Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006671.1 Hibiscus syriacus cultivar Beakdansim tig00016532_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: 77313
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:818 original size:19 final size:19
Alignment explanation
Indices: 794--833 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
784 ACTTTCCTTT
*
794 TAACTCTTAAACCCACGTC
1 TAACTCCTAAACCCACGTC
813 TAACTCCTAAACCCACGTC
1 TAACTCCTAAACCCACGTC
832 TA
1 TA
834 CCGCTGCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.38, G:0.05, T:0.25
Consensus pattern (19 bp):
TAACTCCTAAACCCACGTC
Found at i:2281 original size:19 final size:19
Alignment explanation
Indices: 2257--2298 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
2247 CATCTCGGTG
2257 CCTAACGTCACAAATGTTA
1 CCTAACGTCACAAATGTTA
2276 CCTAACGTCACAAATGTTA
1 CCTAACGTCACAAATGTTA
2295 CCTA
1 CCTA
2299 TTTAGGTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.29, G:0.10, T:0.26
Consensus pattern (19 bp):
CCTAACGTCACAAATGTTA
Found at i:3388 original size:2 final size:2
Alignment explanation
Indices: 3381--3411 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3371 GATTTTCATC
3381 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3412 TATTAATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5030 original size:29 final size:31
Alignment explanation
Indices: 4989--5073 Score: 111
Period size: 29 Copynumber: 2.8 Consensus size: 31
4979 CTTCTCTTCA
* *
4989 TTTGTTTTGTTATTTTATATATTTTA-TTAT
1 TTTGTTTTATTATTTTATTTATTTTACTTAT
5019 TTTGTTTT-TTATTTTATTTATTTTACCTTAT
1 TTTGTTTTATTATTTTATTTATTTTA-CTTAT
* *
5050 TTTCTTTTATTGTTTTATTTATTT
1 TTTGTTTTATTATTTTATTTATTT
5074 CTTAGCCATT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 16 0.33
30 8 0.16
31 11 0.22
32 14 0.29
ACGTcount: A:0.16, C:0.04, G:0.05, T:0.75
Consensus pattern (31 bp):
TTTGTTTTATTATTTTATTTATTTTACTTAT
Found at i:12125 original size:150 final size:151
Alignment explanation
Indices: 11903--12259 Score: 500
Period size: 151 Copynumber: 2.4 Consensus size: 151
11893 GAAAAACCCA
* * * ** * *
11903 ATGTTTATATTCTATTGATATTCAACGAAACAAAACAAATTTGGGTTCTTAATCTCATCTCTGAA
1 ATGTTTATATTTTATTAACATTCAAATAAACAAAACAAATTTGGGTTCTTAATCTTATCTCCGAA
* * * *
11968 CAATAAAGCTTCTTTACTGGGTA-TTATATTCATTTTATTTTCTCGAGAAAATCCGACCAAACGA
66 CAATAAAGCTTCTTTACTGGGTATTTATATTCAATTAATTTTCTCGAGAAAATCCAACCAAACAA
*
12032 ACTACAAGAAGAGAACCCCTT
131 ACTACAAAAAGAGAACCCCTT
*
12053 GTGTTTATATTTTATTAACATTCAAATAAACAAAACAAATTTGGGTTCTTAATCTTATCTCCGAA
1 ATGTTTATATTTTATTAACATTCAAATAAACAAAACAAATTTGGGTTCTTAATCTTATCTCCGAA
* * * * * * *
12118 CAATAAAGTTTCTTTCCTTGGTATTTCTTTTCAATTAATTTTCTCGAGAAAATCTAATCAAACAA
66 CAATAAAGCTTCTTTACTGGGTATTTATATTCAATTAATTTTCTCGAGAAAATCCAACCAAACAA
12183 ACTACAAAAAGAGAACCCCTT
131 ACTACAAAAAGAGAACCCCTT
* * *
12204 ATGTTTATATTTTATTAACTTTCAAATAAACAAAACAAATTTGGATTCCTAATCTT
1 ATGTTTATATTTTATTAACATTCAAATAAACAAAACAAATTTGGGTTCTTAATCTT
12260 GTTTGTGTAT
Statistics
