Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001469.1 Hibiscus syriacus cultivar Beakdansim tig00002845_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: 61666
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:7852 original size:30 final size:31
Alignment explanation
Indices: 7816--7874 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
7806 AGATTCATAA
* *
7816 GTTAAATTGATA-TTTATCTAAATTTCAAAG
1 GTTAAATTAATATTTTATCTAAAGTTCAAAG
*
7846 GTTAAATTAATATTTTATCTGAAGTTCAA
1 GTTAAATTAATATTTTATCTAAAGTTCAA
7875 GGATAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (31 bp):
GTTAAATTAATATTTTATCTAAAGTTCAAAG
Found at i:7884 original size:31 final size:30
Alignment explanation
Indices: 7819--7886 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
7809 TTCATAAGTT
* * *
7819 AAATTGATATTTATCTAAATTTCAAAGGTT
1 AAATTAATATTTATCTAAAGTTCAAAGGTA
*
7849 AAATTAATATTTTATCTGAAGTTC-AAGGATA
1 AAATTAATA-TTTATCTAAAGTTCAAAGG-TA
7880 AAATTAA
1 AAATTAA
7887 AAAATTAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (30 bp):
AAATTAATATTTATCTAAAGTTCAAAGGTA
Found at i:8808 original size:24 final size:24
Alignment explanation
Indices: 8780--8826 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
8770 GATTTAATAG
*
8780 AATGTAACGTTAAATTCTTTAAGT
1 AATGTAACATTAAATTCTTTAAGT
8804 AATGTAACATTAAATTCTTTAAG
1 AATGTAACATTAAATTCTTTAAG
8827 ATCGTCTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (24 bp):
AATGTAACATTAAATTCTTTAAGT
Found at i:11405 original size:16 final size:16
Alignment explanation
Indices: 11384--11414 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11374 TGCAACATTA
*
11384 AACTAAACAAAACAAG
1 AACTAAAAAAAACAAG
11400 AACTAAAAAAAACAA
1 AACTAAAAAAAACAA
11415 TCAAAACACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.16, G:0.03, T:0.06
Consensus pattern (16 bp):
AACTAAAAAAAACAAG
Found at i:11688 original size:85 final size:84
Alignment explanation
Indices: 11546--11716 Score: 297
Period size: 85 Copynumber: 2.0 Consensus size: 84
11536 CTTCACAGAA
*
11546 AAAAAAAAATTAACTCGACGTGTTTAAACTTTGAATGTAGAACCAAATTAGATGACACAGTTGCC
1 AAAAAAAAATTAACTCAACGTGTTTAAACTTTGAATGTAGAACCAAATTAGATGACACAGTTGCC
11611 ACACTTGTATTGTCGTTGT
66 ACACTTGTATTGTCGTTGT
* * *
11630 AAAAAAAATTCTAACTCAACTTGTTTAAACTTTGAATGTAGAACCAAATTAGATGACACATTTGC
1 AAAAAAAAAT-TAACTCAACGTGTTTAAACTTTGAATGTAGAACCAAATTAGATGACACAGTTGC
11695 CACACTTGTATTGTCGTTGT
65 CACACTTGTATTGTCGTTGT
11715 AA
1 AA
11717 CACTCCAAAT
Statistics
Matches: 82, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
84 9 0.11
85 73 0.89
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (84 bp):
AAAAAAAAATTAACTCAACGTGTTTAAACTTTGAATGTAGAACCAAATTAGATGACACAGTTGCC
ACACTTGTATTGTCGTTGT
Found at i:13516 original size:2 final size:2
Alignment explanation
Indices: 13509--13534 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13499 CCGATTTTCA
13509 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
13535 GCATATGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19890 original size:20 final size:19
Alignment explanation
Indices: 19861--19899 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
19851 AGACATGGAA
*
19861 GATTGTAATATTTATTTTT
1 GATTGTAATATTAATTTTT
19880 GATTCGTAATATTAATTTTT
1 GATT-GTAATATTAATTTTT
19900 TTACTTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (19 bp):
GATTGTAATATTAATTTTT
Found at i:19898 original size:19 final size:19
Alignment explanation
Indices: 19861--19898 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
19851 AGACATGGAA
*
19861 GATTGTAATATTTATTTTT
1 GATTGTAATATTTAATTTT
19880 GATTCGTAATA-TTAATTTT
1 GATT-GTAATATTTAATTTT
19899 TTTACTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.58
Consensus pattern (19 bp):
GATTGTAATATTTAATTTT
