Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007379.1 Hibiscus syriacus cultivar Beakdansim tig00019816_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: 78111
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:1925 original size:32 final size:32
Alignment explanation
Indices: 1853--2037 Score: 234
Period size: 32 Copynumber: 5.8 Consensus size: 32
1843 AGTCGAGGGT
* *
1853 TTACCTATGTTTCTACGGAACATATGGACAGAA
1 TTACCTATG-TTCTTCGGAACATATGGACAGGA
*
1886 TTA-CTATG-TCTTTCGGGACATATGGACAGGA
1 TTACCTATGTTC-TTCGGAACATATGGACAGGA
* *
1917 TTACCTATGTTCTTCGGAACATATGTACATGA
1 TTACCTATGTTCTTCGGAACATATGGACAGGA
*
1949 TTACCTATGTTCTTCGGAACATATGAACAGGA
1 TTACCTATGTTCTTCGGAACATATGGACAGGA
* * *
1981 TTTCTTATGTTCTCCGGAACATATGGACA-G-
1 TTACCTATGTTCTTCGGAACATATGGACAGGA
*
2011 TTACATATGTTCTTCGGAACATATGGA
1 TTACCTATGTTCTTCGGAACATATGGA
2038 TAGGTCATTT
Statistics
Matches: 134, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
30 26 0.19
31 21 0.16
32 82 0.61
33 5 0.04
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (32 bp):
TTACCTATGTTCTTCGGAACATATGGACAGGA
Found at i:4918 original size:18 final size:17
Alignment explanation
Indices: 4895--4950 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
4885 AATAATAAAT
4895 TAATTTAAATAAAACTAA
1 TAATTTAAATAAAA-TAA
* *
4913 TAATTT-ATTAAAAATAT
1 TAATTTAAAT-AAAATAA
4930 TATATTTATAATAAAATAA
1 TA-ATTTA-AATAAAATAA
4949 TA
1 TA
4951 GAAAGTTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 6 0.20
18 14 0.47
19 8 0.27
20 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATTTAAATAAAATAA
Found at i:14712 original size:59 final size:59
Alignment explanation
Indices: 14640--14758 Score: 195
Period size: 59 Copynumber: 2.0 Consensus size: 59
14630 AAAGCCAATT
* *
14640 TCAATCATTATTGGCTAGGACTTCTGATCTTAAAC-CACTGTTGATGAGCTTGGAATCGA
1 TCAATCATTATTGGCTAGGACTTCTGATCTTAAACTCA-TGTAGATGAACTTGGAATCGA
*
14699 TCAATCATTATTGGCTAGGACTTCTGATCTTAAACTGATGTAGATGAACTTGGAATCGA
1 TCAATCATTATTGGCTAGGACTTCTGATCTTAAACTCATGTAGATGAACTTGGAATCGA
14758 T
1 T
14759 ATTGAGATGC
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 55 0.98
60 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (59 bp):
TCAATCATTATTGGCTAGGACTTCTGATCTTAAACTCATGTAGATGAACTTGGAATCGA
Found at i:17271 original size:41 final size:41
Alignment explanation
Indices: 17214--17297 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
17204 TTGTAATTTT
* * *
17214 ACAAGAAGATTATCCTGAATTTGACCTTGAGGACAATCTCA
1 ACAAGAAGATTATCCTGAACTTAACCTTGAGGAAAATCTCA
* * *
17255 ACAAGAGGCTTATCCTGAACTTAAGCTTGAGGAAAATCTCA
1 ACAAGAAGATTATCCTGAACTTAACCTTGAGGAAAATCTCA
17296 AC
1 AC
17298 TCCAAGAAGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (41 bp):
ACAAGAAGATTATCCTGAACTTAACCTTGAGGAAAATCTCA
Found at i:18626 original size:9 final size:9
Alignment explanation
Indices: 18612--18637 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
18602 AACATGTCCT
18612 GCACCGACA
1 GCACCGACA
18621 GCACCGACA
1 GCACCGACA
18630 GCACCGAC
1 GCACCGAC
18638 CTTTGCTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.46, G:0.23, T:0.00
Consensus pattern (9 bp):
GCACCGACA
Found at i:22294 original size:17 final size:16
Alignment explanation
