Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009417.1 Hibiscus syriacus cultivar Beakdansim tig00113371_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: 74897
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:824 original size:29 final size:29
Alignment explanation
Indices: 760--817 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
750 TCAATAACTG
760 AAATAAATACAACATACAAATTAGAAACC
1 AAATAAATACAACATACAAATTAGAAACC
*
789 AAATAAATACAAGATACAAATTAGAAACC
1 AAATAAATACAACATACAAATTAGAAACC
818 GATTAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.17
Consensus pattern (29 bp):
AAATAAATACAACATACAAATTAGAAACC
Found at i:2603 original size:2 final size:2
Alignment explanation
Indices: 2592--2623 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2582 AAATTTATTA
2592 AT AT -T 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 AT AT AT A
2624 ATAATTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3686 original size:64 final size:63
Alignment explanation
Indices: 3613--3733 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 63
3603 ATTGTTCAAG
* *
3613 GTGTATCGATGCACATGAAGTGCATCGATGCA-CTAATTTAAAATAAAAACATCGAATGTCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCATCCAA-TT-AAATAAAAACATCGAATGTCATCA
* * *
3677 GTGTATCGATGCACAAGTAGTGCATCGATGCATCCCATTAAATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATG
3734 AGATTTATGC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
63 17 0.33
64 32 0.63
65 2 0.04
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATGTCATCA
Found at i:4432 original size:23 final size:23
Alignment explanation
Indices: 4415--4476 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
4405 ACAATCTTAT
*
4415 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTTCGGTGCAATTCTAC
*
4438 GTGGCACTTCGGTGCAATTCTAC
1 ATGGCACTTCGGTGCAATTCTAC
*
4461 GTGGCACTTCGGTGCA
1 ATGGCACTTCGGTGCA
4477 TTTATATGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.26, G:0.27, T:0.27
Consensus pattern (23 bp):
ATGGCACTTCGGTGCAATTCTAC
Found at i:11390 original size:23 final size:23
Alignment explanation
Indices: 11322--11382 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
11312 CAATCTTATA
* *
11322 TGGCACTACGGTACAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
11345 CGGCACTTCAGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
11368 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
11383 TTTATACGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:12640 original size:31 final size:31
Alignment explanation
Indices: 12569--12640 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
12559 TAAAGAACTA
* * * * *
12569 AAATTGAACGGACTGATAACGTTAGAGACTG
1 AAATTGGACGAACCGATAACATTAGAGAATG
* *
12600 AAATCGGACGAACCGATAACATTAGAGAATT
1 AAATTGGACGAACCGATAACATTAGAGAATG
12631 AAATTGGACG
1 AAATTGGACG
12641 GACTGATGGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.21
Consensus pattern (31 bp):
AAATTGGACGAACCGATAACATTAGAGAATG
Found at i:12760 original size:24 final size:24
Alignment explanation
Indices: 12733--12782 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
12723 CATAATTTAC
12733 CATTATATACCTGACAATGTACTG
1 CATTATATACCTGACAATGTACTG
12757 CATTATATACCTGACAATGTACTG
1 CATTATATACCTGACAATGTACTG
12781 CA
1 CA
12783 GGATATAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (24 bp):
CATTATATACCTGACAATGTACTG
Found at i:12788 original size:24 final size:24
Alignment explanation
