Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000044.1 Hibiscus syriacus cultivar Beakdansim tig00000070_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: 68478
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:11650 original size:5 final size:5
Alignment explanation
Indices: 11640--11677 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
11630 TCAAAATAAT
11640 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
11678 ACTAATAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:16028 original size:15 final size:14
Alignment explanation
Indices: 16008--16047 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
15998 TTTTTTTATC
16008 ATAATTAAAATAAAA
1 ATAATTAAAA-AAAA
*
16023 ATAATTTAAAAAAA
1 ATAATTAAAAAAAA
*
16037 ATAAATAAAAA
1 ATAATTAAAAA
16048 TAATAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
ATAATTAAAAAAAA
Found at i:16045 original size:13 final size:14
Alignment explanation
Indices: 16019--16056 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
16009 TAATTAAAAT
*
16019 AAAAATAATTTAAA
1 AAAAATAATATAAA
16033 AAAAATAA-ATAAA
1 AAAAATAATATAAA
*
16046 AATAATAATAT
1 AAAAATAATAT
16057 TTTATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAATAATATAAA
Found at i:17080 original size:17 final size:18
Alignment explanation
Indices: 17049--17082 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17039 TCCGATTTTA
*
17049 ATTTTTATATTTTAAATT
1 ATTTTTATATATTAAATT
17067 ATTTTT-TATATTAAAT
1 ATTTTTATATATTAAAT
17083 AATAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTTATATATTAAATT
Found at i:18325 original size:11 final size:11
Alignment explanation
Indices: 18309--18371 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
18299 AAAATTACAT
18309 TATTAAAAATA
1 TATTAAAAATA
18320 TATTAAAAATA
1 TATTAAAAATA
* * ***
18331 CACTATTGATA
1 TATTAAAAATA
18342 -ATTATAAAAT-
1 TATTA-AAAATA
18352 T-TTAAAAATA
1 TATTAAAAATA
18362 TATTAAAAAT
1 TATTAAAAAT
18372 TCTATAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:18512 original size:14 final size:14
Alignment explanation
Indices: 18493--18538 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
18483 CAATGAATCC
*
18493 TAAACCCTAAGCTA
1 TAAACCCTAAACTA
18507 TAAACCCTAAACTA
1 TAAACCCTAAACTA
*
18521 TAAACCCTAAACCA
1 TAAACCCTAAACTA
18535 TAAA
1 TAAA
18539 TCTGATTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.50, C:0.28, G:0.02, T:0.20
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:19171 original size:16 final size:16
Alignment explanation
Indices: 19150--19181 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19140 CATTAATATG
*
19150 AAACCTAAATTTAACT
1 AAACCTAAATTAAACT
19166 AAACCTAAATTAAACT
1 AAACCTAAATTAAACT
19182 CACTCACACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (16 bp):
AAACCTAAATTAAACT
Found at i:22685 original size:23 final size:26
Alignment explanation
Indices: 22648--22716 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
22638 TTCTCTTGTG
22648 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
22672 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
22697 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
22717 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:22698 original size:12 final size:12
