Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002617.1 Hibiscus syriacus cultivar Beakdansim tig00005299_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: 60787
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:507 original size:29 final size:30
Alignment explanation
Indices: 467--539 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
457 CAATTTTTTG
* *
467 TTAATGACCAAAATGTAAATTT-TGAAAGT
1 TTAATGACCAAAATATAAATTTGGGAAAGT
*
496 TTAATAGA-CAAAGTATAAATTTGGGAAAGT
1 TTAAT-GACCAAAATATAAATTTGGGAAAGT
* *
526 TTAAGGACCTAAAT
1 TTAATGACCAAAAT
540 GGGAATTTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
29 19 0.54
30 16 0.46
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (30 bp):
TTAATGACCAAAATATAAATTTGGGAAAGT
Found at i:3780 original size:20 final size:22
Alignment explanation
Indices: 3752--3810 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 22
3742 AACTTTATTG
*
3752 AAATAATATTT-ATTATTA-CA
1 AAATAATATTTCAATATTATCA
*
3772 AAATCATATTTCAATATTATCA
1 AAATAATATTTCAATATTATCA
*
3794 AAAT-ATTTTTC-ATATTA
1 AAATAATATTTCAATATTA
3811 AATTTCAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 16 0.47
21 12 0.35
22 6 0.18
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATAATATTTCAATATTATCA
Found at i:16395 original size:30 final size:30
Alignment explanation
Indices: 16359--16420 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
16349 CCTATCGGGC
*
16359 AGTATACTCATAGGAGCATAGACCATTCTT
1 AGTATACTCATAGGAGCAAAGACCATTCTT
*
16389 AGTATACTCATATGAGCAAAGACCATTCTT
1 AGTATACTCATAGGAGCAAAGACCATTCTT
16419 AG
1 AG
16421 CACAAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (30 bp):
AGTATACTCATAGGAGCAAAGACCATTCTT
Found at i:18141 original size:24 final size:25
Alignment explanation
Indices: 18114--18164 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
18104 TTAAGTTTTG
18114 AAAA-CAATTGAAAGTTTAGGTACT
1 AAAATCAATTGAAAGTTTAGGTACT
** * *
18138 AAAATGGATTGATATTTTAGGTACT
1 AAAATCAATTGAAAGTTTAGGTACT
18163 AA
1 AA
18165 GCACATTAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (25 bp):
AAAATCAATTGAAAGTTTAGGTACT
Found at i:18533 original size:7 final size:7
Alignment explanation
Indices: 18523--18548 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18513 TAATAAAAAA
18523 TATATTT
1 TATATTT
18530 TATATTT
1 TATATTT
18537 TATATTT
1 TATATTT
18544 TATAT
1 TATAT
18549 AAATACCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TATATTT
Found at i:22096 original size:19 final size:20
Alignment explanation
Indices: 22069--22107 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
22059 TATACATTGC
*
22069 GTTATGAATCT-AAAGTAAA
1 GTTACGAATCTAAAAGTAAA
22088 GTTACGAATCTAAAAGTAAA
1 GTTACGAATCTAAAAGTAAA
22108 TTATGAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.28
Consensus pattern (20 bp):
GTTACGAATCTAAAAGTAAA
Found at i:22657 original size:21 final size:20
Alignment explanation
Indices: 22624--22678 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
22614 TATGTTTTAG
22624 ATAAAAGATATATTTTATTAAA
1 ATAAAA-ATATATTTT-TTAAA
*
22646 ATAAAAATATATATTTTAAA
1 ATAAAAATATATTTTTTAAA
* *
22666 TTAAAAATTTATT
1 ATAAAAATATATT
22679 AGGCAGTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 15 0.52
21 8 0.28
22 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
ATAAAAATATATTTTTTAAA
Found at i:23034 original size:23 final size:24