Found at i:20881 original size:16 final size:16
Alignment explanation
Indices: 20857--20891 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20847 GACAATTACA
* *
20857 TTTATTTTAATTTATT
1 TTTAATTTAATATATT
20873 TTTAATTTAATATATT
1 TTTAATTTAATATATT
20889 TTT
1 TTT
20892 CTCACTAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTAATTTAATATATT
Found at i:23090 original size:17 final size:17
Alignment explanation
Indices: 23042--23082 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
23032 ATGGTTTTCA
*
23042 GAACCGGACCGGTTAGC
1 GAACCGGATCGGTTAGC
23059 GAACCGGATCGGTTAGC
1 GAACCGGATCGGTTAGC
23076 GAACCGG
1 GAACCGG
23083 TCATGTTACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.27, G:0.37, T:0.12
Consensus pattern (17 bp):
GAACCGGATCGGTTAGC
Found at i:26172 original size:34 final size:36
Alignment explanation
Indices: 26101--26181 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
26091 ATTGAACATA
* * *
26101 TATATATATATATATAAATTTTGATATATTATTATT
1 TATAAATAAATATATAAATTTTGATATATTATAATT
26137 TATAAATAAATATATAAATTATT-A-ATATT-TAATT
1 TATAAATAAATATATAAATT-TTGATATATTATAATT
*
26171 TATTAATAAAT
1 TATAAATAAAT
26182 TGATTAGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
34 14 0.35
35 5 0.12
36 19 0.47
37 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (36 bp):
TATAAATAAATATATAAATTTTGATATATTATAATT
Found at i:26173 original size:15 final size:15
Alignment explanation
Indices: 26145--26178 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
26135 TTTATAAATA
26145 AATATATAAATTATT
1 AATATATAAATTATT
* *
26160 AATATTTAATTTATT
1 AATATATAAATTATT
26175 AATA
1 AATA
26179 AATTGATTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATATAAATTATT
Found at i:29559 original size:26 final size:26
Alignment explanation
Indices: 29530--29612 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 26
29520 TTTAAATAAA
29530 AATAAAATATTTTTAAATTAAGTTAT
1 AATAAAATATTTTTAAATTAAGTTAT
* *
29556 AATAAAATATATTT-AA-TAAGTAAT
1 AATAAAATATTTTTAAATTAAGTTAT
*
29580 -ATAAAAATATTTTTAAGTTAA--TAT
1 AAT-AAAATATTTTTAAATTAAGTTAT
29604 ATATAAAAT
1 A-ATAAAAT
29613 TATATTATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
23 2 0.04
24 19 0.40
25 8 0.17
26 18 0.38
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
AATAAAATATTTTTAAATTAAGTTAT
Found at i:29586 original size:24 final size:25
Alignment explanation
Indices: 29533--29618 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 25
29523 AAATAAAAAT
* *
29533 AAAATATTTTTAAATTAAGTTATA-A
1 AAAATATATTT-AATTAAGTAATATA
29558 TAAAATATATTTAA-TAAGTAATATA
1 -AAAATATATTTAATTAAGTAATATA
*
29583 AAAATATTTTTAAGTTAA-TATATATA
1 AAAATATATTTAA-TTAAGTA-ATATA
*
29609 AAATTATATT
1 AAAATATATT
29619 ATAAATAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
24 20 0.39
25 5 0.10
26 26 0.51
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (25 bp):
AAAATATATTTAATTAAGTAATATA
Found at i:29601 original size:22 final size:24
Alignment explanation
Indices: 29507--29604 Score: 78
Period size: 24 Copynumber: 4.1 Consensus size: 24
29497 CTTATTTTTA
* * * * *
29507 ATAAATTATATTTTTTAAATAAAA
1 ATAAAATATATTTATTAAGTTAAT
*
29531 ATAAAATATTTTTAAATTAAGTT-AT
1 ATAAAATATATTT--ATTAAGTTAAT
*
29556 AATAAAATATATTTAATAAG-TAAT
1 -ATAAAATATATTTATTAAGTTAAT
29580 ATAAAA-ATATTT-TTAAGTTAAT
1 ATAAAATATATTTATTAAGTTAAT
29602 ATA
1 ATA
29605 TATAAAATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
21 4 0.07
22 13 0.22
23 7 0.12
24 18 0.30
25 1 0.02
26 17 0.28
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (24 bp):
ATAAAATATATTTATTAAGTTAAT
Found at i:29627 original size:26 final size:24
Alignment explanation
Indices: 29520--29627 Score: 75
Period size: 26 Copynumber: 4.4 Consensus size: 24
29510 AATTATATTT