Alignment explanation
Indices: 22681--22716 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
22671 TATCATGTTC
22681 TCATATCACATG
1 TCATATCACATG
*
22693 TCATATCACATA
1 TCATATCACATG
22705 TCATATCACATG
1 TCATATCACATG
22717 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:23129 original size:64 final size:63
Alignment explanation
Indices: 23021--23241 Score: 246
Period size: 64 Copynumber: 3.5 Consensus size: 63
23011 TAATGAATGT
* * ** * **
23021 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTATTATTAATGGG
* **
23085 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTT-ATTATTAATGGG
* * ** *
23149 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTTGATGTTT-TTATTTTAAAAGA
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTA--TTAATGGG
**
23213 ATGCATCGATGCACTACCAATGCATCGAT
1 ATGCATCGATGCACTACTTATGCATCGAT
23242 ACACCTTCAA
Statistics
Matches: 135, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
62 3 0.02
63 2 0.01
64 130 0.96
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTATTAATGGG
Found at i:29590 original size:12 final size:12
Alignment explanation
Indices: 29573--29608 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
29563 TATCATGTTC
29573 TCATATCACATG
1 TCATATCACATG
*
29585 TCATATCACATA
1 TCATATCACATG
29597 TCATATCACATG
1 TCATATCACATG
29609 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:30001 original size:64 final size:64
Alignment explanation
Indices: 29918--30134 Score: 224
Period size: 64 Copynumber: 3.4 Consensus size: 64
29908 GAAGGTATGA
* * * *
29918 ATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATT-ATTATTGATGGGATGC
1 ATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGT-TTCATTATTAATGGGATGC
* ** **
29982 ATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGGATGC
1 ATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTTCATTATTAATGGGATGC
* * ** * **
30046 ATCGATGTACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAA-AAGAGTG
1 ATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATG-TTTCATTATTAATGGGA-TG
30109 C
64 C
**
30110 ATCGATGCACTACCAATGCATCGAT
1 ATCGATGCACTACTTATGCATCGAT
30135 ACACCTTCAA
Statistics
Matches: 131, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
63 4 0.03
64 121 0.92
65 6 0.05
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
ATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTTCATTATTAATGGGATGC
Found at i:31288 original size:19 final size:19
Alignment explanation
Indices: 31254--31291 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
31244 TCCTATTCTC
**
31254 TGGTAATCTTTTATTCCAT
1 TGGTAATCTTACATTCCAT
31273 TGGTAATCTTACATTCCAT
1 TGGTAATCTTACATTCCAT
31292 GAACCAAACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (19 bp):
TGGTAATCTTACATTCCAT
Found at i:31946 original size:33 final size:34
Alignment explanation
Indices: 31902--31966 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
31892 ACATCAATCT
* * *
31902 ACTTTCTCTAAAGAAGTGAATAAAC-TTATCACC
1 ACTTTCCCTAAAGAACTAAATAAACTTTATCACC
31935 ACTTTCCCTAAAGAACTAAATAAACTTTATCA
1 ACTTTCCCTAAAGAACTAAATAAACTTTATCA
31967 GGTATGATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 22 0.79
34 6 0.21
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.31