Alignment explanation
Indices: 23000--23060 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
22990 TAAATAAGAA
23000 TCTCTG-TCCTTGTGACACG-CTTT
1 TCTCTGCT-CTTGTGACACGTCTTT
* * *
23023 TCTCTGCTCTTGTGGCATGTTTTT
1 TCTCTGCTCTTGTGACACGTCTTT
23047 TCTCTGCTCTTGTG
1 TCTCTGCTCTTGTG
23061 GCATGTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.45
24 18 0.55
ACGTcount: A:0.05, C:0.26, G:0.20, T:0.49
Consensus pattern (24 bp):
TCTCTGCTCTTGTGACACGTCTTT
Found at i:23052 original size:24 final size:24
Alignment explanation
Indices: 23020--23067 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
23010 TGTGACACGC
23020 TTTTCTCTGCTCTTGTGGCATGTT
1 TTTTCTCTGCTCTTGTGGCATGTT
23044 TTTTCTCTGCTCTTGTGGCATGTT
1 TTTTCTCTGCTCTTGTGGCATGTT
23068 CTTTATGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.04, C:0.21, G:0.21, T:0.54
Consensus pattern (24 bp):
TTTTCTCTGCTCTTGTGGCATGTT
Found at i:24391 original size:21 final size:22
Alignment explanation
Indices: 24362--24504 Score: 62
Period size: 22 Copynumber: 6.4 Consensus size: 22
24352 TTATATATAG
*
24362 TATAATATA-ATATTTTT-AATA
1 TATAATATATA-ATTTTTGAAAA
*
24383 TATATTATATAATTTTTGAAAA
1 TATAATATATAATTTTTGAAAA
* * *
24405 TATAATTTTTAATATATATAT-ATAA
1 TATAATATATAAT-T-T-T-TGAAAA
* * *
24430 CAT-GTATATAATTTTGGAAAA
1 TATAATATATAATTTTTGAAAA
*
24451 TATATATAATATAATTTTTGAATA
1 TATA-AT-ATATAATTTTTGAAAA
* * * * *
24475 CATATTGTATGATTTTTTAAAA
1 TATAATATATAATTTTTGAAAA
24497 TAT-ATATA
1 TATAATATA
24505 ATATATATTA
Statistics
Matches: 87, Mismatches: 25, Indels: 20
0.66 0.19 0.15
Matches are distributed among these distances:
21 23 0.26
22 29 0.33
23 4 0.05
24 24 0.28
25 6 0.07
26 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (22 bp):
TATAATATATAATTTTTGAAAA
Found at i:24406 original size:24 final size:24
Alignment explanation
Indices: 24379--24509 Score: 94
Period size: 24 Copynumber: 5.6 Consensus size: 24
24369 TAATATTTTT
24379 AATATATATTATATAATTTTTGAA
1 AATATATATTATATAATTTTTGAA
* * *
24403 AATATA-ATT-TTTAATATAT--A
1 AATATATATTATATAATTTTTGAA
* * *
24423 TATATAACATGTATATAATTTTGGAA
1 AATAT-ATAT-TATATAATTTTTGAA
*
24449 AATATATATAATATAATTTTTG--
1 AATATATATTATATAATTTTTGAA
* * * *
24471 AATACATATTGTATGATTTTTTAA
1 AATATATATTATATAATTTTTGAA
*
24495 AATATATATAATATA
1 AATATATATTATATA
24510 TATTATATAT
Statistics
Matches: 78, Mismatches: 21, Indels: 16
0.68 0.18 0.14
Matches are distributed among these distances:
20 5 0.06
21 1 0.01
22 26 0.33
23 4 0.05
24 34 0.44
25 3 0.04
26 5 0.06
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (24 bp):
AATATATATTATATAATTTTTGAA
Found at i:24421 original size:14 final size:15
Alignment explanation
Indices: 24388--24422 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
24378 TAATATATAT
24388 TATATAATTTTTGAA
1 TATATAATTTTTGAA
*
24403 AATATAATTTTT-AA
1 TATATAATTTTTGAA
24417 TATATA
1 TATATA
24423 TATATAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
TATATAATTTTTGAA
Found at i:24554 original size:23 final size:23
Alignment explanation
Indices: 24509--24567 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
24499 TATATAATAT
* * *
24509 ATATTATATATGGATTTTGAAAAG
1 ATATTATATATAG-TTTTAAAAAC
24533 ATA-TATGATATAGTTTTAAAAAC
1 ATATTAT-ATATAGTTTTAAAAAC
24556 ATATTATATATA
1 ATATTATATATA
24568 ATATATTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 19 0.63
