Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005167.1 Hibiscus syriacus cultivar Beakdansim tig00011657_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: 73261
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:197 original size:24 final size:24
Alignment explanation
Indices: 137--202 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
127 GAGTAGGGGA
*
137 TTAGGGTTTGAAACCCTAA-TTGTT
1 TTAGGGTTTG-AACCCTAATTTGAT
161 TTAGGGTTTGAACCCTAATTTGAT
1 TTAGGGTTTGAACCCTAATTTGAT
185 TTAGGGTTTGAA-CCTAAT
1 TTAGGGTTTGAACCCTAAT
203 CTGCTAGGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
23 14 0.35
24 26 0.65
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (24 bp):
TTAGGGTTTGAACCCTAATTTGAT
Found at i:318 original size:3 final size:3
Alignment explanation
Indices: 312--364 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
302 AAAAAAAATG
* **
312 TAA TAA TAA TAA TAA TAAA TAA TAA -GA TAA CGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
357 TAA -AA TAA
1 TAA TAA TAA
365 CGGAAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
2 3 0.07
3 35 0.85
4 3 0.07
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:359 original size:23 final size:24
Alignment explanation
Indices: 320--366 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
310 TGTAATAATA
*
320 ATAATAATAAATAATAAGATAACG
1 ATAATAATAAATAATAAAATAACG
344 ATAATAAT-AATAATAAAATAACG
1 ATAATAATAAATAATAAAATAACG
367 GAAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (24 bp):
ATAATAATAAATAATAAAATAACG
Found at i:805 original size:125 final size:132
Alignment explanation
Indices: 649--891 Score: 331
Period size: 125 Copynumber: 1.9 Consensus size: 132
639 GGTTATCAGT
* * *
649 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCA-TCTA-AA-GGTGATAACACGGTTCCTAC-
1 TGACACGGCTCATACATGATGAAGAAATCTGGCCACTCTAGAAGGGTGATAACACGGTTCCTACG
710 TGATGAGGACGGCTGGTTAT-CT-ATGGTGACACGGC-TCATACGTGATGAAGGGTCGGTCTGGG
66 TGATGAGGACGGCTGGTTATCCTAATGGTGACACGGCTTCATACGTGATGAAGGGTCGGTCTGGG
772 GA
131 GA
* * *
774 TGACACGGTTCATACATGATGAA-AAACTCTGGCCACCTTTAGGAAGGGTGATAACTCGGTTCCT
1 TGACACGGCTCATACATGATGAAGAAA-TCTGGCCA-CTCTA-GAAGGGTGATAACACGGTTCCT
* *
838 ACGTGATGAGGACGGCTGGTTATCCTAATGTTGACACGGCTTCCTACGTGATGA
63 ACGTGATGAGGACGGCTGGTTATCCTAATGGTGACACGGCTTCATACGTGATGA
892 GGAAGTCTGG
Statistics
Matches: 100, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
124 2 0.02
125 28 0.28
127 3 0.03
129 2 0.02
130 19 0.19
131 20 0.20
132 2 0.02
133 12 0.12
134 12 0.12
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (132 bp):
TGACACGGCTCATACATGATGAAGAAATCTGGCCACTCTAGAAGGGTGATAACACGGTTCCTACG
TGATGAGGACGGCTGGTTATCCTAATGGTGACACGGCTTCATACGTGATGAAGGGTCGGTCTGGG
GA
Found at i:1832 original size:8 final size:8
Alignment explanation
Indices: 1819--1864 Score: 60
Period size: 9 Copynumber: 5.8 Consensus size: 8
1809 CCTTTATTTA
1819 TTTTTTCT
1 TTTTTTCT
1827 TTTTTTCAT
1 TTTTTTC-T
1836 TTTTTTCAT
1 TTTTTTC-T
1845 TTTTTT-T
1 TTTTTTCT
1852 TTTTTT-T
1 TTTTTTCT
1859 TTTTTT
1 TTTTTT
1865 TAAGTATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
7 14 0.38
8 7 0.19
9 16 0.43
ACGTcount: A:0.04, C:0.07, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTCT
Found at i:16864 original size:2 final size:2
Alignment explanation
Indices: 16853--16886 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