Indices: 12737--12789 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
12727 ATTTACCATT
**
12737 ATATACCTGACAATGTACTGCATT
1 ATATACCTGACAATGTACTGCAGG
12761 ATATACCTGACAATGTACTGCAGG
1 ATATACCTGACAATGTACTGCAGG
12785 ATATA
1 ATATA
12790 ACGAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (24 bp):
ATATACCTGACAATGTACTGCAGG
Found at i:17534 original size:14 final size:15
Alignment explanation
Indices: 17515--17548 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
17505 AATTATTATT
17515 AAATATTA-TTTAAA
1 AAATATTATTTTAAA
17529 AAATATTATTTTAAA
1 AAATATTATTTTAAA
17544 AAATA
1 AAATA
17549 CTAATAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATATTATTTTAAA
Found at i:21334 original size:26 final size:27
Alignment explanation
Indices: 21289--21339 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
21279 GAAATTTGTA
*
21289 AAATATATGATAATATTTTAGAAAAGT
1 AAATATATGATAATATTTTAAAAAAGT
*
21316 AAATATATTAT-ATATTTTAAAAAA
1 AAATATATGATAATATTTTAAAAAA
21340 TGATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (27 bp):
AAATATATGATAATATTTTAAAAAAGT
Found at i:21582 original size:18 final size:19
Alignment explanation
Indices: 21548--21583 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21538 AAAATAATAC
*
21548 ATTTTTATTAATTATAGAG
1 ATTTTTATTAATAATAGAG
21567 ATTTTTATT-ATAATAGA
1 ATTTTTATTAATAATAGA
21584 AGGAAGGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
ATTTTTATTAATAATAGAG
Found at i:21843 original size:6 final size:7
Alignment explanation
Indices: 21834--21892 Score: 63
Period size: 6 Copynumber: 8.6 Consensus size: 7
21824 AAATTAAATT
21834 TATTA-A
1 TATTATA
21840 TATTATA
1 TATTATA
21847 TA-TATA
1 TATTATA
21853 TA-TATA
1 TATTATA
21859 TA-TATA
1 TATTATA
21865 TATATATA
1 TAT-TATA
21873 TATATATA
1 TAT-TATA
21881 TATATATA
1 TAT-TATA
21889 TATT
1 TATT
21893 TATCGGGACG
Statistics
Matches: 50, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
6 23 0.46
7 4 0.08
8 23 0.46
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
TATTATA
Found at i:21850 original size:2 final size:2
Alignment explanation
Indices: 21839--21891 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
21829 AAATTTATTA
21839 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
21880 AT AT AT AT AT AT
1 AT AT AT AT AT AT
21892 TTATCGGGAC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:25875 original size:3 final size:3
Alignment explanation
Indices: 25867--25895 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
25857 TTGAACCTCA
25867 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
25896 AACTTTCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:27238 original size:19 final size:18
Alignment explanation
Indices: 27212--27247 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
27202 GGCTTAATTG
27212 ATTTTTTAAAATTTAATA
1 ATTTTTTAAAATTTAATA
*
27230 ATTTATTTAATATTTAAT
1 ATTT-TTTAAAATTTAAT
27248 TAAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTTTAAAATTTAATA
Found at i:27302 original size:22 final size:23
Alignment explanation
Indices: 27274--27320 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
27264 TAATTTTTCA
*
27274 ATAAATTATAAT-TTTTTATTTT
1 ATAAATTATAATATTTTGATTTT
*
27296 ATAAATTCTAATATTTTGATTTT
1 ATAAATTATAATATTTTGATTTT
27319 AT
1 AT
27321 TTATTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
ATAAATTATAATATTTTGATTTT
Found at i:27348 original size:23 final size:22
Alignment explanation
Indices: 27315--27367 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