Indices: 22237--22296 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
22227 AATTTTTCAT
22237 TATATTATT-TTAAT-
1 TATATTATTATTAATA
22251 TATTATTATTATTAA-A
1 TA-TATTATTATTAATA
*
22267 TAAAATATATTATTATATA
1 T-ATAT-TATTATTA-ATA
22286 TATATTATTAT
1 TATATTATTAT
22297 CATTAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
14 2 0.05
15 7 0.19
16 7 0.19
17 15 0.41
18 4 0.11
19 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATTATTATTAATA
Found at i:22302 original size:37 final size:35
Alignment explanation
Indices: 22237--22308 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 35
22227 AATTTTTCAT
* *
22237 TATATTATTTTAATTATTATTATTATTAAATAAAA
1 TATATTATTATAATTATTATTATCATTAAATAAAA
22272 TATATTATTATATATATATTATTATCATTAAATAAAA
1 TATATTATTATA-AT-TATTATTATCATTAAATAAAA
22309 AATAATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 11 0.33
36 2 0.06
37 20 0.61
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (35 bp):
TATATTATTATAATTATTATTATCATTAAATAAAA
Found at i:22726 original size:24 final size:23
Alignment explanation
Indices: 22675--22739 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
22665 CGGATCCTGC
* **
22675 AAAACAGAAAAGAAGGGAGGACAG
1 AAAACAGAAAAGAA-GAAAAACAG
22699 AAAACAGAAAAGAAGAAAAACAG
1 AAAACAGAAAAGAAGAAAAACAG
*
22722 AAAA-AAAAAAGAAAGAAA
1 AAAACAGAAAAG-AAGAAA
22740 GGAAAGCTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 6 0.17
23 16 0.44
24 14 0.39
ACGTcount: A:0.72, C:0.06, G:0.22, T:0.00
Consensus pattern (23 bp):
AAAACAGAAAAGAAGAAAAACAG
Found at i:23604 original size:18 final size:18
Alignment explanation
Indices: 23581--23639 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
23571 TTGTTTAAAT
23581 ATATTTTAATTTTATATA
1 ATATTTTAATTTTATATA
*
23599 ATATTTTAATTAGTAT-TA
1 ATATTTTAATT-TTATATA
* *
23617 TTATTTTATTTTTA-ATA
1 ATATTTTAATTTTATATA
23634 TATATT
1 -ATATT
23640 ATTTGATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
17 4 0.12
18 26 0.79
19 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
ATATTTTAATTTTATATA
Found at i:23653 original size:24 final size:24
Alignment explanation
Indices: 23592--23654 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 24
23582 TATTTTAATT
*
23592 TTATATAATATTTTAATTAGTATTA
1 TTATATTA-ATTTTAATTAGTATTA
* *
23617 TTATTTTATTTTTAATATA-TATTA
1 TTATATTAATTTTAAT-TAGTATTA
23641 TT-TGATTAATTTTA
1 TTAT-ATTAATTTTA
23655 TAAATTAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 1 0.03
24 22 0.71
25 8 0.26
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (24 bp):
TTATATTAATTTTAATTAGTATTA
Found at i:24360 original size:20 final size:21
Alignment explanation
Indices: 24337--24388 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
24327 AGAAATTAAA
24337 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
24357 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
24379 -ATT-ATTTATT
1 AATTCATTTATT
24389 CTTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:28731 original size:2 final size:2
Alignment explanation
Indices: 28724--28753 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28714 TTATCCTTTA
28724 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28754 CCTTTGTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33791 original size:22 final size:22