16843 AAATTTATTA
16853 AT AT -T 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 A
16887 ATTATTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20505 original size:42 final size:42
Alignment explanation
Indices: 20446--20540 Score: 163
Period size: 42 Copynumber: 2.2 Consensus size: 42
20436 GATGCATTTT
*
20446 TGATGATATGGTCTTGGAATTCACTGATTGCTGGATATTCAC
1 TGATGATATGGTCTTGGAATTCACTAATTGCTGGATATTCAC
20488 TGATGATATGGTCTTGGAATTCACTAATTGCTGGATATTCAC
1 TGATGATATGGTCTTGGAATTCACTAATTGCTGGATATTCAC
*
20530 CGATGAATATG
1 TGATG-ATATG
20541 CATGGTCTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 45 0.90
43 5 0.10
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (42 bp):
TGATGATATGGTCTTGGAATTCACTAATTGCTGGATATTCAC
Found at i:20529 original size:18 final size:17
Alignment explanation
Indices: 20460--20529 Score: 50
Period size: 18 Copynumber: 3.6 Consensus size: 17
20450 GATATGGTCT
*
20460 TGGAATTCACTGATTGC
1 TGGAATTCACTAATTGC
20477 TGGATATTCACTGATGATATGGTC
1 TGGA-ATTCACT-A--AT-T-G-C
20501 TTGGAATTCACTAATTGC
1 -TGGAATTCACTAATTGC
20519 TGGATATTCAC
1 TGGA-ATTCAC
20530 CGATGAATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 17
0.70 0.02 0.28
Matches are distributed among these distances:
17 8 0.19
18 14 0.33
19 1 0.02
20 1 0.02
21 4 0.09
22 1 0.02
23 2 0.05
24 8 0.19
25 4 0.09
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (17 bp):
TGGAATTCACTAATTGC
Found at i:34235 original size:16 final size:16
Alignment explanation
Indices: 34214--34249 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
34204 TGTTATCTCA
34214 CTTTTCAAGCATAATC
1 CTTTTCAAGCATAATC
*
34230 CTTTTCAAGTATAATC
1 CTTTTCAAGCATAATC
34246 CTTT
1 CTTT
34250 ATTGAATCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (16 bp):
CTTTTCAAGCATAATC
Found at i:42321 original size:19 final size:19
Alignment explanation
Indices: 42297--42348 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
42287 AAATGACCAA
42297 CAAATTCGTAACGCAATCT
1 CAAATTCGTAACGCAATCT
*
42316 CAAATTCGTAACGCGATCT
1 CAAATTCGTAACGCAATCT
*
42335 CAAATTCGCAACGC
1 CAAATTCGTAACGC
42349 GAACTCCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.23
Consensus pattern (19 bp):
CAAATTCGTAACGCAATCT
Found at i:42364 original size:20 final size:19
Alignment explanation
Indices: 42297--42572 Score: 124
Period size: 20 Copynumber: 13.9 Consensus size: 19
42287 AAATGACCAA
*
42297 CAAATTCGTAACGC-AATCT
1 CAAATTCGCAACGCGAA-CT
* *
42316 CAAATTCGTAACGCGATCT
1 CAAATTCGCAACGCGAACT
42335 CAAATTCGCAACGCGAACT
1 CAAATTCGCAACGCGAACT
* * *
42354 CCAATTTCGCAACGTGAATT
1 -CAAATTCGCAACGCGAACT
* * ** **
42374 TAACTATCGCATTGCGATTTT
1 CAAAT-TCGCAACGCGA-ACT
*** *
42395 CCAAATTCGCATTACGATAGT
1 -CAAATTCGCAACGCGA-ACT
*** *
42416 CAAATTCGCATTACGATAGT
1 CAAATTCGCAACGCGA-ACT
*
42436 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGA-ACT
* * *
42456 CAAATTCGCAACACAAAAAT
1 CAAATTCGCAACGC-GAACT
*
42476 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAA-CT
* * * * *
42496 GTAAA-TCGCGACACAAAAGT
1 -CAAATTCGCAACGC-GAACT
*
42516 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGA-ACT
*
42536 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGA-ACT
42556 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
42573 AGTCAAATGT
Statistics
Matches: 211, Mismatches: 35, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