27305 AATATTTTGA
27315 TTTT-ATTTATTCTTTTAA-AAC
1 TTTTAATTTATT-TTTTAATAAC
*
27336 TTTTAATTATATTTTTTAATAAT
1 TTTTAATT-TATTTTTTAATAAC
27359 TTTTAATTT
1 TTTTAATTT
27368 TTAAAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 4 0.14
22 10 0.36
23 14 0.50
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTAATTTATTTTTTAATAAC
Found at i:27370 original size:17 final size:17
Alignment explanation
Indices: 27348--27381 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
27338 TTAATTATAT
* *
27348 TTTTTAATAATTTTTAA
1 TTTTTAAAAATATTTAA
27365 TTTTTAAAAATATTTAA
1 TTTTTAAAAATATTTAA
27382 ATATCTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTTAAAAATATTTAA
Found at i:28698 original size:19 final size:19
Alignment explanation
Indices: 28658--28697 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
28648 AAATGATTGT
*
28658 AAATTTTTAATAAAAGTTA
1 AAATTATTAATAAAAGTTA
*
28677 AAATTATTAATCAAA-TTA
1 AAATTATTAATAAAAGTTA
28695 AAA
1 AAA
28698 AGAGTATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AAATTATTAATAAAAGTTA
Found at i:32846 original size:3 final size:3
Alignment explanation
Indices: 32813--32948 Score: 197
Period size: 3 Copynumber: 46.0 Consensus size: 3
32803 GAGGAAGGAG
* * *
32813 GAA GAA -AA GAA TAA GAA GGA GAA GTA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
32860 -AA GAG GAA GGAG GAA -AA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
32904 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
32949 TGACGAGTTA
Statistics
Matches: 119, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
2 6 0.05
3 111 0.93
4 2 0.02
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:34013 original size:46 final size:46
Alignment explanation
Indices: 33929--34029 Score: 157
Period size: 46 Copynumber: 2.2 Consensus size: 46
33919 CATCTTTCCC
* *
33929 GAGGCCATTTATTGCAATAATAATTCACCGTTTAAACTACTTTTCA
1 GAGGCCATTTATTGCAATAATAATGCACCGGTTAAACTACTTTTCA
* * *
33975 GAGGTCATTTATTGCAATAATAATGCACTGGTTCAACTACTTTTCA
1 GAGGCCATTTATTGCAATAATAATGCACCGGTTAAACTACTTTTCA
34021 GAGGCCATT
1 GAGGCCATT
34030 CAATGCAGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (46 bp):
GAGGCCATTTATTGCAATAATAATGCACCGGTTAAACTACTTTTCA
Found at i:34262 original size:34 final size:35
Alignment explanation
Indices: 34200--34265 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 35
34190 TTAATCACTA
* *
34200 TTTTACCTACTTTTCGGTGCTCAATCAATGCACCG
1 TTTTACCTACTTTTCAGAGCTCAATCAATGCACCG
* *
34235 TTTTAGCTACTTTT-AGAGCTCATTCAATGCA
1 TTTTACCTACTTTTCAGAGCTCAATCAATGCA
34266 AAATTCAAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 14 0.52
35 13 0.48
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (35 bp):
TTTTACCTACTTTTCAGAGCTCAATCAATGCACCG
Found at i:41080 original size:23 final size:26
Alignment explanation
Indices: 41040--41090 Score: 72
Period size: 23 Copynumber: 2.1 Consensus size: 26
41030 CTCATGAGTT
*
41040 AAAATTGAGTTTAATTAGA-A-AAAC
1 AAAATTGAGTCTAATTAGAGAGAAAC
41064 AAAATTG-GTCTAATTAGAGAGAAAC
1 AAAATTGAGTCTAATTAGAGAGAAAC
41089 AA
1 AA
41091 GATATTTGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 10 0.42
24 8 0.33
25 6 0.25
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (26 bp):
AAAATTGAGTCTAATTAGAGAGAAAC
Found at i:42408 original size:2 final size:2
Alignment explanation
Indices: 42397--42448 Score: 58
Period size: 2 Copynumber: 27.5 Consensus size: 2
42387 TAAAATCTTG
*
42397 AT AT AT -T AT AT AT A- AA AT AT -T GAT AT AT -T 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
