Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004182.1 Hibiscus syriacus cultivar Beakdansim tig00009148_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: 59811
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:27 original size:18 final size:18
Alignment explanation
Indices: 1--69 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
* *
1 TGGTCCTTCGAGACATAG
1 TGGTCCTTCGGGACACAG
*
19 TGGTGCTTCGGGACACAG
1 TGGTCCTTCGGGACACAG
*
37 TGGCCCTTCGGGACACAG
1 TGGTCCTTCGGGACACAG
*
55 TGGTCCTACGGGACA
1 TGGTCCTTCGGGACA
70 AATTCTACGC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.22
Consensus pattern (18 bp):
TGGTCCTTCGGGACACAG
Found at i:238 original size:14 final size:14
Alignment explanation
Indices: 216--262 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
206 GTGTTTTCTC
*
216 GTGAAATGGTATAT
1 GTGATATGGTATAT
*
230 GTGATATGGGATAT
1 GTGATATGGTATAT
*
244 GTGATAT-GTATAA
1 GTGATATGGTATAT
257 GTGATA
1 GTGATA
263 AGTTAGGATC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 10 0.34
14 19 0.66
ACGTcount: A:0.34, C:0.00, G:0.30, T:0.36
Consensus pattern (14 bp):
GTGATATGGTATAT
Found at i:5228 original size:45 final size:45
Alignment explanation
Indices: 5131--5288 Score: 257
Period size: 45 Copynumber: 3.5 Consensus size: 45
5121 TGGGGTGTTA
*
5131 CATGAAAGGATGCCATATATGAAATGC-TAACTGTGCATTAAAGG
1 CATGAAAGGATGCCATAAATGAAATGCATAACTGTGCATTAAAGG
*
5175 CATGAAAGGATGCCATAAATGAAATGCATAAC-GATGCATGAAAGG
1 CATGAAAGGATGCCATAAATGAAATGCATAACTG-TGCATTAAAGG
* *
5220 AATGAAAGGATGCCATAAATGAAATGCACAACTGTGCATTAAAGG
1 CATGAAAGGATGCCATAAATGAAATGCATAACTGTGCATTAAAGG
5265 CATGAAAGGATGCCATAAATGAAA
1 CATGAAAGGATGCCATAAATGAAA
5289 ATAATGAATA
Statistics
Matches: 105, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
44 27 0.26
45 77 0.73
46 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.20
Consensus pattern (45 bp):
CATGAAAGGATGCCATAAATGAAATGCATAACTGTGCATTAAAGG
Found at i:5306 original size:45 final size:45
Alignment explanation
Indices: 5131--5308 Score: 152
Period size: 45 Copynumber: 4.0 Consensus size: 45
5121 TGGGGTGTTA
* ** ** *
5131 CATGAAAGGATGCCATATATGAAATGCT-AACTGTGCATTAAAGG
1 CATGAAAGGATGCCATAAATGAAATAATGAACAATGTATTAAAGG
* * * *
5175 CATGAAAGGATGCCATAAATGAAATGCAT-AACGATGCATGAAAGG
1 CATGAAAGGATGCCATAAATGAAAT-AATGAACAATGTATTAAAGG
* *
5220 AATGAAAGGATGCCATAAATG--A-AATGCACAACTGTGCATTAAAGG
1 CATGAAAGGATGCCATAAATGAAATAATGAACAA-TGT--ATTAAAGG
*
5265 CATGAAAGGATGCCATAAATGAAAATAATGAATAAT-TATTAAAG
1 CATGAAAGGATGCCATAAATG-AAATAATGAACAATGTATTAAAG
5309 AATAATGGGA
Statistics
Matches: 110, Mismatches: 15, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
41 2 0.02
42 3 0.03
43 3 0.03
44 24 0.22
45 68 0.62
47 1 0.01
48 2 0.02
49 7 0.06
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (45 bp):
CATGAAAGGATGCCATAAATGAAATAATGAACAATGTATTAAAGG
Found at i:9829 original size:3 final size:3
Alignment explanation
Indices: 9821--9857 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
9811 AATTTTAATC
* *
9821 TTA TTA TTA TTA TTA ATG TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
9858 GTTTATTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:9842 original size:18 final size:18
Alignment explanation
Indices: 9815--9853 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
9805 CTATTTAATT
9815 TTAATCTTATTATTATTA
1 TTAATCTTATTATTATTA
*
9833 TTAATGTTATTATTATTA
1 TTAATCTTATTATTATTA
9851 TTA
1 TTA
9854 TTATGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
TTAATCTTATTATTATTA
Found at i:11532 original size:2 final size:2
Alignment explanation
Indices: 11525--11560 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
11515 TGCTAATCGT
11525 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11561 GGTTTATCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14184 original size:20 final size:19
Alignment explanation
Indices: 14161--14226 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
14151 AAAAAAGGGA
*
14161 AAAGAAGAAAATAAAAAAAC
1 AAAGAA-AAAAGAAAAAAAC
*
14181 AAAGAAAAAAGAAAAAAAT
1 AAAGAAAAAAGAAAAAAAC
* * *
14200 AAAAAATAAAAG-CAAAAAT
1 AAAGAA-AAAAGAAAAAAAC
14219 AAAGAAAA
1 AAAGAAAA
14227 TAATTAAAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 2 0.05
19 27 0.68
20 11 0.28
ACGTcount: A:0.82, C:0.03, G:0.09, T:0.06
Consensus pattern (19 bp):
AAAGAAAAAAGAAAAAAAC
Found at i:14184 original size:27 final size:26