19 43 0.20
20 145 0.69
21 20 0.09
22 3 0.01
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.24
Consensus pattern (19 bp):
CAAATTCGCAACGCGAACT
Found at i:42453 original size:40 final size:40
Alignment explanation
Indices: 42409--42580 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
42399 ATTCGCATTA
** * *
42409 CGATAGTCAAATTCGCATTACGATAGTCAAATTCGCAACG
1 CGATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACG
*
42449 CGATAGTCAAATTCGCAACACAAAAATCAAATTCGCAACG
1 CGATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACG
* *
42489 CGAATTTGT-AAA-TCGCGACACAAAAGTCAAATTCGCAACG
1 CG-A-TAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACG
* * *
42529 CGATAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACG
1 CGATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACG
*
42569 CGAAAGTCAAAT
1 CGATAGTCAAAT
42581 GTTTTTACGT
Statistics
Matches: 114, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
38 3 0.03
39 4 0.04
40 100 0.88
41 4 0.04
42 3 0.03
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (40 bp):
CGATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACG
Found at i:42576 original size:20 final size:20
Alignment explanation
Indices: 42413--42580 Score: 178
Period size: 20 Copynumber: 8.4 Consensus size: 20
42403 GCATTACGAT
*** *
42413 AGTCAAATTCGCATTACGAT
1 AGTCAAATTCGCAACGCGAA
*
42433 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAA
* *
42453 AGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACGCGAA
*
42473 AATCAAATTCGCAACGCGAA
1 AGTCAAATTCGCAACGCGAA
* * * *
42493 TTTGT-AAA-TCGCGACACAAA
1 --AGTCAAATTCGCAACGCGAA
*
42513 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAA
*
42533 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAA
42553 AGTCAAATTCGCAACGCGAA
1 AGTCAAATTCGCAACGCGAA
42573 AGTCAAAT
1 AGTCAAAT
42581 GTTTTTACGT
Statistics
Matches: 124, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
18 2 0.02
19 3 0.02
20 115 0.93
21 3 0.02
22 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAA
Found at i:42737 original size:22 final size:22
Alignment explanation
Indices: 42712--42754 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
42702 GGCGACATCC
42712 GTCCCCATCTCCGACGAAATCT
1 GTCCCCATCTCCGACGAAATCT
*
42734 GTCCCTATCTCCGACGAAATC
1 GTCCCCATCTCCGACGAAATC
42755 CGTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.40, G:0.14, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCT
Found at i:42763 original size:20 final size:21
Alignment explanation
Indices: 42708--42765 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
42698 CTACGGCGAC
*
42708 ATCCGTCCCCATCTCCGACGAA
1 ATCCGT-CCTATCTCCGACGAA
*
42730 ATCTGTCCCTATCTCCGACGAA
1 ATCCGT-CCTATCTCCGACGAA
42752 ATCCGT-CTATCTCC
1 ATCCGTCCTATCTCC
42766 ATCTCTCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 8 0.24
22 25 0.76
ACGTcount: A:0.21, C:0.41, G:0.12, T:0.26
Consensus pattern (21 bp):
ATCCGTCCTATCTCCGACGAA
Found at i:43045 original size:20 final size:19
Alignment explanation
Indices: 43010--43063 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
43000 AAATCGCAAC
*
43010 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCATT
*
43029 GCGATTTTCATTTTCGCATT
1 GCGATTTT-AGTTTCGCATT
*
43049 GCGAATTTAAGTTTC
1 GCG-ATTTTAGTTTC
43064 AGAAACTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 8 0.28
