Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002132.1 Hibiscus syriacus cultivar Beakdansim tig00004361_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: 97427
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1265 original size:23 final size:23
Alignment explanation
Indices: 1239--1291 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1229 CATTTTATAT
1239 GGCACTTCAGTGCAATTCTACGC
1 GGCACTTCAGTGCAATTCTACGC
* * *
1262 GGCACTTCGGTGTAATTCTACGT
1 GGCACTTCAGTGCAATTCTACGC
1285 GGCACTT
1 GGCACTT
1292 GGTGTATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (23 bp):
GGCACTTCAGTGCAATTCTACGC
Found at i:1305 original size:22 final size:23
Alignment explanation
Indices: 1239--1305 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
1229 CATTTTATAT
* * *
1239 GGCACTTCAGTGCAATTCTACGC
1 GGCACTTCGGTGTAATTATACGC
* *
1262 GGCACTTCGGTGTAATTCTACGT
1 GGCACTTCGGTGTAATTATACGC
*
1285 GGCACTT-GGTGTATTTATACG
1 GGCACTTCGGTGTAATTATACG
1306 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 12 0.31
23 27 0.69
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.33
Consensus pattern (23 bp):
GGCACTTCGGTGTAATTATACGC
Found at i:2409 original size:59 final size:60
Alignment explanation
Indices: 2310--2485 Score: 220
Period size: 58 Copynumber: 3.0 Consensus size: 60
2300 GTCTGTTCTA
* * *
2310 ATCTTCCATATTGGCCTCCTAGATCATAGTGGTCTAGGGTAAGTCCTTATGGATG-TCTGT
1 ATCTTCCATATTGGACTCCTAGATCCTAGTGGTATAGGGTAAGTCCTTATGGATGAT-TGT
*
2370 ATCTTCCATATTGGACT-CTATATCCTAGTGGTATAGGGTAAGTCC-TATGGATGATTGT
1 ATCTTCCATATTGGACTCCTAGATCCTAGTGGTATAGGGTAAGTCCTTATGGATGATTGT
* * * *
2428 ATCTTCCATA-TAGACTCCTAGAT-CTA-TAGGTTTAGGGTAAGCCCTTATGGATGCTTGT
1 ATCTTCCATATTGGACTCCTAGATCCTAGT-GGTATAGGGTAAGTCCTTATGGATGATTGT
2486 TCTCGGGTAT
Statistics
Matches: 103, Mismatches: 9, Indels: 10
0.84 0.07 0.08
Matches are distributed among these distances:
56 1 0.01
57 22 0.21
58 38 0.37
59 26 0.25
60 16 0.16
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (60 bp):
ATCTTCCATATTGGACTCCTAGATCCTAGTGGTATAGGGTAAGTCCTTATGGATGATTGT
Found at i:4763 original size:22 final size:25
Alignment explanation
Indices: 4735--4782 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 25
4725 AAACATCCTA
*
4735 TTAATAATAT-ATATGA-AC-ATAT
1 TTAATAACATCATATGACACGATAT
4757 TTAATAACATCATATGACACGATAT
1 TTAATAACATCATATGACACGATAT
4782 T
1 T
4783 AAGATAGTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 9 0.41
23 6 0.27
24 2 0.09
25 5 0.23
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (25 bp):
TTAATAACATCATATGACACGATAT
Found at i:37427 original size:121 final size:121
Alignment explanation
Indices: 37300--37541 Score: 457
Period size: 121 Copynumber: 2.0 Consensus size: 121
37290 TAAAACAATG
* *
37300 TTCGTAGATCGTCATAGAATTTTTCTAATTTAATTCTCTCCCCTTTAACAAAATGAGAAGATAAT
1 TTCGTAGATCGTCATAGAATTTTCCTAATTTAAATCTCTCCCCTTTAACAAAATGAGAAGATAAT
37365 CCATACAAAATGTAACTTTTAAAATAAAATTCATTTAATATTTTTAATTTAAAGTA
66 CCATACAAAATGTAACTTTTAAAATAAAATTCATTTAATATTTTTAATTTAAAGTA
37421 TTCGTAGATCGTCATAGAATTTTCCTAATTTAAATCTCTCCCCTTTAACAAAATGAGAAGATAAT
1 TTCGTAGATCGTCATAGAATTTTCCTAATTTAAATCTCTCCCCTTTAACAAAATGAGAAGATAAT
*
37486 CCATACAAAATGTAACTTTTAAAATAAAATTGATTTAATATTTTTAATTTAAAGTA
66 CCATACAAAATGTAACTTTTAAAATAAAATTCATTTAATATTTTTAATTTAAAGTA
37542 ATAATTTTAA
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 118 1.00
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (121 bp):
TTCGTAGATCGTCATAGAATTTTCCTAATTTAAATCTCTCCCCTTTAACAAAATGAGAAGATAAT
CCATACAAAATGTAACTTTTAAAATAAAATTCATTTAATATTTTTAATTTAAAGTA
Found at i:39081 original size:17 final size:17
Alignment explanation
