Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003644.1 Hibiscus syriacus cultivar Beakdansim tig00007743_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: 100910
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1757 original size:19 final size:19
Alignment explanation
Indices: 1733--1771 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1723 GCCAATCACT
1733 CCAACATCTCAAGCTATCG
1 CCAACATCTCAAGCTATCG
1752 CCAACATCTCAAGCTATCG
1 CCAACATCTCAAGCTATCG
1771 C
1 C
1772 GCTGTTGGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.38, G:0.10, T:0.21
Consensus pattern (19 bp):
CCAACATCTCAAGCTATCG
Found at i:4664 original size:17 final size:18
Alignment explanation
Indices: 4642--4679 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
4632 TGCCATGTGG
4642 ATAAGGTTTAGGGTGT-T
1 ATAAGGTTTAGGGTGTAT
4659 ATAAGGTTTAGGGTGTAT
1 ATAAGGTTTAGGGTGTAT
4677 ATA
1 ATA
4680 TATTTCTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (18 bp):
ATAAGGTTTAGGGTGTAT
Found at i:14668 original size:30 final size:28
Alignment explanation
Indices: 14624--14698 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 28
14614 AGAGGAAAAG
* *
14624 AAAAAAAAGGGAAAAATCAAAATAATGA
1 AAAAAAAAGAGAAAAATCAAAAGAATGA
*
14652 AAAATGAAAAGAGAAAAGA-GAAAAGAATGA
1 AAAA--AAAAGAGAAAA-ATCAAAAGAATGA
*
14682 ATAAAAAAGAGAAAAAT
1 AAAAAAAAGAGAAAAAT
14699 GGAGAAATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 1 0.03
28 15 0.38
30 22 0.56
31 1 0.03
ACGTcount: A:0.72, C:0.01, G:0.17, T:0.09
Consensus pattern (28 bp):
AAAAAAAAGAGAAAAATCAAAAGAATGA
Found at i:15819 original size:55 final size:55
Alignment explanation
Indices: 15753--16563 Score: 699
Period size: 55 Copynumber: 14.7 Consensus size: 55
15743 TTGAAGCATC
* * *
15753 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGAAGCGAACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAAACACGATTGTTG
* * * * *
15808 AAGATTGTTCGAGTCTAATACTCTCTAAAGGAATAAGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAAACACGATTGTTG
* * * *
15863 AAGATTGTTCGAGTCTTATCCTCTCTGAAGGAATAGGGAGCAGACATGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAAACACGATTGTTG
* *
15918 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATATGGAG-AATACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAA-ACACGATTGTTG
* * * * *
15973 AAGATTTTTTGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAAACACGATTGTTG
* * *
16028 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTATTG
1 AAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAAACACGATTGTTG
* * * *
16083 AAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACATGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAAACACGATTGTTG
* * * * * * **
16138 AAG-TTGTTCGAGT-TCTATACTCCCTAAAGAAAGAGGGGGCAAACCCG-TGGGAAG
1 AAGATTGTTCGAGTCT-TATACTCCCTGAAGGAATAGGGAGCAAACACGAT-TGTTG
* * * * * * * **
16192 AAGA-TGTTCGAGT-TCCATACTCCCTAAAGAAAGAGGGAGCGAACCCG-TAGGAAG
1 AAGATTGTTCGAGTCT-TATACTCCCTGAAGGAATAGGGAGCAAACACGAT-TGTTG
* * * * *
16246 AAGA-TGTTCGAGT-TCTATACTCCCTGAAAGAA-AGTGGGAGCGAACCCGTTTGTAG
1 AAGATTGTTCGAGTCT-TATACTCCCTGAAGGAATA--GGGAGCAAACACGATTGTTG
*
16301 AAGATTGTTCGAGT-TCTATACTCCCTGAAGTG-ATAGGGAGCAAACTCG-TTGTTCAG
1 AAGATTGTTCGAGTCT-TATACTCCCTGAAG-GAATAGGGAGCAAACACGATTGTT--G
* * * **
16357 AAGATTGCTCGAGT-TCTATACTCCCTGAAGCG-ATAGGAAGCAAACTC-ATTTGCAG
1 AAGATTGTTCGAGTCT-TATACTCCCTGAAG-GAATAGGGAGCAAACACGA-TTGTTG
* * *
16412 AAGATTCTTCGAGATC-TATACTCCCTGAAGCAATAGGGAGCAAACTCG-TTGTTCAG
1 AAGATTGTTCGAG-TCTTATACTCCCTGAAGGAATAGGGAGCAAACACGATTGTT--G
* * * * **
16468 AAGATTGTTCGAGT-TCTATACTCCCTGAAGCAATAGGAAGCAAACTCGTTTGCAG
1 AAGATTGTTCGAGTCT-TATACTCCCTGAAGGAATAGGGAGCAAACACGATTGTTG