Alignment explanation
Indices: 14138--14229 Score: 94
Period size: 27 Copynumber: 3.4 Consensus size: 26
14128 ATATCAAAGT
** **
14138 GAAAAAAATAGGAAAAAAAGGGAAAA
1 GAAAAAAATAAAAAAAAAAGAAAAAA
*
14164 GAAGAAAATAAAAAAACAAAGAAAAAA
1 GAAAAAAATAAAAAAA-AAAGAAAAAA
*
14191 GAAAAAAATAAAAAATAAAAGCAAAAA
1 GAAAAAAATAAAAAA-AAAAGAAAAAA
*
14218 TAAAGAAAATAA
1 GAAA-AAAATAA
14230 TTAAAGAACA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
26 13 0.24
27 34 0.62
28 8 0.15
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (26 bp):
GAAAAAAATAAAAAAAAAAGAAAAAA
Found at i:15979 original size:37 final size:39
Alignment explanation
Indices: 15934--16021 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 39
15924 TGAGAATTTT
** *
15934 AAAACAAATTTTTGTCTCGCTTGAGACA-ATTT-CTTTC
1 AAAACAAATTTTCATCTCACTTGAGACATATTTCCTTTC
* *
15971 AAAACAAA-TTTCATCTCACTTGAGACATTTTTCCTTTG
1 AAAACAAATTTTCATCTCACTTGAGACATATTTCCTTTC
16009 AAATACAAATTTT
1 AAA-ACAAATTTT
16022 GAATTTGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
36 16 0.38
37 11 0.26
38 7 0.17
39 5 0.12
40 3 0.07
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.40
Consensus pattern (39 bp):
AAAACAAATTTTCATCTCACTTGAGACATATTTCCTTTC
Found at i:16586 original size:15 final size:15
Alignment explanation
Indices: 16544--16586 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
16534 TGTTTTTGTC
*
16544 TCTTTTGAGAAAGTT
1 TCTTTTGAGAAATTT
*
16559 TATTTTGAGAAATTT
1 TCTTTTGAGAAATTT
*
16574 TCTTTTGAAAAAT
1 TCTTTTGAGAAAT
16587 CTTTGAGTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (15 bp):
TCTTTTGAGAAATTT
Found at i:17471 original size:63 final size:65
Alignment explanation
Indices: 17298--17477 Score: 197
Period size: 64 Copynumber: 2.8 Consensus size: 65
17288 ATAAAACAAA
* *
17298 CATCATTGAGATCGTTTCCCTTGAAACGAATTTTATCTCATTTGAGAC--TTTCCCATGAAACAT
1 CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCATTTGAGACAGTTTCCCATGAAACAT
* * * * * * * *
17361 CGATATCTGAGAACGTTTCCCTTAAAATCAAATTTTGTCTCACTTGAGACAGTTT-CCTTTAAAC
1 C-ATCTTTGAGATCGTTTCCCTTGAAA-CGAATTTTGTCTCATTTGAGACAGTTTCCCATGAAAC
*
17425 GT
64 AT
* *
17427 CATCTTTGAG-TCGTTTCCCTTGAAACGAATTTTGTCTCTTTTGAGATAGTT
1 CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCATTTGAGACAGTT
17478 GCTTTTGAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 8
0.78 0.16 0.07
Matches are distributed among these distances:
63 23 0.24
64 33 0.35
65 26 0.28
66 9 0.10
67 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (65 bp):
CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCATTTGAGACAGTTTCCCATGAAACAT
Found at i:17528 original size:28 final size:28
Alignment explanation
Indices: 17496--17560 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
17486 AACACGTCAC
* *
17496 CTTTGAGTTTGTTT-TTCTTGAAACAAAT
1 CTTTGAGTCTATTTCTT-TTGAAACAAAT
*
17524 CTTTGAGTCTATTTCTTTTTAAACAAAT
1 CTTTGAGTCTATTTCTTTTGAAACAAAT
17552 CTTTGAGTC
1 CTTTGAGTC
17561 GGTTTCCCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 31 0.94
29 2 0.06
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (28 bp):
CTTTGAGTCTATTTCTTTTGAAACAAAT
Found at i:17575 original size:28 final size:28
Alignment explanation
Indices: 17512--17575 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
17502 GTTTGTTTTT
* *
17512 CTTGAAACAAATCTTTGAGTCTATTTCT
1 CTTGAAACAAATCTTTGAGTCGATTTCC
* * *
17540 TTTTAAACAAATCTTTGAGTCGGTTTCC
1 CTTGAAACAAATCTTTGAGTCGATTTCC
17568 CTTGAAAC
1 CTTGAAAC
17576 CATAATCACA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (28 bp):
CTTGAAACAAATCTTTGAGTCGATTTCC
Found at i:17792 original size:93 final size:93
Alignment explanation
Indices: 17631--17856 Score: 301
Period size: 93 Copynumber: 2.4 Consensus size: 93
17621 TGTCATCCCC
* * * * ** *
17631 TGACCAGACCTCCTCATCATGTAGGAGTCACGTCACCCCTAGATAACCAGCCGTCCTCATCGCCT
1 TGACCAGAACTCTTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCATCCTCATCGCCT
17696 AGGAACCGAGTTATCACT-TTCCTAAAGA
66 AGGAACCGAGTTATCA-TATTCCTAAAGA
* * *
17724 TGACCAGAACTCTTCATCGCGTAGGAGCCGTGTCACCCCTAGATAACCAGTCATCCTCATCGCGT
1 TGACCAGAACTCTTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCATCCTCATCGCCT
*
17789 AGGAACCGAGTTATCATATTCCTAAATA
66 AGGAACCGAGTTATCATATTCCTAAAGA
* * *
17817 TGACCATAACTCTTCATCACGTATGAGTCGTGTCATCCCC
1 TGACCAGAACTCTTCATCACGTAGGAGCCGTGTCA-CCCC
17857 CGACCAGATT
Statistics