Indices: 39059--39093 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
39049 TTTTAAATCA
39059 CAAAATAACCGAAAGAC
1 CAAAATAACCGAAAGAC
*
39076 CAAAATAACCGTAAGAC
1 CAAAATAACCGAAAGAC
39093 C
1 C
39094 CTCTAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.26, G:0.11, T:0.09
Consensus pattern (17 bp):
CAAAATAACCGAAAGAC
Found at i:42785 original size:51 final size:51
Alignment explanation
Indices: 42709--42811 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
42699 ATTATCATAA
42709 ATATTATTATTTTTAATATTTTTGATAAAAAAATCGATGAATGAATTTTGG
1 ATATTATTATTTTTAATATTTTTGATAAAAAAATCGATGAATGAATTTTGG
42760 ATATTATTATTTTTAATATTTTTGATAAAAAAATCGATGAATGAATTTTGG
1 ATATTATTATTTTTAATATTTTTGATAAAAAAATCGATGAATGAATTTTGG
42811 A
1 A
42812 GAGCAAGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (51 bp):
ATATTATTATTTTTAATATTTTTGATAAAAAAATCGATGAATGAATTTTGG
Found at i:44107 original size:13 final size:13
Alignment explanation
Indices: 44050--44110 Score: 61
Period size: 13 Copynumber: 4.5 Consensus size: 13
44040 TTTCTGTTTT
44050 AATATTTATTT-A
1 AATATTTATTTAA
* *
44062 AATATTAATCTAA
1 AATATTTATTTAA
*
44075 AATATTTATAAGTAA
1 AATATTTAT--TTAA
44090 TAATATTTATTTAA
1 -AATATTTATTTAA
44104 AATATTT
1 AATATTT
44111 TCAATTATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
12 9 0.22
13 16 0.40
14 3 0.08
15 3 0.08
16 9 0.22
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (13 bp):
AATATTTATTTAA
Found at i:44848 original size:23 final size:22
Alignment explanation
Indices: 44806--44889 Score: 141
Period size: 22 Copynumber: 3.7 Consensus size: 22
44796 AGCATTTTTT
44806 AAAATGATATATTTTTTTGATAGC
1 AAAATG-TATA-TTTTTTGATAGC
44830 AAAATGATATATTTTTTGATAGC
1 AAAATG-TATATTTTTTGATAGC
44853 AAAATGTATATTTTTTGATAGC
1 AAAATGTATATTTTTTGATAGC
44875 AAAATGTATATTTTT
1 AAAATGTATATTTTT
44890 CTTGAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
22 31 0.52
23 18 0.30
24 11 0.18
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (22 bp):
AAAATGTATATTTTTTGATAGC
Found at i:52084 original size:22 final size:21
Alignment explanation
Indices: 52054--52121 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 21
52044 GTAAAATATT
*
52054 GTATGAACAATACCATGAAAA
1 GTATAAACAATACCATGAAAA
52075 GTAATAAACAATACCATGAACAA
1 GT-ATAAACAATACCATGAA-AA
*
52098 TGT-TAAACAATACCATGAACA
1 -GTATAAACAATACCATGAAAA
52119 GTA
1 GTA
52122 CCGTGAAGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 2 0.05
21 3 0.07
22 32 0.78
23 2 0.05
24 2 0.05
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.21
Consensus pattern (21 bp):
GTATAAACAATACCATGAAAA
Found at i:57438 original size:2 final size:2
Alignment explanation
Indices: 57431--57478 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
57421 CATATACTAC
57431 TA TA TA TA 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 TA TA TA TA
57473 TA TA TA
1 TA TA TA
57479 AAAAAAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58526 original size:140 final size:140
Alignment explanation
Indices: 58369--58791 Score: 830
Period size: 140 Copynumber: 3.0 Consensus size: 140
58359 TAGAAATTTA
58369 AAATT-GGGTCTAAAATTTTAATTTTCTCTTTTTAAAAATAATGGGTATGCAAAATATTTATTTT
1 AAATTGGGGTCTAAAATTTTAATTTTCTCTTTTTAAAAATAATGGGTATGCAAAATATTTATTTT
58433 TTCTTGTTTCCTTAACATATCAAGTTAAATTTAATTATTTTCCCAAAATAATGGAATGCAACCGC
66 TTCTTGTTTCCTTAACATATCAAGTTAAATTTAATTATTTTCCCAAAATAATGGAATGCAACCGC
58498 CCTTGCCGTC
131 CCTTGCCGTC
58508 AAATTGGGGTCTAAAATTTTAATTTTCTCTTTTTAAAAATAATGGGTATGCAAAATATTTATTTT
1 AAATTGGGGTCTAAAATTTTAATTTTCTCTTTTTAAAAATAATGGGTATGCAAAATATTTATTTT
58573 TTCTTGTTTCCTTAACATATCAAGTTAAATTTAATTATTTTCCCAAAATAATGGAATGCAACCGC