Matches: 182, Mismatches: 24, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
150 77 0.42
151 105 0.58
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (151 bp):
ATGTTTATATTTTATTAACATTCAAATAAACAAAACAAATTTGGGTTCTTAATCTTATCTCCGAA
CAATAAAGCTTCTTTACTGGGTATTTATATTCAATTAATTTTCTCGAGAAAATCCAACCAAACAA
ACTACAAAAAGAGAACCCCTT
Found at i:14517 original size:28 final size:28
Alignment explanation
Indices: 14477--14536 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
14467 ATGTATAAGA
14477 GTCGGAGCAACACAGCTTTGTGCTGAAG
1 GTCGGAGCAACACAGCTTTGTGCTGAAG
14505 GTCGGAGCAACACAGCTTTGTGCTGAAG
1 GTCGGAGCAACACAGCTTTGTGCTGAAG
14533 GTCG
1 GTCG
14537 TATAAGCCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.23, C:0.22, G:0.33, T:0.22
Consensus pattern (28 bp):
GTCGGAGCAACACAGCTTTGTGCTGAAG
Found at i:30170 original size:24 final size:24
Alignment explanation
Indices: 30138--30193 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
30128 CTGTGACTTG
*
30138 TTCGTTTCATCTATTTTTTTCTCA
1 TTCGCTTCATCTATTTTTTTCTCA
30162 TTCGCTTCATCTATTTTTTTCTCA
1 TTCGCTTCATCTATTTTTTTCTCA
30186 TTCGCTTC
1 TTCGCTTC
30194 CCTATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.11, C:0.25, G:0.05, T:0.59
Consensus pattern (24 bp):
TTCGCTTCATCTATTTTTTTCTCA
Found at i:31651 original size:2 final size:2
Alignment explanation
Indices: 31646--31679 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
31636 ATATATATAT
* *
31646 AC AC AC AC AC AC AC GC GC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
31680 TAACTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.50, G:0.06, T:0.00
Consensus pattern (2 bp):
AC
Found at i:34219 original size:3 final size:3
Alignment explanation
Indices: 34211--34241 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
34201 GGTATTAAGC
34211 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
34242 GATAGGGTAA
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:35021 original size:31 final size:31
Alignment explanation
Indices: 34985--35044 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
34975 AACTTAAAAG
* *
34985 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
35016 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
35045 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:35680 original size:20 final size:20
Alignment explanation
Indices: 35655--35708 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 20
35645 TATTTAAACT
*
35655 TAAATAAAAAATAATTAAAA
1 TAAATATAAAATAATTAAAA
* *
35675 TAAATATAAAAT-TTTAATA
1 TAAATATAAAATAATTAAAA
35694 -AAATATAAAATAATT
1 TAAATATAAAATAATT
35709 TATATGATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 11 0.38
19 7 0.24
20 11 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAATATAAAATAATTAAAA
Found at i:35787 original size:14 final size:14
Alignment explanation
Indices: 35739--35823 Score: 67
Period size: 14 Copynumber: 6.5 Consensus size: 14
35729 ATCTATAATA
*
35739 TAATATTAAAAAAG
1 TAATATTAAAAAAT
*
35753 TAATATT---TAAT