*
29520 TTTAAATAA-A-A-ATAAAATATT
1 TTTAAATAATATATATAAAATATA
29541 TTTAAATTAAGT-TATAATAAAATATA
1 TTTAAA-TAA-TATAT-ATAAAATATA
*
29567 TTT-AATAAGTA-ATATAAAAATATT
1 TTTAAATAA-TATATAT-AAAATATA
*
29591 TTTAAGTTAATATATATAAAATTATA
1 TTTAA-ATAATATATATAAAA-TATA
29617 TTATAAATAAT
1 TT-TAAATAAT
29628 TCGGGTCACG
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
21 6 0.09
22 3 0.04
23 2 0.03
24 18 0.26
25 9 0.13
26 28 0.41
27 3 0.04
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.43
Consensus pattern (24 bp):
TTTAAATAATATATATAAAATATA
Found at i:29899 original size:38 final size:38
Alignment explanation
Indices: 29834--29951 Score: 123
Period size: 38 Copynumber: 3.1 Consensus size: 38
29824 TTTAAAAAAT
*
29834 AATTTAGAATGTTAATGTGAAATAATTTAATAAATTAAG
1 AATTTAGAATGTT-ATGTGAAATAATTTAAGAAATTAAG
* * *
29873 AATTTAGAACGTTATGTGCCAA-AATTTAAGAAATTAGG
1 AATTTAGAATGTTATGTG-AAATAATTTAAGAAATTAAG
* * * *
29911 ATTTTAGAATGTTAGAGTGAAATAATTTGAG-AATTATG
1 AATTTAGAATGTTA-TGTGAAATAATTTAAGAAATTAAG
29949 AAT
1 AAT
29952 AAAAAATTCA
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
38 41 0.63
39 24 0.37
ACGTcount: A:0.44, C:0.03, G:0.17, T:0.36
Consensus pattern (38 bp):
AATTTAGAATGTTATGTGAAATAATTTAAGAAATTAAG
Found at i:30365 original size:34 final size:34
Alignment explanation
Indices: 30321--30388 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
30311 AAGTATGACT
*
30321 AAATTGAGAGAATATGTAAATAACATAGACCAAA
1 AAATTAAGAGAATATGTAAATAACATAGACCAAA
30355 AAATTAAGAGAATATGTAAATAACATAGACCAAA
1 AAATTAAGAGAATATGTAAATAACATAGACCAAA
30389 TATGTGATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.57, C:0.09, G:0.13, T:0.21
Consensus pattern (34 bp):
AAATTAAGAGAATATGTAAATAACATAGACCAAA
Found at i:34682 original size:185 final size:184
Alignment explanation
Indices: 34460--34830 Score: 618
Period size: 185 Copynumber: 2.0 Consensus size: 184
34450 AAATTAAATG
* *
34460 TTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAAT-AAAAATTTCA
1 TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAATTT-A
34524 GATAAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAAT
65 GATAAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAAT
* *
34589 TGAGTTTTAAATTGTTTGGGCTTAGGCTAAATGTTATATATAATATATTTAATAT
130 TGAGTTTTAAATGGTTTGGGCTGAGGCTAAATGTTATATATAATATATTTAATAT
34644 TTTTTAATTAAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAATTTA
1 TTTTTAATTAAAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAATTTA
* ** *
34709 TATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAAT
65 GATAAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAAT
* * *
34774 TGGGTTTTAAATGGTTTGGGCTGAGTCTATATGTTATATATAATATATTTAATAT
130 TGAGTTTTAAATGGTTTGGGCTGAGGCTAAATGTTATATATAATATATTTAATAT
34829 TT
1 TT
34831 AAAATTTAAT
Statistics
Matches: 174, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
184 15 0.09
185 151 0.87
186 8 0.05
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (184 bp):
TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAATTTAG
ATAAAATTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
GAGTTTTAAATGGTTTGGGCTGAGGCTAAATGTTATATATAATATATTTAATAT
Found at i:42828 original size:30 final size:29
Alignment explanation
Indices: 42773--42865 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 29
42763 TCGAAGGACC
*
42773 ACTATCCATATGTTCTGAAGAACATAGGTA
1 ACTATCCATATG-TCTGAAGGACATAGGTA
* * *
42803 ACTGTCTATATGTCCTTAAGGACATAGGTAA
1 ACTATCCATATGT-CTGAAGGACATAGGT-A
*
42834 ACTATCCATATGTCTAGAAAGACATAGGTA
1 ACTATCCATATGTCT-GAAGGACATAGGTA
42864 AC
1 AC
42866 CCTCGACTCT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
29 1 0.02
30 28 0.54
31 23 0.44
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (29 bp):
ACTATCCATATGTCTGAAGGACATAGGTA