* * * *
16523 AAGATTCTTCAAGATC-TATACTCCCTGAAGCAATACGGAGC
1 AAGATTGTTCGAG-TCTTATACTCCCTGAAGGAATAGGGAGC
16564 GAACGCGTGT
Statistics
Matches: 658, Mismatches: 72, Indels: 52
0.84 0.09 0.07
Matches are distributed among these distances:
53 3 0.00
54 120 0.18
55 409 0.62
56 118 0.18
57 8 0.01
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (55 bp):
AAGATTGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAAACACGATTGTTG
Found at i:24269 original size:15 final size:15
Alignment explanation
Indices: 24231--24269 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
24221 CTACATAGAG
24231 CGATGAAGAAGGTTC
1 CGATGAAGAAGGTTC
*
24246 TGATGAAGAAGGTTC
1 CGATGAAGAAGGTTC
*
24261 CGATAAAGA
1 CGATGAAGA
24270 GGAACAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.31, T:0.21
Consensus pattern (15 bp):
CGATGAAGAAGGTTC
Found at i:28293 original size:23 final size:22
Alignment explanation
Indices: 28251--28311 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 22
28241 ATAGGGCAGA
* *
28251 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
28273 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
28296 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
28312 CAGGGGAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:34807 original size:20 final size:21
Alignment explanation
Indices: 34775--34814 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
34765 TATGCAAGTG
34775 TAAAAATGCTAAATG-AAAAA
1 TAAAAATGCTAAATGCAAAAA
34795 TAAATAATG-TAAATGCAAAA
1 TAAA-AATGCTAAATGCAAAA
34815 GGCATCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (21 bp):
TAAAAATGCTAAATGCAAAAA
Found at i:35026 original size:21 final size:21
Alignment explanation
Indices: 35000--35043 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
34990 AGTAGAATGA
*
35000 TCTTGTGTATAGTGGGCCACC
1 TCTTGTGTATAGTGAGCCACC
35021 TCTTGTGTATAGTGAGCCACC
1 TCTTGTGTATAGTGAGCCACC
35042 TC
1 TC
35044 ACTCATCTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.34
Consensus pattern (21 bp):
TCTTGTGTATAGTGAGCCACC
Found at i:35078 original size:22 final size:22
Alignment explanation
Indices: 35053--35100 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
35043 CACTCATCTG
35053 TGCTATCTCTTCGCCCATCATA
1 TGCTATCTCTTCGCCCATCATA
35075 TGCTATCTCTTCGCCCATCATA
1 TGCTATCTCTTCGCCCATCATA
35097 TGCT
1 TGCT
35101 TGCATTCCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.17, C:0.35, G:0.10, T:0.38
Consensus pattern (22 bp):
TGCTATCTCTTCGCCCATCATA
Found at i:37276 original size:37 final size:39
Alignment explanation
Indices: 37235--37314 Score: 112
Period size: 36 Copynumber: 2.1 Consensus size: 39
37225 TATATCAAAG
* *
37235 ATAAAAATAAAATAAAATAAA-AATAGAATGAGAT-AAA
1 ATAAAAATAAAATAAAATAAACAAGAGAATAAGATAAAA
*
37272 AT-AAAATAAAATAAAATAAACAAGATAATAAGATAAAA
1 ATAAAAATAAAATAAAATAAACAAGAGAATAAGATAAAA
37310 ATAAA
1 ATAAA
37315 GCAAAAACCA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 18 0.49
37 12 0.32
38 5 0.14
39 2 0.05
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.19
Consensus pattern (39 bp):
ATAAAAATAAAATAAAATAAACAAGAGAATAAGATAAAA
Found at i:37307 original size:5 final size:5
Alignment explanation
Indices: 37238--37291 Score: 72
Period size: 5 Copynumber: 10.6 Consensus size: 5
37228 ATCAAAGATA
* * *
37238 AAAAT AAAAT AAAAT AAAAAT AGAAT GAGAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
37289 AAA
1 AAA
37292 CAAGATAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
5 37 0.88
6 5 0.12
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:38199 original size:35 final size:35
Alignment explanation