24 11 0.37
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (23 bp):
ATATTATATATAGTTTTAAAAAC
Found at i:24591 original size:3 final size:3
Alignment explanation
Indices: 24583--24618 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
24573 TTAGTAGATA
24583 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
24619 GTACTCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:25777 original size:201 final size:201
Alignment explanation
Indices: 25355--25888 Score: 686
Period size: 201 Copynumber: 2.7 Consensus size: 201
25345 TTCTTTAAGG
* * * * *
25355 CGAGTTCTTTAAGCCAAGAAGAATACCAAGGTTGATTGTGATTTGGCAA-AAATGAACCATTTCA
1 CGAGGTCTTTAAGCCAAGAAGAAGACCAAGGTTGACTGCGATTTGGCAACAAA-GAACCATTTCC
* * * * * *
25419 GAGTCAAAATTCGACATAGCTTAAGGAGAAAAA-AACTATTTGTTGAGTAAAAGCTTTC-AGTTT
65 CAATTAAAATTCGACATAGCTTAA-GACAAAAAGAGCTATTTGTCGAGTAAAAGCTTTCAAGTTT
* * * * *
25482 GATTCCATTCAGCACGAGGGCGTATTAACTGCATGGTAACAACGAGGAATTATATTCCGGTTAAA
129 GATTCCATTCAGCACGAGGGCGCATCAACTGCATGGTAACAACGAAGAACTACATTCCGGTTAAA
25547 TTTTAAAC
194 TTTTAAAC
*
25555 CGAGGTCTTTAAGCCAAGAAGAAGACCAAGGTTGACTGCGATTTGACAACAAAGAACCATTTCCC
1 CGAGGTCTTTAAGCCAAGAAGAAGACCAAGGTTGACTGCGATTTGGCAACAAAGAACCATTTCCC
*
25620 AATTAAAATTCGACATAGCTTAAGACAAAAAGAGCTATTTGTCGAGTAAAAGCTTTCAAGTTCGA
66 AATTAAAATTCGACATAGCTTAAGACAAAAAGAGCTATTTGTCGAGTAAAAGCTTTCAAGTTTGA
* * * * **
25685 TTCCATTCAGCATGAGGGCGCATCAA-TCGCATGGTATCAGCGAAGAACTACCTTTTGGTTAAAT
131 TTCCATTCAGCACGAGGGCGCATCAACT-GCATGGTAACAACGAAGAACTACATTCCGGTTAAAT
25749 TTTAAAC
195 TTTAAAC
* *
25756 CGAGGTCTTTAAGCCAAGAAGAATG-CCAAGGTTAACTACGATTTGGCAACAAAGAACCATTT-C
1 CGAGGTCTTTAAGCCAAGAAGAA-GACCAAGGTTGACTGCGATTTGGCAACAAAGAACCATTTCC
* * * * *
25819 CTAGTAAATATTTGACATAGCTTAAGGCAAAAAGAGTTATTTGTCGAGTAAAAGC-TTCAGAGTT
65 CAATTAAA-ATTCGACATAGCTTAAGACAAAAAGAGCTATTTGTCGAGTAAAAGCTTTCA-AGTT
25883 TGATTC
128 TGATTC
25889 TACTTAGCTC
Statistics
Matches: 294, Mismatches: 33, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
199 7 0.02
200 110 0.37
201 176 0.60
202 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (201 bp):
CGAGGTCTTTAAGCCAAGAAGAAGACCAAGGTTGACTGCGATTTGGCAACAAAGAACCATTTCCC
AATTAAAATTCGACATAGCTTAAGACAAAAAGAGCTATTTGTCGAGTAAAAGCTTTCAAGTTTGA
TTCCATTCAGCACGAGGGCGCATCAACTGCATGGTAACAACGAAGAACTACATTCCGGTTAAATT
TTAAAC
Found at i:26780 original size:27 final size:29
Alignment explanation
Indices: 26741--26796 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
26731 TTACTATCAC
*
26741 ATTTGTATATATATAT-GTTATAGTATTTT
1 ATTTGTATATATATATAG-TATAATATTTT
26770 ATTT-TAT-TATATATAGTATAATATTTT
1 ATTTGTATATATATATAGTATAATATTTT
26797 TTAATATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 17 0.68
28 4 0.16
29 4 0.16
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (29 bp):
ATTTGTATATATATATAGTATAATATTTT
Found at i:26785 original size:22 final size:20
Alignment explanation
Indices: 26759--26804 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
26749 ATATATATGT
**
26759 TATAGTATTTTATTTTATTATA
1 TATAGTATAATATTTT-TTA-A
26781 TATAGTATAATATTTTTTAA
1 TATAGTATAATATTTTTTAA
26801 TATA
1 TATA
26805 CATATTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 3 0.14
22 14 0.64
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (20 bp):
TATAGTATAATATTTTTTAA
Found at i:26804 original size:24 final size:23
Alignment explanation