42436 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
42449 AGGTATGTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
1 4 0.09
2 39 0.89
3 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42434 original size:24 final size:22
Alignment explanation
Indices: 42387--42432 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
42377 CAAAGCTTAT
*
42387 TAAAATCTTGATATATTATATA
1 TAAAATATTGATATATTATATA
42409 TAAAATATTGATATATTATATA
1 TAAAATATTGATATATTATATA
42431 TA
1 TA
42433 TATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (22 bp):
TAAAATATTGATATATTATATA
Found at i:49891 original size:14 final size:14
Alignment explanation
Indices: 49874--49925 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
49864 GTTAAAAAAA
49874 TATTATTAAATTAT
1 TATTATTAAATTAT
49888 TATTATTAAATTAT
1 TATTATTAAATTAT
* *
49902 TATTATTAATTTTAG
1 TATTATTAA-ATTAT
49917 TATTATTAA
1 TATTATTAA
49926 GTGTGTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
14 23 0.66
15 12 0.34
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
TATTATTAAATTAT
Found at i:62872 original size:6 final size:6
Alignment explanation
Indices: 62861--62914 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
62851 AAATAAAAAG
* *
62861 ATGAAA ATGAAAA ATGAAA AGGAAA A--AAA ATGAAAA ATGAAA AAG-AA
1 ATGAAA ATG-AAA ATGAAA ATGAAA ATGAAA ATG-AAA ATGAAA ATGAAA
62908 ATGAAA A
1 ATGAAA A
62915 AATAAAAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
4 4 0.10
5 4 0.10
6 20 0.50
7 12 0.30
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (6 bp):
ATGAAA
Found at i:62876 original size:7 final size:7
Alignment explanation
Indices: 62851--62928 Score: 51
Period size: 7 Copynumber: 11.4 Consensus size: 7
62841 AAAAGGGAAC
*
62851 AAATAAA
1 AAATGAA
62858 AAGATG-A
1 AA-ATGAA
62865 AAATGAA
1 AAATGAA
62872 AAATGAA
1 AAATGAA
**
62879 AAGGAAAAA
1 AA--ATGAA
62888 AAATGAA
1 AAATGAA
62895 AAATGAA
1 AAATGAA
62902 AAA-G--
1 AAATGAA
62906 AAATGAAA
1 AAATG-AA
62914 AAAT-AA
1 AAATGAA
62920 AAA-GAA
1 AAATGAA
62926 AAA
1 AAA
62929 GGAGGGTTTG
Statistics
Matches: 57, Mismatches: 5, Indels: 19
0.70 0.06 0.23
Matches are distributed among these distances:
4 3 0.05
5 1 0.02
6 14 0.25
7 28 0.49
8 6 0.11
9 5 0.09
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (7 bp):
AAATGAA
Found at i:62894 original size:23 final size:23
Alignment explanation
Indices: 62864--62929 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 23
62854 TAAAAAGATG
*
62864 AAAATGAAAAATGAAAAGGAAAA
1 AAAATGAAAAATGAAAAAGAAAA
62887 AAAATGAAAAATGAAAAAGAAATGAA
1 AAAATGAAAAATGAAAAAG-AA--AA
62913 AAAAT-AAAAA-GAAAAAG
1 AAAATGAAAAATGAAAAAG
62930 GAGGGTTTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
23 18 0.46
24 9 0.23
25 5 0.13
26 7 0.18
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (23 bp):
AAAATGAAAAATGAAAAAGAAAA
Found at i:62909 original size:18 final size:18
Alignment explanation
Indices: 62872--62926 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
62862 TGAAAATGAA
*
62872 AAATG-AAAAGGAAAAA-
1 AAATGAAAAATGAAAAAG
62888 AAATGAAAAATGAAAAAG
1 AAATGAAAAATGAAAAAG
62906 AAATGAAAAAAT-AAAAAG
1 AAATG-AAAAATGAAAAAG
62924 AAA
1 AAA
62927 AAGGAGGGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
16 5 0.14
17 10 0.29
18 14 0.40
19 6 0.17
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (18 bp):
AAATGAAAAATGAAAAAG
Found at i:64028 original size:135 final size:136
Alignment explanation