Alignment explanation
Indices: 33762--33816 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
33752 ATCTACACTC
*
33762 TTCAAAGATGATAGGTTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
33784 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
33806 TTCAAAAATGA
1 TTCAAAGATGA
33817 AAGCTTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:34636 original size:77 final size:77
Alignment explanation
Indices: 34492--35285 Score: 1443
Period size: 77 Copynumber: 10.4 Consensus size: 77
34482 CTATTTCCCA
*
34492 CATCTATAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
34556 AATCCTTCGGGT
66 AAGCCTTCGGGT
34568 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
34633 AATCCTTCGGGT
66 AAGCCTTCGGGT
*
34645 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
* *
34710 AATCCTTCAGGT
66 AAGCCTTCGGGT
34722 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
34787 AAGCCTTAGGGT
66 AAGCCTTCGGGT
34799 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
34864 AATCCTTCGGGT
66 AAGCCTTCGGGT
*
34876 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
34941 AATCCTTCGGGT
66 AAGCCTTCGGGT
34953 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
35018 AAGCCTTAGGGT
66 AAGCCTTCGGGT
35030 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
35094 AAGCCTTCGGGT
66 AAGCCTTCGGGT
35106 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
35170 AAGCCTTCGAGT
66 AAGCCTTCGGGT
35182 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
35246 AAGCCTTTGGGT
66 AAGCCTTCGGGT
35258 CATCTGTAAGTCCTTCAGTGCATGATGT
1 CATCTGTAAGTCCTTCAGTGCATGATGT
35286 GTTCAATATT
Statistics
Matches: 700, Mismatches: 17, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
76 251 0.36
77 449 0.64
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (77 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAGCCTTCGGGT
Found at i:35460 original size:35 final size:32
Alignment explanation
Indices: 35409--35475 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 32
35399 AATTTTTCAT
*
35409 TATATTATTTTAATTATTATTATTAAATAAAA
1 TATATTATTTTAATTATTATCATTAAATAAAA
35441 TATATTATTATATATATTATTATCATTAAATAAAA
1 TATATTATT-T-TA-ATTATTATCATTAAATAAAA
35476 AATAATAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 9 0.29
33 1 0.03
34 2 0.06
35 19 0.61
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATTATTTTAATTATTATCATTAAATAAAA
Found at i:35894 original size:24 final size:24
Alignment explanation
Indices: 35843--35909 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
35833 CGGATCCTGC
* **
35843 AAAACAGAAAAGAAGGGAGGACAG
1 AAAACAGAAAAGAAGGAAAAACAG
35867 AAAACAGAAAAGAA-GAAAAACAG
1 AAAACAGAAAAGAAGGAAAAACAG
* *
35890 AAAAAAAAAAAGAAAGGAAA
1 AAAACAGAAAAG-AAGGAAA
35910 GCTTACCGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 16 0.44
24 16 0.44
25 4 0.11
ACGTcount: A:0.72, C:0.06, G:0.22, T:0.00
Consensus pattern (24 bp):
AAAACAGAAAAGAAGGAAAAACAG
Found at i:36762 original size:18 final size:18
Alignment explanation
Indices: 36739--36799 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
36729 TTGTTTAAAT
36739 ATATTTTAATTTTATATA
1 ATATTTTAATTTTATATA
*
36757 ATATTTTAATTAGTAT-TA