1 TAATATTAAAAAAT
*
35764 TTAT-TTAAAAAAT
1 TAATATTAAAAAAT
35777 TAATATT--AAAAT
1 TAATATTAAAAAAT
* *
35789 TAATATCTATAATA-
1 TAATAT-TAAAAAAT
35803 TAATATTAAAAAAT
1 TAATATTAAAAAAT
35817 TAATATT
1 TAATATT
35824 TAATTTATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
10 2 0.04
11 5 0.09
12 11 0.20
13 12 0.22
14 22 0.40
15 3 0.05
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (14 bp):
TAATATTAAAAAAT
Found at i:35794 original size:64 final size:65
Alignment explanation
Indices: 35718--35846 Score: 242
Period size: 64 Copynumber: 2.0 Consensus size: 65
35708 TTATATGATA
35718 TAAAATTAAATATCTATAATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAAATATCTATAATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAAATTAATAT
*
35783 TAAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAAATATCTATAATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAAATTAATAT
35847 CTATAATATA
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
64 56 0.89
65 7 0.11
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.43
Consensus pattern (65 bp):
TAAAATTAAATATCTATAATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:35807 original size:26 final size:27
Alignment explanation
Indices: 35777--35864 Score: 105
Period size: 24 Copynumber: 3.4 Consensus size: 27
35767 TTTAAAAAAT
35777 TAATATT-AAAATTAATATCTATAATA
1 TAATATTAAAAATTAATATCTATAATA
35803 TAATATTAAAAAATTAATAT-T-TAAT-
1 TAATATT-AAAAATTAATATCTATAATA
*
35828 TTAT-TTAAAAAATTAATATCTATAATA
1 TAATATT-AAAAATTAATATCTATAATA
*
35855 TAAAATTAAA
1 TAATATTAAA
35865 TATAAAACCT
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
24 15 0.28
25 4 0.08
26 15 0.28
27 6 0.11
28 13 0.25
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
TAATATTAAAAATTAATATCTATAATA
Found at i:35840 original size:24 final size:28
Alignment explanation
Indices: 35777--35864 Score: 116
Period size: 28 Copynumber: 3.4 Consensus size: 28
35767 TTTAAAAAAT
35777 TAATATT--AAAATTAATATCTATAATA
1 TAATATTAAAAAATTAATATCTATAATA
35803 TAATATTAAAAAATTAATAT-T-TAAT-
1 TAATATTAAAAAATTAATATCTATAATA
*
35828 TTAT-TTAAAAAATTAATATCTATAATA
1 TAATATTAAAAAATTAATATCTATAATA
*
35855 TAAAATTAAA
1 TAATATTAAA
35865 TATAAAACCT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
24 15 0.28
25 4 0.08
26 15 0.28
27 3 0.06
28 16 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
TAATATTAAAAAATTAATATCTATAATA
Found at i:35867 original size:64 final size:64
Alignment explanation
Indices: 35718--35869 Score: 236
Period size: 64 Copynumber: 2.4 Consensus size: 64
35708 TTATATGATA
35718 TAAAATTAAATATCTATAATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAAA-ATCTATAATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAAATTAATAT
* *
35783 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAAAATCTATAATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAAATTAATAT
*
35847 CTATAATATAAAAT-TA-AATATAA
1 -TAAAAT-TAAAATCTATAATATAA
35870 AACCTCTTTG
Statistics
