Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007813.1 Hibiscus syriacus cultivar Beakdansim tig00110144_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: 170288
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:19488 original size:23 final size:24
Alignment explanation
Indices: 19439--19491 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
19429 TTCTTTGCTT
* *
19439 TTTC-TTCTTTTGAGTGCTGGATT
1 TTTCTTTCTTTTGAGTGCTGCATC
*
19462 TTTCTTTCTTTTGAGTGCTTCA-C
1 TTTCTTTCTTTTGAGTGCTGCATC
19485 TTTCTTT
1 TTTCTTT
19492 TCTGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGCTGCATC
Found at i:21022 original size:18 final size:18
Alignment explanation
Indices: 20999--21042 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
20989 GTCTCCTTCT
20999 AGCTAGCTTGAGTTGTGG
1 AGCTAGCTTGAGTTGTGG
21017 AGCTAGCTTGAGTTGTGG
1 AGCTAGCTTGAGTTGTGG
21035 AGCTAGCT
1 AGCTAGCT
21043 AGAAAACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.14, G:0.36, T:0.32
Consensus pattern (18 bp):
AGCTAGCTTGAGTTGTGG
Found at i:22154 original size:13 final size:12
Alignment explanation
Indices: 22120--22161 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
22110 TTGCAATTCC
*
22120 TTTATCTT-TTC
1 TTTATCTTATTT
22131 TTTATCTT-TTT
1 TTTATCTTATTT
*
22142 TTAATCTTATTT
1 TTTATCTTATTT
22154 TTTATCTT
1 TTTATCTT
22162 GTTTCGAGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATCTTATTT
Found at i:22523 original size:19 final size:19
Alignment explanation
Indices: 22495--22534 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
22485 ATTTTTTTTC
22495 AAAAAAGCAAAAAAG-CAA
1 AAAAAAGCAAAAAAGCCAA
22513 AAAACAAGCAAAAAAGCCAA
1 AAAA-AAGCAAAAAAGCCAA
22533 AA
1 AA
22535 TTTCAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.20
19 11 0.55
20 5 0.25
ACGTcount: A:0.75, C:0.15, G:0.10, T:0.00
Consensus pattern (19 bp):
AAAAAAGCAAAAAAGCCAA
Found at i:27930 original size:24 final size:25
Alignment explanation
Indices: 27885--27952 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 25
27875 TTAAAAACAA
* *
27885 AACAAAAACAAAAAAGGAAAAA-AC
1 AACAAAAAAAAAAAAGCAAAAATAC
* *
27909 AACAAAAAAAAAAAAGCCAAAATTTC
1 AACAAAAAAAAAAAAG-CAAAAATAC
27935 -A-AAAAAAAAAAAAGCAAA
1 AACAAAAAAAAAAAAGCAAA
27953 CGAAAGTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 4 0.11
24 28 0.74
25 5 0.13
26 1 0.03
ACGTcount: A:0.78, C:0.12, G:0.06, T:0.04
Consensus pattern (25 bp):
AACAAAAAAAAAAAAGCAAAAATAC
Found at i:30203 original size:18 final size:18
Alignment explanation
Indices: 30180--30222 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
30170 AACTGAATCT
30180 ACCAAACCAGAATCCAAG
1 ACCAAACCAGAATCCAAG
30198 ACCAAACCAGAATCCAAG
1 ACCAAACCAGAATCCAAG
30216 ACCAAAC
1 ACCAAAC
30223 AATGCTGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.51, C:0.35, G:0.09, T:0.05
Consensus pattern (18 bp):
ACCAAACCAGAATCCAAG
Found at i:31883 original size:43 final size:43
Alignment explanation
Indices: 31822--31907 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
31812 TTAAGCATGC
31822 TACTATTCCAAGAATTGAACATATAAAAAATGTATATCACGAT