Consensus pattern (34 bp):
ACTTTCCCTAAAGAACTAAATAAACTTTATCACC
Found at i:35411 original size:18 final size:18
Alignment explanation
Indices: 35388--35422 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
35378 TTGTCACTAA
35388 AATTTAACAA-AAAATAAT
1 AATTTAA-AAGAAAATAAT
35406 AATTTAAAAGAAAATAA
1 AATTTAAAAGAAAATAA
35423 CTTCAGTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (18 bp):
AATTTAAAAGAAAATAAT
Found at i:35622 original size:20 final size:20
Alignment explanation
Indices: 35597--35635 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35587 AACACAACTA
35597 TTCGCAACGCGAATCTCGTT
1 TTCGCAACGCGAATCTCGTT
* *
35617 TTCGCAACTCGAATTTCGT
1 TTCGCAACGCGAATCTCGT
35636 ATATAGGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (20 bp):
TTCGCAACGCGAATCTCGTT
Found at i:41690 original size:8 final size:8
Alignment explanation
Indices: 41677--41717 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
41667 CTCATTTTCA
41677 GAGAATTT
1 GAGAATTT
41685 GAGAATTT
1 GAGAATTT
*
41693 -AGAGTTT
1 GAGAATTT
*
41700 GGGAATTT
1 GAGAATTT
41708 GAGAATTT
1 GAGAATTT
41716 GA
1 GA
41718 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:42129 original size:128 final size:128
Alignment explanation
Indices: 41788--42543 Score: 1304
Period size: 128 Copynumber: 5.9 Consensus size: 128
41778 TAATCGGAGT
41788 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
41853 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
41916 ACTATTCACATGAAGGCGCGTT-CCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
41980 CATTGCCCTATTATGTCACTCACGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
42043 ACTATTCACATGAAGGAGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGGGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
42108 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
42171 ACTATTCACATGAAGGTGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
42236 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGGTATATCAGTACCTATTATTT-
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*** * *
42298 -CTAAGGGGACTTGAAGGTGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTT
1 ACT-A-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTT
*
42362 ATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTGCCTATTATTTC
64 ATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** * *
42427 TC-AGGGGACTTGAAGGCGCGTTCCCGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTA
42491 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
42544 AATCAGGTAA
Statistics
Matches: 607, Mismatches: 16, Indels: 10
0.96 0.03 0.02
Matches are distributed among these distances:
126 2 0.00
127 126 0.21
128 478 0.79
130 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:42974 original size:31 final size:34
Alignment explanation
Indices: 42903--43000 Score: 130
Period size: 31 Copynumber: 3.0 Consensus size: 34
42893 AAATTTAATG
*
42903 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* *
42937 TTAAATTTCGAATAATATTATTT-T-TTTT-ATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* *
42968 TTAAATTTCGAATAATAAAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
43001 AACATTTATC
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
31 23 0.42