Matches: 81, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
64 60 0.74
65 16 0.20
66 5 0.06
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (64 bp):
TAAAATTAAAATCTATAATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:43914 original size:23 final size:23
Alignment explanation
Indices: 43873--43916 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
43863 GTAATAAATG
* * *
43873 TAAAATTTTATATATTAAAAAAA
1 TAAAATTTTAGAAAATAAAAAAA
43896 TAAAATTTTAGAAAATAAAAA
1 TAAAATTTTAGAAAATAAAAA
43917 TAAATGGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
TAAAATTTTAGAAAATAAAAAAA
Found at i:44267 original size:18 final size:19
Alignment explanation
Indices: 44233--44268 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
44223 AAATTATACT
*
44233 TAAATTAATATTTAAAATC
1 TAAATTAATAGTTAAAATC
44252 TAAATTAAT-GTTAAAAT
1 TAAATTAATAGTTAAAAT
44269 AATAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAATTAATAGTTAAAATC
Found at i:44274 original size:19 final size:19
Alignment explanation
Indices: 44233--44280 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
44223 AAATTATACT
* *
44233 TAAATTAATATTTAAAATC
1 TAAATTAATAGTTAAAATA
44252 TAAATTAAT-GTTAAAATAA
1 TAAATTAATAGTTAAAAT-A
44271 TAAAATTAAT
1 T-AAATTAAT
44281 TAATTAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.28
19 10 0.40
20 8 0.32
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TAAATTAATAGTTAAAATA
Found at i:46433 original size:242 final size:239
Alignment explanation
Indices: 46004--46467 Score: 628
Period size: 242 Copynumber: 1.9 Consensus size: 239
45994 TAAACTAGTC
* * * *
46004 GATCTAGCCGAATACACGTCGATTCGAGTTTGTTGAAACCTTGAATAGATATGTTTGATCTTCAA
1 GATCTAGCAGAATACACATCAATTCGAGCTTGTTGAAACCTTGAATAGATATGTTTGATCTTCAA
* * * *
46069 AGAGCAAGCTCTGTACCCGTTGGATTTGGATCAACTCAATTTTGCTCCTACATGGTCTTCTGAGC
66 AAAGCAAGCTCTGTACACGTTGGACTTGGATCAACTCAATTTTGCTCCTACATGGTCTTCTAAGC
* *
46134 CAACCACCTTGTGATTTGTCGGTAGAATGTTGGACTCCTAGTCCCGAGATTATACCCTGGCGATT
131 CAACCACCATGTGATTTGTCGGTAGAATGTTGGACTCCTAGTCCCGAGATTATACCCTGGCAATT
46199 TCAATAGAACC-AGAAATGTCTTACTTTGAGTAGTGTGACCAGTT
196 TCAATAGAACCGA-AAATGTCTTACTTTGAGTAGTGTGACCAGTT
*
46243 GATCTAGCAGAATACACATCAATTTGAGCTTGTTG-AACCTTGAAT-GCATATGTTTGATCTTCA
1 GATCTAGCAGAATACACATCAATTCGAGCTTGTTGAAACCTTGAATAG-ATATGTTTGATCTTCA
* * * * ** *
46306 AAAAGCAAGCTTTGTACACTTTTGACTTGGATCGACTCGGTTTTGCTCCTATATGGTGTTACTTC
65 AAAAGCAAGCTCTGTACACGTTGGACTTGGATCAACTCAATTTTGCTCCTACAT-G-G-T-CTTC
** * *
46371 TAAGCCAACGGCCATGTGATTTGTTGGTAGAATGTTGGACTCCTAGTCTCGAGATTATACCCTGG
126 TAAGCCAACCACCATGTGATTTGTCGGTAGAATGTTGGACTCCTAGTCCCGAGATTATACCCTGG
* * *
46436 CAATTTCGATCGTACCGAAAATGTCTTACTTT
191 CAATTTCAATAGAACCGAAAATGTCTTACTTT
46468 TGAGCTGTGT
Statistics
Matches: 194, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
237 1 0.01
238 70 0.36
239 31 0.16
240 1 0.01
241 1 0.01
242 89 0.46
243 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (239 bp):
GATCTAGCAGAATACACATCAATTCGAGCTTGTTGAAACCTTGAATAGATATGTTTGATCTTCAA