1 TACTATTCCAAGAATTGAACATATAAAAAATGTATATCACGAT
31865 TACTATTCCAAGAATTGAACATATAAAAAATGTATATCACGAT
1 TACTATTCCAAGAATTGAACATATAAAAAATGTATATCACGAT
31908 AACTCGGATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (43 bp):
TACTATTCCAAGAATTGAACATATAAAAAATGTATATCACGAT
Found at i:33719 original size:11 final size:11
Alignment explanation
Indices: 33693--33731 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
33683 TGCTGGAAAC
33693 AAGATTAAAAA
1 AAGATTAAAAA
33704 TAAGATTAAAAA
1 -AAGATTAAAAA
33716 AAGA-TAAAGAA
1 AAGATTAAA-AA
33727 AAGAT
1 AAGAT
33732 AAAGGAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.16
11 10 0.40
12 11 0.44
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (11 bp):
AAGATTAAAAA
Found at i:34019 original size:14 final size:14
Alignment explanation
Indices: 34000--34031 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
33990 AGCTTCGAAG
34000 GCACAAGGCAATCA
1 GCACAAGGCAATCA
34014 GCACAAGGCAATCA
1 GCACAAGGCAATCA
34028 GCAC
1 GCAC
34032 TTGCAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.31, G:0.22, T:0.06
Consensus pattern (14 bp):
GCACAAGGCAATCA
Found at i:38445 original size:11 final size:12
Alignment explanation
Indices: 38410--38452 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
38400 TGCTGGAAAC
*
38410 AAGATTAAAGAT
1 AAGATTAAAGAA
38422 AAGATTAAA-AA
1 AAGATTAAAGAA
38433 AAGA-TAAAGAA
1 AAGATTAAAGAA
38444 AAGA-TAAAG
1 AAGATTAAAG
38453 GAAATGCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 4 0.14
11 16 0.55
12 9 0.31
ACGTcount: A:0.67, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
AAGATTAAAGAA
Found at i:43241 original size:8 final size:8
Alignment explanation
Indices: 43230--43279 Score: 64
Period size: 8 Copynumber: 5.9 Consensus size: 8
43220 AAATTTTGGC
43230 TTTTTTTG
1 TTTTTTTG
43238 TTTTTTTG
1 TTTTTTTG
*
43246 TTTATTTTT
1 TTT-TTTTG
43255 TTTTTTTG
1 TTTTTTTG
43263 CCTTTTTTTG
1 --TTTTTTTG
43273 TTTTTTT
1 TTTTTTT
43280 TTAAATAGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
8 22 0.59
9 7 0.19
10 8 0.22
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.86
Consensus pattern (8 bp):
TTTTTTTG
Found at i:43252 original size:27 final size:26
Alignment explanation
Indices: 43229--43280 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
43219 GAAATTTTGG
43229 CTTTTTTTG-TTTTTTTGTTTATTTT
1 CTTTTTTTGCTTTTTTTGTTTATTTT
* *
43254 TTTTTTTTGCCTTTTTTTGTTTTTTTT
1 CTTTTTTTG-CTTTTTTTGTTTATTTT
43281 TAAATAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 8 0.35
27 15 0.65
ACGTcount: A:0.02, C:0.06, G:0.08, T:0.85
Consensus pattern (26 bp):
CTTTTTTTGCTTTTTTTGTTTATTTT
Found at i:43636 original size:11 final size:11
Alignment explanation
Indices: 43610--43648 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
43600 TGCTCGAAAC
43610 AAGATTAAAAA
1 AAGATTAAAAA
43621 TAAGATTAAAAA
1 -AAGATTAAAAA
43633 AAGA-TAAAGAA
1 AAGATTAAA-AA
43644 AAGAT
1 AAGAT
43649 AAAGGAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.16
11 10 0.40
12 11 0.44
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (11 bp):