66 TTCTTGTTTCCTTAACATATCAAGTTAAATTTAATTATTTTCCCAAAATAATGGAATGCAACCGC
58638 CCTTGCCGTC
131 CCTTGCCGTC
58648 AAATTGGGGTCTAAAATTTTAATTTTCTCTTTTTAAAAATAATGGGTATGCAAAATATTTATTTT
1 AAATTGGGGTCTAAAATTTTAATTTTCTCTTTTTAAAAATAATGGGTATGCAAAATATTTATTTT
*
58713 TTCTTGTTTCCTTAACATATCAAGTTAAATTTAATTATTTTCCCAAAATAATGGGATGCAACCGC
66 TTCTTGTTTCCTTAACATATCAAGTTAAATTTAATTATTTTCCCAAAATAATGGAATGCAACCGC
58778 CCTTGCCGTC
131 CCTTGCCGTC
58788 AAAT
1 AAAT
58792 CCATACATAC
Statistics
Matches: 282, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
139 5 0.02
140 277 0.98
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.41
Consensus pattern (140 bp):
AAATTGGGGTCTAAAATTTTAATTTTCTCTTTTTAAAAATAATGGGTATGCAAAATATTTATTTT
TTCTTGTTTCCTTAACATATCAAGTTAAATTTAATTATTTTCCCAAAATAATGGAATGCAACCGC
CCTTGCCGTC
Found at i:66652 original size:128 final size:123
Alignment explanation
Indices: 66474--66735 Score: 463
Period size: 128 Copynumber: 2.1 Consensus size: 123
66464 TACGACATAT
66474 TATATTATATTATTTATATTATATATATTATATTATATTATATTATATTATTATATTATATTATA
1 TATATTATATTATTTATATTATATATATTATATTATATTATATTATATTATTATATTATATTATA
66539 TTATATTATATTATATTATATATATTATATATATATATATTATATTATATATATTATTATA
66 TTATATTATATTATATTATATATATTATAT-TATAT-TATTATATTATATATA-TATTATA
66600 TATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATTATATTATATTA
1 TATATTATATTAT-TTATATTATA-TATATTATATTATATTATATTATATTATTATATTATATTA
*
66665 TATTATATTATATTATATTATATTTATTATATTATATTATTATATTATATATATATTATA
64 TATTATATTATATTATATTATATATATTATATTATATTATTATATTATATATATATTATA
66725 T-TATTATATTA
1 TATATTATATTA
66736 AGAAAGTAGC
Statistics
Matches: 133, Mismatches: 1, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
124 10 0.08
125 8 0.06
126 29 0.22
127 15 0.11
128 71 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (123 bp):
TATATTATATTATTTATATTATATATATTATATTATATTATATTATATTATTATATTATATTATA
TTATATTATATTATATTATATATATTATATTATATTATTATATTATATATATATTATA
Found at i:66709 original size:133 final size:131
Alignment explanation
Indices: 66470--66733 Score: 437
Period size: 133 Copynumber: 2.0 Consensus size: 131
66460 ATTTTACGAC
66470 ATATTATATTATATTATTTATATTATATATATTATATTATATTATATTATATTATTATATTATAT
1 ATATTATATTATATTATTTATATTATATATATTATATTATATTATATTATATTATTATATTATAT
66535 TATATTATATTATATTATATTATATATATTATATATATATATATTATAT-TATA-TATATTATTA
66 TATATTATATTATATTATATTATATATATTATATA-AT-TATATTATATATATATTATATTATTA
66598 TAT
129 TAT
66601 ATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTAT-TATATTATATTA
1 ATATTATATTATATTAT-TTATATTATA-TATATTATATTATATTATATTATAT-TATTATATTA
*
66665 TATTATATTATATTATATTATATT-TATTATATTATATTATTATATTATATATATATTATATTAT
63 TATTATATTATATTATATTATATTATA-TATATTATATAATTATATTATATATATATTATATTAT
66729 TATAT
127 TATAT
66734 TAAGAAAGTA
Statistics
Matches: 126, Mismatches: 1, Indels: 10
0.92 0.01 0.07
Matches are distributed among these distances:
131 27 0.21
132 19 0.15
133 80 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (131 bp):
ATATTATATTATATTATTTATATTATATATATTATATTATATTATATTATATTATTATATTATAT
TATATTATATTATATTATATTATATATATTATATAATTATATTATATATATATTATATTATTATA
T
Found at i:66735 original size:5 final size:5
Alignment explanation
Indices: 66470--66728 Score: 398
Period size: 5 Copynumber: 53.4 Consensus size: 5
66460 ATTTTACGAC
66470 ATATT ATATT ATATT AT-TT ATATT ATA-T ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
66518 ATA-T -TATT ATATT ATATT ATATT ATATT ATATT ATATT ATA-T ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
66565 ATA-T ATATAT ATATT ATATT ATA-T ATATT ATTATAT ATATT ATATT