Indices: 26771--26819 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
26761 TAGTATTTTA
* *
26771 TTTTATTATATATAGTATAATATT
1 TTTTAATATACATAGTATAAT-TT
*
26795 TTTTAATATACATATTATAATTT
1 TTTTAATATACATAGTATAATTT
26818 TT
1 TT
26820 GAAAATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTTAATATACATAGTATAATTT
Found at i:26830 original size:15 final size:15
Alignment explanation
Indices: 26810--26843 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
26800 ATATACATAT
26810 TATAATTTTTGAAA-A
1 TATAATTTTT-AAATA
26825 TATAATTTTTAAATA
1 TATAATTTTTAAATA
26840 TATA
1 TATA
26844 TAATATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TATAATTTTTAAATA
Found at i:27024 original size:24 final size:24
Alignment explanation
Indices: 26997--27046 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
26987 AGTAGATATG
26997 TTGTTGTTGTTATTATTATTATTA
1 TTGTTGTTGTTATTATTATTATTA
*
27021 TTGTTGTTGTTGTTATTATTATTA
1 TTGTTGTTGTTATTATTATTATTA
27045 TT
1 TT
27047 ATTTACTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.00, G:0.14, T:0.68
Consensus pattern (24 bp):
TTGTTGTTGTTATTATTATTATTA
Found at i:27025 original size:27 final size:27
Alignment explanation
Indices: 26995--27049 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
26985 TTAGTAGATA
26995 TGTTGTTGTTGTTATTATTATTATTAT
1 TGTTGTTGTTGTTATTATTATTATTAT
27022 TGTTGTTGTTGTTATTATTATTATTAT
1 TGTTGTTGTTGTTATTATTATTATTAT
27049 T
1 T
27050 TACTAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.67
Consensus pattern (27 bp):
TGTTGTTGTTGTTATTATTATTATTAT
Found at i:27026 original size:21 final size:21
Alignment explanation
Indices: 27000--27043 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
26990 AGATATGTTG
27000 TTGTTGTTATTATTATTATTA
1 TTGTTGTTATTATTATTATTA
* *
27021 TTGTTGTTGTTGTTATTATTA
1 TTGTTGTTATTATTATTATTA
27042 TT
1 TT
27044 ATTATTTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.00, G:0.14, T:0.68
Consensus pattern (21 bp):
TTGTTGTTATTATTATTATTA
Found at i:27039 original size:3 final size:3
Alignment explanation
Indices: 27006--27049 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
26996 GTTGTTGTTG
* * * *
27006 TTA TTA TTA TTA TTA TTG TTG TTG TTG TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
27050 TACTAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:27833 original size:2 final size:2
Alignment explanation
Indices: 27826--27851 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27816 AAAAATACCC
27826 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
27852 TTCCAATTAA
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:28768 original size:32 final size:32
Alignment explanation
Indices: 28722--28803 Score: 128
Period size: 32 Copynumber: 2.6 Consensus size: 32
28712 AAAAATCGGG
* * *
28722 TTCGGTTCGAGTCGGGTTTTTTAAGTTTAATA
1 TTCGGGTCGGGTCGGGTTTTTTAAGTGTAATA
*
28754 TTCGGGTCGGGTCGGGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTTTAAGTGTAATA
28786 TTCGGGTCGGGTCGGGTT
1 TTCGGGTCGGGTCGGGTT
28804 CGGGTTTAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.12, C:0.11, G:0.35, T:0.41
Consensus pattern (32 bp):
TTCGGGTCGGGTCGGGTTTTTTAAGTGTAATA
Found at i:29064 original size:22 final size:22
Alignment explanation
Indices: 29036--29103 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
29026 CGGGTTGGGC
29036 CTCGGGTGGAGCTTCCATTGTT
1 CTCGGGTGGAGCTTCCATTGTT