1 ATATTTTAATT-TTATATA
* *
36775 TTATTTTATTTTTAATATA
1 ATATTTTAATTTT-ATATA
*
36794 TTATTT
1 ATATTT
36800 GATTAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 1 0.03
18 24 0.67
19 11 0.31
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
ATATTTTAATTTTATATA
Found at i:42066 original size:19 final size:19
Alignment explanation
Indices: 42044--42082 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
42034 ATGATAATAT
42044 CCCAAATATGAATTAATTA
1 CCCAAATATGAATTAATTA
42063 CCCAAATATGAATTAATTA
1 CCCAAATATGAATTAATTA
42082 C
1 C
42083 AACACAAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.31
Consensus pattern (19 bp):
CCCAAATATGAATTAATTA
Found at i:43084 original size:84 final size:84
Alignment explanation
Indices: 42975--43170 Score: 200
Period size: 84 Copynumber: 2.3 Consensus size: 84
42965 TTGATCTCTT
* * *
42975 CGGAGAAGAAAGTCACC-ACGGGTTCTGGTCTTTCCATTAAC-CCGGAGAAGAAACTCATCAATG
1 CGGAGAGGAAAGTCACCAAC-AGTTCTGGTCTTTCCATT-ACTCCGGAGAAGAAACTCATCAACG
* *
43038 GTGCTGGTGCTTCGGTCACTT
64 GTGCTGGCGCTTCGGTCACTC
* * *** * * *
43059 CGGA-AGAGAAAGTCATCAACAGTTCTGGTGTTTGGGTTTCTCCGGAGAAGAAAGTCATCAGCGG
1 CGGAGAG-GAAAGTCACCAACAGTTCTGGTCTTTCCATTACTCCGGAGAAGAAACTCATCAACGG
* *
43123 TTCTGGCGTTTCGGTCACTC
65 TGCTGGCGCTTCGGTCACTC
*
43143 CGGAGAGGAAATTCACCAACAGTTCTGG
1 CGGAGAGGAAAGTCACCAACAGTTCTGG
43171 ACCTTCTGGT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
83 2 0.02
84 85 0.93
85 4 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (84 bp):
CGGAGAGGAAAGTCACCAACAGTTCTGGTCTTTCCATTACTCCGGAGAAGAAACTCATCAACGGT
GCTGGCGCTTCGGTCACTC
Found at i:43087 original size:42 final size:41
Alignment explanation
Indices: 42912--43170 Score: 155
Period size: 42 Copynumber: 6.2 Consensus size: 41
42902 GTCTTGGTAG
* * * *
42912 GTTCTGGTGCTTT-GGTTACTCCTGAGAAGAGAGTCATAAACA
1 GTTCTGGTG-TTTCGGTCACTCCGGAG-AGAAAGTCATCAACA
* * * * * * *
42954 ATTCTGGTGTTTTGATCTCTTCGGAGAAGAAAGTCA-CCACGG
1 GTTCTGGTGTTTCGGTCACTCCGGAG-AGAAAGTCATCAAC-A
* ** * * **
42996 GTTCTGGTCTTTCCATTAAC-CCGGAGAAGAAACTCATCAATG
1 GTTCTGGTGTTT-CGGTCACTCCGGAG-AGAAAGTCATCAACA
* * *
43038 GTGCTGGTGCTTCGGTCACTTCGGAAGAGAAAGTCATCAACA
1 GTTCTGGTGTTTCGGTCACTCCGG-AGAGAAAGTCATCAACA
* ** * *
43080 GTTCTGGTGTTTGGGTTTCTCCGGAGAAGAAAGTCATCAGCG
1 GTTCTGGTGTTTCGGTCACTCCGGAG-AGAAAGTCATCAACA
* * *
43122 GTTCTGGCGTTTCGGTCACTCCGGAGAGGAAATTCACCAACA
1 GTTCTGGTGTTTCGGTCACTCCGGAGA-GAAAGTCATCAACA
43164 GTTCTGG
1 GTTCTGG
43171 ACCTTCTGGT
Statistics
Matches: 162, Mismatches: 47, Indels: 16
0.72 0.21 0.07
Matches are distributed among these distances:
41 12 0.07
42 144 0.89
43 6 0.04
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (41 bp):
GTTCTGGTGTTTCGGTCACTCCGGAGAGAAAGTCATCAACA
Found at i:43321 original size:84 final size:83
Alignment explanation
Indices: 43210--43592 Score: 354
Period size: 84 Copynumber: 4.6 Consensus size: 83
43200 AGAAAGTAAG
* * * * * * * *
43210 TTCGGTGAAGAAGGTCATCCACGGTTCTGGTGGTTCTCTTCCTTCTGAGATGAAAGTCAT-TATT
1 TTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGCTTCCTTCGGAGAAGAAAGTCATCT-TT
*
43274 GGTACTGGTGTATCGGTTCC
65 GGTTCTGGTGT-TCGGTTCC
*
43294 TTCGGAGAAGAAAGTCAACAACAGTTCTGGTGTTTCGGC-TCCTTCGGAGAAGAAA-TCCATCTT