32 5 0.09
33 5 0.09
34 22 0.40
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:43549 original size:21 final size:20
Alignment explanation
Indices: 43522--43612 Score: 101
Period size: 21 Copynumber: 4.3 Consensus size: 20
43512 GGTATAAAAC
*
43522 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
43542 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
43563 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
* * *
43584 CCCTACAGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
43605 CCCTGCGG
1 -CCTGCGG
43613 AGATGGCATA
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
20 3 0.05
21 57 0.90
22 3 0.05
ACGTcount: A:0.21, C:0.27, G:0.33, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:43582 original size:42 final size:42
Alignment explanation
Indices: 43519--43612 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
43509 TATGGTATAA
* * *
43519 AACCCTGCGGGCTAGGCATGTAA-CCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGTAACCCT-ACAGGCTAGGAATGT
* *
43561 AACCCTGCGGGCTCGGAATGTAACCCTACAGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGTAACCCTACAGGCTAGGAATGT
43603 AACCCTGCGG
1 AACCCTGCGG
43613 AGATGGCATA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 43 0.93
43 3 0.07
ACGTcount: A:0.22, C:0.28, G:0.32, T:0.18
Consensus pattern (42 bp):
AACCCTGCGGGCTAGGAATGTAACCCTACAGGCTAGGAATGT
Found at i:45251 original size:28 final size:28
Alignment explanation
Indices: 45198--45256 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
45188 TTATAAAAAA
* * *
45198 TAAAATTAATATAAATTCATAATAACTT
1 TAAAATTAAAATAAATTAATAATAACAT
*
45226 TAAAA-TAAAATAAATTAAATATTAACAT
1 TAAAATTAAAATAAATT-AATAATAACAT
45254 TAA
1 TAA
45257 TTATAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (28 bp):
TAAAATTAAAATAAATTAATAATAACAT
Found at i:49822 original size:18 final size:18
Alignment explanation
Indices: 49799--49837 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
49789 GATTTTAAGT
49799 ATGTGTTTTGATCATTAG
1 ATGTGTTTTGATCATTAG
49817 ATGTGTTTTGATCATTAG
1 ATGTGTTTTGATCATTAG
49835 ATG
1 ATG
49838 ATAACTAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (18 bp):
ATGTGTTTTGATCATTAG
Found at i:51798 original size:22 final size:22
Alignment explanation
Indices: 51772--51912 Score: 180
Period size: 22 Copynumber: 6.4 Consensus size: 22
51762 TATATTAGTC
*
51772 CTTCGAGACGTATCCAGTGGTT
1 CTTCGGGACGTATCCAGTGGTT
*
51794 CTTCGGGACGTATCCAGTGGTC
1 CTTCGGGACGTATCCAGTGGTT
51816 CTTCGGGACGTATCCAGTGG-T
1 CTTCGGGACGTATCCAGTGGTT
* *
51837 CATTCGGGATGTATCCAGTGGTC
1 C-TTCGGGACGTATCCAGTGGTT
*
51860 CTTCAGGACGTATCCAGTGG-T
1 CTTCGGGACGTATCCAGTGGTT
*
51881 CATTCGGGACGTATCTAGTGG-T
1 C-TTCGGGACGTATCCAGTGGTT
51903 CATTCGGGAC
1 C-TTCGGGAC
51913 ACAGTGGTCA
Statistics
Matches: 106, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
21 2 0.02
22 103 0.97
23 1 0.01
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.29
Consensus pattern (22 bp):
CTTCGGGACGTATCCAGTGGTT
Found at i:51832 original size:44 final size:44
Alignment explanation
Indices: 51769--51931 Score: 237
Period size: 44 Copynumber: 3.8 Consensus size: 44
51759 GGGTATATTA
*
51769 GTCCTTCGAGACGTATCCAGTGGTTC-TTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTGG-TCATTCGGGACGTATCCAGTG