1 ATATT ATAT-T ATATT ATATT ATATT ATATT A-TAT-T ATATT ATATT
66611 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATA-T -TATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
66659 ATATT ATATT ATATT ATATT ATATT ATATT -TATT ATATT ATA-T -TATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
66706 ATATT ATATAT ATATT ATATT AT
1 ATATT ATAT-T ATATT ATATT AT
66729 TATATTAAGA
Statistics
Matches: 238, Mismatches: 0, Indels: 32
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.03
4 30 0.13
5 184 0.77
6 16 0.07
7 2 0.01
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:67098 original size:3 final size:3
Alignment explanation
Indices: 67090--67186 Score: 167
Period size: 3 Copynumber: 32.0 Consensus size: 3
67080 CCATATTGAT
*
67090 TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
67136 TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
67184 TTA
1 TTA
67187 AATATATTAA
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
3 86 0.97
4 3 0.03
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:78228 original size:160 final size:159
Alignment explanation
Indices: 77947--78267 Score: 576
Period size: 160 Copynumber: 2.0 Consensus size: 159
77937 CTTTGACAGG
77947 CAGAATGGCTAGATGACAGATGTTATTATCTGAGTTTGATATTGTATATGTCAACCAAAAAGCGA
1 CAGAATGGCTAGA-GACAGATGTTATTATCTGAGTTTGATATTGTATATGTCAACCAAAAAGCGA
78012 TAAAGGAGTGTCATAGCTGATTTTCTGGCCAGTCGTGTATCAAATGATTATCAGCCTTTGAGTTT
65 TAAAGGAGTGTCATAGCTGATTTTCTGGCCAGTCGTGTATCAAATGATTATCAGCCTTTGAGTTT
78077 CAA-TTTCCCGATGAAGATTTGTTGTGCATAT
130 CAATTTTCCCGATGAAGA-TTGTT-TGCATAT
78108 CAGAATGGCTAGA-ACAGATGTTATTATCTGAGTTTGATATTGTATATGTCAACC-AAAAGCGAT
1 CAGAATGGCTAGAGACAGATGTTATTATCTGAGTTTGATATTGTATATGTCAACCAAAAAGCGAT
78171 AAAAGGAAGTGTCATAGCTGATTTTCTGGCCAGTCGTGTATCAAATGATTATCAGCCTTTGAGTT
66 -AAAGG-AGTGTCATAGCTGATTTTCTGGCCAGTCGTGTATCAAATGATTATCAGCCTTTGAGTT
78236 TCAATTTTCCCGATGAAGATTGTTTGCATAT
129 TCAATTTTCCCGATGAAGATTGTTTGCATAT
78267 C
1 C
78268 CATGAATGAA
Statistics
Matches: 157, Mismatches: 0, Indels: 8
0.95 0.00 0.05
Matches are distributed among these distances:
158 9 0.06
159 54 0.34
160 67 0.43
161 27 0.17
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.35
Consensus pattern (159 bp):
CAGAATGGCTAGAGACAGATGTTATTATCTGAGTTTGATATTGTATATGTCAACCAAAAAGCGAT
AAAGGAGTGTCATAGCTGATTTTCTGGCCAGTCGTGTATCAAATGATTATCAGCCTTTGAGTTTC
AATTTTCCCGATGAAGATTGTTTGCATAT
Found at i:79916 original size:9 final size:9
Alignment explanation
Indices: 79902--79941 Score: 57
Period size: 8 Copynumber: 4.6 Consensus size: 9
79892 AAGCTTGAAA
79902 AAAAAAGAG
1 AAAAAAGAG
79911 AAAAAAGA-
1 AAAAAAGAG
79919 AAAAAA-AG
1 AAAAAAGAG
79927 AAAAAAGAAG
1 AAAAAAG-AG
79937 AAAAA
1 AAAAA
79942 GGGGGGGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 1 0.04
8 12 0.43
9 8 0.29
10 7 0.25
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:79923 original size:16 final size:16
Alignment explanation
Indices: 79901--79942 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
79891 TAAGCTTGAA
79901 AAAAAAAGAGAAAAAAG
1 AAAAAAA-AGAAAAAAG
79918 AAAAAAAAGAAAAAAG
1 AAAAAAAAGAAAAAAG
*
79934 AAGAAAAAG
1 AAAAAAAAG
79943 GGGGGGTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAG
Found at i:79942 original size:9 final size:9
Alignment explanation
Indices: 79900--79941 Score: 66
Period size: 9 Copynumber: 4.6 Consensus size: 9
79890 TTAAGCTTGA
79900 AAAAAAAAG
1 AAAAAAAAG
*
79909 AGAAAAAAG
1 AAAAAAAAG
79918 AAAAAAAAG
1 AAAAAAAAG
79927 AAAAAAGAAG
1 AAAAAA-AAG
79937 AAAAA
1 AAAAA
79942 GGGGGGGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
9 22 0.73
10 8 0.27
