Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006945.1 Hibiscus syriacus cultivar Beakdansim tig00017849_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: 76508
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1881 original size:17 final size:16
Alignment explanation
Indices: 1855--1906 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
1845 TTCTAAATGT
*
1855 TTACAGTTATCAGATA
1 TTACAATTATCAGATA
*
1871 TATACAATTATCATATGA
1 T-TACAATTATCAGAT-A
1889 TTACAATTATCAGATA
1 TTACAATTATCAGATA
1905 TT
1 TT
1907 TTACAGTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 4 0.13
17 25 0.81
18 2 0.06
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (16 bp):
TTACAATTATCAGATA
Found at i:2895 original size:20 final size:21
Alignment explanation
Indices: 2870--2909 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
2860 CTCTACATGG
2870 TAGTATCAATACCA-TAGGCA
1 TAGTATCAATACCATTAGGCA
2890 TAGTATCAATACCATTAGGC
1 TAGTATCAATACCATTAGGC
2910 CCCAACGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (21 bp):
TAGTATCAATACCATTAGGCA
Found at i:3062 original size:10 final size:10
Alignment explanation
Indices: 3049--3074 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3039 AAACACTCCC
3049 AACGGCTATA
1 AACGGCTATA
3059 AACGGCTATA
1 AACGGCTATA
3069 AACGGC
1 AACGGC
3075 CACAACATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (10 bp):
AACGGCTATA
Found at i:9405 original size:29 final size:30
Alignment explanation
Indices: 9344--9406 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 30
9334 TGACATGATA
*
9344 TACATGCTTATATGAATATGCAATATGTAT
1 TACATGCTTATATGAATATGCAAGATGTAT
9374 TACATG-TTATATGAA-ATGACATAGATGT-T
1 TACATGCTTATATGAATATG-CA-AGATGTAT
9403 TACA
1 TACA
9407 CATACATATG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 3 0.10
29 16 0.53
30 11 0.37
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (30 bp):
TACATGCTTATATGAATATGCAAGATGTAT
Found at i:10291 original size:21 final size:21
Alignment explanation
Indices: 10265--10346 Score: 164
Period size: 21 Copynumber: 3.9 Consensus size: 21
10255 TACGAAAGTT
10265 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAGTGCATCGATGC
10286 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAGTGCATCGATGC
10307 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAGTGCATCGATGC
10328 ACTGTAGCAGTGCATCGAT
1 ACTGTAGCAGTGCATCGAT
10347 ACACAATTGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATGC
Found at i:10389 original size:12 final size:12
Alignment explanation
Indices: 10372--10405 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
10362 GAAATTTTTC
10372 ACTGTTCATAGT
1 ACTGTTCATAGT
*
10384 ACTGTTCATGGT
1 ACTGTTCATAGT
*
10396 ACTATTCATA
1 ACTGTTCATA
10406 CCATATAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (12 bp):
ACTGTTCATAGT
Found at i:15754 original size:20 final size:20
Alignment explanation
Indices: 15729--15809 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
15719 ATATTTGATT
15729 TTTTATAATAATTAACTTGA
1 TTTTATAATAATTAACTTGA
*
15749 TTTTATAATAATTTAAGTATATATTTGA
1 -TTT-T-ATAA--TAA-T-TA-ACTTGA
*
15777 TTTTATAATAATTTACTTGA
1 TTTTATAATAATTAACTTGA
15797 TTTTATAATAATT
1 TTTTATAATAATT
15810 TATGTATGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
20 18 0.36
21 4 0.08
22 2 0.04
23 7 0.14
25 7 0.14
26 2 0.04
27 5 0.10
28 5 0.10
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTTATAATAATTAACTTGA
Found at i:15785 original size:48 final size:48
Alignment explanation
Indices: 15717--15842 Score: 189
Period size: 48 Copynumber: 2.6 Consensus size: 48
15707 TTATGTACAC
15717 ATATATTTGATTTTTTATAATAATTAACTTGATTTTATAATAATTTAAGT
1 ATATATTTGA--TTTTATAATAATTAACTTGATTTTATAATAATTTAAGT
* *
15767 ATATATTTGATTTTATAATAATTTACTTGATTTTATAATAATTTATGT