AAGATTAAAAA
Found at i:48083 original size:50 final size:50
Alignment explanation
Indices: 47979--48085 Score: 119
Period size: 50 Copynumber: 2.1 Consensus size: 50
47969 TCACACTCCA
* * * * * *
47979 ATTTGCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATATTATCGT
1 ATTTTCCTTTTCATCGCGACTAGGAGGGCTCGATAGAGACATATCATCGT
*
48029 ATTTTCCTTTTCATTGCGACTAGGAGGGCTCGATAG-GACATTATCCATCG-
1 ATTTTCCTTTTCATCGCGACTAGGAGGGCTCGATAGAGACA-TAT-CATCGT
48079 ATTTTCC
1 ATTTTCC
48086 ACATATCCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
49 3 0.06
50 41 0.85
51 4 0.08
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (50 bp):
ATTTTCCTTTTCATCGCGACTAGGAGGGCTCGATAGAGACATATCATCGT
Found at i:48220 original size:23 final size:22
Alignment explanation
Indices: 48182--48224 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
48172 CAATTCCTTT
48182 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTTCTTTATCTTGTTTTA
*
48204 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
48225 CCAGCACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTA
Found at i:53613 original size:19 final size:20
Alignment explanation
Indices: 53575--53617 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
53565 TAAACCCCTT
*
53575 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
53595 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
53614 TGAA
1 TGAA
53618 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:58425 original size:19 final size:20
Alignment explanation
Indices: 58401--58440 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
58391 TATCCTTTCT
58401 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
58420 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
58440 T
1 T
58441 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:62178 original size:89 final size:90
Alignment explanation
Indices: 62026--62191 Score: 280
Period size: 89 Copynumber: 1.9 Consensus size: 90
62016 TATAACACAC
* * **
62026 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGAATTTTATTATTTCAAATTAATTAAATCTAT
62091 ATTTAATTAATTAGAATTTAATAAT
66 ATTTAATTAATTAGAATTTAATAAT
*
62116 CCTTTTATATCCAAGTTACCCTAATCATATCA-GAATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGAATTTTATTATTTCAAATTAATTAAATCTAT
62180 ATTTAATTAATT
66 ATTTAATTAATT
62192 TAAATTAAAT
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
89 42 0.59
90 29 0.41
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGAATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTAGAATTTAATAAT
Found at i:67741 original size:36 final size:35
Alignment explanation
Indices: 67694--67805 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
67684 TAAGATACTA
67694 CCTATAACATCACCATCTTCTATCACCATTTTCACG
1 CCTATAACATCACCATCTTCTATCACCA-TTTCACG
* *
67730 CCTATAACATCACCATCTTCCATCACCATTACACG
1 CCTATAACATCACCATCTTCTATCACCATTTCACG
** * * * *
67765 CCTATATTATCATCAACTTCTATTACCATTTCAGG
1 CCTATAACATCACCATCTTCTATCACCATTTCACG
67800 CCTATA
1 CCTATA
67806 TAACCACCAA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 39 0.59