Matches: 116, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
92 1 0.01
93 111 0.96
94 4 0.03
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (93 bp):
TGACCAGAACTCTTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCATCCTCATCGCCT
AGGAACCGAGTTATCATATTCCTAAAGA
Found at i:18106 original size:3 final size:3
Alignment explanation
Indices: 18098--18144 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
18088 AATTTTAATC
* * *
18098 TTA TTA TTA TTA TTA TTA TTA ATA ATG TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
18145 GTTGAGTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:18942 original size:75 final size:77
Alignment explanation
Indices: 18839--19032 Score: 315
Period size: 76 Copynumber: 2.6 Consensus size: 77
18829 AACCGTTGTA
* * *
18839 CAAGGGGGAATCGGTACCCCCT-TGGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGG
1 CAAGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGG
18902 AGCAAAACCATT
66 AGCAAAACCATT
*
18914 CAAGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGG
1 CAAGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGG
*
18978 AGCCAAACCATT
66 AGCAAAACCATT
18990 C-AGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTC
1 CAAGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTC
19033 TAAGCAATCT
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
75 48 0.43
76 63 0.57
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.22
Consensus pattern (77 bp):
CAAGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGG
AGCAAAACCATT
Found at i:19676 original size:17 final size:17
Alignment explanation
Indices: 19654--19689 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
19644 TCATAAATCC
*
19654 AAAATCCAACAATCCAA
1 AAAATCAAACAATCCAA
19671 AAAATCAAACAATCCAA
1 AAAATCAAACAATCCAA
19688 AA
1 AA
19690 TATAATGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.64, C:0.25, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAATCAAACAATCCAA
Found at i:21717 original size:20 final size:21
Alignment explanation
Indices: 21671--21731 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
21661 TTCCCATGTG
21671 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
21694 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
21714 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
21732 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:27589 original size:75 final size:75
Alignment explanation
Indices: 27482--27688 Score: 310
Period size: 75 Copynumber: 2.7 Consensus size: 75
27472 GTTGTACAAG
* * *
27482 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAGCA
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAGCA
27546 AAACCATTCA
66 AAACCATTCA
* * *
27556 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAGCA
27621 AAACCATTCA
66 AAACCATTCA
*
27631 GGGGGAATCGGTTCCTCCTATGGGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAATT
1 GGGGGAATCGGTTCCTCCTAT--GGGGGGAATCGGTTCCCTCCGAGCATA-CTGGAATT
27689 TTTGACTTTG
Statistics
Matches: 120, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
74 17 0.14
75 72 0.60
77 31 0.26
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (75 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAGCA
AAACCATTCA
Found at i:29607 original size:2 final size:2
Alignment explanation
Indices: 29600--29681 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
29590 TGCTAATCGT
29600 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29642 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29682 AATGGTTTAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:37464 original size:4 final size:4
Alignment explanation
Indices: 37455--37502 Score: 96
Period size: 4 Copynumber: 12.0 Consensus size: 4
37445 ATTAGCTTCA
37455 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
37503 TTCTATTGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:43524 original size:42 final size:40
Alignment explanation
Indices: 43453--43548 Score: 102
Period size: 42 Copynumber: 2.3 Consensus size: 40
43443 AAATAGTAAG
* * *
43453 TCCTTTGGCCATCAGTAAGTCTTTCGAGCATGATGATGAAA
1 TCCTTTGGCCATCAGTAAGCCTTTAGAGCAAGATGAT-AAA
* * *
43494 TCCTTTAGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAG
1 TCCTTT-GGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
*
43535 TCCTTCGGGCCATC
1 TCCTT-TGGCCATC
43549 CATAAGACCT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