1 ATATATTTGATTTTATAATAATTAACTTGATTTTATAATAATTTAAGT
* **
15815 ATGTATTCAATTTTATAATAATTAACTT
1 ATATATTTGATTTTATAATAATTAACTT
15843 AATTAACTTG
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
48 60 0.86
50 10 0.14
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (48 bp):
ATATATTTGATTTTATAATAATTAACTTGATTTTATAATAATTTAAGT
Found at i:15810 original size:20 final size:20
Alignment explanation
Indices: 15773--15811 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
15763 AAGTATATAT
15773 TTGATTTTATAATAATTTAC
1 TTGATTTTATAATAATTTAC
15793 TTGATTTTATAATAATTTA
1 TTGATTTTATAATAATTTA
15812 TGTATGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (20 bp):
TTGATTTTATAATAATTTAC
Found at i:15880 original size:34 final size:34
Alignment explanation
Indices: 15842--15907 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
15832 ATAATTAACT
15842 TAATTAACTTGATTTTATAAAAATTTATGTATAG
1 TAATTAACTTGATTTTATAAAAATTTATGTATAG
* *
15876 TAATTAACTTTATTTTATAATAATTTATGTAT
1 TAATTAACTTGATTTTATAAAAATTTATGTAT
15908 TTTTTAGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (34 bp):
TAATTAACTTGATTTTATAAAAATTTATGTATAG
Found at i:16380 original size:6 final size:5
Alignment explanation
Indices: 16372--16415 Score: 52
Period size: 6 Copynumber: 8.0 Consensus size: 5
16362 TAAATTGAAA
16372 TATTT ATATTT ATATTT TATTGT TATTT TATTT TATTCT TATTT
1 TATTT -TATTT -TATTT TATT-T TATTT TATTT TATT-T TATTT
16416 ATAAATTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (5 bp):
TATTT
Found at i:16405 original size:16 final size:17
Alignment explanation
Indices: 16378--16418 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
16368 GAAATATTTA
*
16378 TATTTATATTTTATTGT
1 TATTTATATTTTATTCT
16395 TATTT-TATTTTATTCT
1 TATTTATATTTTATTCT
16411 TATTTATA
1 TATTTATA
16419 AATTTTCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (17 bp):
TATTTATATTTTATTCT
Found at i:16417 original size:10 final size:10
Alignment explanation
Indices: 16372--16415 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 10
16362 TAAATTGAAA
16372 TATTTATATTT
1 TATTT-TATTT
16383 ATATTTTATTGT
1 -TATTTTATT-T
16395 TATTTTATTT
1 TATTTTATTT
16405 TATTCTTATTT
1 TATT-TTATTT
16416 ATAAATTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.17
11 19 0.63
12 6 0.20
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (10 bp):
TATTTTATTT
Found at i:16837 original size:21 final size:21
Alignment explanation
Indices: 16775--16830 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
16765 TAAATATATG
16775 TCCACCACTATGCTC-CCTCAT
1 TCCACCACTATGCTCTCC-CAT
16796 TCCACCACTATGCTCTCCCAT
1 TCCACCACTATGCTCTCCCAT
* *
16817 TGCACCACTTTGCT
1 TCCACCACTATGCT
16831 TTTCCATCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.18, C:0.45, G:0.07, T:0.30
Consensus pattern (21 bp):
TCCACCACTATGCTCTCCCAT
Found at i:17712 original size:3 final size:3
Alignment explanation
Indices: 17704--17742 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
17694 AATTAAATAG
17704 TAT TAT TAT TAT TAT TAT TAT TA- TAT TA- TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17743 ATTTTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.18
3 27 0.82
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:17722 original size:15 final size:14
Alignment explanation
Indices: 17704--17742 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
17694 AATTAAATAG
17704 TATTATTATTATTA
1 TATTATTATTATTA
17718 TTATTATTA-TATTA
1 -TATTATTATTATTA
17732 TATTA-TATTAT
1 TATTATTATTAT
17743 ATTTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.09
13 8 0.35
14 5 0.22
15 8 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:17732 original size:5 final size:5
Alignment explanation
Indices: 17704--17745 Score: 57
Period size: 5 Copynumber: 7.8 Consensus size: 5