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:81220 original size:83 final size:83
Alignment explanation
Indices: 81081--81843 Score: 1204
Period size: 83 Copynumber: 9.2 Consensus size: 83
81071 ACTGAAACAA
*
81081 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAATC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
81146 AATCATTGAATTTGAAAG
66 AATCATTGAATTTGAAAG
* * *
81164 ATGAATGTGCTCATAGCATCTCCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
*
81229 AATCATTGAAATT-AGAAG
66 AATCATTGAATTTGA-AAG
* *
81247 ATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAATC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
81312 AATCATTGAATTTGAAAG
66 AATCATTGAATTTGAAAG
* **
81330 ATGAATGTGCTCATAGCATCTCCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAATT
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
81395 AATCATTGAATTTGAAAG
66 AATCATTGAATTTGAAAG
* * *
81413 ATGAATGTGCTCATAGCATCTCCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
81478 AATCATTGAATTTGAAAG
66 AATCATTGAATTTGAAAG
* * *
81496 AGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGGTCTGATTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
* *
81561 AATCATTGAAATTGGAAG
66 AATCATTGAATTTGAAAG
* *
81579 ATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
* *
81644 AATCATTGAAATTGGAAG
66 AATCATTGAATTTGAAAG
* * *
81662 ATGAATATGATCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
* *
81727 AATCATTGAAATTGGAAG
66 AATCATTGAATTTGAAAG
* * * *
81745 ATGAATATGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
* *
81810 AATCATTAAATTTAAAAG
66 AATCATTGAATTTGAAAG
*
81828 ATGAATTTGCTCATAG
1 ATGAATGTGCTCATAG
81844 TAGAAATAAG
Statistics
Matches: 638, Mismatches: 40, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
82 1 0.00
83 636 1.00
84 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (83 bp):
ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
AATCATTGAATTTGAAAG
Found at i:82824 original size:113 final size:113
Alignment explanation
Indices: 82626--83478 Score: 1234
Period size: 113 Copynumber: 7.5 Consensus size: 113
82616 GCAAAGATTT
* *
82626 AAATCCATTACTTGATGGATTAGATTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
82691 AAGGAAGAAGAAGTTCATAATGAGAAAAATTTTTTCAACCTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * **
82739 AAATCCATCATTTGATGGATCAGCTTTTCCAG-AGGAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAA
* *
82803 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
65 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * * *
82852 AAATTCATCA-TATGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AAATCCATCACT-TGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA--C-TCATCT
*
82916 GAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAGA-TTTTTGCTC
62 GAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCA-ACCTTTTGCTC
* ** **
82968 AAATCCATCACTTGATAGATCCGCTTTTCCAG-AGGAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAA
83032 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
83081 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATATGAAG
1 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
83146 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
83194 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
83259 AAGAATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
83307 AAATCTATCACTTGATAGATTAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
83372 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAGA-TTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCA-ACCTTTTGCTC
* * ** *
83420 AAATCCATCACTTGATGGGTCAATTTTTCCAG--AGAAGTTCATAATGAGAAGAACTCATC