1 TTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTC-GCTTCCTTCGGAGAAGAAAGT-CATCTT
43357 TGGTTCTGGTG-T---TT-C
64 TGGTTCTGGTGTTCGGTTCC
* * * *
43372 TGT-GGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGATTCCTTCCGACAAGAAATTCATCTTT
1 T-TCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGCTTCCTTCGGAGAAGAAAGTCATCTTT
* * *
43436 GGTGCTGTTGCTTCGGTTCA
65 GGTTCTGGTG-TTCGGTTCC
* **** * * *
43456 TTCGGAGAAGAAATTCATCGTTGGTTCTTGTGTTTCTG-TTCTTTCGGAGAAGAAAGTCATCATT
1 TTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTC-GCTTCCTTCGGAGAAGAAAGTCATCTTT
* *
43520 GGTTCTGGCGTTTTGGTTCC
65 GGTTCTGGTG-TTCGGTTCC
* * *
43540 TTCTGAGAAGAAAGTCATCAACAGTTCTGGCGTTTCGGTTCCTTCGGAGAAGA
1 TTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGCTTCCTTCGGAGAAGA
43593 TGAAAGCCAT
Statistics
Matches: 241, Mismatches: 43, Indels: 30
0.77 0.14 0.10
Matches are distributed among these distances:
77 1 0.00
78 63 0.26
79 4 0.02
80 1 0.00
82 1 0.00
83 5 0.02
84 163 0.68
85 3 0.01
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (83 bp):
TTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGCTTCCTTCGGAGAAGAAAGTCATCTTTG
GTTCTGGTGTTCGGTTCC
Found at i:43324 original size:42 final size:42
Alignment explanation
Indices: 43210--43664 Score: 312
Period size: 42 Copynumber: 10.9 Consensus size: 42
43200 AGAAAGTAAG
* * * * * **
43210 TTCGGTGAAGAAGGTCATCCACGGTTCTGGTGGTTCTCTTCC
1 TTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGGTTCC
* * * *** * *
43252 TTCTGAGATGAAAGTCATTATTGGTACTGGTGTATCGGTTCC
1 TTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGGTTCC
* *
43294 TTCGGAGAAGAAAGTCAACAACAGTTCTGGTGTTTCGGCTCC
1 TTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGGTTCC
****
43336 TTCGGAGAAGAAA-TCCATCTTTGGTTCTGGTGTTTC---T--
1 TTCGGAGAAGAAAGT-CATCAACAGTTCTGGTGTTTCGGTTCC
* *
43373 GT-GGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGATTCC
1 TTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGGTTCC
* * * **** * * * *
43414 TTCCGACAAGAAATTCATCTTTGGTGCTGTTGCTTCGGTTCA
1 TTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGGTTCC
* **** * * *
43456 TTCGGAGAAGAAATTCATCGTTGGTTCTTGTGTTTCTGTTCT
1 TTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGGTTCC
*** * *
43498 TTCGGAGAAGAAAGTCATCATTGGTTCTGGCGTTTTGGTTCC
1 TTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGGTTCC
* *
43540 TTCTGAGAAGAAAGTCATCAACAGTTCTGGCGTTTCGGTTCC
1 TTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGGTTCC
* * **
43582 TTCGGAGAAGATGAAAGCCATCAACAGTTCTGGTGTTTCGGGTAT
1 TTCGGAG-A-A-GAAAGTCATCAACAGTTCTGGTGTTTCGGTTCC
* * * *
43627 TTCAGACAAGAAAGTCATCGACGGTTCTGGTGTTTCGG
1 TTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGG
43665 CTACTCAGTC
Statistics
Matches: 324, Mismatches: 78, Indels: 22
0.76 0.18 0.05
Matches are distributed among these distances:
36 27 0.08
37 2 0.01
39 2 0.01
41 2 0.01
42 254 0.78
43 2 0.01
44 2 0.01
45 33 0.10
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (42 bp):
TTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGGTTCC
Found at i:43399 original size:36 final size:38
Alignment explanation
Indices: 43295--43407 Score: 106
Period size: 36 Copynumber: 2.9 Consensus size: 38
43285 ATCGGTTCCT
* *