Indices: 38176--38248 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
38166 TCGAGCAATA
38176 AAAAATAAAA-TGTTAGAAAGTTAGTTCAAACAAAT
1 AAAAATAAAAGT-TTAGAAAGTTAGTTCAAACAAAT
*
38211 AAAAATAAAAGTTTAGAAAGTTAGTTCAAATAAA-
1 AAAAATAAAAGTTTAGAAAGTTAGTTCAAACAAAT
38245 AAAA
1 AAAA
38249 GAGTTAGCGG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
34 4 0.11
35 31 0.86
36 1 0.03
ACGTcount: A:0.60, C:0.04, G:0.11, T:0.25
Consensus pattern (35 bp):
AAAAATAAAAGTTTAGAAAGTTAGTTCAAACAAAT
Found at i:45216 original size:22 final size:22
Alignment explanation
Indices: 45188--45413 Score: 311
Period size: 22 Copynumber: 10.5 Consensus size: 22
45178 ATTTTAAAAT
45188 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
45210 TTTATTTTAAAATAT--A---A
1 TTTATTTTAAAATATGGATTGA
*** **
45227 AAAACATTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
**
45249 TTTATTTTAAAATATGGA-AAA
1 TTTATTTTAAAATATGGATTGA
* *
45270 ATTATTTTAAAATCTGGATTGA
1 TTTATTTTAAAATATGGATTGA
*
45292 TTTATTTTAAAATATGAATTGA
1 TTTATTTTAAAATATGGATTGA
45314 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
45336 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
*
45358 TTTATTTTTAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
45380 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
45402 TTTATTTTAAAA
1 TTTATTTTAAAA
45414 AATTTATTAT
Statistics
Matches: 176, Mismatches: 22, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
17 11 0.06
19 1 0.01
20 1 0.01
21 17 0.10
22 146 0.83
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.48
Consensus pattern (22 bp):
TTTATTTTAAAATATGGATTGA
Found at i:46855 original size:2 final size:2
Alignment explanation
Indices: 46850--46939 Score: 173
Period size: 2 Copynumber: 45.5 Consensus size: 2
46840 AATATTTTTA
46850 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
46892 AT AT AT A- 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
46933 AT AT AT A
1 AT AT AT A
46940 CTTATAATTT
Statistics
Matches: 87, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 86 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48455 original size:2 final size:2
Alignment explanation
Indices: 48444--48511 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
48434 GTTGGTCTCA
48444 AT AT -T 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
48485 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
48512 ACTCAATTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56957 original size:43 final size:44
Alignment explanation
Indices: 56900--56984 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 44
56890 TTTTAAAAAT
*
56900 TATTAATTTACTAATAGATAATAAAA-ATAATAAATTATTAATA
1 TATTAATTTACTAATAAATAATAAAATATAATAAATTATTAATA
* * * *
56943 TATTAGTTTTCTAATAAATAATAAAATATATTACATTATTAA
1 TATTAATTTACTAATAAATAATAAAATATAATAAATTATTAA
56985 CTAATTATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 23 0.64
44 13 0.36
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (44 bp):
TATTAATTTACTAATAAATAATAAAATATAATAAATTATTAATA
Found at i:59132 original size:2 final size:2
Alignment explanation
Indices: 59125--59154 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
59115 TACCACAACA
59125 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
59155 GATTATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59883 original size:2 final size:2
Alignment explanation
Indices: 59876--59902 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59866 TATAGACGTA
59876 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
59903 ATTTTCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61120 original size:29 final size:28
Alignment explanation