Found at i:42858 original size:31 final size:30
Alignment explanation
Indices: 42773--42864 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 30
42763 TCGAAGGACC
42773 ACTATCCATATGTTCTG-AAGAACATAGGT-A
1 ACTATCCATATG-TCTGAAAG-ACATAGGTAA
* * * *
42803 ACTGTCTATATGTCCTTAAGGACATAGGTAA
1 ACTATCCATATGT-CTGAAAGACATAGGTAA
42834 ACTATCCATATGTCTAGAAAGACATAGGTAA
1 ACTATCCATATGTCT-GAAAGACATAGGTAA
42865 CCCTCGACTC
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
29 1 0.02
30 22 0.44
31 27 0.54
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (30 bp):
ACTATCCATATGTCTGAAAGACATAGGTAA
Found at i:43106 original size:15 final size:15
Alignment explanation
Indices: 43083--43112 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43073 CACATAAACT
*
43083 CATATCTTCTTATCA
1 CATAGCTTCTTATCA
43098 CATAGCTTCTTATCA
1 CATAGCTTCTTATCA
43113 TATCATTCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.27, G:0.03, T:0.43
Consensus pattern (15 bp):
CATAGCTTCTTATCA
Found at i:43696 original size:22 final size:22
Alignment explanation
Indices: 43671--43719 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
43661 TTCGTTACTC
* *
43671 TATAACTTATATCACATGTTCA
1 TATAACTCATATAACATGTTCA
* * *
43693 TATAGCTCATATAACATTTTCT
1 TATAACTCATATAACATGTTCA
43715 TATAA
1 TATAA
43720 TCACACACAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (22 bp):
TATAACTCATATAACATGTTCA
Found at i:45958 original size:17 final size:17
Alignment explanation
Indices: 45936--45968 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
45926 TCATAATCAA
*
45936 GTCATAAATCCGTCTTT
1 GTCATAAATCAGTCTTT
45953 GTCATAAATCAGTCTT
1 GTCATAAATCAGTCTT
45969 CCCAGATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.39
Consensus pattern (17 bp):
GTCATAAATCAGTCTTT
Found at i:51441 original size:20 final size:20
Alignment explanation
Indices: 51418--51505 Score: 61
Period size: 21 Copynumber: 4.3 Consensus size: 20
51408 CAATTCGCTT
*
51418 TGCGATTAAGTAAATCGCAA
1 TGCGATTAAGAAAATCGCAA
**
51438 TGCGAATTTGGAAAATCGCAA
1 TGCG-ATTAAGAAAATCGCAA
* **
51459 TGCGA-TACTGACTATCGCAA
1 TGCGATTA-AGAAAATCGCAA
* * *
51479 CGCGATAATACAAAATCGCAA
1 TGCGATTA-AGAAAATCGCAA
51500 TGCGAT
1 TGCGAT
51506 ACTGACTTTC
Statistics
Matches: 50, Mismatches: 15, Indels: 5
0.71 0.21 0.07
Matches are distributed among these distances:
19 1 0.02
20 18 0.36
21 31 0.62
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (20 bp):
TGCGATTAAGAAAATCGCAA
Found at i:51476 original size:41 final size:41
Alignment explanation
Indices: 51449--51546 Score: 169
Period size: 41 Copynumber: 2.4 Consensus size: 41
51439 GCGAATTTGG
51449 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
* *
51490 AAAATCGCAATGCGATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
*
51531 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
51547 TTTCAAAGCG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.21
Consensus pattern (41 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
Found at i:51519 original size:20 final size:20
Alignment explanation
Indices: 51452--51546 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 20
51442 AATTTGGAAA
51452 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
51472 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
51493 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * * *
51513 TTCGCAACGAGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
51533 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
51547 TTTCAAAGCG
Statistics
Matches: 57, Mismatches: 13, Indels: 9
0.72 0.16 0.11
Matches are distributed among these distances:
19 4 0.07
20 27 0.47
21 24 0.42
22 2 0.04
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:51741 original size:22 final size:22