36 27 0.41
ACGTcount: A:0.29, C:0.34, G:0.04, T:0.33
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCTATCACCATTTCACG
Found at i:67990 original size:15 final size:15
Alignment explanation
Indices: 67952--67990 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
67942 CTTTGATAAC
67952 ATTTATTTCCATTTCA
1 ATTT-TTTCCATTTCA
* *
67968 ATTCTTTCCATTTCT
1 ATTTTTTCCATTTCA
67983 ATTTTTTC
1 ATTTTTTC
67991 TTCTTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTTTCCATTTCA
Found at i:78470 original size:11 final size:11
Alignment explanation
Indices: 78454--78501 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
78444 AAATTTTGGA
*
78454 TTTTTTGGCTTT
1 TTTTTTGTC-TT
78466 TTTTTTGTCTT
1 TTTTTTGTCTT
*
78477 TTTTTTGTTTT
1 TTTTTTGTCTT
78488 TTTTTTGT-TT
1 TTTTTTGTCTT
78498 TTTT
1 TTTT
78502 GAAAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
10 6 0.18
11 20 0.59
12 8 0.24
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.85
Consensus pattern (11 bp):
TTTTTTGTCTT
Found at i:85335 original size:5 final size:5
Alignment explanation
Indices: 85321--85356 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
85311 TCCAACAATC
85321 AAAA- AAAAG AAAAG AAAAG AAAAG AAAAG -AAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
85357 GTTGAAGCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:85343 original size:15 final size:15
Alignment explanation
Indices: 85321--85356 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
85311 TCCAACAATC
85321 AAAA-AAAAGAAAAG
1 AAAAGAAAAGAAAAG
85335 AAAAGAAAAGAAAAG
1 AAAAGAAAAGAAAAG
85350 -AAAGAAA
1 AAAAGAAA
85357 GTTGAAGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAGAAAAG
Found at i:86617 original size:24 final size:22
Alignment explanation
Indices: 86578--86632 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
86568 AGTGACCAAC
* *
86578 AAGACATGTCCTTTGACATTTCA
1 AAGA-ATGTCCTTTGAAATTTAA
*
86601 AAGGATGTACCTCTTGAAATTTAA
1 AAGAATGT-CCT-TTGAAATTTAA
86625 AAGAATGT
1 AAGAATGT
86633 GCCAATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 4 0.15
23 6 0.23
24 16 0.62
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (22 bp):
AAGAATGTCCTTTGAAATTTAA
Found at i:90499 original size:28 final size:27
Alignment explanation
Indices: 90468--90529 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
90458 AAGAAAAATT
*
90468 AGAAAACAAAGTGAAGCACTC-AAAAGAA
1 AGAAAACAAA-TCAAGCACTCAAAAAG-A
*
90496 AGAAAAACAAATCCAGCACTCAAAAAGA
1 AG-AAAACAAATCAAGCACTCAAAAAGA
90524 AGAAAA
1 AGAAAA
90530 GAAAAGAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 4 0.13
28 13 0.43
29 13 0.43
ACGTcount: A:0.63, C:0.16, G:0.15, T:0.06
Consensus pattern (27 bp):
AGAAAACAAATCAAGCACTCAAAAAGA
Found at i:97926 original size:13 final size:13
Alignment explanation
Indices: 97908--97933 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
97898 TGGCCAAAGA
97908 TGAAAAGGTATGT
1 TGAAAAGGTATGT
97921 TGAAAAGGTATGT
1 TGAAAAGGTATGT
97934 GAGATGTGTT
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:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:99835 original size:16 final size:17