Indices: 61076--61145 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 28
61066 GCTTTATTGA
* *
61076 GTCTCTCGACTATTAGAAGTTATAAAATG
1 GTCTC-CGACTATTAGAAATTACAAAATG
61105 GTCCTCCGACTATTAGAAATTACAAAATG
1 GT-CTCCGACTATTAGAAATTACAAAATG
61134 GTCTCCGACTAT
1 GTCTCCGACTAT
61146 AGAGTGTTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 10 0.26
29 25 0.66
30 3 0.08
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (28 bp):
GTCTCCGACTATTAGAAATTACAAAATG
Found at i:61628 original size:26 final size:26
Alignment explanation
Indices: 61593--61646 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
61583 ATATTTATTA
*
61593 TATCTGAAATTATATGTT-AACATTTT
1 TATCTGAAATT-TATGTTAAAAATTTT
* *
61619 TATCTTAAATTTATTTTAAAAATTTT
1 TATCTGAAATTTATGTTAAAAATTTT
61645 TA
1 TA
61647 ATTGTTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (26 bp):
TATCTGAAATTTATGTTAAAAATTTT
Found at i:61644 original size:25 final size:26
Alignment explanation
Indices: 61593--61644 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
61583 ATATTTATTA
* *
61593 TATCTGAAATTATATGTTAACATTTT
1 TATCTGAAATTATATGTTAAAAATTT
* *
61619 TATCTTAAATT-TATTTTAAAAATTT
1 TATCTGAAATTATATGTTAAAAATTT
61644 T
1 T
61645 TAATTGTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (26 bp):
TATCTGAAATTATATGTTAAAAATTT
Found at i:64035 original size:4 final size:4
Alignment explanation
Indices: 64026--64060 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
64016 CCCATGACGC
64026 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
64061 CAGAATTGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:66806 original size:18 final size:18
Alignment explanation
Indices: 66783--66840 Score: 91
Period size: 18 Copynumber: 3.3 Consensus size: 18
66773 AAGGAGGGGT
66783 GGGAGAGAGTAGTAGTTA
1 GGGAGAGAGTAGTAGTTA
66801 GGGAGAGAGTAGTAGTTA
1 GGGAGAGAGTAGTAGTTA
* *
66819 GGGAG-GAGCAGTAGTCA
1 GGGAGAGAGTAGTAGTTA
66836 GGGAG
1 GGGAG
66841 GAGCAGATGG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
17 15 0.39
18 23 0.61
ACGTcount: A:0.31, C:0.03, G:0.48, T:0.17
Consensus pattern (18 bp):
GGGAGAGAGTAGTAGTTA
Found at i:67379 original size:23 final size:23
Alignment explanation
Indices: 67326--67412 Score: 95
Period size: 23 Copynumber: 3.8 Consensus size: 23
67316 CAAAAATGCA
*
67326 AATGGGTACCGATACCCC-TATG
1 AATGGGTACCAATACCCCTTATG
* * *
67348 TATGAGTATCAATACCCCTTATG
1 AATGGGTACCAATACCCCTTATG
** *
67371 AATGGGTATGAATGCCCCTTATG
1 AATGGGTACCAATACCCCTTATG
*
67394 AATGGGTACCGATACCCCT
1 AATGGGTACCAATACCCCT
67413 ATGGGTATCA
Statistics
Matches: 52, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 14 0.27
23 38 0.73
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (23 bp):
AATGGGTACCAATACCCCTTATG
Found at i:67418 original size:18 final size:18
Alignment explanation
Indices: 67395--67448 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
67385 CCCCTTATGA
67395 ATGGGTACCGATACCCCT
1 ATGGGTACCGATACCCCT
* *
67413 ATGGGTATCAATA-CCC-
1 ATGGGTACCGATACCCCT
*
67429 -TGTGTACCGATACCCCT
1 ATGGGTACCGATACCCCT
67446 ATG
1 ATG
67449 ACTGGGTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 9 0.32
16 3 0.11
17 3 0.11
18 13 0.46
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (18 bp):
ATGGGTACCGATACCCCT
Found at i:75997 original size:65 final size:64
Alignment explanation
Indices: 75926--76070 Score: 166
Period size: 64 Copynumber: 2.2 Consensus size: 64
75916 TACACTAGGG
* * *
75926 GTGCATCGATGCATAAAATACATTCGATGTTTTAAACA-AGCCTGGAGTGCATCGATGCATGGTT
1 GTGCATCGATACACAAAATACATTCGATG-TTTAAA-ATAGCCAGGAGTGCATCGATGCATGGTT
75990 T
64 T
* * ** **
75991 GTGCATCGGTACACAAAATGCATTCGATGTTTAAAATATTCAGGAGTGCATCGATGCATGCCTT