Alignment explanation
Indices: 51713--51756 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
51703 CACTCTCTCA
51713 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
51735 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
51757 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:53424 original size:18 final size:18
Alignment explanation
Indices: 53398--53445 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
53388 TCCACTTCGG
53398 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
53416 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
53434 GAGCCATCACCT
1 GAGCCATCACCT
53446 AATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:54020 original size:20 final size:19
Alignment explanation
Indices: 53986--54040 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
53976 TAGTTTACTT
*
53986 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGACTA
*
54005 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGACTA
*
54025 TCGCAATGCGAAATGA
1 TCGCAACGCGAAATGA
54041 AAATCACAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:54081 original size:19 final size:19
Alignment explanation
Indices: 54024--54117 Score: 68
Period size: 19 Copynumber: 5.5 Consensus size: 19
54014 GGAAATGGCT
54024 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
54043 ATCACAA--CGACAA-G---
1 ATCGCAATGCGA-AATGAAA
54057 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
54076 ATCGCAA--CGACAA-G---
1 ATCGCAATGCGA-AATGAAA
*
54090 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
54109 ATCGCAATG
1 ATCGCAATG
54118 TGATTTATGT
Statistics
Matches: 58, Mismatches: 3, Indels: 28
0.65 0.03 0.31
Matches are distributed among these distances:
14 13 0.22
15 4 0.07
16 8 0.14
17 8 0.14
18 4 0.07
19 21 0.36
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:54112 original size:33 final size:33
Alignment explanation
Indices: 54024--54115 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
54014 GGAAATGGCT
*
54024 ATCGCAATGCGAAATGAAAATCACAACGACAAG
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAG
54057 ATCGCAATGCGAAATGAAAATCGCAACGACAAG
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAG
*
54090 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
54116 TGTGATTTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAG
Found at i:54171 original size:33 final size:33
Alignment explanation
Indices: 54134--54206 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
54124 ATGTTTCACG
* *
54134 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATCTTGTCGTTACGATTTTCATTTCGCA
54167 TTGCGATCTTGTCGTTACGATTTTCATTTCGCA
1 TTGCGATCTTGTCGTTACGATTTTCATTTCGCA
54200 TTGCGAT
1 TTGCGAT
54207 AGCCATTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATCTTGTCGTTACGATTTTCATTTCGCA
Found at i:54172 original size:19 final size:19
Alignment explanation
Indices: 54148--54206 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
54138 GATTTTGTCG
54148 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
54167 TTGCGA---TC-TTGTCG--
1 TTGCGATTTTCATT-TCGCA
*
54181 TTACGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
54200 TTGCGAT
1 TTGCGAT
54207 AGCCATTTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 2 0.06
16 5 0.16
17 5 0.16
18 2 0.06
19 12 0.39
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:54225 original size:20 final size:20
Alignment explanation
Indices: 54191--54265 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
54181 TTACGATTTT
*
54191 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
54210 CATTTCCGCGTTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
54230 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
*
54250 CATTTTCGCGTTGCGA
1 CATTTCCGCGTTGCGA