Alignment explanation
Indices: 99797--99837 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
99787 ATTAGAGTTA
*
99797 AGTTATGTTTAGTTTATT
1 AGTTAT-TTTAGTTCATT
99815 A-TTATTTTAG-TCATT
1 AGTTATTTTAGTTCATT
99830 AGTTATTT
1 AGTTATTT
99838 AGGACCTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.24
16 11 0.52
17 4 0.19
18 1 0.05
ACGTcount: A:0.24, C:0.02, G:0.12, T:0.61
Consensus pattern (17 bp):
AGTTATTTTAGTTCATT
Found at i:100249 original size:22 final size:22
Alignment explanation
Indices: 100224--100265 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
100214 CAATTCATTT
100224 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
100246 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
100266 ACAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:104917 original size:22 final size:22
Alignment explanation
Indices: 104892--104933 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
104882 CAATTCATTT
104892 ATCTT-TTCTTTATCTTGTTTTC
1 ATCTTATT-TTTATCTTGTTTTC
104914 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
104934 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.12, C:0.14, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTC
Found at i:110899 original size:9 final size:9
Alignment explanation
Indices: 110887--110953 Score: 59
Period size: 9 Copynumber: 7.4 Consensus size: 9
110877 TTTTTTGAAA
*
110887 TTTTGGCTT
1 TTTTGCCTT
110896 TTTTGGCTCTTT
1 TTTT-GC-C-TT
*
110908 TTTTG-TTT
1 TTTTGCCTT
110916 TTTTGCCTT
1 TTTTGCCTT
*
110925 TTTT--TTT
1 TTTTGCCTT
110932 TTTTGCCTT
1 TTTTGCCTT
110941 TTTTGCCTT
1 TTTTGCCTT
110950 TTTT
1 TTTT
110954 TTTGTTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
7 6 0.13
8 7 0.15
9 25 0.53
10 1 0.02
11 2 0.04
12 6 0.13
ACGTcount: A:0.00, C:0.13, G:0.12, T:0.75
Consensus pattern (9 bp):
TTTTGCCTT
Found at i:110916 original size:18 final size:17
Alignment explanation
Indices: 110894--110944 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 17
110884 AAATTTTGGC
*
110894 TTTTTTGGCTCTTTTTTT
1 TTTTTTTGC-CTTTTTTT
110912 GTTTTTTTGCC-TTTTTT
1 -TTTTTTTGCCTTTTTTT
110929 TTTTTTTGCCTTTTTT
1 TTTTTTTGCCTTTTTT
110945 GCCTTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 10 0.33
17 11 0.37
18 1 0.03
19 8 0.27
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (17 bp):
TTTTTTTGCCTTTTTTT
Found at i:110932 original size:16 final size:17
Alignment explanation
Indices: 110906--110945 Score: 73
Period size: 16 Copynumber: 2.4 Consensus size: 17
110896 TTTTGGCTCT
110906 TTTTTTGTTTTTTTGCC
1 TTTTTTGTTTTTTTGCC
110923 TTTTTT-TTTTTTTGCC
1 TTTTTTGTTTTTTTGCC
110939 TTTTTTG
1 TTTTTTG
110946 CCTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (17 bp):
TTTTTTGTTTTTTTGCC
Found at i:110951 original size:21 final size:20
Alignment explanation
Indices: 110887--110965 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 20
110877 TTTTTTGAAA
* * *
110887 TTTTGGCTTTTTTGGCTCTT
1 TTTTTGCTTTTTTGCCTTTT
*
110907 TTTTTGTTTTTTTGCCTTTTTTTT
1 TTTTTGCTTTTTTGCC----TTTT
110931 TTTTTGCCTTTTTTGCCTTTT