17694 AATTAAATAG
17704 TATTA TTATTA TTATTA TTATTA TATTA TATTA TATTA TATT
1 TATTA -TATTA -TATTA -TATTA TATTA TATTA TATTA TATT
17746 TTAAAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 19 0.53
6 17 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TATTA
Found at i:19850 original size:80 final size:80
Alignment explanation
Indices: 19685--19891 Score: 219
Period size: 80 Copynumber: 2.6 Consensus size: 80
19675 GGCCAATCAT
* * * * *
19685 GATGCATGCAAGAGAGGCTGGGAAGACGCATGGAAAGTCATGCGTCTTTGAGAGATTTTCGGGGT
1 GATGCATGCAAGAGGGGATGGGAAGACGCATGGAAAGCCATGCGTCTTCGAGAGATGTTCGGGGT
***
19750 TGGTCCACGTCATTT
66 TGGTCCACGTCAGCA
* * * *
19765 G-TGCATGCAAGAGGGGATGGGGAAGATGCATGGAAAGCCATGTGTCTTCGAGGGGTGTTCGGGG
1 GATGCATGCAAGAGGGGAT-GGGAAGACGCATGGAAAGCCATGCGTCTTCGAGAGATGTTCGGGG
19829 TTGGTCCACGT-AGCA
65 TTGGTCCACGTCAGCA
* * **
19844 GATGCATGC-AGA-GGG--GGGAAGACACATTGAAAGGAATGCGTCTTCGAG
1 GATGCATGCAAGAGGGGATGGGAAGACGCATGGAAAGCCATGCGTCTTCGAG
19892 TTGGCCATTG
Statistics
Matches: 107, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
75 27 0.25
78 3 0.03
79 20 0.19
80 57 0.53
ACGTcount: A:0.25, C:0.15, G:0.38, T:0.22
Consensus pattern (80 bp):
GATGCATGCAAGAGGGGATGGGAAGACGCATGGAAAGCCATGCGTCTTCGAGAGATGTTCGGGGT
TGGTCCACGTCAGCA
Found at i:25584 original size:54 final size:54
Alignment explanation
Indices: 25525--26099 Score: 781
Period size: 54 Copynumber: 10.6 Consensus size: 54
25515 ATTTCTTTAT
* * * * ** ** **
25525 AATGCACTCGTAGTGCCCATACGGTTATTCATAAACATATTATGAATTCTATGA
1 AATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGA
** ** *
25579 AATGCACACTTAGTGCCGAAACGGTTATTCATAAACATATTATGAATTCCATGA
1 AATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGA
* * * * * *
25633 AATGCACACTTATTGCCGAAATGATTCTTCATCTACATAGGATGAATTCTGTGA
1 AATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGA
* *
25687 AATGTACACTTAGTGCCGAAACGGTTATTCATCCATATAGGATGAATTCCGTGA
1 AATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGA
* * * *
25741 AATGTACACTTAGTGCCGAAACGATTATTCATCCACATAGGATAAATTTCGTGA
1 AATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGA
* * * *
25795 AATGCACACTTAGTGCCGAAACGATTATTCTTCTACATAGGATGAATTTCGTGA
1 AATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGA
*
25849 AATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCCTGA
1 AATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGA
* *
25903 AATGCACACTTAGTGCCGAAACGGTTATTCATCCACATATGATGAATTCCCTGA
1 AATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGA
* *
25957 AATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATAAATTTCGTGA
1 AATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGA
* ** *
26011 AATACACACTTAGTGTTGAAACGGTTATTCATCCACATAGGATGAATTTCGTGA
1 AATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGA
*
26065 AATGCACACTTAGTGTCGAAACGGTTATTCATCCA
1 AATGCACACTTAGTGCCGAAACGGTTATTCATCCA
26100 TTAAATACAT
Statistics
Matches: 474, Mismatches: 47, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 474 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (54 bp):
AATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGA
Found at i:31070 original size:18 final size:18
Alignment explanation
Indices: 31047--31087 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
31037 CTCATCTTGA
31047 GCTCTTTCAATCGCCTTC
1 GCTCTTTCAATCGCCTTC
31065 GCTCTTTCAATCGCCTTC
1 GCTCTTTCAATCGCCTTC
31083 GCTCT
1 GCTCT
31088 ATTTATCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.39, G:0.12, T:0.39
Consensus pattern (18 bp):
GCTCTTTCAATCGCCTTC
Found at i:32096 original size:45 final size:46
Alignment explanation
Indices: 32047--32137 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
32037 AAACATCGAA
* * * *
32047 TGCATTTTATGTATCGATGGAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