1 GTGCATCGATACACAAAATACATTCGATGTTTAAAATAGCCAGGAGTGCATCGATGCATGGTTT
* *
76055 GTGTATCGGTACACAA
1 GTGCATCGATACACAA
76071 TGCATTCAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
63 1 0.01
64 43 0.62
65 25 0.36
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (64 bp):
GTGCATCGATACACAAAATACATTCGATGTTTAAAATAGCCAGGAGTGCATCGATGCATGGTTT
Found at i:78792 original size:23 final size:21
Alignment explanation
Indices: 78721--78794 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 21
78711 AGAGTGTATT
78721 GATGCACATTCAGGACGTGCATC
1 GATGCACATTCAGGA--TGCATC
* * *
78744 GGTGCACCTTCATGGAT-AATC
1 GATGCACATTCA-GGATGCATC
78765 GATGCACATTCAAGGGATGCATC
1 GATGCACATTC-A-GGATGCATC
78788 GATGCAC
1 GATGCAC
78795 TAATGAGTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
21 12 0.29
22 6 0.15
23 20 0.49
24 3 0.07
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (21 bp):
GATGCACATTCAGGATGCATC
Found at i:84409 original size:22 final size:22
Alignment explanation
Indices: 84381--84492 Score: 84
Period size: 22 Copynumber: 5.6 Consensus size: 22
84371 CACCTACCTT
**
84381 ATACCCCTATGAATGGGTATTA
1 ATACCCCTATGAATGGGTACCA
*
84403 ATACCCCTATGAATGGGTACCG
1 ATACCCCTATGAATGGGTACCA
*
84425 ATACCCC--T--ATGGGTATCA
1 ATACCCCTATGAATGGGTACCA
*
84443 ATA-CCC--TG--T--GTACCG
1 ATACCCCTATGAATGGGTACCA
* *
84458 ATACCCCTATGACTGGGTATCA
1 ATACCCCTATGAATGGGTACCA
84480 ATACCCCTATGAA
1 ATACCCCTATGAA
84493 GGCTCAAACA
Statistics
Matches: 72, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
15 7 0.10
16 3 0.04
17 5 0.07
18 13 0.18
20 2 0.03
22 42 0.58
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (22 bp):
ATACCCCTATGAATGGGTACCA
Found at i:84438 original size:18 final size:18
Alignment explanation
Indices: 84415--84468 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
84405 ACCCCTATGA
84415 ATGGGTACCGATACCCCT
1 ATGGGTACCGATACCCCT
* *
84433 ATGGGTATCAATA-CCC-
1 ATGGGTACCGATACCCCT
*
84449 -TGTGTACCGATACCCCT
1 ATGGGTACCGATACCCCT
84466 ATG
1 ATG
84469 ACTGGGTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 9 0.32
16 3 0.11
17 3 0.11
18 13 0.46
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (18 bp):
ATGGGTACCGATACCCCT
Found at i:84723 original size:20 final size:22
Alignment explanation
Indices: 84685--84724 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
84675 GTTTTACAGA
84685 AAAATCATCCCCAAACGGCTTC
1 AAAATCATCCCCAAACGGCTTC
84707 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
84725 ATACACATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTTC
Found at i:87081 original size:18 final size:18
Alignment explanation
Indices: 87058--87116 Score: 82
Period size: 18 Copynumber: 3.1 Consensus size: 18
87048 TATATAATTG
87058 TTAACAATTGATATCTTT
1 TTAACAATTGATATCTTT
87076 TTAACAATTGATATCCTTT
1 TTAACAATTGATAT-CTTT
*
87095 TGTAAACAACTGATATCTTT
1 T-T-AACAATTGATATCTTT
87115 TT
1 TT
87117 CATTAAACAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 14 0.38
19 6 0.16
20 6 0.16
21 11 0.30
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47
Consensus pattern (18 bp):
TTAACAATTGATATCTTT
Found at i:87374 original size:23 final size:23
Alignment explanation
Indices: 87337--87401 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
87327 ATGGGTACTG
87337 ATACCCC-TATGAATGGGTATCA
1 ATACCCCTTATGAATGGGTATCA
*
87359 ATACCCCTTATGAATGAGTATCA
1 ATACCCCTTATGAATGGGTATCA
*
87382 ATACCCCTTATGAATTGGTA
1 ATACCCCTTATGAATGGGTA
87402 CTGATACCCC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 7 0.18
23 32 0.82
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (23 bp):
ATACCCCTTATGAATGGGTATCA