1 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATC
83479 AAGAGCTTAT
Statistics
Matches: 673, Mismatches: 54, Indels: 27
0.89 0.07 0.04
Matches are distributed among these distances:
111 1 0.00
112 26 0.04
113 544 0.81
114 4 0.01
115 2 0.00
116 94 0.14
117 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATTAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:83739 original size:3 final size:3
Alignment explanation
Indices: 83731--83812 Score: 137
Period size: 3 Copynumber: 27.0 Consensus size: 3
83721 CCATATTGAT
*
83731 TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
83777 TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
83813 AATATATTAA
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
3 71 0.96
4 3 0.04
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:84121 original size:19 final size:19
Alignment explanation
Indices: 84097--84135 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
84087 AACGCCGTCC
84097 ACGCCATGGCTATGGGGTG
1 ACGCCATGGCTATGGGGTG
84116 ACGCCATGGCTATGGGGTG
1 ACGCCATGGCTATGGGGTG
84135 A
1 A
84136 GTCACACTGG
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:0.18, C:0.21, G:0.41, T:0.21
Consensus pattern (19 bp):
ACGCCATGGCTATGGGGTG
Found at i:91583 original size:184 final size:184
Alignment explanation
Indices: 91265--91652 Score: 629
Period size: 184 Copynumber: 2.1 Consensus size: 184
91255 ATTAAATTTT
* *
91265 AAATTTTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
* * *
91330 TTTAAGATCTAATAACTTTTAAACCTATATCAATATTAATTAATTAAAAAAATTATATAAATATT
66 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATATAAATATT
*
91395 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
*
91449 AAATATTATATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
*
91514 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAATTTA-ACTGAAAT-
66 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATA-T-AAATA
*
91577 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTAATTAAA
129 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
* * *
91633 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
91653 AATTAGAAAA
Statistics
Matches: 189, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
183 9 0.05
184 176 0.93
185 4 0.02
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATATAAATATT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
Found at i:96197 original size:46 final size:45
Alignment explanation
Indices: 96099--96204 Score: 133
Period size: 45 Copynumber: 2.3 Consensus size: 45
96089 GTGCACTAAG
* * *
96099 AGTGCAACGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
* *
96144 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTC
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCAC
*
96190 AGTGCATCGGTGCAT
1 AGTGCATCGATGCAT
96205 GGTATGTGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
45 28 0.53
46 22 0.42
47 3 0.06
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (45 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
Found at i:96279 original size:65 final size:63
Alignment explanation
Indices: 96145--96290 Score: 163
Period size: 65 Copynumber: 2.3 Consensus size: 63
96135 AATAGCCAGA
*
96145 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGTAT
* **
96210 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGG-A
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGGTA
96272 TT
63 -T
*
96274 GGTGCATCGGTGCATCA
1 -GTGCATCGATGCATCA
96291 CTTTGATAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
62 3 0.04
63 4 0.06
64 21 0.30
65 42 0.60
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTAT
Done.