Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001929.1 Hibiscus syriacus cultivar Beakdansim tig00003901_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: 67338
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6175 original size:14 final size:14
Alignment explanation
Indices: 6156--6186 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6146 TTTTATTTTT
6156 AATAAAAATTAATA
1 AATAAAAATTAATA
*
6170 AATAAAAATTATTA
1 AATAAAAATTAATA
6184 AAT
1 AAT
6187 TTAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AATAAAAATTAATA
Found at i:7243 original size:45 final size:45
Alignment explanation
Indices: 7162--7484 Score: 494
Period size: 45 Copynumber: 7.3 Consensus size: 45
7152 ATTATTCATT
*
7162 ATTTCCATTTATGGCATCCTTTCATG-CTTTATTGCACCGTTATGC
1 ATTT-CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
7207 ATTTCATTTATGGCATCCTTTCATACCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
7252 A-TTCATTTATGGTATCCTTTCATGACTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
7296 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACTGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
7341 ATTTCATTTATGGCATCATTTCATGCCTTTAATG--CCG-TATAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
7383 ATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * **
7428 ATTTCATTTATGACATCCTTTCTTGCCTTTAATGCACTATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
7473 ATTTCATTTATG
1 ATTTCATTTATG
7485 TAATAAAAAA
Statistics
Matches: 256, Mismatches: 17, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
42 36 0.14
43 2 0.01
44 64 0.25
45 154 0.60
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:7409 original size:87 final size:89
Alignment explanation
Indices: 7162--7484 Score: 456
Period size: 87 Copynumber: 3.6 Consensus size: 89
7152 ATTATTCATT
* *
7162 ATTTCCATTTATGGCATCCTTTCATG-CTTTATTGCACCGTTATGCATTTCATTTATGGCATCCT
1 ATTT-CATTTATGGCATCCTTTCATGCCTTTAATG-ACCGTTATACATTTCATTTATGGCATCCT
*
7226 TTCATACCTTTAATGCACCGTTATGC
64 TTCATGCCTTTAATGCACCGTTATGC
* * *
7252 A-TTCATTTATGGTATCCTTTCATGACTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTT
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATG-ACCGTTATACATTTCATTTATGGCATCCTT
*
7316 TCATGCCTTTAATGCACTGTTATGC
65 TCATGCCTTTAATGCACCGTTATGC
* *
7341 ATTTCATTTATGGCATCATTTCATGCCTTTAATG-CCG-TATACATTTCATTTATGACATCCTTT
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGACCGTTATACATTTCATTTATGGCATCCTTT
7404 CATGCCTTTAATGCACCGTTATGC
66 CATGCCTTTAATGCACCGTTATGC
* * ** *
7428 ATTTCATTTATGACATCCTTTCTTGCCTTTAATGCACTATTATGCATTTCATTTATG
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATG-ACCGTTATACATTTCATTTATG
7485 TAATAAAAAA
Statistics
Matches: 212, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
87 78 0.37
88 23 0.11
89 65 0.31
90 46 0.22
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (89 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGACCGTTATACATTTCATTTATGGCATCCTTT
CATGCCTTTAATGCACCGTTATGC
Found at i:7437 original size:132 final size:133
Alignment explanation
Indices: 7162--7484 Score: 499
Period size: 132 Copynumber: 2.4 Consensus size: 133
7152 ATTATTCATT
* * *
7162 ATTTCCATTTATGGCATCCTTTCATG-CTTTATTGCACCGTTATGCATTTCATTTATGGCATCCT
1 ATTT-CATTTATGGCATCCTTTCATGCCTTTAATGCACTGTTATGCATTTCATTTATGGCATCAT
* **
7226 TTCATACCTTTAATGCACCGTTATGCATTCATTTATGGTATCCTTTCATGACTTTAATGCACCGT
65 TTCATACCTTTAATG-ACCGTTATACATTCATTTATGACATCCTTTCATGACTTTAATGCACCGT
7291 TATGC
129 TATGC
7296 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACTGTTATGCATTTCATTTATGGCATCATT
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACTGTTATGCATTTCATTTATGGCATCATT
* *
7361 TCATGCCTTTAATG-CCG-TATACATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTT
66 TCATACCTTTAATGACCGTTATACA-TTCATTTATGACATCCTTTCATGACTTTAATGCACCGTT
7424 ATGC
130 ATGC
* * *
7428 ATTTCATTTATGACATCCTTTCTTGCCTTTAATGCACTATTATGCATTTCATTTATG
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACTGTTATGCATTTCATTTATG
7485 TAATAAAAAA
Statistics
Matches: 176, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
131 5 0.03
132 97 0.55
133 21 0.12
134 53 0.30
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (133 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACTGTTATGCATTTCATTTATGGCATCATT
TCATACCTTTAATGACCGTTATACATTCATTTATGACATCCTTTCATGACTTTAATGCACCGTTA
TGC
Found at i:8662 original size:17 final size:18
Alignment explanation
Indices: 8640--8673 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
8630 ATACCCTTTC
*
8640 AATTA-TCCTTTTACTTA
1 AATTATTCCTTATACTTA
8657 AATTATTCCTTATACTT
1 AATTATTCCTTATACTT
8674 TAACATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTATTCCTTATACTTA
Found at i:14087 original size:45 final size:45
Alignment explanation
Indices: 14037--14228 Score: 312
Period size: 45 Copynumber: 4.3 Consensus size: 45
14027 ATTATTCATT
* *
14037 ATTTCATTTATGGCATCCTTTCATGCTTTTAATGTACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
14082 ATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
**
14127 ATTTCATTTATGGTGTCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
14172 ATTTCATTTATGGCATCTTTTCATGCCTTTAATGCACCGTTATTC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
14217 ATTTCATTTATG
1 ATTTCATTTATG
14229 TAACAAAACA
Statistics
Matches: 135, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 135 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:14217 original size:23 final size:23
Alignment explanation
Indices: 14146--14218 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
14136 ATGGTGTCCT
14146 TTCATGCCTTTAATGCACCGTTA
1 TTCATGCCTTTAATGCACCGTTA
* * * *
14169 TGCATTTCATTT-ATGGCATC-TT-
1 TTCA-TGCCTTTAAT-GCACCGTTA
14191 TTCATGCCTTTAATGCACCGTTA
1 TTCATGCCTTTAATGCACCGTTA
14214 TTCAT
1 TTCAT
14219 TTCATTTATG
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
21 9 0.24
22 7 0.19
23 12 0.32
24 9 0.24
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (23 bp):
TTCATGCCTTTAATGCACCGTTA
Found at i:17931 original size:31 final size:31
Alignment explanation
Indices: 17895--17953 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
17885 AAATTCAAGA
*
17895 GTTAAATTAATATTTTATCTAAAGTTTATAG
1 GTTAAATTAATATTTTATCTAAAATTTATAG
*
17926 GTTAAATTAATCTTTTATCTAAAATTTA
1 GTTAAATTAATATTTTATCTAAAATTTA
17954 GCACCAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (31 bp):
GTTAAATTAATATTTTATCTAAAATTTATAG
Found at i:18233 original size:14 final size:15
Alignment explanation
Indices: 18195--18235 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
18185 GTTTTTTCGG
18195 TTCGGTTCGGGTTTT
1 TTCGGTTCGGGTTTT
18210 TTAACGGTTCGGG-TTT
1 TT--CGGTTCGGGTTTT
18226 TTCGGTTCGG
1 TTCGGTTCGG
18236 TTCGGTTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.33
15 2 0.08
16 5 0.21
17 9 0.38
ACGTcount: A:0.05, C:0.15, G:0.34, T:0.46
Consensus pattern (15 bp):
TTCGGTTCGGGTTTT
Found at i:18413 original size:5 final size:5
Alignment explanation
Indices: 18405--18429 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
18395 TTTAAAGCCA
18405 AACCG AACCG AACCG AACCG AACCG
1 AACCG AACCG AACCG AACCG AACCG
18430 TTTTACTCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.20, T:0.00
Consensus pattern (5 bp):
AACCG
Found at i:22345 original size:22 final size:22
Alignment explanation
Indices: 22317--22359 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
22307 TTGTAAAATA
22317 TCGGGGATCCCTACGATTATTT
1 TCGGGGATCCCTACGATTATTT
*
22339 TCGGGGATCCCTACGGTTATT
1 TCGGGGATCCCTACGATTATT
22360 CACACGTGTA
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:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (22 bp):
TCGGGGATCCCTACGATTATTT
Found at i:22794 original size:40 final size:40
Alignment explanation
Indices: 22745--22820 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
22735 ATACCTAAAG
22745 TTTAATTTTTGTTTCATTTTAGTATCC-CGTCGTTAAAAAC
1 TTTAATTTTTGTTTCATTTTAGTA-CCTCGTCGTTAAAAAC
*