43295 TCGGAGAAGAAAGTCAACAACAGTTCTGGTGTTTCGGCTCCT
1 TCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTT---CT-CG
****
43337 TCGGAGAAGAAA-TCCATCTTTGGTTCTGGTGTTTCT-G
1 TCGGAGAAGAAAGT-CATCAACAGTTCTGGTGTTTCTCG
43374 T-GGAGAAGAAAGTCATCAACAGTTCTGGTGTTTC
1 TCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTC
43408 GATTCCTTCC
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
36 27 0.46
37 2 0.03
39 2 0.03
41 1 0.02
42 27 0.46
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (38 bp):
TCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCTCG
Found at i:43454 original size:162 final size:164
Alignment explanation
Indices: 43209--43584 Score: 377
Period size: 162 Copynumber: 2.3 Consensus size: 164
43199 AAGAAAGTAA
* * * * * ** * * *
43209 GTTCGGTGAAGAAGGTCATCCACGGTTCTGGTGGTTCTCTTCCTTCTGAGATGAAAGTCATTATT
1 GTTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGATTCCTTCCGACAAGAAAGTCATTATT
*
43274 GGTACTGGTGTATCGGTTCCTTCGGAGAAGAAAGTCAACAACAGTTCTGGTGTTTCGGCTCCTTC
66 GGTACTGGTGTATCGGTTCATTCGGAGAAGAAAGTCAACAACAGTTCTGGTGTTTCGGCTCCTTC
* *
43339 GGAGAAGAAA-TCCATCTTTGGTTCTGGTGTTTCT-
131 GGAGAAGAAAGT-CATCATTGGTTCTGGCGTTT-TG
*
43373 G-T-GGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGATTCCTTCCGACAAGAAATTCATCT-T
1 GTTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGATTCCTTCCGACAAGAAAGTCAT-TAT
* * * * **** * * * *
43435 TGGTGCTGTTGCT-TCGGTTCATTCGGAGAAGAAATTCATCGTTGGTTCTTGTGTTTCTGTTCTT
65 TGGTACTGGTG-TATCGGTTCATTCGGAGAAGAAAGTCAACAACAGTTCTGGTGTTTCGGCTCCT
43499 TCGGAGAAGAAAGTCATCATTGGTTCTGGCGTTTTG
129 TCGGAGAAGAAAGTCATCATTGGTTCTGGCGTTTTG
* * *
43535 GTTCCTTCTGAGAAGAAAGTCATCAACAGTTCTGGCGTTTCGGTTCCTTC
1 G----TTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGATTCCTTC
43585 GGAGAAGATG
Statistics
Matches: 173, Mismatches: 29, Indels: 16
0.79 0.13 0.07
Matches are distributed among these distances:
161 1 0.01
162 127 0.73
163 4 0.02
164 1 0.01
167 1 0.01
168 39 0.23
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (164 bp):
GTTCGGAGAAGAAAGTCATCAACAGTTCTGGTGTTTCGATTCCTTCCGACAAGAAAGTCATTATT
GGTACTGGTGTATCGGTTCATTCGGAGAAGAAAGTCAACAACAGTTCTGGTGTTTCGGCTCCTTC
GGAGAAGAAAGTCATCATTGGTTCTGGCGTTTTG
Found at i:45602 original size:36 final size:35
Alignment explanation
Indices: 45561--45681 Score: 152
Period size: 36 Copynumber: 3.4 Consensus size: 35
45551 TAATTATAAT
*
45561 GACCACATGTTAGTAATCGAACGATTAAGTAGATAC
1 GACCACGTGTTAGTAATC-AACGATTAAGTAGATAC
*
45597 GACCACGTGTTAATAATCAAACGATTAAGTAGATAC
1 GACCACGTGTTAGTAATC-AACGATTAAGTAGATAC
* * *
45633 GACCACGTATTAGTAATCAAGCAATTAAGTAGATAT
1 GACCACGTGTTAGTAATCAA-CGATTAAGTAGATAC
* *
45669 GAACATGTGTTAG
1 GACCACGTGTTAG
45682 AGCATAATAA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
35 2 0.03
36 72 0.97
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (35 bp):
GACCACGTGTTAGTAATCAACGATTAAGTAGATAC
Found at i:46534 original size:103 final size:103
Alignment explanation
Indices: 46342--46572 Score: 259
Period size: 103 Copynumber: 2.2 Consensus size: 103
46332 ATTAAGTCGA
* ** * *
46342 TACTGAACATGTGTTAGAAATCAACTGATTCTGTAGCTCTAAGCACATGCTACAATGAACGTATT
1 TACTGAACACGTGTTAGAAATCAACCCAATCTGTAGCTCTAAGCACATGCTACAATGAACGGATT
* *
46407 GAGTGGTTCTAAGCATGTTCTAGAAACTAAC-GATTGAG