41 19 0.42
42 26 0.58
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (40 bp):
TCCTTTGGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
Found at i:43873 original size:80 final size:80
Alignment explanation
Indices: 43769--44064 Score: 278
Period size: 80 Copynumber: 3.6 Consensus size: 80
43759 CAATAACTGC
* *
43769 CATCAATAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTAATTTGTAAGCCTTCACCGAAGA
1 CATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGA
43834 GTAGTGAAGCAAATT
66 GTAGTGAAGCAAATT
* * * ** ** ** * *
43849 CATCAGTAAATCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTATTTCGAGC-AT
1 CATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTAATTTGTAAG-CCTTC-ACCGAA
*
43913 GA-T-GATGAAGTC--CTT
64 GAGTAG-TGAAG-CAAATT
* * * *
43928 CGGGCCATCAGTAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTAATTGGTAAGCCTTCACC
1 -----CATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTAATTTGTAAGCCTTCACC
* *
43993 GAAGAGTAGAGAAGCAAATC
61 GAAGAGTAGTGAAGCAAATT
* *
44013 CATCAATAAGTCTTTTGAGCATGATGATGAAATCCTTCGGGTCATTTGTAAG
1 CATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTAATTTGTAAG
44065 TCTTTCGAGC
Statistics
Matches: 167, Mismatches: 35, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
79 3 0.02
80 95 0.57
81 7 0.04
82 4 0.02
83 7 0.04
84 49 0.29
85 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (80 bp):
CATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGA
GTAGTGAAGCAAATT
Found at i:43887 original size:22 final size:21
Alignment explanation
Indices: 43862--43971 Score: 66
Period size: 22 Copynumber: 5.2 Consensus size: 21
43852 CAGTAAATCT
43862 TTCGAGCATGATGATGAAGTCC
1 TTCGAGCATGATGAT-AAGTCC
* * **
43884 TTCGGGCCATCA-G-TAAGTAT
1 TTCGAG-CATGATGATAAGTCC
43904 TTCGAGCATGATGATGAAGTCC
1 TTCGAGCATGATGAT-AAGTCC
* * *
43926 TTCGGGCCATCA-G-TAAGTCT
1 TTCGAG-CATGATGATAAGTCC
* *
43946 TTCGAGTATGATGATTAAATCC
1 TTCGAGCATGATGA-TAAGTCC
43968 TTCG
1 TTCG
43972 GGTAATTGGT
Statistics
Matches: 64, Mismatches: 16, Indels: 16
0.67 0.17 0.17
Matches are distributed among these distances:
19 7 0.11
20 21 0.33
21 3 0.05
22 25 0.39
23 8 0.12
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (21 bp):
TTCGAGCATGATGATAAGTCC
Found at i:43907 original size:20 final size:20
Alignment explanation
Indices: 43878--43949 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
43868 CATGATGATG
*
43878 AAGTCCTTCGGGCCATCAGT
1 AAGTCTTTCGGGCCATCAGT
* * *
43898 AAGTATTTCGAG-CATGATGAT
1 AAGTCTTTCGGGCCATCA-G-T
*
43919 GAAGTCCTTCGGGCCATCAGT
1 -AAGTCTTTCGGGCCATCAGT
43940 AAGTCTTTCG
1 AAGTCTTTCG
43950 AGTATGATGA
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
19 4 0.10
20 19 0.49
21 2 0.05
22 10 0.26
23 4 0.10
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (20 bp):
AAGTCTTTCGGGCCATCAGT
Found at i:43966 original size:164 final size:163
Alignment explanation
Indices: 43767--44098 Score: 511
Period size: 164 Copynumber: 2.0 Consensus size: 163
43757 ATCAATAACT
* *
43767 GCCATCAATAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTAATTTGTAAGCCTTCACCGAA
1 GCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTGGTAAGCCTTCACCGAA
* * * *
43832 GAGTAGTGAAGCAAATTCATCAGTAAATCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATCAG
66 GAGTAGAGAAGCAAATCCATCAATAAATCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAG
*
43897 TAAGTATTTCGAGCATGATGATGAAGTCCTTCGG
131 TAAGTATTTCGAGCAAGATGAT-AAGTCCTTCGG
* *
43931 GCCATCAGTAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTAATTGGTAAGCCTTCACCGAA
1 GCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTGGTAAGCCTTCACCGAA
* * * **
43996 GAGTAGAGAAGCAAATCCATCAATAAGTCTTTTGAGCATGATGATGAAATCCTTCGGGTCATTTG
66 GAGTAGAGAAGCAAATCCATCAATAAATCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAG
* *
44061 TAAGTCTTTCGAGCAAGTTGATAAGTCCTTCGG
131 TAAGTATTTCGAGCAAGATGATAAGTCCTTCGG
44094 GCCAT
1 GCCAT
44099 TTTAAGCCTT
Statistics
Matches: 152, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
163 16 0.11
164 136 0.89
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (163 bp):
GCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTGGTAAGCCTTCACCGAA
GAGTAGAGAAGCAAATCCATCAATAAATCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAG
TAAGTATTTCGAGCAAGATGATAAGTCCTTCGG
Found at i:43984 original size:42 final size:42
Alignment explanation