Found at i:87446 original size:33 final size:35
Alignment explanation
Indices: 87399--87465 Score: 93
Period size: 37 Copynumber: 1.9 Consensus size: 35
87389 TTATGAATTG
*
87399 GTACTGATACCCC-TA-TGGGTATCAATACCCTGT
1 GTACCGATACCCCTTACTGGGTATCAATACCCTGT
87432 GTACCGATACCCCTATTACTGGGTATCAATACCC
1 GTACCGATACCCC--TTACTGGGTATCAATACCC
87466 CTATGAAGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 12 0.41
36 2 0.07
37 15 0.52
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.28
Consensus pattern (35 bp):
GTACCGATACCCCTTACTGGGTATCAATACCCTGT
Found at i:87964 original size:33 final size:33
Alignment explanation
Indices: 87922--87991 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
87912 TTTTGTAAAG
* *
87922 GGGAAAGGTTCCAGCTGATCCCGTGAAAAGCTA
1 GGGAAAGGTTCCAGCTGAGCCCGTGAAAAACTA
* * *
87955 GGGAAAGGTTCTAGTTTAGCCCGTGAAAAACTA
1 GGGAAAGGTTCCAGCTGAGCCCGTGAAAAACTA
87988 GGGA
1 GGGA
87992 GTTGTAAAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.20
Consensus pattern (33 bp):
GGGAAAGGTTCCAGCTGAGCCCGTGAAAAACTA
Found at i:88523 original size:15 final size:15
Alignment explanation
Indices: 88499--88528 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
88489 GGGAAGTTGG
*
88499 ATTTTTAAAAAAAAT
1 ATTTTAAAAAAAAAT
88514 ATTTTAAAAAAAAAT
1 ATTTTAAAAAAAAAT
88529 TAAAAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTTTAAAAAAAAAT
Found at i:88538 original size:21 final size:22
Alignment explanation
Indices: 88508--88553 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 22
88498 GATTTTTAAA
88508 AAAAATATTTTAAAAAAAAAT-T
1 AAAAATA-TTTAAAAAAAAATAT
*
88530 AAAAA-ATTTAGAAAAAAATAT
1 AAAAATATTTAAAAAAAAATAT
88551 AAA
1 AAA
88554 CATGTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 5 0.23
22 5 0.23
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAAATATTTAAAAAAAAATAT
Found at i:89584 original size:14 final size:14
Alignment explanation
Indices: 89565--89594 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
89555 ATTTTTAATT
89565 TCGAGTTATTCAAG
1 TCGAGTTATTCAAG
*
89579 TCGAGTTATTCGAG
1 TCGAGTTATTCAAG
89593 TC
1 TC
89595 AACTCGAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (14 bp):
TCGAGTTATTCAAG
Found at i:91415 original size:28 final size:28
Alignment explanation
Indices: 91384--91450 Score: 134
Period size: 28 Copynumber: 2.4 Consensus size: 28
91374 TCTTTCTGTG
91384 ACACACTTTATCCATTTGTTCCCTTCAA
1 ACACACTTTATCCATTTGTTCCCTTCAA
91412 ACACACTTTATCCATTTGTTCCCTTCAA
1 ACACACTTTATCCATTTGTTCCCTTCAA
91440 ACACACTTTAT
1 ACACACTTTAT
91451 GTTATCAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.27, C:0.31, G:0.03, T:0.39
Consensus pattern (28 bp):
ACACACTTTATCCATTTGTTCCCTTCAA
Found at i:99967 original size:30 final size:30
Alignment explanation
Indices: 99912--99996 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
99902 TTTGACCAGT
*
99912 GACTAAAATGTA-AGTTTTG-AAAGTTTAGAG
1 GACTAAAAT-TATAATTTTGAAAAGTTTAG-G
*
99942 G-CT-AAAGTATAAATTTTGAAAAGTTTAGG
1 GACTAAAATTAT-AATTTTGAAAAGTTTAGG
*
99971 GACTAAAATTATAATTTTTAAAAGTT
1 GACTAAAATTATAATTTTGAAAAGTT
99997 ATATATTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
27 2 0.04
28 3 0.07
29 10 0.22
30 25 0.54
31 6 0.13
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.36
Consensus pattern (30 bp):
GACTAAAATTATAATTTTGAAAAGTTTAGG
Found at i:99992 original size:15 final size:17
Alignment explanation
Indices: 99974--100005 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
99964 GTTTAGGGAC
99974 TAAAA-TTATA-ATTTT
1 TAAAAGTTATATATTTT
99989 TAAAAGTTATATATTTT
1 TAAAAGTTATATATTTT
100006 ATCTTGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TAAAAGTTATATATTTT
Done.