54266 AAGTATGTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 5 0.10
20 47 0.90
ACGTcount: A:0.16, C:0.27, G:0.24, T:0.33
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:54276 original size:20 final size:19
Alignment explanation
Indices: 54211--54290 Score: 79
Period size: 20 Copynumber: 4.1 Consensus size: 19
54201 TGCGATAGCC
* * *
54211 ATTTCCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGAAAG-T
* *
54231 ATTTCCGCGTTGCGATAGT
1 ATTTTCGCGTTGCGAAAGT
54250 CATTTTCGCGTTGCGAAAGT
1 -ATTTTCGCGTTGCGAAAGT
*
54270 ATGTTTCGTGTTGCGAAAGT
1 AT-TTTCGCGTTGCGAAAGT
54290 A
1 A
54291 AACTATTCTT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
19 2 0.04
20 52 0.96
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (19 bp):
ATTTTCGCGTTGCGAAAGT
Found at i:54691 original size:42 final size:42
Alignment explanation
Indices: 54632--54711 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
54622 AACTCACCTG
* *
54632 TCATCCCTCAAGAGTCTCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCTCCCCCAACCGTTCAAGAGGCCCCTA
*
54674 TCATCCCTCAAGAGTCTCCCCCCACCGTTCAAGAGGCC
1 TCATCCCTCAAGAGTCTCCCCCAACCGTTCAAGAGGCC
54712 ACTGTCATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.41, G:0.15, T:0.21
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCTCCCCCAACCGTTCAAGAGGCCCCTA
Found at i:56323 original size:19 final size:19
Alignment explanation
Indices: 56299--56373 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
56289 ATCGCAACGA
56299 GAAAATCGCAACGCGAAAT
1 GAAAATCGCAACGCGAAAT
*
56318 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGCGAAAT
*
56337 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGCGAAAT
*
56356 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGCGAAA
56374 ATCGCAATGC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.49, C:0.17, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAAATCGCAACGCGAAAT
Found at i:56326 original size:33 final size:33
Alignment explanation
Indices: 56270--56385 Score: 133
Period size: 33 Copynumber: 3.3 Consensus size: 33
56260 AAACAGACTG
* **
56270 TCGCAACACGAAAATGATTATCGCAACGAGAAAA
1 TCGCAACGCG-AAATGAAAATCGCAACGAGAAAA
56304 TCGCAACGCGAAATGAAAATCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAATCGCAA--CG--A-GAAAA
*
56342 TCGCAATGCGAAATGAAAATCGCAACGAGAAAA
1 TCGCAACGCGAAATGAAAATCGCAACGAGAAAA
*
56375 TCGCAATGCGA
1 TCGCAACGCGA
56386 TTTTCATTTC
Statistics
Matches: 73, Mismatches: 4, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
33 29 0.40
34 10 0.14
35 2 0.03
36 2 0.03
37 1 0.01
38 29 0.40
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.14
Consensus pattern (33 bp):
TCGCAACGCGAAATGAAAATCGCAACGAGAAAA
Found at i:56429 original size:20 final size:20
Alignment explanation
Indices: 56404--56459 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
56394 TCGCGTTGCG
* *
56404 ATTTTCTCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
56424 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
56444 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
56460 TTCCCCGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.14, C:0.21, G:0.23, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:56859 original size:21 final size:20
Alignment explanation
Indices: 56806--56887 Score: 137
Period size: 20 Copynumber: 4.0 Consensus size: 20
56796 TGTATTATCT
* *
56806 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
56826 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
56846 CGTTGCGAAAAGTCAGAATCG
1 CGTTGCG-AAAGTCAGAATCG
56867 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
56887 C
1 C
56888 AATTTTTGTG
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
20 39 0.66
21 20 0.34
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:56860 original size:41 final size:40