Indices: 43849--43973 Score: 205
Period size: 42 Copynumber: 3.0 Consensus size: 42
43839 GAAGCAAATT
*
43849 CATCAGTAAATCTTTCGAGCATGATGATGAAGTCCTTCGGGC
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGC
*
43891 CATCAGTAAGTATTTCGAGCATGATGATGAAGTCCTTCGGGC
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGC
* * *
43933 CATCAGTAAGTCTTTCGAGTATGATGATTAAATCCTTCGGG
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGG
43974 TAATTGGTAA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGC
Found at i:44100 original size:41 final size:41
Alignment explanation
Indices: 44019--44104 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 41
44009 AATCCATCAA
* * *
44019 TAAGTCTTTTGAGCATGATGATGAAATCCTTCGGGTCATTT
1 TAAGTCTTTCGAGCAAGATGATGAAATCCTTCGGGCCATTT
* *
44060 GTAAGTCTTTCGAGCAAGTTGAT-AAGTCCTTCGGGCCATTT
1 -TAAGTCTTTCGAGCAAGATGATGAAATCCTTCGGGCCATTT
44101 TAAG
1 TAAG
44105 CCTTCTCGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 4 0.10
41 16 0.41
42 19 0.49
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.36
Consensus pattern (41 bp):
TAAGTCTTTCGAGCAAGATGATGAAATCCTTCGGGCCATTT
Found at i:44539 original size:53 final size:53
Alignment explanation
Indices: 44476--44835 Score: 474
Period size: 53 Copynumber: 6.8 Consensus size: 53
44466 AGAATCAAAC
44476 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
*
44529 CAGAAGATTGTTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* *
44582 CAGAAGATTATTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* ** * * *
44635 CAGAAGATTGTTCGAGTTTTACTCTTTGAAGCAAGTGAGAGCGAACCCGTAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
** * *
44688 CAGAAGATCATTCGAGTTCTACTCCCTGAAACAAGAGGGA-CTGAACCCGCTAGT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGC-GAACCCG-TAGG
* * ***
44742 C-GAAGATTGTTCGAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCCATTTTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCC-GTAGG
* *
44795 TAGAAGATTGTTCGAGTTCCTTAATCCCTGAA-CAAGAGGGA
1 CAGAAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGA
44836 ACAGACCCGT
Statistics
Matches: 270, Mismatches: 30, Indels: 12
0.87 0.10 0.04
Matches are distributed among these distances:
52 1 0.00
53 230 0.85
54 20 0.07
55 9 0.03
56 10 0.04
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:47145 original size:29 final size:29
Alignment explanation
Indices: 47112--47174 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
47102 TTGAATATTG
47112 TAAAATTCATATTTGTTGTTTTATGGGAT
1 TAAAATTCATATTTGTTGTTTTATGGGAT
47141 TAAAATTCATATTTGTTGTTTTATGGGAT
1 TAAAATTCATATTTGTTGTTTTATGGGAT
47170 TAAAA
1 TAAAA
47175 GTCAAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.49
Consensus pattern (29 bp):
TAAAATTCATATTTGTTGTTTTATGGGAT
Found at i:49516 original size:61 final size:60
Alignment explanation
Indices: 49334--49504 Score: 173
Period size: 61 Copynumber: 2.8 Consensus size: 60
49324 TATTTTCATA
* * * * * *
49334 ATATTTTTCTAAAATGGTATATATATGATTTTGGATAAGAATTACCCAATACATTTTTGTATG
1 ATATTTTACT-AAATGGT-TATAGATGATTTTGGGTATGAATTACCAAATACA-TTTTATATG
* * * * *
49397 AAATTTTACTAAATGATTTTAGATGATTTCGGGATATG-ATTACCCAAATGCATTTTATATG
1 ATATTTTACTAAATGGTTATAGATGATTTTGGG-TATGAATTA-CCAAATACATTTTATATG
* *
49458 ATATTTTGCTAAATGGTTATGGATGATTTTGGGTATGAATTACCAAA
1 ATATTTTACTAAATGGTTATAGATGATTTTGGGTATGAATTACCAAA
49505 CTCACCTTTA
Statistics
Matches: 88, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
60 9 0.10
61 55 0.62
62 16 0.18
63 8 0.09
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (60 bp):
ATATTTTACTAAATGGTTATAGATGATTTTGGGTATGAATTACCAAATACATTTTATATG
Found at i:51366 original size:34 final size:34
Alignment explanation
Indices: 51327--51405 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
51317 TGAACATATA
* * *
51327 TAAACGAATATGTTCGCGAACATTATACAAACAC
1 TAAACGAACATGTTCACGAACATTAAACAAACAC
* * **
51361 TAAACGAGCATGTTCATGAATGTTAAACAAACAC
1 TAAACGAACATGTTCACGAACATTAAACAAACAC
51395 TAAACGAACAT
1 TAAACGAACAT
51406 TAAACGAATG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (34 bp):
TAAACGAACATGTTCACGAACATTAAACAAACAC
Found at i:51404 original size:11 final size:11
Alignment explanation
Indices: 51384--51426 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
51374 TCATGAATGT
*
51384 TAAACAAACAC
1 TAAACGAACAC
*
51395 TAAACGAACAT
1 TAAACGAACAC
**
51406 TAAACGAATGC
1 TAAACGAACAC
51417 TAAACGAACA