66 GAGAGGTTCTAAGCACGTTCTAGAAACT-ACTGATTGAG
* * * * *
46445 TACTGAACACGTGTTAGTAATCAACCCAATCAT-TAGCTCTAAGTACATTCTATAATTAACGGAT
1 TACTGAACACGTGTTAGAAATCAACCCAATC-TGTAGCTCTAAGCACATGCTACAATGAACGGAT
* * *
46509 TGAGAGGTTCTGAGCACGTTTTAGAAACTACTGATTGAT
65 TGAGAGGTTCTAAGCACGTTCTAGAAACTACTGATTGAG
* * * *
46548 TACTGAGCAGGTGTTTGCAATCAAC
1 TACTGAACACGTGTTAGAAATCAAC
46573 AGTTTGAGTA
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
102 2 0.02
103 104 0.97
104 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (103 bp):
TACTGAACACGTGTTAGAAATCAACCCAATCTGTAGCTCTAAGCACATGCTACAATGAACGGATT
GAGAGGTTCTAAGCACGTTCTAGAAACTACTGATTGAG
Found at i:48469 original size:269 final size:266
Alignment explanation
Indices: 47981--48477 Score: 798
Period size: 269 Copynumber: 1.9 Consensus size: 266
47971 CCATGAATCA
*
47981 TATATGCATCTGGTTGGAAACATTGAATACAGAAGTGTTTATGGTTATATTCTCAACTAATATGC
1 TATATGCATCTGGTTGGAAACATTGAATACAGAAGTGTTTATGGTTATAATCTCAACTAATATGC
* * * *
48046 AAGGAAGTTCATTTAGTGCTAGAATATTCATGTTTTTTTACTTTGTTTTGATTTCTAATTCGTGC
66 AAGGAAGTCCATTAAGTGCCAGAATATTCATGTTTTTTTACTTTGTTTTGACTTCTAATTCGTGC
*
48111 CCCATACAAAATGCTGGGTTGTTGCTGTTTAAAGCTTCAGCCTAACTGAAAGATCATGTCATTCA
131 CCCATACAAAATGCTGGGTTGTTGCTGTTTAAAGCTTCAGCCTAACTGAAAGACCATGTCATTCA
*
48176 CCCCATTGTTGTTGACATCTTGAAAATGTTCCATGAGCACAAACGTTTTGACGACAACGTGGCAG
196 CACCATTGTTGTTGACATCTTGAAAATGTTCCATGAGCACAAACGTTTTGACGACAACGTGGCAG
48241 GTGTCG
261 GTGTCG
* * ** * *
48247 TATATGTATCTTGTTGGAAACATTGAATACA-AAGGTGTTTATGGTTATAATCTCTGCTCATGTG
1 TATATGCATCTGGTTGGAAACATTGAATACAGAA-GTGTTTATGGTTATAATCTCAACTAATATG
48311 CAAGGAAGTCCATTAAGTGCCAGAATATTCATGTGTTTTTTTACTTTGTTTTGACTTCTAATTCA
65 CAAGGAAGTCCATTAAGTGCCAGAATATTCA--TGTTTTTTTACTTTGTTTTGACTTCTAATTC-
* * *
48376 GTGCTCCATACAAAATGCTGGGTTGTTGTTGTTTAAAGCTTCAGCCTAACTGAAAGGCCATGTCA
127 GTGCCCCATACAAAATGCTGGGTTGTTGCTGTTTAAAGCTTCAGCCTAACTGAAAGACCATGTCA
*
48441 TTCACACCATTGTTGTTGCCATCTTGAAAATGTTCCA
192 TTCACACCATTGTTGTTGACATCTTGAAAATGTTCCA
48478 CGAAATGACA
Statistics
Matches: 210, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
265 2 0.01
266 82 0.39
268 30 0.14
269 96 0.46
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (266 bp):
TATATGCATCTGGTTGGAAACATTGAATACAGAAGTGTTTATGGTTATAATCTCAACTAATATGC
AAGGAAGTCCATTAAGTGCCAGAATATTCATGTTTTTTTACTTTGTTTTGACTTCTAATTCGTGC
CCCATACAAAATGCTGGGTTGTTGCTGTTTAAAGCTTCAGCCTAACTGAAAGACCATGTCATTCA
CACCATTGTTGTTGACATCTTGAAAATGTTCCATGAGCACAAACGTTTTGACGACAACGTGGCAG
GTGTCG
Found at i:52106 original size:55 final size:55
Alignment explanation
Indices: 52004--52107 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
51994 TGCAGAAAGA
** * * *
52004 AGAAAGCGTTTAGTTTGCACAATGCAGCTATGTAGAGAGAGAAAAAAATACGAAT
1 AGAAAGCACTTAGTCTGCACAATGCAGCCATGTAGAGAGAAAAAAAAATACGAAT
52059 AGAAAGCACTTAGTCTGCACAATGCAGCCACT-TAGAGA-ACAAAAAAAAT
1 AGAAAGCACTTAGTCTGCACAATGCAGCCA-TGTAGAGAGA-AAAAAAAAT
52108 GTTAATAGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 40 0.95
56 1 0.02
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.19
Consensus pattern (55 bp):
AGAAAGCACTTAGTCTGCACAATGCAGCCATGTAGAGAGAAAAAAAAATACGAAT
Found at i:71256 original size:23 final size:23
Alignment explanation