20 17 0.59
21 4 0.14
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCATT
Found at i:45040 original size:12 final size:12
Alignment explanation
Indices: 45023--45064 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
45013 TTTTTCGGCA
*
45023 TTATTTATTTAT
1 TTATTTATTAAT
*
45035 TTATTTACTAAT
1 TTATTTATTAAT
*
45047 TTATGTATTAAT
1 TTATTTATTAAT
45059 TTATTT
1 TTATTT
45065 TCAGCGGCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (12 bp):
TTATTTATTAAT
Found at i:45249 original size:21 final size:21
Alignment explanation
Indices: 45225--45326 Score: 87
Period size: 21 Copynumber: 4.9 Consensus size: 21
45215 TCAAGAGATG
45225 CCTCCCATCGTTCAAGAGGCC
1 CCTCCCATCGTTCAAGAGGCC
* * * * *
45246 CCTCTCATCATTGAAGAAGTC
1 CCTCCCATCGTTCAAGAGGCC
* *
45267 CCTTCCACCGTTCAAGAGGCC
1 CCTCCCATCGTTCAAGAGGCC
** *
45288 CCTGTCATCGTTCAAGAGGTC
1 CCTCCCATCGTTCAAGAGGCC
* **
45309 CCGCCCGCCGTTCAAGAG
1 CCTCCCATCGTTCAAGAG
45327 CCCGATTCAC
Statistics
Matches: 60, Mismatches: 21, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.21, C:0.37, G:0.21, T:0.22
Consensus pattern (21 bp):
CCTCCCATCGTTCAAGAGGCC
Found at i:45255 original size:42 final size:43
Alignment explanation
Indices: 45208--45326 Score: 145
Period size: 42 Copynumber: 2.8 Consensus size: 43
45198 GATGCACCTA
* *
45208 TCATCATTCAAGAGA-TGCCTCCCATCGTTCAAGAGGCCCCTC
1 TCATCATTCAAGAGAGTCCCTCCCACCGTTCAAGAGGCCCCTC
* * *
45250 TCATCATTGAAGA-AGTCCCTTCCACCGTTCAAGAGGCCCCTG
1 TCATCATTCAAGAGAGTCCCTCCCACCGTTCAAGAGGCCCCTC
* * *
45292 TCATCGTTCAAGAG-GTCCCGCCCGCCGTTCAAGAG
1 TCATCATTCAAGAGAGTCCCTCCCACCGTTCAAGAG
45327 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.02
42 64 0.98
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (43 bp):
TCATCATTCAAGAGAGTCCCTCCCACCGTTCAAGAGGCCCCTC
Found at i:46779 original size:61 final size:62
Alignment explanation
Indices: 46679--46818 Score: 194
Period size: 66 Copynumber: 2.2 Consensus size: 62
46669 TTTTACATTG
*
46679 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
* * *
46739 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA--TTTTT-CTTGATTAATTGATTTGT
46804 A
62 A
46805 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
46819 GTTTCTAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
60 17 0.24
61 18 0.26
64 4 0.06
66 31 0.44
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.51
Consensus pattern (62 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
Found at i:46901 original size:20 final size:20
Alignment explanation
Indices: 46876--46953 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 20
46866 TGTTGAAGGT
*
46876 TCAAATTCGTAACGCGAAAG
1 TCAAATTCGCAACGCGAAAG
*
46896 TCAAATTCGCAACTCGAAAG
1 TCAAATTCGCAACGCGAAAG
*
46916 TCAAATTCGCAACTCGAAAG
1 TCAAATTCGCAACGCGAAAG
*
46936 TTAAATTCGCAACGCGAA
1 TCAAATTCGCAACGCGAA
46954 TTTGGCTATC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.21
Consensus pattern (20 bp):
TCAAATTCGCAACGCGAAAG
Found at i:47233 original size:39 final size:39
Alignment explanation
Indices: 47179--47265 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
47169 TCAAGTTGTA
47179 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
* *
47218 GATTTTGATTTCCTTTTGTTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
47257 GATTTTGAT
1 GATTTTGAT