1 TAAACGAACA
51427 TGTTAGTGAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.56, C:0.21, G:0.09, T:0.14
Consensus pattern (11 bp):
TAAACGAACAC
Found at i:51409 original size:22 final size:22
Alignment explanation
Indices: 51383--51427 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
51373 TTCATGAATG
51383 TTAAACAAACACTAAACGAACA
1 TTAAACAAACACTAAACGAACA
* **
51405 TTAAACGAATGCTAAACGAACA
1 TTAAACAAACACTAAACGAACA
51427 T
1 T
51428 GTTAGTGAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.20, G:0.09, T:0.18
Consensus pattern (22 bp):
TTAAACAAACACTAAACGAACA
Found at i:51797 original size:2 final size:2
Alignment explanation
Indices: 51790--51833 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
51780 TATTCTTATG
51790 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51832 TA
1 TA
51834 CTTGTGAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52021 original size:36 final size:36
Alignment explanation
Indices: 51968--52049 Score: 130
Period size: 36 Copynumber: 2.3 Consensus size: 36
51958 TATATCCCTA
*
51968 AAATCAATCTTAGCCTTCACGAAATAGTAGTGAAGC
1 AAATCAATCTTAACCTTCACGAAATAGTAGTGAAGC
*
52004 AAATCAAT-TTAAACCTTCACGGAATAGTAGTGAAGC
1 AAATCAATCTT-AACCTTCACGAAATAGTAGTGAAGC
52040 AAATCAATCT
1 AAATCAATCT
52050 CGAGTCTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
35 2 0.05
36 39 0.93
37 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (36 bp):
AAATCAATCTTAACCTTCACGAAATAGTAGTGAAGC
Found at i:52182 original size:47 final size:47
Alignment explanation
Indices: 52112--52584 Score: 428
Period size: 47 Copynumber: 9.6 Consensus size: 47
52102 TCTCGAGTCT
* *
52112 TATCTCCCTAAAAGAAGATTGGAGCAGATTCGTCTTCCCTTGGATCA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCA
* * ** * *
52159 TATCTCCCTGAAAGAAGAGTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCT
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTT-C-----CCT-TGGA-TCA
*
52214 TATCTCCCTGAAAGAAGAGTGGAGAAGATTCGTCTTCCCTTGGATCA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCA
*
52261 TATCTCCCTGAAAGAAGAGTGGACCAGATTCGTCTTCCCTTGGATCA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCA
* * ** * *
52308 TATCTCCCTGAAAGAAGAGTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCT
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTT-C-----CCT-TGGA-TCA
* *
52363 TATCTCCCTGAAAGAAGAGTAGAGAAGATTCGTCTTCCCTTGGATCA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCA
*
52410 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCATCTTCCCTTGGAT-A
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCA
* * * * * *
52456 GTATCTCCCTTAAAGAAGAATGGAGCAGATCCGTTTTACAAAGATTTCTT-GAGTCT
1 -TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTT-C-------CCTTGGA-TCA
* *
52512 TATCTCCCTGAAAGAAGAGTGGAGCATATTCGTCTTCCCTTGGATCG
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCA
* * *
52559 TATCTCCCTAAAAAAATAGTGGAGCA
1 TATCTCCCTGAAAGAAGAGTGGAGCA
52585 TACCCGTTTT
Statistics
Matches: 346, Mismatches: 52, Indels: 56
0.76 0.11 0.12
Matches are distributed among these distances:
46 1 0.00
47 215 0.62
48 11 0.03
49 2 0.01
53 2 0.01
54 11 0.03
55 104 0.30
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (47 bp):
TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCA
Found at i:52237 original size:102 final size:102
Alignment explanation
Indices: 52057--52639 Score: 597
Period size: 102 Copynumber: 5.8 Consensus size: 102
52047 TCTCGAGTCT
* * * *
52057 TATCTCCCTAAAAGAAGAGTGGAGAATATCCGTTTTACAAAGATTTCTCGAGTCTTATCTCCCTA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATCCGTTTTACAAAGATTTCTCGAGTCTTATCTCCCTG
*
52122 AAAGAAGATTGGAGCAGATTCGTCTTCCCTTGGATCA
66 AAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCA
*
52159 TATCTCCCTGAAAGAAGAGTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCTTATCTCCCTG
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATCCGTTTTACAAAGATTTCTCGAGTCTTATCTCCCTG
*
52224 AAAGAAGAGTGGAGAAGATTCGTCTTCCCTTGGATCA
66 AAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCA
* * * ** * *
52261 TATCTCCCTGAAAGAAGAGTGGACCAGATTCGTCTT-C-----CCT-TGGA-TCATATCTCCCTG
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATCCGTTTTACAAAGATTTCTCGAGTCTTATCTCCCTG
* * ** * *
52318 AAAGAAGAGTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCT
66 AAAGAAGAGTGGAGCAGATTCGTCTT-C-----CCT-TGGA-TCA
* * * * ** * *
