCCAGGGGATACCGA-TTCCCCCAG
*
108982 GGGGAACAGATTCCCCCCAGGGGGTACCGATTCCCCC
1 GGGGAACAGATTCCCCCCAGGGGATACCGATTCCCCC
109019 TGTCTAACGG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 7 0.20
40 28 0.80
ACGTcount: A:0.19, C:0.36, G:0.29, T:0.16
Consensus pattern (39 bp):
GGGGAACAGATTCCCCCCAGGGGATACCGATTCCCCCAG
Found at i:111800 original size:19 final size:20
Alignment explanation
Indices: 111761--111802 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
111751 ATCAGATTGT
111761 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
111781 CCAGGGGG-AGCAGATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
111801 CC
1 CC
111803 TGTCTAACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.19, C:0.38, G:0.31, T:0.12
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Done.