AAAGCAAGCTCTGTACACGTTGGACTTGGATCAACTCAATTTTGCTCCTACATGGTCTTCTAAGC
CAACCACCATGTGATTTGTCGGTAGAATGTTGGACTCCTAGTCCCGAGATTATACCCTGGCAATT
TCAATAGAACCGAAAATGTCTTACTTTGAGTAGTGTGACCAGTT
Found at i:47888 original size:44 final size:44
Alignment explanation
Indices: 47834--47967 Score: 200
Period size: 44 Copynumber: 3.1 Consensus size: 44
47824 AATTTTGATT
* *
47834 CTATCCGTGTTTGTTACTATCTTTATTTTATGATTTCGATTCGA
1 CTATCCGTGTTTGTTACGATCATTATTTTATGATTTCGATTCGA
* * *
47878 CTATCCGTGTTTGTCACGAACATTATTTTATGATTTTGATT--A
1 CTATCCGTGTTTGTTACGATCATTATTTTATGATTTCGATTCGA
*
47920 CTATCCGTGTTTGTTACGATCATTATTTTAGGATTTCGATTCGA
1 CTATCCGTGTTTGTTACGATCATTATTTTATGATTTCGATTCGA
47964 CTAT
1 CTAT
47968 GGAAGTATCG
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
42 38 0.48
44 41 0.52
ACGTcount: A:0.21, C:0.16, G:0.15, T:0.49
Consensus pattern (44 bp):
CTATCCGTGTTTGTTACGATCATTATTTTATGATTTCGATTCGA
Found at i:47944 original size:42 final size:42
Alignment explanation
Indices: 47818--47960 Score: 189
Period size: 42 Copynumber: 3.4 Consensus size: 42
47808 ATGATCTCGG
* * * *
47818 TTTTATAATTTTGATT-CTATCCGTGTTTGTTACTATCTTTA
1 TTTTATGATTTCGATTACTATCCGTGTTTGTTACGATCATTA
* *
47859 TTTTATGATTTCGATTCGACTATCCGTGTTTGTCACGAACATTA
1 TTTTATGATTTCGATT--ACTATCCGTGTTTGTTACGATCATTA
*
47903 TTTTATGATTTTGATTACTATCCGTGTTTGTTACGATCATTA
1 TTTTATGATTTCGATTACTATCCGTGTTTGTTACGATCATTA
*
47945 TTTTAGGATTTCGATT
1 TTTTATGATTTCGATT
47961 CGACTATGGA
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
41 14 0.16
42 38 0.43
44 36 0.41
ACGTcount: A:0.21, C:0.13, G:0.14, T:0.52
Consensus pattern (42 bp):
TTTTATGATTTCGATTACTATCCGTGTTTGTTACGATCATTA
Found at i:51531 original size:38 final size:38
Alignment explanation
Indices: 51480--51553 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
51470 CGTTATTGAG
* * * *
51480 TTATTTCATAAATGAAATGACAATCAACTTTGATATGT
1 TTATCTCACAAATGAAATAACAATCAACTTTAATATGT
* *
51518 TTATCTCACAAATGAATTAACAATCGACTTTAATAT
1 TTATCTCACAAATGAAATAACAATCAACTTTAATAT
51554 ATTTCGATTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38
Consensus pattern (38 bp):
TTATCTCACAAATGAAATAACAATCAACTTTAATATGT
Found at i:53981 original size:38 final size:38
Alignment explanation
Indices: 53930--54003 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
53920 CGTTATTGAG
* * * *
53930 TTATTTCATAAATGAAATGACAATCAACTTTGATATGT
1 TTATCTCACAAATGAAATAACAATCAACTTTAATATGT
* *
53968 TTATCTCACAAATGAATTAACAATCGACTTTAATAT
1 TTATCTCACAAATGAAATAACAATCAACTTTAATAT
54004 ATTTCGATTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38
Consensus pattern (38 bp):
TTATCTCACAAATGAAATAACAATCAACTTTAATATGT
Found at i:54826 original size:21 final size:21
Alignment explanation
Indices: 54787--54826 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
54777 ACGCGTTTAA
**
54787 TACCTAAACTATCCGTTTTGG
1 TACCTAAACTATCAATTTTGG
*
54808 TACCTAAACTTTCAATTTT
1 TACCTAAACTATCAATTTT
54827 TTCAAAACCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.42
Consensus pattern (21 bp):