1 TTTTTG-CTTTTTTGCCTTTT
*
110952 TTTTTGTTTTTTTG
1 TTTTTGCTTTTTTG
110966 AAAAAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 20 0.42
21 10 0.21
24 9 0.19
25 9 0.19
ACGTcount: A:0.00, C:0.11, G:0.13, T:0.76
Consensus pattern (20 bp):
TTTTTGCTTTTTTGCCTTTT
Found at i:124984 original size:17 final size:16
Alignment explanation
Indices: 124962--124999 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
124952 CTATCCTTCT
124962 TTATTTCATTTCATTC
1 TTATTTCATTTCATTC
124978 GTTATTTCATTTCATTC
1 -TTATTTCATTTCATTC
124995 TTATT
1 TTATT
125000 ATTTATTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.18, C:0.16, G:0.03, T:0.63
Consensus pattern (16 bp):
TTATTTCATTTCATTC
Found at i:126062 original size:23 final size:23
Alignment explanation
Indices: 126032--126079 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
126022 TAGAGGATTA
126032 AATGTTAAGAGACTTCATCACCC
1 AATGTTAAGAGACTTCATCACCC
126055 AATGTTAAGAGACTTCATCACCC
1 AATGTTAAGAGACTTCATCACCC
126078 AA
1 AA
126080 ATATGCTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (23 bp):
AATGTTAAGAGACTTCATCACCC
Found at i:127519 original size:453 final size:445
Alignment explanation
Indices: 126642--127529 Score: 1204
Period size: 445 Copynumber: 2.0 Consensus size: 445
126632 ACCGTGATAT
* * *
126642 AGTTCAGCCTAGCCTCACTTGGATGGATGGTAAATTCAATGTTATACCTTTGATTGCTTCGATAT
1 AGTTCAACCTAGCCTCACTTGGATGGATGGTAAAGTCAAGGTTATACCTTTGATTGCTTCGATAT
* * *
126707 AGGAAAGCAACAAGGATCTTGCACAAACAAGAAAGTTAGAATAAAATGGTTAAATGGAAGTAATG
66 AGGAAAGCAACAAGGATCATGCACAAACAAGAAAGTCAGAATAAAATAGTTAAATGGAAGTAATG
* * * *
126772 AAATGGAAAGATAAATATGGCAATGAAATATATACATAAGTTGGTGATATGTTTAAAGGAAGTGA
131 AAATGGAAAGACAAATATGGCAATGAAATATATACATAAGTCGGTGATATGTTTAAACGAAATGA
* *
126837 GGAAGTATGATAATGGAAGTAGAATTAAGGTGATGGAGAATAAGATGAAAGGTAATATCTCAAAG
196 GGAAGTATGATAATGAAAGTAGAATGAAGGTGATGGAGAATAAGATGAAAGGTAATATCTCAAAG
* * *
126902 AAGACTCAAAGAAGAACTAATGTTAAATAACAAAGACCCAAACTTTATATTGCTTCTTTAAGGGG
261 AAGACTCAAAGAAGAACCAATGTTAAAGAACAAAGACCCAAACTTTATATTACTTCTTTAAGGGG
* * * *
126967 TGGTAAACAAGGAATTTTGACCCACTATCTATAAAGAGATAGGAACTAGAAATATCATGATGAAA
326 TGGTAAACAAGGAACTTTGACCCACTATCCATAAAGAGATAGGAACCAGAAATATCAAGATGAAA
*
127032 TAGATAGGGGCGACGCCACAAGCATATGCTTGATAAG-CTGATAAAGTTCTGATGC
391 TAGATAGGGGCGACGCCACAAGCATATACTTGATAAGTC-GATAAAGTTCTGATGC
* * * *
127087 AGTTCAACCTAGCCTCACTTGGATGGATGGTAGAGTCAAGGTTGTACCTTTGATTGTTTCGATCT
1 AGTTCAACCTAGCCTCACTTGGATGGATGGTAAAGTCAAGGTTATACCTTTGATTGCTTCGATAT
127152 AGGAAAGCAACAAGGATCATGCACAAACAAGAAAGCTCA-AA-AAAATAGTTAAATGGGAAGTAA
66 AGGAAAGCAACAAGGATCATGCACAAACAAGAAAG-TCAGAATAAAATAGTTAAAT-GGAAGTAA
* *
127215 TGAAATGGAAAGACAAATATGGAAGCGGAAT-ATATATATATATATATGTCGGTGATATGTTTAA
129 TGAAATGGAAAGACAAATAT-G--GC--AATGA-A-ATATATACATAAGTCGGTGATATGTTTAA
* * *
127279 ACGAAATGATGAAGTATGGTAATGAAAGTAGAATGAAGTGGTGATGGAG-ATGAATATGAAAGG-
187 ACGAAATGAGGAAGTATGATAATGAAAGTAGAATGAA--GGTGATGGAGAAT-AAGATGAAAGGT
* *
127342 AAGTATCTCAAAGAAGACTCAAATAAGAACCAATGTTAAAGAACAAAGACCCATACTTTATATTA
249 AA-TATCTCAAAGAAGACTCAAAGAAGAACCAATGTTAAAGAACAAAGACCCAAACTTTATATTA