22785 TTTAGTTTTTGTTTCATTTTAGTACCTCGTCGTTAA
1 TTTAATTTTTGTTTCATTTTAGTACCTCGTCGTTAA
22821 GTCTTAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
39 2 0.06
40 32 0.94
ACGTcount: A:0.21, C:0.14, G:0.12, T:0.53
Consensus pattern (40 bp):
TTTAATTTTTGTTTCATTTTAGTACCTCGTCGTTAAAAAC
Found at i:36048 original size:21 final size:21
Alignment explanation
Indices: 36022--36064 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
36012 TTTCTGGGTT
* *
36022 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
36043 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
36064 A
1 A
36065 CGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:36169 original size:68 final size:67
Alignment explanation
Indices: 36044--36195 Score: 214
Period size: 68 Copynumber: 2.3 Consensus size: 67
36034 ACCCATTCAA
* * *
36044 GGGGAACCGATACCCCTTCAACGAAATGAATTTCCAGAATGCAAGAGGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCCAG
36109 GG
66 GG
* * * **
36111 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAACCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACG-AAATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCCA
36176 GGG
65 GGG
*
36179 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
36196 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 21 0.28
68 54 0.72
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.16
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCCAG
GG
Found at i:36532 original size:29 final size:29
Alignment explanation
Indices: 36498--36567 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
36488 CATATTATGA
**
36498 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
36527 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
36556 TACATGACATGA
1 TACATGACATGA
36568 TTATGCAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:36625 original size:30 final size:31
Alignment explanation
Indices: 36583--36642 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
36573 CAGAAAAGTT
*
36583 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
36614 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
36643 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:36890 original size:22 final size:22
Alignment explanation
Indices: 36862--36906 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
36852 TTATGGACAT
36862 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
36884 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
36906 A
1 A
36907 TTTATACGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:36914 original size:22 final size:22
Alignment explanation
Indices: 36862--36914 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
36852 TTATGGACAT
*
36862 AATTCTACGGGCACTTCGGTGC
1 AATTATACGGGCACTTCGGTGC
*
36884 AATTCTACGGGCACTTCGGTGC
1 AATTATACGGGCACTTCGGTGC
*
36906 ATTTATACG
1 AATTATACG
36915 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (22 bp):
AATTATACGGGCACTTCGGTGC
Found at i:42966 original size:21 final size:21
Alignment explanation
Indices: 42940--42982 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42930 TTTCTGGGTT
* *
42940 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
42961 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
42982 A
1 A
42983 CGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:43070 original size:72 final size:71
Alignment explanation
Indices: 42962--43104 Score: 205
Period size: 72 Copynumber: 2.0 Consensus size: 71
42952 ACCCATTCAA
* * *
42962 GGGGAACCGATACCCCTTCAACGAAATGAATTTCCAGAATGCAAGAGGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCCAG
43027 GGGGGG
66 GGGGGG
* * * **
43033 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAACCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACG-AAATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCCA
43098 GGGGGGG
65 GGGGGGG
43105 AACCGATTCC
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
71 21 0.33
72 42 0.67
ACGTcount: A:0.28, C:0.25, G:0.31, T:0.16