*
32092 TGCATTTGATGCATCGATGCACAAGACTATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
32138 GTTTTTCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 19 0.47
46 21 0.52
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:35859 original size:21 final size:21
Alignment explanation
Indices: 35817--35860 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
35807 ACTCAGGGAG
* *
35817 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
35838 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
35859 CT
1 CT
35861 CCTCCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:36993 original size:20 final size:20
Alignment explanation
Indices: 36964--37001 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
36954 TTTCAAAGTG
36964 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
36984 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
37002 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:37070 original size:45 final size:46
Alignment explanation
Indices: 37021--37111 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
37011 AAACATCGAA
* *
37021 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
*
37066 TGCATTTGATGCATCGATGCACAAGACTATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
37112 GCTTTTCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.50
46 21 0.50
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:37127 original size:46 final size:45
Alignment explanation
Indices: 37032--37128 Score: 115
Period size: 46 Copynumber: 2.1 Consensus size: 45
37022 GCATTTTATG
* * **
37032 CATCGATGCACATACCATGCATCGATGCACTCAGTGCATTTGATG
1 CATCGATGCACAGACCATGCATCGATGCACTCAGTGCATTTAAAA
* *
37077 CATCGATGCACAAGACTATGCATCGATGCACTCAG-GCTTTTCAAAA
1 CATCGATGCAC-AGACCATGCATCGATGCACTCAGTGCATTT-AAAA
37123 CATCGA
1 CATCGA
37129 ATGTATTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
45 16 0.36
46 28 0.64
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (45 bp):
CATCGATGCACAGACCATGCATCGATGCACTCAGTGCATTTAAAA
Found at i:43184 original size:54 final size:54
Alignment explanation
Indices: 43136--43689 Score: 750
Period size: 54 Copynumber: 10.3 Consensus size: 54
43126 TAGTACCCAT
** ** * * *
43136 ACGGTTATTCATAAACATATTACGAATTCCGTGAAATGCACATTTAGTACCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* *
43190 ACGGTTATTCATCCACATAAGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
*** * * *
43244 ATAATTATTCATCCACATAGGATAAATTCCATGAAATGCACACTTAGTGCTGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* ** * *
43298 ACGATTATTCATCCACATAGGATGAATTCCGTGAAATGCATGCTCAGTACCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* * *
43352 ATGGTTATTCATCCACATAGGATGAATTCCATGAAATGCACACTCAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* * *
43406 ACGGTTATTCATCCATATAGTATGAATTCCGTGAAATGCACACGTAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
** * * *
43460 ACAATTATTCATCCACATATGATGAATTCCGTGAAATGCACACTCAGTGCTGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
*
43514 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGTACACTTAGTGCCG-A
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* *
43567 GCAGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* * *
43621 ACGGTTATTCATCCACATAGAATGAATTCTGTGAAATGCACACTCAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
**
43675 AAAGTTATTCATCCA
1 ACGGTTATTCATCCA
43690 TTAAATAATG
Statistics
Matches: 438, Mismatches: 61, Indels: 2
0.87 0.12 0.00
Matches are distributed among these distances:
53 50 0.11
54 388 0.89
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (54 bp):
ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
Found at i:43935 original size:20 final size:21
Alignment explanation
Indices: 43910--43961 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