* *
127407 CTTCTTTAAGGGGTGGTAAACAAGG-ACTTTGACCTACTATCCATAAAGAGATAGGAACCAGAAG
313 CTTCTTTAAGGGGTGGTAAACAAGGAACTTTGACCCACTATCCATAAAGAGATAGGAACCAGAAA
* * *
127471 TATCAAGGTG-AA-A-A-AGGGGATTGACGCCACAAGTATAAAATACTTGATAAGTCGATAAA
378 TATCAAGATGAAATAGATAGGGG--CGACGCCACAAGCAT---ATACTTGATAAGTCGATAAA
127530 AGTCACCAGG
Statistics
Matches: 388, Mismatches: 36, Indels: 30
0.85 0.08 0.07
Matches are distributed among these distances:
444 12 0.03
445 121 0.31
446 3 0.01
448 7 0.02
449 2 0.01
450 18 0.05
451 59 0.15
452 46 0.12
453 119 0.31
454 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (445 bp):
AGTTCAACCTAGCCTCACTTGGATGGATGGTAAAGTCAAGGTTATACCTTTGATTGCTTCGATAT
AGGAAAGCAACAAGGATCATGCACAAACAAGAAAGTCAGAATAAAATAGTTAAATGGAAGTAATG
AAATGGAAAGACAAATATGGCAATGAAATATATACATAAGTCGGTGATATGTTTAAACGAAATGA
GGAAGTATGATAATGAAAGTAGAATGAAGGTGATGGAGAATAAGATGAAAGGTAATATCTCAAAG
AAGACTCAAAGAAGAACCAATGTTAAAGAACAAAGACCCAAACTTTATATTACTTCTTTAAGGGG
TGGTAAACAAGGAACTTTGACCCACTATCCATAAAGAGATAGGAACCAGAAATATCAAGATGAAA
TAGATAGGGGCGACGCCACAAGCATATACTTGATAAGTCGATAAAGTTCTGATGC
Found at i:131110 original size:9 final size:9
Alignment explanation
Indices: 131089--131125 Score: 65
Period size: 9 Copynumber: 4.0 Consensus size: 9
131079 TGCTTCAACA
131089 TTCTTTCTTT
1 TTCTTT-TTT
131099 TTCTTTTTT
1 TTCTTTTTT
131108 TTCTTTTTT
1 TTCTTTTTT
131117 TTCTTTTTT
1 TTCTTTTTT
131126 GAGTGCTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 21 0.78
10 6 0.22
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:131112 original size:15 final size:15
Alignment explanation
Indices: 131092--131124 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
131082 TTCAACATTC
131092 TTTCTTTTTCTTTTT
1 TTTCTTTTTCTTTTT
131107 TTTCTTTTT-TTTCTT
1 TTTCTTTTTCTTT-TT
131122 TTT
1 TTT
131125 TGAGTGCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTCTTTTTCTTTTT
Found at i:131162 original size:22 final size:22
Alignment explanation
Indices: 131116--131167 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
131106 TTTTCTTTTT
131116 TTTCTTTTTTGAGTGCTTTCAA
1 TTTCTTTTTTGAGTGCTTTCAA
* *
131138 TTTCTTCTTTTGAGTGCTTTGAT
1 TTTCTT-TTTTGAGTGCTTTCAA
131161 TTTCTTT
1 TTTCTTT
131168 GCTGGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.10, C:0.13, G:0.13, T:0.63
Consensus pattern (22 bp):
TTTCTTTTTTGAGTGCTTTCAA
Found at i:146941 original size:25 final size:25
Alignment explanation
Indices: 146913--146968 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
146903 GCCATGTGTT
*
146913 TTGCATGTGATCAGTCCCTTGTTCC
1 TTGCATGTGATCAGTCCCATGTTCC
146938 TTGCATGTGATCAGTCCCATGTTCC
1 TTGCATGTGATCAGTCCCATGTTCC
146963 TTGCAT
1 TTGCAT
146969 ATGGTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.39
Consensus pattern (25 bp):
TTGCATGTGATCAGTCCCATGTTCC
Found at i:155577 original size:6 final size:6
Alignment explanation
Indices: 155552--155594 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
155542 CAAAAGCAAC
*
155552 AAAAAG AGAAAG AAAGAAG AAAAAG AAAAAG -AAAAG AAAAAG A
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