Indices: 63783--64131 Score: 549
Period size: 135 Copynumber: 2.6 Consensus size: 136
63773 GGTGAACCAG
* *
63783 CATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATG
* * *
63848 AGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTTGAATCAGTGACACCTTGCTTGAAG
66 AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
*
63913 GATCAG
131 GATCAA
*
63919 TATTTCCAATGGAGAGTTCATAATGA-AAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATG
* *
63983 AGAAGAGCTTGTTCGACCTATCACTCGATTCATAACATTTCGAATCAGTGACACCTCGCTTGAGG
66 AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
64048 GATCAA
131 GATCAA
* ** * *
64054 CATTTCCAGTAAAGAGTTCATAATGAGAAGAACTCATCAAAC-GAGGAAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATG
*
64118 AGAAGAACTTGTTC
66 AGAAGAGCTTGTTC
64132 AACTTCGCAT
Statistics
Matches: 196, Mismatches: 16, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
135 158 0.81
136 38 0.19
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (136 bp):
CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATG
AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
GATCAA
Found at i:64249 original size:225 final size:219
Alignment explanation
Indices: 63920--64349 Score: 634
Period size: 225 Copynumber: 1.9 Consensus size: 219
63910 AAGGATCAGT
*
63920 ATTTCCAATGGAGAGTTCATAATGAAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAG
1 ATTTCCAATGGAGAGCTCATAATGAAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAG
*
63985 AAGAGCTTGTTCGACCTATCACTCGATTCATAACATTTCGAATCAGTGACACCTCGCTTGAGGGA
66 AAGAGCTTGTTCGACCTATCACTCGATTCATAACATTTCGAATCAGTGAC-CCTAGCTTGAGGGA
64050 TCAACATTTCCAGTAAAGAGTTCATAATGAGAAGAACTCAT-CAAACGAGGAAGAAGAAGTTCAT
130 TCAACATTTCCAG--AAGAGTTCATAATGAGAAGAACTCATCCAAA--AGG-AG-A-AAGTTCAT
64114 AATGAGAAGAACTTGTTCAACTTCGCATCAAC
188 AATGAGAAGAACTTGTTCAACTTCGCATCAAC
* * *
64146 ATTTTCAATGGAGGGCTCATAATGAGAAGAACTCGTCCGAA-AGAGGGAGAAGAAGTTCATAATG
1 ATTTCCAATGGAGAGCTCATAATGA-AAGAACTCATCC-AACAGAGGGAGAAGAAGTTCATAATG
* *
64210 AG-A-AGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATTAGTGACCCTAGCTTGAGGG
64 AGAAGAGCTTGTTCGACCTATCACTCGATTCATAACATTTCGAATCAGTGACCCTAGCTTGAGGG
** * * *
64273 ATTGATATTTTCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAAGTTCATAATGAG
129 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCAAAAGGAGAAAGTTCATAATGAG
64338 AAGAACTTGTTC
194 AAGAACTTGTTC
64350 CTTTCAAGTC
Statistics
Matches: 189, Mismatches: 12, Indels: 14
0.88 0.06 0.07
Matches are distributed among these distances:
218 26 0.14
219 1 0.01
220 2 0.01
221 3 0.02
222 26 0.14
223 3 0.02
224 22 0.12
225 45 0.24
226 23 0.12
227 36 0.19
228 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.25
Consensus pattern (219 bp):
ATTTCCAATGGAGAGCTCATAATGAAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAG
AAGAGCTTGTTCGACCTATCACTCGATTCATAACATTTCGAATCAGTGACCCTAGCTTGAGGGAT
CAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCAAAAGGAGAAAGTTCATAATGAGAA
GAACTTGTTCAACTTCGCATCAAC
Found at i:64541 original size:92 final size:89
Alignment explanation
Indices: 64378--64542 Score: 251
Period size: 92 Copynumber: 1.8 Consensus size: 89
64368 AAAGAGATGG
64378 ATCAACATTTCCAATGGAGTTCATAATAAGAAGAACTCATCCAATGAGAGAGAAGAAGTTCATAA
1 ATCAACATTTCCAATGGAGTTCATAATAAGAAGAACTCATCCAATGAGAGAGAAGAAGTTCATAA
64443 TGAGAAGAACTTGTTCAACTTCGC
66 TGAGAAGAACTTGTTCAACTTCGC
* * * *
64467 ATCAATATTTTCAATGGAGAGTTCATAATGAA-AAGAACTCATCCGATAGAGGGAGAAGAAGTTC
1 ATCAACATTTCCAAT-G-GAGTTCATAAT-AAGAAGAACTCATCCAAT-GAGAGAGAAGAAGTTC