* *
29058 CTCGGGTCGG-G--T---TGGGT
1 CTCGGGT-GGAGCTTCCATTGTT
29075 CTCGGGTGGAGCTTCCATTGTT
1 CTCGGGTGGAGCTTCCATTGTT
29097 CTCGGGT
1 CTCGGGT
29104 CGGGTGGACC
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
16 2 0.06
17 11 0.31
19 1 0.03
20 1 0.03
22 18 0.51
23 2 0.06
ACGTcount: A:0.06, C:0.22, G:0.38, T:0.34
Consensus pattern (22 bp):
CTCGGGTGGAGCTTCCATTGTT
Found at i:29065 original size:39 final size:39
Alignment explanation
Indices: 29020--29108 Score: 169
Period size: 39 Copynumber: 2.3 Consensus size: 39
29010 TTTATTTTGG
29020 TCGGGTCGGGTTGGGCCTCGGGTGGAGCTTCCATTGTTC
1 TCGGGTCGGGTTGGGCCTCGGGTGGAGCTTCCATTGTTC
*
29059 TCGGGTCGGGTTGGGTCTCGGGTGGAGCTTCCATTGTTC
1 TCGGGTCGGGTTGGGCCTCGGGTGGAGCTTCCATTGTTC
29098 TCGGGTCGGGT
1 TCGGGTCGGGT
29109 GGACCAAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.04, C:0.21, G:0.43, T:0.31
Consensus pattern (39 bp):
TCGGGTCGGGTTGGGCCTCGGGTGGAGCTTCCATTGTTC
Found at i:29472 original size:18 final size:18
Alignment explanation
Indices: 29449--29485 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
29439 CAATTCTTAC
*
29449 AGATTTCAATTCCTTCAT
1 AGATTTCAATTCCCTCAT
29467 AGATTTCAATTCCCTCAT
1 AGATTTCAATTCCCTCAT
29485 A
1 A
29486 ATCATTCCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (18 bp):
AGATTTCAATTCCCTCAT
Found at i:33006 original size:5 final size:5
Alignment explanation
Indices: 32996--33031 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
32986 TTTTGCCAAG
* *
32996 ATAAA ATAAA ATACA ATAAA ATAAA ACAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
33032 ATGAAAAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:33428 original size:30 final size:30
Alignment explanation
Indices: 33357--33429 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
33347 CTAAAACAAC
* *
33357 AAAACAGAAACTTAAAATATTAAAATAATA
1 AAAACAGAAAGTTAAAAGATTAAAATAATA
* *
33387 AAAACATAAAGTTAAAGGATTAAAATAGA-A
1 AAAACAGAAAGTTAAAAGATTAAAATA-ATA
*
33417 AAAATAGAAAGTT
1 AAAACAGAAAGTT
33430 CAGGGACTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 35 0.97
31 1 0.03
ACGTcount: A:0.64, C:0.04, G:0.10, T:0.22
Consensus pattern (30 bp):
AAAACAGAAAGTTAAAAGATTAAAATAATA
Found at i:34234 original size:18 final size:16
Alignment explanation
Indices: 34211--34246 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
34201 ATAAGAGGTC
34211 TTTCTTTCTCTTTTTACT
1 TTTCTTTCT-TTTTT-CT
34229 TTTCTTTCTTTTTTCT
1 TTTCTTTCTTTTTTCT
34245 TT
1 TT
34247 CTGAGTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 5 0.28
18 9 0.50
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTCTTTCTTTTTTCT
Found at i:35450 original size:133 final size:132
Alignment explanation
Indices: 35053--35533 Score: 551
Period size: 133 Copynumber: 3.6 Consensus size: 132
35043 ATCGTCTAAA
* * * * ** * *
35053 GGTGGCACGACTCCTACGAGATGAGGAGATCTGGTCGGTGGGTGACACGACTCATACGTGATGAA
1 GGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGG-GGATGACACGGTTCCTACGCGATGAA
* * * * *
35118 GA-GTTATGTCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCGATGAGGACAGTTGGTTAT
65 GACGGTATGGCCATCTTTAGG-AGGGTGATAACACGGTTCCTACGTGATGAGGATAATTGGTTAT
35182 CTAGG
129 C-AGG
* * * * *
35187 GGTGACACGGCTCCAACGTGATGAGGAGGTCTGGTCGAGGATTACACGGTTCCTACGCGATGAGG
1 GGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGATGACACGGTTCCTACGCGATGAAG
* * * * * *