*
51813 GTCCTTCGGGACGTATCCAGTGGTCATTCGGGATGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTGGTCATTCGGGACGTATCCAGTG
* *
51857 GTCCTTCAGGACGTATCCAGTGGTCATTCGGGACGTATCTAGTG
1 GTCCTTCGGGACGTATCCAGTGGTCATTCGGGACGTATCCAGTG
*
51901 GTCATTCGGGAC--A--CAGTGGTCATTCGGGACG
1 GTCCTTCGGGACGTATCCAGTGGTCATTCGGGACG
51932 AATACTGAAC
Statistics
Matches: 111, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
40 18 0.16
42 1 0.01
43 2 0.02
44 90 0.81
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.28
Consensus pattern (44 bp):
GTCCTTCGGGACGTATCCAGTGGTCATTCGGGACGTATCCAGTG
Found at i:51887 original size:66 final size:66
Alignment explanation
Indices: 51781--51911 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
51771 CCTTCGAGAC
* * *
51781 GTATCCAGTGGTTCTTCGGGACGTATCCAGTGGTCCTTCGGGACGTATCCAGTGGTCATTCGGGA
1 GTATCCAGTGGTCCTTCAGGACGTATCCAGTGGTCATTCGGGACGTATCCAGTGGTCATTCGGGA
51846 T
66 T
*
51847 GTATCCAGTGGTCCTTCAGGACGTATCCAGTGGTCATTCGGGACGTATCTAGTGGTCATTCGGGA
1 GTATCCAGTGGTCCTTCAGGACGTATCCAGTGGTCATTCGGGACGTATCCAGTGGTCATTCGGGA
51912 CACAGTGGTC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.17, C:0.22, G:0.31, T:0.30
Consensus pattern (66 bp):
GTATCCAGTGGTCCTTCAGGACGTATCCAGTGGTCATTCGGGACGTATCCAGTGGTCATTCGGGA
T
Found at i:51920 original size:18 final size:20
Alignment explanation
Indices: 51786--51932 Score: 138
Period size: 22 Copynumber: 7.0 Consensus size: 20
51776 GAGACGTATC
51786 CAGTGGTTC-TTCGGGACGTAT
1 CAGTGG-TCATTCGGGACG-AT
*
51807 CCAGTGGTCCTTCGGGACGTAT
1 -CAGTGGTCATTCGGGACG-AT
*
51829 CCAGTGGTCATTCGGGATGTAT
1 -CAGTGGTCATTCGGGACG-AT
* *
51851 CCAGTGGTCCTTCAGGACGTAT
1 -CAGTGGTCATTCGGGACG-AT
51873 CCAGTGGTCATTCGGGACGTAT
1 -CAGTGGTCATTCGGGACG-AT
51895 CTAGTGGTCATTCGGGAC-A-
1 C-AGTGGTCATTCGGGACGAT
51914 CAGTGGTCATTCGGGACGA
1 CAGTGGTCATTCGGGACGA
51933 ATACTGAACA
Statistics
Matches: 115, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
18 16 0.14
19 2 0.02
20 1 0.01
21 3 0.03
22 93 0.81
ACGTcount: A:0.18, C:0.22, G:0.32, T:0.28
Consensus pattern (20 bp):
CAGTGGTCATTCGGGACGAT
Found at i:52794 original size:23 final size:23
Alignment explanation
Indices: 52768--52831 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
52758 CAGCTCATGT
*
52768 AAATGCACCGAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
52791 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
*
52814 AAATGCACCGTAGTGCCA
1 AAATGCACCGAAGTGCCA
52832 TATAATGTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.33, C:0.27, G:0.27, T:0.14
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:54646 original size:16 final size:17
Alignment explanation
Indices: 54625--54658 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
54615 CACATACACA
*
54625 TATTCAA-ACTCATTTC
1 TATTCAATAATCATTTC
54641 TATTCAATAATCATTTC
1 TATTCAATAATCATTTC
54658 T
1 T
54659 TTAACCTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTCAATAATCATTTC
Found at i:61803 original size:641 final size:639
Alignment explanation
Indices: 60125--62039 Score: 3441
Period size: 640 Copynumber: 3.0 Consensus size: 639
60115 AAATATTAAA
60125 AGTTACGAGTTTAAAGTTGAAATATTAAGAATCATAGTATGGTATCCCTCTAAAGAATAAGTGTT
1 AGTTACGAGTTTAAAGTTGAAATATTAAGAATCATAGTATGGTATCCCTCTAAAGAATAAGTGTT