Consensus pattern (71 bp):
GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCCAG
GGGGGG
Found at i:43454 original size:29 final size:29
Alignment explanation
Indices: 43420--43489 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
43410 CATATTATGA
**
43420 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
43449 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
43478 TACATGACATGA
1 TACATGACATGA
43490 TTATGCAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:43547 original size:30 final size:31
Alignment explanation
Indices: 43505--43564 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
43495 CAGAAAAGTT
*
43505 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
43536 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
43565 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:43810 original size:22 final size:22
Alignment explanation
Indices: 43782--43826 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
43772 TTATGGACAT
43782 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
43804 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
43826 A
1 A
43827 TTTATACGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:43834 original size:22 final size:22
Alignment explanation
Indices: 43782--43834 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
43772 TTATGGACAT
*
43782 AATTCTACGGGCACTTCGGTGC
1 AATTATACGGGCACTTCGGTGC
*
43804 AATTCTACGGGCACTTCGGTGC
1 AATTATACGGGCACTTCGGTGC
*
43826 ATTTATACG
1 AATTATACG
43835 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (22 bp):
AATTATACGGGCACTTCGGTGC
Found at i:46608 original size:54 final size:54
Alignment explanation
Indices: 46526--46869 Score: 467
Period size: 54 Copynumber: 6.4 Consensus size: 54
46516 ATTTTTTTAT
*
46526 GTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATTAACAACC
1 GTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACAACC
*
46580 GTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATACGTTTATGAACAACC
1 GTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACAACC
* * *
46634 GTATCGACACTAAGTGTACAAACCAC-GAAATTCATAATAAGTTTATGAACAACC
1 GTATCGGCACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACAACC
* * * * *
46688 GTATCGACACTAAGTGTACAAACCACAAAATTCATAATAAGTTTATGAACGACC
1 GTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACAACC
* * ** **
46742 GTATCGACACTAAATGTGCAACCCATGGAATTCATAATAAGTTTATGAATGACC
1 GTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACAACC
* ** *
46796 GTATCAGCACTAAGTGTGCAACCCAC-GAAATTCATAACGAGTTTATGAATAACC
1 GTATCGGCACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACAACC
*
46850 GTATCGGCACTACGTGTGCA
1 GTATCGGCACTAAGTGTGCA
46870 CCCTACGGAA
Statistics
Matches: 263, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
53 2 0.01
54 261 0.99
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.25
Consensus pattern (54 bp):
GTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACAACC
Found at i:46674 original size:27 final size:27
Alignment explanation
Indices: 46644--46729 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
46634 GTATCGACAC
46644 TAAGTGTACAAACCACGAAATTCATAA
1 TAAGTGTACAAACCACGAAATTCATAA
* ** * * * *
46671 TAAGTTTATGAACAACCG-TA-TCGACAC
1 TAAGTGTACAAACCA-CGAAATTC-ATAA
*
46698 TAAGTGTACAAACCACAAAATTCATAA
1 TAAGTGTACAAACCACGAAATTCATAA
46725 TAAGT
1 TAAGT
46730 TTATGAACGA
Statistics
Matches: 40, Mismatches: 15, Indels: 8
0.63 0.24 0.13
Matches are distributed among these distances:
26 3 0.08
27 33 0.82
28 4 0.10
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (27 bp):
TAAGTGTACAAACCACGAAATTCATAA
Found at i:59207 original size:42 final size:43
Alignment explanation
Indices: 59026--59234 Score: 287
Period size: 43 Copynumber: 4.9 Consensus size: 43
59016 ACATAATCCA
* * *
59026 CCTTTGTTGTGTGTAAGGGTAAGTCTTACAGTTCCCCCAGG-T
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTT
* * *
59068 CCTTTTGCTGTGTGCAAGGGTATGCCTTACAGTTCCCCCAAGTC