35252 AC-GAATGGCCATCTTTAGGA--GTGATAATACGGTTCCTATGTGATAAGGATAACTGATTATCA
66 ACGGTATGGCCATCTTTAGGAGGGTGATAACACGGTTCCTACGTGATGAGGATAATTGGTTATCA
35314 GG
131 GG
* * *
35316 GGTGACACAACTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACGGTTCTTACGCGATGAG
1 GGTGACACGACTCCTACGTGATGAGGAGGTCTGGTC-GGGGATGACACGGTTCCTACGCGATGAA
* *
35381 GACGGTA-GACCATCTTTAGGTAGGGTGATAACACGGTTCCTACGTGATGAGGATGATTGGTTAT
65 GACGGTATGGCCATCTTTAGG-AGGGTGATAACACGGTTCCTACGTGATGAGGATAATTGGTTAT
35445 CAGG
129 CAGG
* * ** *
35449 GGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGAGAGATGACATAGTTCCTACGTGATGAA
1 GGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCG-GGGATGACACGGTTCCTACGCGATGAA
*
35514 GATGGTA-GGCCATCTTTAGG
65 GACGGTATGGCCATCTTTAGG
35534 GATTATGGTT
Statistics
Matches: 292, Mismatches: 48, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
129 36 0.12
130 73 0.25
131 3 0.01
132 2 0.01
133 146 0.50
134 32 0.11
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.25
Consensus pattern (132 bp):
GGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGATGACACGGTTCCTACGCGATGAAG
ACGGTATGGCCATCTTTAGGAGGGTGATAACACGGTTCCTACGTGATGAGGATAATTGGTTATCA
GG
Found at i:35529 original size:263 final size:263
Alignment explanation
Indices: 35053--35533 Score: 675
Period size: 263 Copynumber: 1.8 Consensus size: 263
35043 ATCGTCTAAA
* * * *
35053 GGTGGCACGACTCCTACGAGATGAGGAGATCTGGTCGGTGGGTGACACGACTCATACGTGATGAA
1 GGTGACACAACTCCTACGAGATGAGGAGATCTGGTCGGTGGATGACACGACTCATACGCGATGAA
* *
35118 GAGTTATGTCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCGATGAGGACAGTTGGTTATC
66 GAGGTATGACCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCGATGAGGACAGTTGGTTATC
* *
35183 TAGGGGTGACACGGCTCCAACGTGATGAGGAGGTCTGGTCGAGGATTACACGGTTCCTACGCGAT
131 TAGGGGTGACACGGCTCCAACGTGATGAGGAGGTCTGGTCGAGGATGACACAGTTCCTACGCGAT
*
35248 GAGGACGAATGGCCATCTTTAGGAGTGATAATACGGTTCCTATGTGATAAGGATAACTGATTATC
196 GAAGACGAATGGCCATCTTTAGGAGTGATAATACGGTTCCTATGTGATAAGGATAACTGATTATC
35313 AGG
261 AGG
* * ** *
35316 GGTGACACAACTCCTACGTGATGAGGAGGTCTGGTCAGG-GGATGACACGGTTCTTACGCGATGA
1 GGTGACACAACTCCTACGAGATGAGGAGATCTGGTC-GGTGGATGACACGACTCATACGCGATGA
* * * *
35380 GGACGGTA-GACCATCTTTAGGTAGGGTGATAACACGGTTCCTACGTGATGAGGA-TGATTGGTT
65 AGA-GGTATGACCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCGATGAGGACAG-TTGGTT
* *
35443 ATC-AGGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGAGAGATGACATAGTTCCTACG
128 ATCTAGGGGTGACACGGCTCCAACGTGATGAGGAGGTCTGGTCGAG-GATGACACAGTTCCTACG
* * *
35507 TGATGAAGATG-GTAGGCCATCTTTAGG
192 CGATGAAGACGAAT-GGCCATCTTTAGG
35534 GATTATGGTT
Statistics
Matches: 190, Mismatches: 23, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
262 43 0.23
263 142 0.75
264 5 0.03
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.25
Consensus pattern (263 bp):
GGTGACACAACTCCTACGAGATGAGGAGATCTGGTCGGTGGATGACACGACTCATACGCGATGAA
GAGGTATGACCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCGATGAGGACAGTTGGTTATC
TAGGGGTGACACGGCTCCAACGTGATGAGGAGGTCTGGTCGAGGATGACACAGTTCCTACGCGAT
GAAGACGAATGGCCATCTTTAGGAGTGATAATACGGTTCCTATGTGATAAGGATAACTGATTATC
AGG
Found at i:35725 original size:37 final size:37
Alignment explanation
Indices: 35606--35742 Score: 174
Period size: 37 Copynumber: 3.7 Consensus size: 37
35596 GACAAAATTC
*
35606 GTTTCAAGGGAAAC-GATCTCAAAGATA--TTTGTTTT
1 GTTTCAAGTGAAACAGA-CTCAAAGATATTTTTGTTTT