64531 ATAATGAGAAGA
62 ATAATGAGAAGA
64543 GTTTTTTGAC
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
89 13 0.19
90 1 0.01
91 25 0.37
92 29 0.43
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (89 bp):
ATCAACATTTCCAATGGAGTTCATAATAAGAAGAACTCATCCAATGAGAGAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACTTCGC
Found at i:64745 original size:330 final size:326
Alignment explanation
Indices: 64051--64745 Score: 1007
Period size: 327 Copynumber: 2.1 Consensus size: 326
64041 CTTGAGGGAT
64051 CAACATTTCCAGTAAAGAGTTCATAATGAGAAGAACTCATCAAACGAGGAAGAAGAAGTTCATAA
1 CAACATTTCC--T-AAGAGTTCATAATGAGAAGAACTCATCAAACGAGGAAGAAGAAGTTCATAA
* * *
64116 TGAGAAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGGGCTCATAATGAGAAGAACTCG
63 TGAGAAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGAACTCA
*
64181 TCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGCTTGTTCGACCTATCACTCGATTCATGACAT
128 TCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGCTTGTTCGACCTATCACTCGATTCACGACAT
* * * * *
64246 TTCGAATTAGTGACCCTAGCTTGAGGGATTGATATTTTCAGAAGAGTTCATAATGAGAAGAACTC
193 TTCGAATCAATGACCCTAGCTTGAGGGATCGACATTTCCAGAAGAGTTCATAATGAGAAGAACTC
* * * *
64311 ATCCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAGTCCATCACAGAAAGAGAT
258 ATCATAAAGGAGAAAGTTCATAATGAGAAGAACTTATTCCTTTCAAATCCACCACAGAAAGAGAT
* *
64376 GGAT
323 GAAC
* * *
64380 CAACATTTCC-AATGGAGTTCATAATAAGAAGAACTCATCCAATGA-GAGAGAAGAAGTTCATAA
1 CAACATTTCCTAA--GAGTTCATAATGAGAAGAACTCATCAAACGAGGA-AGAAGAAGTTCATAA
* *
64443 TGAGAAGAACTTGTTCAACTTCGCATCAATATTTTCAATGGAGAGTTCATAATGAAAAGAACTCA
63 TGAGAAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGAACTCA
* * * * *
64508 TCCGATAGAGGGAGAAGAAGTTCATAATGAGAAGAGTTTTTTGACCTATCACTTGATTCACGACA
128 TCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAG-CTTGTTCGACCTATCACTCGATTCACGACA
* *
64573 TTTCGAATCAATGATGCCTCGCTTGAGGGATCGACATTTCCATGAAGAGTTCATAATGAGAAGAA
192 TTTCGAATCAATGA-CCCTAGCTTGAGGGATCGACATTTCCA-GAAGAGTTCATAATGAGAAGAA
* **
64638 CTCATCATAAAGGAGAAAGTTCATAATGAGAAGAACTTATTCCTTTCAAATTCACCACAGATGGA
255 CTCATCATAAAGGAGAAAGTTCATAATGAGAAGAACTTATTCCTTTCAAATCCACCACAGAAAGA
*
64703 GGTGAAC
320 GATGAAC
64710 CAACATTTCCTGAAGAGTTCATAATGAGAAGAACTC
1 CAACATTTCCT-AAGAGTTCATAATGAGAAGAACTC
64746 GTCCTAAAGG
Statistics
Matches: 326, Mismatches: 32, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
325 2 0.01
326 2 0.01
327 136 0.42
328 37 0.11
329 32 0.10
330 115 0.35
332 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (326 bp):
CAACATTTCCTAAGAGTTCATAATGAGAAGAACTCATCAAACGAGGAAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGAACTCATCC
GAAAGAGGGAGAAGAAGTTCATAATGAGAAGCTTGTTCGACCTATCACTCGATTCACGACATTTC
GAATCAATGACCCTAGCTTGAGGGATCGACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATC
ATAAAGGAGAAAGTTCATAATGAGAAGAACTTATTCCTTTCAAATCCACCACAGAAAGAGATGAA
C
Found at i:64935 original size:13 final size:13
Alignment explanation
Indices: 64909--64957 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
64899 GTTAAAAAAA
64909 TATTATTAAATTAT
1 TATTATT-AATTAT
64923 TATTATTAATTAT
1 TATTATTAATTAT
** *
64936 TATTATTTTTTAG
1 TATTATTAATTAT
64949 TATTATTAA
1 TATTATTAA
64958 GTGTGTTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 23 0.77
14 7 0.23
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TATTATTAATTAT
Found at i:64939 original size:16 final size:15
Alignment explanation
Indices: 64909--64956 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