52363 TATCTCCCTGAAAGAAGAGTAGAGAAGATTCGTCTT-C-----CCT-TGGA-TCATATCTCCCTG
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATCCGTTTTACAAAGATTTCTCGAGTCTTATCTCCCTG
*
52420 AAAGAAGAGTGGAGCAGATTCATCTTCCCTTGGAT-A
66 AAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCA
* * *
52456 GTATCTCCCTTAAAGAAGAATGGAGCAGATCCGTTTTACAAAGATTTCTTGAGTCTTATCTCCCT
1 -TATCTCCCTGAAAGAAGAGTGGAGCAGATCCGTTTTACAAAGATTTCTCGAGTCTTATCTCCCT
* *
52521 GAAAGAAGAGTGGAGCATATTCGTCTTCCCTTGGATCG
65 GAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCA
* * * * * *
52559 TATCTCCCTAAAAAAATAGTGGAGCATACCCGTTTTACAAAGATTTCTCGAGTCTTATCTCACTG
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATCCGTTTTACAAAGATTTCTCGAGTCTTATCTCCCTG
*
52624 GAAGAAGAGTGGAGCA
66 AAAGAAGAGTGGAGCA
52640 TATTTGTTTT
Statistics
Matches: 410, Mismatches: 53, Indels: 36
0.82 0.11 0.07
Matches are distributed among these distances:
94 66 0.16
95 8 0.02
96 2 0.00
100 2 0.00
101 8 0.02
102 324 0.79
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (102 bp):
TATCTCCCTGAAAGAAGAGTGGAGCAGATCCGTTTTACAAAGATTTCTCGAGTCTTATCTCCCTG
AAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCA
Found at i:52327 original size:149 final size:149
Alignment explanation
Indices: 52112--52744 Score: 856
Period size: 149 Copynumber: 4.2 Consensus size: 149
52102 TCTCGAGTCT
* *
52112 TATCTCCCTAAAAGAAGATTGGAGCAGATTCGTCTTCCCTTGGATCATATCTCCCTGAAAGAAGA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCATATCTCCCTGAAAGAAGA
52177 GTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGAAGA
66 GTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGAAGA
52242 TTCGTCTTCCCTTGGATCA
131 TTCGTCTTCCCTTGGATCA
*
52261 TATCTCCCTGAAAGAAGAGTGGACCAGATTCGTCTTCCCTTGGATCATATCTCCCTGAAAGAAGA
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCATATCTCCCTGAAAGAAGA
*
52326 GTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCTTATCTCCCTGAAAGAAGAGTAGAGAAGA
66 GTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGAAGA
52391 TTCGTCTTCCCTTGGATCA
131 TTCGTCTTCCCTTGGATCA
* *
52410 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCATCTTCCCTTGGAT-AGTATCTCCCTTAAAGAAG
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCA-TATCTCCCTGAAAGAAG
* * * * *
52474 AATGGAGCAGATCCGTTTTACAAAGATTTCTTGAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAT
65 AGTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGAAG
*
52539 ATTCGTCTTCCCTTGGATCG
130 ATTCGTCTTCCCTTGGATCA
* * * * ** * ** * * *
52559 TATCTCCCTAAAAAAATAGTGGAGCATACCCGTTTTACAAAGATTTCTCGAGTCTTATCTCACTG
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTT-C-----CCT-TGGA-TCATATCTCCCTG
* * ** * *
52624 GAAGAAGAGTGGAGCATATTTGTTTTACAAAGATTTCTCAAGTCTTATCTCCCTGAAAGAAGAGT
58 AAAGAAGAGTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCTTATCTCCCTGAAAGAAGAGT
* **
52689 GGA-ACAGATTCGTTTTCCCTTTAATCA
123 GGAGA-AGATTCGTCTTCCCTTGGATCA
*
52716 TATCTCCCTGAAAGAAGAGTGAAGCAGAT
1 TATCTCCCTGAAAGAAGAGTGGAGCAGAT
52745 CTATTTTACA
Statistics
Matches: 426, Mismatches: 47, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
148 1 0.00
149 310 0.73
150 1 0.00
155 1 0.00
156 3 0.01
157 110 0.26
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (149 bp):
TATCTCCCTGAAAGAAGAGTGGAGCAGATTCGTCTTCCCTTGGATCATATCTCCCTGAAAGAAGA
GTGGAGCAGATCCGTTTTACAAAGATTTATCGAGTCTTATCTCCCTGAAAGAAGAGTGGAGAAGA
TTCGTCTTCCCTTGGATCA
Found at i:52680 original size:157 final size:156
Alignment explanation
Indices: 52457--52799 Score: 443
Period size: 157 Copynumber: 2.2 Consensus size: 156
52447 CCTTGGATAG
* * **
52457 TATCTCCCTTAAAGAAGAATGGAGCAGATCCGTTTTACAAAGATTTCTTGAGTCTTATCTCCCTG
1 TATCTCACTGAAAGAAG-ATGGAGCAGATCCGTTTTACAAAGATTTCTCAAGTCTTATCTCCCTG
* * * * * * *
52522 AAAGAAGAGTGGAGCATATTCGTCTTCCCTTGGATCGTATCTCCCTAAAAAAATAGTGGAGCATA
65 AAAGAAGAGTGGAACAGATTCGTCTTCCCTTGAATCATATCTCCCTAAAAAAAGAGTGAAGCAGA
*
52587 CCCGTTTTACAAAGATTTCTCGAGTCT
130 CCCATTTTACAAAGATTTCTCGAGTCT
* * **
52614 TATCTCACTGGAAGAAGAGTGGAGCATATTTGTTTTACAAAGATTTCTCAAGTCTTATCTCCCTG
1 TATCTCACTGAAAGAAGA-TGGAGCAGATCCGTTTTACAAAGATTTCTCAAGTCTTATCTCCCTG
* * * *
52679 AAAGAAGAGTGGAACAGATTCGTTTTCCCTTTAATCATATCTCCCTGAAAGAAGAGTGAAGCAGA
65 AAAGAAGAGTGGAACAGATTCGTCTTCCCTTGAATCATATCTCCCTAAAAAAAGAGTGAAGCAGA
* * *
52744 TCTATTTTACAAAGATTTCTTGAGTCT
130 CCCATTTTACAAAGATTTCTCGAGTCT
*
52771 TATCTCCCTGAAAGAAGCATGGAGCAGAT
1 TATCTCACTGAAAGAAG-ATGGAGCAGAT
52800 TCGTCTTCCC