* *
35641 GTTTCAAGGGAAACAAACTCAAAGATGATTTTTGTTTT
1 GTTTCAAGTGAAACAGACTCAAAGAT-ATTTTTGTTTT
* *
35679 GTTTCAAGTGAAACAGACTCAAATAT-TTCTTTGCTTT
1 GTTTCAAGTGAAACAGACTCAAAGATATT-TTTGTTTT
35716 GTTTCAAGTGAAACAGACTCAAAGATA
1 GTTTCAAGTGAAACAGACTCAAAGATA
35743 AGTGTTTTTA
Statistics
Matches: 90, Mismatches: 6, Indels: 9
0.86 0.06 0.09
Matches are distributed among these distances:
35 23 0.26
36 4 0.04
37 32 0.36
38 31 0.34
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (37 bp):
GTTTCAAGTGAAACAGACTCAAAGATATTTTTGTTTT
Found at i:36050 original size:32 final size:32
Alignment explanation
Indices: 36005--36065 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
35995 ACATCTTGAT
*
36005 GTTGAATCCCCAAATATGCCCCAACATTCGAC
1 GTTGAATCCCCAAAGATGCCCCAACATTCGAC
* *
36037 GTTGAATCTCCAAAGATGCCCCATCATTC
1 GTTGAATCCCCAAAGATGCCCCAACATTC
36066 ATTGTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.30, C:0.33, G:0.13, T:0.25
Consensus pattern (32 bp):
GTTGAATCCCCAAAGATGCCCCAACATTCGAC
Found at i:48843 original size:26 final size:26
Alignment explanation
Indices: 48814--48865 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
48804 ATGCATAATA
48814 TGTTGAAACTCAAAAATAAATAAAAG
1 TGTTGAAACTCAAAAATAAATAAAAG
48840 TGTTGAAACTCAAAAATAAATAAAAG
1 TGTTGAAACTCAAAAATAAATAAAAG
48866 GATCGTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.23
Consensus pattern (26 bp):
TGTTGAAACTCAAAAATAAATAAAAG
Found at i:49791 original size:32 final size:32
Alignment explanation
Indices: 49755--49819 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
49745 AAAACAACAC
* *
49755 AAATAGAAACTTAAAGGATTAAAATAATAAAA
1 AAATAGAAACTTAAAAGACTAAAATAATAAAA
* *
49787 AAATAGAAAGTTAAAAGACTAAAATAGTAAAA
1 AAATAGAAACTTAAAAGACTAAAATAATAAAA
49819 A
1 A
49820 TAGAAAGTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.66, C:0.03, G:0.11, T:0.20
Consensus pattern (32 bp):
AAATAGAAACTTAAAAGACTAAAATAATAAAA
Found at i:51241 original size:3 final size:3
Alignment explanation
Indices: 51233--51293 Score: 99
Period size: 3 Copynumber: 20.7 Consensus size: 3
51223 AAAAATAACC
51233 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
51281 A-A TATA AT- ATA AT
1 ATA -ATA ATA ATA AT
51294 TATATTTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 3 0.05
3 51 0.93
4 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:53278 original size:21 final size:21
Alignment explanation
Indices: 53236--53278 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
53226 TATTTTGATA
*
53236 TTATGATTGATATTTATAAAT
1 TTATGATTGATATATATAAAT
* * *
53257 TTATGTTTGGTATATATTAAT
1 TTATGATTGATATATATAAAT
53278 T
1 T
53279 AATTCAAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (21 bp):
TTATGATTGATATATATAAAT
Found at i:53724 original size:18 final size:18
Alignment explanation
Indices: 53703--53737 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53693 TTGGATATGA
*
53703 ATTGTATATTAAATTTGG
1 ATTGCATATTAAATTTGG
*
53721 ATTGCATATTGAATTTG
1 ATTGCATATTAAATTTG
53738 AGTTTTAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.49
Consensus pattern (18 bp):
ATTGCATATTAAATTTGG
Found at i:55832 original size:21 final size:21
Alignment explanation
Indices: 55808--55849 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
55798 AGTAATGTAT
* *
55808 AATTTATTATTTATTCATTAA
1 AATTTATTATTAATTAATTAA
*
55829 AATTTTTTATTAATTAATTAA