64899 GTTAAAAAAA
64909 TATTATTAA-ATTAT
1 TATTATTAATATTAT
64923 TATTATTAATTATTAT
1 TATTATTAA-TATTAT
* *
64939 TATTTTTTAGTATTAT
1 TA-TTATTAATATTAT
64955 TA
1 TA
64957 AGTGTGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 9 0.31
16 15 0.52
17 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (15 bp):
TATTATTAATATTAT
Found at i:67369 original size:93 final size:94
Alignment explanation
Indices: 67233--67419 Score: 315
Period size: 93 Copynumber: 2.0 Consensus size: 94
67223 TCACTTTTAT
* *
67233 TTTCGTTATACTTAAGGGTATTTTTTCATTTTAGCCAATTAGAAGTATTTTAGTAACTTATCCTA
1 TTTCGTTATACTTAAGGGTATTTTTTAATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTA
* *
67298 AATCTTTTATTATTAGA-CCCTTAATCCAC
66 AATCTTTTATTA-GACATCCCTTAATCCAC
67327 TTTCGTTATACTTAAGGGTA-TTTTTAATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTA
1 TTTCGTTATACTTAAGGGTATTTTTTAATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTA
67391 AATCTTTTATTAGACATCCCTTAATCCAC
66 AATCTTTTATTAGACATCCCTTAATCCAC
67420 AAACATTTAG
Statistics
Matches: 88, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
92 2 0.02
93 66 0.75
94 20 0.23
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.45
Consensus pattern (94 bp):
TTTCGTTATACTTAAGGGTATTTTTTAATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTA
AATCTTTTATTAGACATCCCTTAATCCAC
Found at i:67609 original size:20 final size:20
Alignment explanation
Indices: 67581--67631 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
67571 TCTACCTTCG
* *
67581 ATATGGATACTTGATGAACA
1 ATATCGATACTTCATGAACA
*
67601 ATATCGATACTTCTTGAACA
1 ATATCGATACTTCATGAACA
*
67621 ATATTGATACT
1 ATATCGATACT
67632 CTTAGTCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (20 bp):
ATATCGATACTTCATGAACA
Found at i:68582 original size:2 final size:2
Alignment explanation
Indices: 68575--68611 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
68565 CATGACCTCA
68575 AT AT AT AT AT 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 AT AT AT AT AT A
68612 GCTTGATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:71123 original size:32 final size:32
Alignment explanation
Indices: 71086--71228 Score: 96
Period size: 32 Copynumber: 4.5 Consensus size: 32
71076 AACTGACGAA
*
71086 TGATATGTATCACATCACTCAAAGTGATGATG
1 TGATATGTATCACATCACTCAAAATGATGATG
* * **
71118 TGATATTTGTCATGTCACTCAAAATGATGATG
1 TGATATGTATCACATCACTCAAAATGATGATG
* * * *
71150 TTCATATG--TCAAATCATTTAAAATGATGAT-
1 -TGATATGTATCACATCACTCAAAATGATGATG
* * * * * *
71180 TAACATATATCACATCACTTAAAGTAATGATG
1 TGATATGTATCACATCACTCAAAATGATGATG
*
71212 T-AGTATGTATCATATCA
1 TGA-TATGTATCACATCA
71229 ATAATTAGAT
Statistics
Matches: 85, Mismatches: 21, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
29 4 0.05
31 37 0.44
32 39 0.46
33 5 0.06
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (32 bp):
TGATATGTATCACATCACTCAAAATGATGATG
Found at i:71187 original size:31 final size:31
Alignment explanation
Indices: 71132--71213 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
71122 ATTTGTCATG
* * *
71132 TCACTCAAAATGATGATGTTCATATGTCAAA
1 TCACTTAAAATGATGATGTACATATATCAAA
* *
71163 TCATTTAAAATGATGAT-TAACATATATCACA
1 TCACTTAAAATGATGATGT-ACATATATCAAA
* *
71194 TCACTTAAAGTAATGATGTA
1 TCACTTAAAATGATGATGTA
71214 GTATGTATCA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
30 1 0.02
31 39 0.95
32 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.34
Consensus pattern (31 bp):
TCACTTAAAATGATGATGTACATATATCAAA
Done.