Indices: 71203--71257 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
71193 AACTCTACCA
* *
71203 AAAGACAGAGATAAACATGCCAC
1 AAAGACATACATAAACATGCCAC
* *
71226 AAAGACATACATAAACGTGTCAC
1 AAAGACATACATAAACATGCCAC
71249 AAAGACATA
1 AAAGACATA
71258 ATTATTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.53, C:0.20, G:0.15, T:0.13
Consensus pattern (23 bp):
AAAGACATACATAAACATGCCAC
Found at i:73110 original size:23 final size:23
Alignment explanation
Indices: 73084--73135 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
73074 TTATATGATA
** *
73084 GTTTAGCGTTTGTGAATATGTTC
1 GTTTAGCGTTCATGAACATGTTC
*
73107 GTTTAGCGTTCATGAACATTTTC
1 GTTTAGCGTTCATGAACATGTTC
73130 GTTTAG
1 GTTTAG
73136 AATAAAGAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.19, C:0.12, G:0.23, T:0.46
Consensus pattern (23 bp):
GTTTAGCGTTCATGAACATGTTC
Found at i:76674 original size:39 final size:39
Alignment explanation
Indices: 76626--76710 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
76616 CTAGAAACCC
* *
76626 TAATTCTACCTTATTACTTGTTTGATATATAATCTAGTG
1 TAATCCTACCCTATTACTTGTTTGATATATAATCTAGTG
76665 TAATCCTACCCTATTACTTGTTTGATATATAATCTAGTG
1 TAATCCTACCCTATTACTTGTTTGATATATAATCTAGTG
76704 TAATCCT
1 TAATCCT
76711 GGAATATTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.46
Consensus pattern (39 bp):
TAATCCTACCCTATTACTTGTTTGATATATAATCTAGTG
Found at i:76974 original size:171 final size:172
Alignment explanation
Indices: 76662--77181 Score: 806
Period size: 171 Copynumber: 3.0 Consensus size: 172
76652 ATATAATCTA
*
76662 GTGT-AATCCTACCCTATTACTTGTTTGATATATAATCTAGTGTAATCCTGGAATATTGATAAAG
1 GTGTAAATTCTACCCTATTACTTGTTTGATATATAATCTAGTGTAATCCTGGAATATTGATAAAG
*
76726 TTAATA-ATTTCCCCTCTCTAAAAAAAACTGGAGAACTTGATCTGGTTTTTGGTGAGGAATATTT
66 TTAATATATTTCCCCTCTCT--AAAAAACTGGAGAACTTGATCT-GTTTTTGGTGAGGTATATTT
76790 AGGGACAAATATGTTCTAGGAGACGAATTTATTAAATTTTAGAGG
128 AGGGACAAATATGTTCTAGGAGACGAATTTATTAAATTTTAGAGG
76835 GTGTAAATTCTA-CCTATTACTTGTTTGATATATAATC-AGTGTAATCCTGGAATATTGATAAAG
1 GTGTAAATTCTACCCTATTACTTGTTTGATATATAATCTAGTGTAATCCTGGAATATTGATAAAG
* *
76898 TTAATATATTTCCCCTCTCTAAAAACCTGGAGAACTTTATCTAGTTTTTGGTGAGGTATATTTAG
66 TTAATATATTTCCCCTCTCTAAAAAACTGGAGAACTTGATCT-GTTTTTGGTGAGGTATATTTAG
* *
76963 GAACAAATATGTTCTAGGAGACGAATTTATTAAATTTTAGAGC
130 GGACAAATATGTTCTAGGAGACGAATTTATTAAATTTTAGAGG
77006 GTGTAAATTCTACCCTATTACTTGTTTGATATATAATCTAGTGTAATCCTGGAATATTGATAAAG
1 GTGTAAATTCTACCCTATTACTTGTTTGATATATAATCTAGTGTAATCCTGGAATATTGATAAAG
* * *
77071 TTAATAATATTT-CCCTCTCTTAAAAAACTAGAGAACTTGATCTGGTTTT--TGAGATATA-TTA
66 TTAAT-ATATTTCCCCTCTC-TAAAAAACTGGAGAACTTGATCTGTTTTTGGTGAGGTATATTTA
* * * *
77132 GGGATAAATATGTTTTAGAAGACGAATTTATTAAATTTTATAGG
129 GGGACAAATATGTTCTAGGAGACGAATTTATTAAATTTTAGAGG
77176 GT-TAAA
1 GTGTAAA
77182 ACATGATATC
Statistics
Matches: 323, Mismatches: 18, Indels: 16
0.90 0.05 0.04
Matches are distributed among these distances:
169 4 0.01
170 43 0.13
171 102 0.32
172 57 0.18
173 85 0.26
174 32 0.10
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (172 bp):
GTGTAAATTCTACCCTATTACTTGTTTGATATATAATCTAGTGTAATCCTGGAATATTGATAAAG
TTAATATATTTCCCCTCTCTAAAAAACTGGAGAACTTGATCTGTTTTTGGTGAGGTATATTTAGG
GACAAATATGTTCTAGGAGACGAATTTATTAAATTTTAGAGG
Done.