*
60190 TATCCTAGTTTTGTAAATCCATCATCTCTAAGAACACCCTGTAGATACTTCTAAATGAGACATTT
66 TATCCTAGTTTTGTAAATCCATCATCTCTAAGAACACCCTGCAGATACTTCTAAATGAGACATTT
*
60255 TCGCCTGTACATCATAAGAAGCTATCTGATCTGAGCCTTTGACCATTGGGATAGGGGATTTGCAT
131 TCGCCTGTACATCATAAGAAGCTACCTGATCTGAGCCTTTGACCATTGGGATAGGGGATTTGCAT
60320 TGATTCTTAAATTGCTTCGTTAATTTATGAGAGATGATTATGAATTATTTTGTAAATTATGATAG
196 TGATTCTTAAATTGCTTCGTTAATTTATGAGAGATGATTATGAATTATTTTGTAAATTATGATAG
* * *
60385 ATTCCTTCGTAAGTTATAGGAGACGCCTTTAAGTGAGATGTCTCTAATGGGATGTCAACTAGTAA
261 ATGCCTTCGTAAGTTATGGGAGACTCCTTTAAGTGAGATGTCTCTAATGGGATGTCAACTAGTAA
* *
60450 GATGAATCTATGACTCTCGACCTAAATCGAAATGGGTGAATCATCAAAGTCTCACATGATTTATT
326 GATGAATCTATGACTCTCGATCTAAATCGAAATGGGTGAATCGTCAAAGTCTCACATGATTTATT
60515 G-----T-TTTTTTTTTCTCGACAATATTATTTTATTAATAAATAATCAAACAAGTCTAACATGA
391 GTTTTTTCTTTTTTTTTCTCGACAATATTATTTTATTAATAAATAATCAAACAAGTCTAACATGA
* *
60574 GTTATATGCATCGTTAAAAACCTTTATGAACCTAACAAGAGAAAAAGAGTACAAACAACCAGGGA
456 GTTATATGCATCGTTAAAAACCTTTATAAACCTAACAAGAGGAAAAGAGTACAAACAACCAGGGA
* *
60639 AAATACACGCGATCGCTCAAAGAGAAGGCAGACACAAAAGACTATTAATACTCCACTACAACAAC
521 AAATCCGCGCGATCGCTCAAAGAGAAGGCAGACACAAAAGACTATTAATACTCCACTACAACAAC
60704 TCACAAAGAGTATAGCACAACTCTTCAACAACTTCTTAAAAAATAAAAAACTCT
586 TCACAAAGAGTATAGCACAACTCTTCAACAACTTCTTAAAAAATAAAAAACTCT
60758 AGTTACGAGTTTAAAGTTGAAATATTAAGAATCATAGTAT-GTATCCCTCTAAAGAATAAGTGTT
1 AGTTACGAGTTTAAAGTTGAAATATTAAGAATCATAGTATGGTATCCCTCTAAAGAATAAGTGTT
60822 TATCCTAGTTTTGTAAATCCATCATCTCTAAGAACACCCTGCAGATACTTCTAAATGAGACATTT
66 TATCCTAGTTTTGTAAATCCATCATCTCTAAGAACACCCTGCAGATACTTCTAAATGAGACATTT
* * * *
60887 TCACCTGTACATCATAATAAGCTACATGATTTGAGCCTTTGACCATTGGGATAGGGGATTTGCAT
131 TCGCCTGTACATCATAAGAAGCTACCTGATCTGAGCCTTTGACCATTGGGATAGGGGATTTGCAT
60952 TGATTCTTAAATTGCTTCGTTAATTTATGAGAGATGATTATGAATTATTTTGTAAATTATGATAG
196 TGATTCTTAAATTGCTTCGTTAATTTATGAGAGATGATTATGAATTATTTTGTAAATTATGATAG
* * * *
61017 ATGCCTTTGTAGGTTATGGGAGACTCCTTTAAGTGAGATATCTCTAATGGGATGTCTACTAGTAA
261 ATGCCTTCGTAAGTTATGGGAGACTCCTTTAAGTGAGATGTCTCTAATGGGATGTCAACTAGTAA
61082 GATGAATCTATGACTCTCGATCTAAATCGAAATGGGTGAATCGTCAAAGTCTCACATGATTTATT
326 GATGAATCTATGACTCTCGATCTAAATCGAAATGGGTGAATCGTCAAAGTCTCACATGATTTATT
*
61147 GTTTATTTCTTTTTTTTTACTCGACAATATTATTTTATTAATAAATAATAAAACAAGTCTAACAT
391 GTTT-TTTCTTTTTTTTT-CTCGACAATATTATTTTATTAATAAATAATCAAACAAGTCTAACAT
*
61212 GAGTTATATGCATCGTTAAAAACCTTTACAAACCTAACAAGAGGAAAAGAGTACAAACAACCAGG
454 GAGTTATATGCATCGTTAAAAACCTTTATAAACCTAACAAGAGGAAAAGAGTACAAACAACCAGG
*
61277 GAAAATCCGCGCGATAGCTCAAAGAGAAGGCAGACACAAAAGACTATTAATACTCCACTACAACA
519 GAAAATCCGCGCGATCGCTCAAAGAGAAGGCAGACACAAAAGACTATTAATACTCCACTACAACA
61342 ACTCACAAAGAGTATAGCACAACTCTTCAACAACTTCTTAAAAAATAAAAAACTCT
584 ACTCACAAAGAGTATAGCACAACTCTTCAACAACTTCTTAAAAAATAAAAAACTCT
61398 AGTTACGAGTTTAAAGTTGAAATATTAAGAATCATAGTATGGTATCCCTCTAAAGAATAAGTGTT
1 AGTTACGAGTTTAAAGTTGAAATATTAAGAATCATAGTATGGTATCCCTCTAAAGAATAAGTGTT
*
61463 TATCCTAGTTTTGTAAATCCATCATCTCTAAGAACACCCTACAGATACTTCTAAATGAGACATTT
66 TATCCTAGTTTTGTAAATCCATCATCTCTAAGAACACCCTGCAGATACTTCTAAATGAGACATTT
61528 TCGCCTGTACATCATAAGAAGCTACCTGATCTGAGCCTTTGACCATTGGGATAGGGGATTTGCAT
131 TCGCCTGTACATCATAAGAAGCTACCTGATCTGAGCCTTTGACCATTGGGATAGGGGATTTGCAT
*