1 AATTTATTATTAATTAATTAA
55850 TCAATTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTTATTATTAATTAATTAA
Found at i:55843 original size:11 final size:12
Alignment explanation
Indices: 55829--55874 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
55819 TATTCATTAA
55829 AATT-TTTTATT
1 AATTATTTTATT
* * *
55840 AATTAATTAATC
1 AATTATTTTATT
55852 AATTATTTTATT
1 AATTATTTTATT
55864 -ATTATTTTATT
1 AATTATTTTATT
55875 TTAATATTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
11 15 0.54
12 13 0.46
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (12 bp):
AATTATTTTATT
Found at i:55864 original size:8 final size:8
Alignment explanation
Indices: 55853--55898 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
55843 TAATTAATCA
55853 ATTATTTT
1 ATTATTTT
55861 ATTATTATT
1 ATTATT-TT
55870 -TTATTTT
1 ATTATTTT
*
55877 AATA-TTT
1 ATTATTTT
*
55884 ATTATTTG
1 ATTATTTT
55892 ATTATTT
1 ATTATTT
55899 AATTGTAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
7 8 0.25
8 22 0.69
9 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (8 bp):
ATTATTTT
Found at i:58328 original size:13 final size:13
Alignment explanation
Indices: 58312--58336 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58302 TTTTTGCCTC
58312 TTATTTTGTTTTG
1 TTATTTTGTTTTG
58325 TTATTTTGTTTT
1 TTATTTTGTTTT
58337 ATATAAAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.12, T:0.80
Consensus pattern (13 bp):
TTATTTTGTTTTG
Found at i:59032 original size:26 final size:26
Alignment explanation
Indices: 58998--59048 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
58988 GGTATGCTTT
*
58998 ATGTCATGTTTAAT-ATTTGTTGTTTA
1 ATGTAATGTTT-ATGATTTGTTGTTTA
*
59024 ATGTAATGTTTATGGTTTGTTGTTT
1 ATGTAATGTTTATGATTTGTTGTTT
59049 TTATAGTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.20, C:0.02, G:0.20, T:0.59
Consensus pattern (26 bp):
ATGTAATGTTTATGATTTGTTGTTTA
Found at i:60027 original size:82 final size:83
Alignment explanation
Indices: 59888--60280 Score: 440
Period size: 82 Copynumber: 4.8 Consensus size: 83
59878 CATTTCAGGT
* * *
59888 GTTTTCCATTATTATCCAGAGAATCTCTACCATGTCATAGTGTTTCATCCTATCCGAAATGAAAG
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAG
** *
59953 GCGCGCTCCA-GGGAAGT
66 GCGCATTCCACGGGAAGC
* * * *
59970 GCTTTCCATTATTATTCAGAGAATCTTTGTCATGTCATAGTGTTTCATTCCATCCGAAATGAAAG
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAG
*
60035 GCGCATTCCAGGGGAA-C
66 GCGCATTCCACGGGAAGC
* * * * *
60052 GTTTTCCATTATTATTCATAGAATCTCTGTCATGTCATAGTCTTCCATCCCAT-CGAAAAGAAAG
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAG
* ** *
60116 GTGTGTTCTACGGGAAGC
66 GCGCATTCCACGGGAAGC
* * * * *
60134 ATTTTCCATTATTATTCATAGAATCTCTACCATGTCAGAGTG-TTCTATCCCATCTGAAAT-AAA
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTC-ATCCCATCCGAAATGAAA
* *
60197 GACGCATTCTA-GGAGAAGC
65 GGCGCATTCCACGG-GAAGC
* * *
60216 GTTTTCCATTATTATTCCGAGAATCTCTGCCATATCATAGTG-TTCTATGCCATCCGAAATGAAA
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTC-ATCCCATCCGAAATGAAA
60280 G
65 G
60281 AATCATGTTC
Statistics
Matches: 263, Mismatches: 42, Indels: 11
0.83 0.13 0.03
Matches are distributed among these distances:
81 25 0.10
82 225 0.86
83 13 0.05
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (83 bp):
GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAG
GCGCATTCCACGGGAAGC
Done.