Alignment explanation
Indices: 56806--56887 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 40
56796 TGTATTATCT
* *
56806 CGTTGCGATAGTCAGAATCTCGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGAATCG
56846 CGTTGCGAAAAGTCAGAATCGCGTTGCGAAAGTCAGAATCG
1 CGTTGCG-AAAGTCAGAATCGCGTTGCGAAAGTCAGAATCG
56887 C
1 C
56888 AATTTTTGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 7 0.18
41 32 0.82
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (40 bp):
CGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGAATCG
Found at i:57596 original size:24 final size:24
Alignment explanation
Indices: 57569--57622 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
57559 GTATTTGAAA
*
57569 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
57593 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
57617 TTTGAT
1 TTTGAT
57623 GATGTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:57814 original size:12 final size:12
Alignment explanation
Indices: 57797--57821 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57787 ATATAATCCT
57797 GAAGAAGAAAAA
1 GAAGAAGAAAAA
57809 GAAGAAGAAAAA
1 GAAGAAGAAAAA
57821 G
1 G
57822 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:60176 original size:18 final size:18
Alignment explanation
Indices: 60110--60177 Score: 65
Period size: 18 Copynumber: 4.1 Consensus size: 18
60100 CTTAATGTCT
*
60110 ATCGCAATGCGAAATAAA
1 ATCGCAATGCGAAATGAA
*
60128 ATCGCAAT--GAGA-G-A
1 ATCGCAATGCGAAATGAA
*
60142 ATCGTAATGCG-AATGAA
1 ATCGCAATGCGAAATGAA
*
60159 ATCGCAATGTGAAATGAA
1 ATCGCAATGCGAAATGAA
60177 A
1 A
60178 ATCACAACGA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
14 8 0.21
15 1 0.03
16 5 0.13
17 10 0.26
18 15 0.38
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.19
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:60204 original size:50 final size:51
Alignment explanation
Indices: 60110--60222 Score: 140
Period size: 50 Copynumber: 2.2 Consensus size: 51
60100 CTTAATGTCT
* * * *
60110 ATCGCAATGCGAAATAAAATCGCAATGAGAGAATCGTAATGCG-AATG-AA
1 ATCGCAATGCGAAATAAAATCACAACGAGAGAATCGCAAAGCGAAATGAAA
* *
60159 ATCGCAATGTGAAATGAAAATCACAACGAGGGAATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAAT-AAAATCACAACGAGAGAATCGCAAAGCGAAATGAAA
*
60211 ATCGCAACGCGA
1 ATCGCAATGCGA
60223 TTTTAGTTTC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
49 14 0.26
50 23 0.43
51 4 0.08
52 12 0.23
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (51 bp):
ATCGCAATGCGAAATAAAATCACAACGAGAGAATCGCAAAGCGAAATGAAA
Found at i:60234 original size:19 final size:19
Alignment explanation
Indices: 60212--60253 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
60202 GAAATGAAAA
60212 TCGCAACGCGATTTTAGTT
1 TCGCAACGCGATTTTAGTT
***
60231 TCGCGTTGCGATTTTAGTT
1 TCGCAACGCGATTTTAGTT
60250 TCGC
1 TCGC
60254 GTTGCGATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
TCGCAACGCGATTTTAGTT
Found at i:60254 original size:19 final size:19
Alignment explanation
Indices: 60219--60262 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
60209 AAATCGCAAC
60219 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
60238 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
60257 GCGATT
1 GCGATT
60263 CTCTCGTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.11, C:0.16, G:0.27, T:0.45
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:60420 original size:14 final size:14
Alignment explanation
Indices: 60401--60437 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
60391 CATCAATTAA
60401 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
60415 ACAAATCATCTTTT
1 ACAAATCAACTTTT
60429 ACAAATCAA
1 ACAAATCAA
60438 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Done.