Statistics
Matches: 158, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
156 1 0.01
157 156 0.99
158 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (156 bp):
TATCTCACTGAAAGAAGATGGAGCAGATCCGTTTTACAAAGATTTCTCAAGTCTTATCTCCCTGA
AAGAAGAGTGGAACAGATTCGTCTTCCCTTGAATCATATCTCCCTAAAAAAAGAGTGAAGCAGAC
CCATTTTACAAAGATTTCTCGAGTCT
Found at i:52704 original size:55 final size:55
Alignment explanation
Indices: 52589--52803 Score: 209
Period size: 55 Copynumber: 4.1 Consensus size: 55
52579 GGAGCATACC
* * * * *
52589 CGTTTTACAAAGATTTCTCGAGTCTTATCTCACTGGAAGAAGAGTGGAGCATATT
1 CGTTTTACAAAGATTTCTCAAGTCTTATCTCCCTGAAAGAAGAGTGGAACAGATT
*
52644 TGTTTTACAAAGATTTCTCAAGTCTTATCTCCCTGAAAGAAGAGTGGAACAGATT
1 CGTTTTACAAAGATTTCTCAAGTCTTATCTCCCTGAAAGAAGAGTGGAACAGATT
** *
52699 CGTTTT-C----CCTT-T-AA-TCATATCTCCCTGAAAGAAGAGT-GAAGCAGA-T
1 CGTTTTACAAAGATTTCTCAAGTCTTATCTCCCTGAAAGAAGAGTGGAA-CAGATT
* ** *
52745 CTATTTTACAAAGATTTCTTGAGTCTTATCTCCCTGAAAGAAGCA-TGGAGCAGATT
1 C-GTTTTACAAAGATTTCTCAAGTCTTATCTCCCTGAAAGAAG-AGTGGAACAGATT
52801 CGT
1 CGT
52804 CTTCCCTTGG
Statistics
Matches: 130, Mismatches: 17, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
46 5 0.04
47 30 0.23
48 3 0.02
49 1 0.01
50 2 0.02
52 2 0.02
53 1 0.01
54 2 0.02
55 79 0.61
56 5 0.04
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (55 bp):
CGTTTTACAAAGATTTCTCAAGTCTTATCTCCCTGAAAGAAGAGTGGAACAGATT
Found at i:52720 original size:102 final size:101
Alignment explanation
Indices: 52614--52911 Score: 339
Period size: 102 Copynumber: 2.9 Consensus size: 101
52604 TCTCGAGTCT
* * * *
52614 TATCTCACTGGAAGAAGAGTGGAGCATATTTGTTTTACAAAGATTTCTCAAGTCTTATCTCCCTG
1 TATCTC-CTGAAAGAAGAGTGGAGCAGATCTGTTTTACAAAGATTTCTTAAGTCTTATCTCCCTG
* *
52679 AAAGAAGAGTGGAACAGATTCGTTTTCCCTTTAATCA
65 AAAGAAGAGTGGAACAGATTCGTCTTCCCTTGAATCA
* * *
52716 TATCTCCCTGAAAGAAGAGTGAAGCAGATCTATTTTACAAAGATTTCTTGAGTCTTATCTCCCTG
1 TATCT-CCTGAAAGAAGAGTGGAGCAGATCTGTTTTACAAAGATTTCTTAAGTCTTATCTCCCTG
* * *
52781 AAAGAAGCA-TGGAGCAGATTCGTCTTCCCTTGGATCT
65 AAAGAAG-AGTGGAACAGATTCGTCTTCCCTTGAATCA
* * * * *
52818 TATCTTCCTAAAAAAAGAGTGGAGCAGACCCGTTTT-CTAAAGATTTCTTAAGTCTGATCTCCCC
1 TATC-TCCTGAAAGAAGAGTGGAGCAGATCTGTTTTAC-AAAGATTTCTTAAGTCTTATCT-CCC
* * * *
52882 TGAATGAATAGTGGAACAGACTCATCTTCC
63 TGAAAGAAGAGTGGAACAGATTCGTCTTCC
52912 AAAATTGATC
Statistics
Matches: 165, Mismatches: 25, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
101 1 0.01
102 135 0.82
103 29 0.18
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (101 bp):
TATCTCCTGAAAGAAGAGTGGAGCAGATCTGTTTTACAAAGATTTCTTAAGTCTTATCTCCCTGA
AAGAAGAGTGGAACAGATTCGTCTTCCCTTGAATCA
Found at i:54520 original size:16 final size:15
Alignment explanation
Indices: 54492--54521 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
54482 CATATTTATT
54492 ATTTAATTATATTTA
1 ATTTAATTATATTTA
54507 ATTTAATATATATTT
1 ATTTAAT-TATATTT
54522 TTAAGTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTAATTATATTTA
Found at i:55248 original size:34 final size:33
Alignment explanation
Indices: 55210--55309 Score: 103
Period size: 34 Copynumber: 3.0 Consensus size: 33
55200 TGAACATATA
*
55210 TAAACGAATATGTTCACGAACGTTATACGAACAC
1 TAAACGAA-ATGTTCACGAACGTTAAACGAACAC
* * * *
55244 TAAACGAACTGTTCATGAATGTTAAACAAACAC
1 TAAACGAAATGTTCACGAACGTTAAACGAACAC
* *
55277 TAACAC-ACCATGTTTACGAACGTTAAACGAACA
1 TAA-ACGA-AATGTTCACGAACGTTAAACGAACA
55310 TGTTTACGAA
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
33 24 0.45
34 29 0.55
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.23
Consensus pattern (33 bp):
TAAACGAAATGTTCACGAACGTTAAACGAACAC
Found at i:55312 original size:23 final size:23
Alignment explanation
Indices: 55285--55333 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
55275 ACTAACACAC
55285 CATGTTTACGAACGTTAAACGAA
1 CATGTTTACGAACGTTAAACGAA
55308 CATGTTTACGAACGTTAAACGAA
1 CATGTTTACGAACGTTAAACGAA
55331 CAT
1 CAT
55334 ATTCACTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (23 bp):
CATGTTTACGAACGTTAAACGAA
Found at i:56941 original size:10 final size:10
Alignment explanation
Indices: 56926--56951 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
56916 AAATGTATCA
56926 GATGTAAACG
1 GATGTAAACG
56936 GATGTAAACG
1 GATGTAAACG
56946 GATGTA
1 GATGTA
56952 GAACAGAGAT
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:0.08, G:0.31, T:0.23
Consensus pattern (10 bp):
GATGTAAACG
Done.