47266 GAGCATCAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:47598 original size:18 final size:18
Alignment explanation
Indices: 47575--47611 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
47565 CGAAATTTAT
47575 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
47593 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
47611 A
1 A
47612 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:47812 original size:20 final size:20
Alignment explanation
Indices: 47787--47826 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
47777 TGTCACATGG
*
47787 TTTGACTATCGCGTTACGAA
1 TTTGACTATCACGTTACGAA
47807 TTTGACTATCACGTTACGAA
1 TTTGACTATCACGTTACGAA
47827 ATTGGAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (20 bp):
TTTGACTATCACGTTACGAA
Found at i:48055 original size:17 final size:18
Alignment explanation
Indices: 48015--48055 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
48005 ATTATTTTTT
*
48015 AATTTTTTAATAATAAAA
1 AATTATTTAATAATAAAA
48033 ATATTATTTAA-AATAAAA
1 A-ATTATTTAATAATAAAA
48051 AATTA
1 AATTA
48056 AGAAAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 9 0.43
19 8 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTATTTAATAATAAAA
Found at i:48340 original size:10 final size:10
Alignment explanation
Indices: 48325--48349 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
48315 AATTATAAGA
48325 TTAAATATTT
1 TTAAATATTT
48335 TTAAATATTT
1 TTAAATATTT
48345 TTAAA
1 TTAAA
48350 AAAATTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTAAATATTT
Found at i:52666 original size:2 final size:2
Alignment explanation
Indices: 52659--52685 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52649 GTTGTTTTTA
52659 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
52686 ATAAAAATAA
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:52901 original size:17 final size:18
Alignment explanation
Indices: 52861--52901 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
52851 TTTTAGAATT
52861 AGAAATATAAAATATAAA
1 AGAAATATAAAATATAAA
* *
52879 ATAAATAT-AAATATATA
1 AGAAATATAAAATATAAA
52896 AGAAAT
1 AGAAAT
52902 CAGATACTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (18 bp):
AGAAATATAAAATATAAA
Found at i:68168 original size:21 final size:20
Alignment explanation
Indices: 68144--68182 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
68134 TTGGTCACAT
*
68144 AATTTTTAAAGCTTATAATAC
1 AATTATTAAA-CTTATAATAC
*
68165 AATTATTAAACTTTTAAT
1 AATTATTAAACTTATAAT
68183 TCATTTTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (20 bp):
AATTATTAAACTTATAATAC
Found at i:69845 original size:13 final size:13
Alignment explanation
Indices: 69829--69854 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
69819 TTAATAAAGT
69829 TTAAATTTAAAAA
1 TTAAATTTAAAAA
69842 TTAAATTTAAAAA
1 TTAAATTTAAAAA
69855 ACTCAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAATTTAAAAA
Found at i:71441 original size:32 final size:32
Alignment explanation
Indices: 71404--71466 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
71394 TATTCGGGTT
**
71404 GATTTTTTAAGTGTGCTATTCGGGTCGGGTCG
1 GATTTTTTAAGTGTAATATTCGGGTCGGGTCG
71436 GATTTTTTAAGTGTAATATTCGGGTCGGGTC
1 GATTTTTTAAGTGTAATATTCGGGTCGGGTC
71467 AGGTTCGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.16, C:0.11, G:0.32, T:0.41
Consensus pattern (32 bp):
GATTTTTTAAGTGTAATATTCGGGTCGGGTCG
Done.