1 CC-TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTT
* *
59112 CCTTTGATGTGTGCAAGGGTAAGCCTTATAGTTCCCCCAGGTT
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTT
* **
59155 CCTTTGCTGTGTGTAAGGGTAAGCCTTACAGTT-TTCCAGGTT
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTT
59197 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGCTTCCCC
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAG-TTCCCC
59235 AAGCTCTTTT
Statistics
Matches: 144, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
42 39 0.27
43 102 0.71
44 3 0.02
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (43 bp):
CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTT
Found at i:61222 original size:13 final size:13
Alignment explanation
Indices: 61201--61235 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
61191 GTCACAACTC
* *
61201 GACCTGACCCGTT
1 GACCCGACCCATT
61214 GACCCGACCCATT
1 GACCCGACCCATT
61227 GACCCGACC
1 GACCCGACC
61236 TGATCCGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.20, C:0.46, G:0.20, T:0.14
Consensus pattern (13 bp):
GACCCGACCCATT
Found at i:61235 original size:18 final size:18
Alignment explanation
Indices: 61214--61254 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
61204 CTGACCCGTT
61214 GACCCGACCCATTGACCC
1 GACCCGACCCATTGACCC
* * *
61232 GACCTGATCCGTTGACCC
1 GACCCGACCCATTGACCC
61250 GACCC
1 GACCC
61255 ATTGACCGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.20, C:0.46, G:0.20, T:0.15
Consensus pattern (18 bp):
GACCCGACCCATTGACCC
Found at i:61235 original size:31 final size:31
Alignment explanation
Indices: 61200--61261 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
61190 GGTCACAACT
61200 CGACCTGACCCGTTGACCCGACCCATTGACC
1 CGACCTGACCCGTTGACCCGACCCATTGACC
*
61231 CGACCTGATCCGTTGACCCGACCCATTGACC
1 CGACCTGACCCGTTGACCCGACCCATTGACC
61262 GTTGACCGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.19, C:0.44, G:0.19, T:0.18
Consensus pattern (31 bp):
CGACCTGACCCGTTGACCCGACCCATTGACC
Found at i:63495 original size:41 final size:43
Alignment explanation
Indices: 63415--63591 Score: 229
Period size: 41 Copynumber: 4.2 Consensus size: 43
63405 TTACCGTTAT
*
63415 AGTTCCCCTAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTAC
1 AGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTAC
*
63458 AGTTCCCCCAAGTCCCTTTG-T-TGTGCAAGGGTAAGCCTTAC
1 AGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTAC
* * *
63499 AGTTCCTCCAGGTTCCTTTG-TGTGTGTAAGGGTAAGCCTTAC
1 AGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTAC
* * * *
63541 AGTT--TCCAGGTTCCTTTGTTCTGTGCAAGGGTAAGCCTTAC
1 AGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTAC
*
63582 AGTTTCCCCA
1 AGTTCCCCCA
63592 AGCTGTTTTA
Statistics
Matches: 121, Mismatches: 9, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
40 14 0.12
41 62 0.51
42 24 0.20
43 21 0.17
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.33
Consensus pattern (43 bp):
AGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTAC
Found at i:63531 original size:83 final size:84
Alignment explanation
Indices: 63415--63590 Score: 243
Period size: 83 Copynumber: 2.1 Consensus size: 84
63405 TTACCGTTAT
63415 AGTTCCCCTAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAAGTCCCTTTG-T
1 AGTTCCCCTAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTT--CCCAAGTCCCTTTGTT
63479 -TGTGCAAGGGTAAGCCTTAC
64 CTGTGCAAGGGTAAGCCTTAC
* * * * *
63499 AGTTCCTCC-AGGTTCCTTTG-TGTGTGTAAGGGTAAGCCTTACAGTTTCCAGGTTCCTTTGTTC
1 AGTTCC-CCTAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCAAGTCCCTTTGTTC
63562 TGTGCAAGGGTAAGCCTTAC
65 TGTGCAAGGGTAAGCCTTAC
63582 AGTTTCCCC
1 AG-TTCCCC
63591 AAGCTGTTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
81 11 0.13
82 1 0.01
83 49 0.59
84 20 0.24
85 2 0.02
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (84 bp):
AGTTCCCCTAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCAAGTCCCTTTGTTCT
GTGCAAGGGTAAGCCTTAC
Done.