155595 CTCCTACATC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
7 6 0.18
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:155586 original size:11 final size:11
Alignment explanation
Indices: 155552--155594 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 11
155542 CAAAAGCAAC
155552 AAAAAGAGAAAG
1 AAAAAGA-AAAG
155564 AAAGAAGAAAAAG
1 AAA-AAG-AAAAG
155577 AAAAAGAAAAG
1 AAAAAGAAAAG
155588 AAAAAGA
1 AAAAAGA
155595 CTCCTACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 12 0.41
12 6 0.21
13 10 0.34
14 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:155588 original size:17 final size:19
Alignment explanation
Indices: 155552--155594 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
155542 CAAAAGCAAC
*
155552 AAAAAGAGAAAGAAAGAAG
1 AAAAAGAAAAAGAAAGAAG
155571 AAAAAGAAAAAG-AA-AAG
1 AAAAAGAAAAAGAAAGAAG
155588 AAAAAGA
1 AAAAAGA
155595 CTCCTACATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.43
18 2 0.09
19 11 0.48
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAAGAAAGAAG
Found at i:156980 original size:24 final size:24
Alignment explanation
Indices: 156948--157018 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
156938 AGACATGTGT
156948 CACTTGAAGTGCCAAAAGTTATGC
1 CACTTGAAGTGCCAAAAGTTATGC
*** * * *
156972 CACTTGAAGTTAAAAAAGATGTGT
1 CACTTGAAGTGCCAAAAGTTATGC
156996 CACTTGAAGTGCCAAAAGTTATG
1 CACTTGAAGTGCCAAAAGTTATG
157019 ATTATTGAAG
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (24 bp):
CACTTGAAGTGCCAAAAGTTATGC
Found at i:159660 original size:11 final size:11
Alignment explanation
Indices: 159604--159660 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
159594 ACAATCTGTC
159604 CATCACCATTAT
1 CATCACCATT-T
* *
159616 CA-CGCCTATAT
1 CATCACC-ATTT
159627 CATCACCATATT
1 CATCACCAT-TT
159639 CCATCACCATTT
1 -CATCACCATTT
159651 CATCACCATT
1 CATCACCATT
159661 AAATCATCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
11 18 0.49
12 10 0.27
13 9 0.24
ACGTcount: A:0.30, C:0.37, G:0.02, T:0.32
Consensus pattern (11 bp):
CATCACCATTT
Found at i:165264 original size:11 final size:11
Alignment explanation
Indices: 165208--165264 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
165198 ACAATCTGTC
165208 CATCACCATTAT
1 CATCACCATT-T
* *
165220 CA-CGCCTATAT
1 CATCACC-ATTT
165231 CATCACCATATT
1 CATCACCAT-TT
165243 CCATCACCATTT
1 -CATCACCATTT
165255 CATCACCATT
1 CATCACCATT
165265 AAATCATCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
11 18 0.49
12 10 0.27
13 9 0.24
ACGTcount: A:0.30, C:0.37, G:0.02, T:0.32
Consensus pattern (11 bp):
CATCACCATTT
Found at i:167028 original size:14 final size:15
Alignment explanation
Indices: 166997--167039 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
166987 TTTGGAGTGC
166997 AAAGAAAGAAAAAGA
1 AAAGAAAGAAAAAGA
**
167012 AAAG-AAGAAAATTA
1 AAAGAAAGAAAAAGA
167026 AAAGCAAAGAAAAA
1 AAAG-AAAGAAAAA
167040 AAGGTGAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 12 0.52
15 4 0.17
16 7 0.30
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (15 bp):
AAAGAAAGAAAAAGA
Done.