43900 TGTTTTGAAT
*
43910 GGTATCGATACCT-TCCCTTC
1 GGTATCGATACCTCCCCCTTC
43930 GGTATCGATA-CTCCCCCTTC
1 GGTATCGATACCTCCCCCTTC
43950 GGTATCGATACC
1 GGTATCGATACC
43962 GATTAAATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.90
21 1 0.03
ACGTcount: A:0.17, C:0.35, G:0.17, T:0.31
Consensus pattern (21 bp):
GGTATCGATACCTCCCCCTTC
Found at i:48279 original size:13 final size:13
Alignment explanation
Indices: 48261--48286 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48251 GTTCTTAGGT
48261 CAACTATCCCCAA
1 CAACTATCCCCAA
48274 CAACTATCCCCAA
1 CAACTATCCCCAA
48287 TACGCCTTGG
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:0.46, G:0.00, T:0.15
Consensus pattern (13 bp):
CAACTATCCCCAA
Found at i:51961 original size:24 final size:24
Alignment explanation
Indices: 51933--51985 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
51923 ATAAAACTAC
*
51933 AACACTAGTTGCGGCTAATTTACA
1 AACACTAGATGCGGCTAATTTACA
51957 AACACTAGATGCGGCTAATTTACA
1 AACACTAGATGCGGCTAATTTACA
51981 AACAC
1 AACAC
51986 AACCACGCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (24 bp):
AACACTAGATGCGGCTAATTTACA
Found at i:57494 original size:159 final size:156
Alignment explanation
Indices: 57309--57613 Score: 418
Period size: 159 Copynumber: 1.9 Consensus size: 156
57299 CCCAATTTCA
* *
57309 TTATTTCCTCAATTCATCCTTCATTTTATG-TCCATTTTTCACCAAATTTGA-ACCACATGC-CC
1 TTATTTCCTCAATTCATCATTCATTTTAAGCT-CATTTTTCACCAAATTTGAGA-CACATGCTCC
* * * * * *
57371 TAAACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTTTTTATAACAATTGTTTTTTAT
64 TAAACCATACTAGAATACATGTGTACTTTCAATT--TC-TCTTTTTGATAACAAATATTTTAT-T
*
57436 TTTCAATTTAGTTTTTCAATTTTCATAATCTT
125 TTTCAATTTAGTTCTTCAATTTTCATAATCTT
* * * *
57468 TTATTTCTTCAATTCATCATTTATTTTAAGCTCTTTTTTTACCAAATTTGAGACACATGCTCCTA
1 TTATTTCCTCAATTCATCATTCATTTTAAGCTCATTTTTCACCAAATTTGAGACACATGCTCCTA
57533 AACCATACTAGAATACATGTGTACTTTCAATTTCTCTTTTTGATAACAAATATTTTATTTTTCAA
66 AACCATACTAGAATACATGTGTACTTTCAATTTCTCTTTTTGATAACAAATATTTTATTTTTCAA
57598 TTTAGTTCTTCAATTT
131 TTTAGTTCTTCAATTT
57614 GTGATTTATT
Statistics
Matches: 130, Mismatches: 13, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
156 22 0.17
157 19 0.15
158 2 0.02
159 50 0.38
160 37 0.28
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (156 bp):
TTATTTCCTCAATTCATCATTCATTTTAAGCTCATTTTTCACCAAATTTGAGACACATGCTCCTA
AACCATACTAGAATACATGTGTACTTTCAATTTCTCTTTTTGATAACAAATATTTTATTTTTCAA
TTTAGTTCTTCAATTTTCATAATCTT
Found at i:59321 original size:23 final size:20
Alignment explanation
Indices: 59265--59322 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 20
59255 CAAGAATTCA
*
59265 TTATGGTATTGATACTCCCC
1 TTATGGTATCGATACTCCCC
* *
59285 TT-GGGTATCAATACTCCCC
1 TTATGGTATCGATACTCCCC
59304 TTTTTATGGTATCGATACT
1 ---TTATGGTATCGATACT
59323 AAATTTTCCC
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 14 0.48
20 2 0.07
22 2 0.07
23 11 0.38
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (20 bp):
TTATGGTATCGATACTCCCC
Found at i:72781 original size:13 final size:13
Alignment explanation
Indices: 72763--72788 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
72753 GTTCTTAGGT
72763 CAACTATCCCCAA
1 CAACTATCCCCAA
72776 CAACTATCCCCAA
1 CAACTATCCCCAA
72789 TACGCCTTGG
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:0.46, G:0.00, T:0.15
Consensus pattern (13 bp):
CAACTATCCCCAA
Found at i:76439 original size:24 final size:24
Alignment explanation
Indices: 76411--76463 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
76401 ATAAAACTAC
*
76411 AACACTAGTTGCGGCTAATTTACA
1 AACACTAGATGCGGCTAATTTACA
76435 AACACTAGATGCGGCTAATTTACA
1 AACACTAGATGCGGCTAATTTACA
76459 AACAC
1 AACAC
76464 AACCACGCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (24 bp):
AACACTAGATGCGGCTAATTTACA
Done.