61593 TGATTCTTAAATTACTTCGTTAATTTATGAGAGATGATTATGAATTATTTTGTAAATTATGATAG
196 TGATTCTTAAATTGCTTCGTTAATTTATGAGAGATGATTATGAATTATTTTGTAAATTATGATAG
*
61658 ATGCCTTCGTACGTTATGGGAGA-TCCTTTAAGTGAGATGTCTCTAATGGGATGTCAACTAGTAA
261 ATGCCTTCGTAAGTTATGGGAGACTCCTTTAAGTGAGATGTCTCTAATGGGATGTCAACTAGTAA
*
61722 GATGAATCTATGACTCTCGATCTAAATCGAAATGGGTGAATCGTCAAAGTCTCATATGATTTATT
326 GATGAATCTATGACTCTCGATCTAAATCGAAATGGGTGAATCGTCAAAGTCTCACATGATTTATT
*
61787 GTTTCTTTCTTTTTTTTGCTCGACAATATTATTTTATTAATAAATAATCAAACAAGTCTAACATG
391 GTTT-TTTCTTTTTTTTTCTCGACAATATTATTTTATTAATAAATAATCAAACAAGTCTAACATG
61852 AGTTATATGCATCGTTAAAAACCTTTATAAACCTAACAAGAGGAAAAGAGTACAAACAACCAGGG
455 AGTTATATGCATCGTTAAAAACCTTTATAAACCTAACAAGAGGAAAAGAGTACAAACAACCAGGG
* * *
61917 AAAATCCGCGCAATCTCTCAAATAGAAGGCAGACACAAAAGACTATTAATACTCCACTACAACAA
520 AAAATCCGCGCGATCGCTCAAAGAGAAGGCAGACACAAAAGACTATTAATACTCCACTACAACAA
*
61982 CTCACAAAGAGTATAACACAACTCTTCAACAACTTCTTCTTAAAAAATAAAAAACTCT
585 CTCACAAAGAGTATAGCACAACTCTTCAACAA---CTTCTTAAAAAATAAAAAACTCT
62040 TCAACATCTA
Statistics
Matches: 1228, Mismatches: 42, Indels: 15
0.96 0.03 0.01
Matches are distributed among these distances:
632 335 0.27
633 40 0.03
638 1 0.00
639 211 0.17
640 384 0.31
641 234 0.19
642 23 0.02
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (639 bp):
AGTTACGAGTTTAAAGTTGAAATATTAAGAATCATAGTATGGTATCCCTCTAAAGAATAAGTGTT
TATCCTAGTTTTGTAAATCCATCATCTCTAAGAACACCCTGCAGATACTTCTAAATGAGACATTT
TCGCCTGTACATCATAAGAAGCTACCTGATCTGAGCCTTTGACCATTGGGATAGGGGATTTGCAT
TGATTCTTAAATTGCTTCGTTAATTTATGAGAGATGATTATGAATTATTTTGTAAATTATGATAG
ATGCCTTCGTAAGTTATGGGAGACTCCTTTAAGTGAGATGTCTCTAATGGGATGTCAACTAGTAA
GATGAATCTATGACTCTCGATCTAAATCGAAATGGGTGAATCGTCAAAGTCTCACATGATTTATT
GTTTTTTCTTTTTTTTTCTCGACAATATTATTTTATTAATAAATAATCAAACAAGTCTAACATGA
GTTATATGCATCGTTAAAAACCTTTATAAACCTAACAAGAGGAAAAGAGTACAAACAACCAGGGA
AAATCCGCGCGATCGCTCAAAGAGAAGGCAGACACAAAAGACTATTAATACTCCACTACAACAAC
TCACAAAGAGTATAGCACAACTCTTCAACAACTTCTTAAAAAATAAAAAACTCT
Found at i:62731 original size:3 final size:3
Alignment explanation
Indices: 62723--62753 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
62713 GGACTTAAAA
62723 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
62754 CATTATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:63093 original size:19 final size:19
Alignment explanation
Indices: 63071--63129 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
63061 CAACCCTCTG
* *
63071 TCCCACCGATAACGAGCCA
1 TCCCACCAACAACGAGCCA
63090 TCCCACCAACAACGAGCCA
1 TCCCACCAACAACGAGCCA
**
63109 TCCCACCAACGTCGAGCCA
1 TCCCACCAACAACGAGCCA
63128 TC
1 TC
63130 GAATGTTCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.31, C:0.46, G:0.14, T:0.10
Consensus pattern (19 bp):
TCCCACCAACAACGAGCCA
Found at i:68426 original size:22 final size:22
Alignment explanation
Indices: 68396--68448 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
68386 AGGCAATATT
68396 TTTCAAAATTCATTTTGATGTG
1 TTTCAAAATTCATTTTGATGTG
*
68418 TTTCGAAATTCATTTTGATGTG
1 TTTCAAAATTCATTTTGATGTG
68440 -TTCAAAATT
1 TTTCAAAATT
68449 TGAAAATCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 8 0.28
22 21 0.72
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.49
Consensus pattern (22 bp):
TTTCAAAATTCATTTTGATGTG
Done.