TACCTAAACTATCAATTTTGG
Found at i:56322 original size:30 final size:31
Alignment explanation
Indices: 56270--56346 Score: 120
Period size: 30 Copynumber: 2.5 Consensus size: 31
56260 AAAAATTAAA
*
56270 AGTTTAGGTACTAAAATTGAGTAAATTTGAT
1 AGTTTAGGTACTAAAATGGAGTAAATTTGAT
56301 AGTTTAGGTACTAAAA-GGAGTAAATTTGAT
1 AGTTTAGGTACTAAAATGGAGTAAATTTGAT
*
56331 AGTTTGGGTACATAAA
1 AGTTTAGGTAC-TAAA
56347 GGCACGGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 23 0.53
31 20 0.47
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (31 bp):
AGTTTAGGTACTAAAATGGAGTAAATTTGAT
Found at i:56622 original size:23 final size:23
Alignment explanation
Indices: 56596--56706 Score: 80
Period size: 23 Copynumber: 5.2 Consensus size: 23
56586 ACACAATAAT
56596 AACACTGGGAATCATTACATTGA
1 AACACTGGGAATCATTACATTGA
* * *
56619 AACA-T---AATCA-CACAATAA
1 AACACTGGGAATCATTACATTGA
56637 TAACACTGGGAATCATTACATTGA
1 -AACACTGGGAATCATTACATTGA
* * *
56661 AACA-T---AATCA-CACAATAA
1 AACACTGGGAATCATTACATTGA
56679 TAACACTGGGAATCATTACATTGA
1 -AACACTGGGAATCATTACATTGA
56703 AACA
1 AACA
56707 TAATCACACA
Statistics
Matches: 64, Mismatches: 12, Indels: 24
0.64 0.12 0.24
Matches are distributed among these distances:
18 10 0.16
19 18 0.28
20 2 0.03
22 2 0.03
23 22 0.34
24 10 0.16
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.23
Consensus pattern (23 bp):
AACACTGGGAATCATTACATTGA
Found at i:56629 original size:42 final size:42
Alignment explanation
Indices: 56570--56717 Score: 287
Period size: 42 Copynumber: 3.5 Consensus size: 42
56560 TCTTAAATTG
*
56570 ACATTCAAACATAATCACACAATAATAACACTGGGAATCATT
1 ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
56612 ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
1 ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
56654 ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
1 ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
56696 ACATTGAAACATAATCACACAA
1 ACATTGAAACATAATCACACAA
56718 ATCCATTAAT
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 105 1.00
ACGTcount: A:0.49, C:0.20, G:0.08, T:0.23
Consensus pattern (42 bp):
ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
Found at i:56641 original size:19 final size:19
Alignment explanation
Indices: 56577--56683 Score: 56
Period size: 19 Copynumber: 5.2 Consensus size: 19
56567 TTGACATTCA
56577 AACATAATCACACAATAAT
1 AACATAATCACACAATAAT
* * *
56596 AACACTGGGAATCATTACATTGA-
1 AACA-T---AATCA-CACAATAAT
56619 AACATAATCACACAATAAT
1 AACATAATCACACAATAAT
* * *
56638 AACACTGGGAATCATTACATTGA-
1 AACA-T---AATCA-CACAATAAT
56661 AACATAATCACACAATAAT
1 AACATAATCACACAATAAT
56680 AACA
1 AACA
56684 CTGGGAATCA
Statistics
Matches: 64, Mismatches: 12, Indels: 24
0.64 0.12 0.24
Matches are distributed among these distances:
18 10 0.16
19 22 0.34
20 2 0.03
22 2 0.03
23 18 0.28
24 10 0.16
ACGTcount: A:0.50, C:0.20, G:0.07, T:0.22
Consensus pattern (19 bp):
AACATAATCACACAATAAT
Found at i:59240 original size:24 final size:23
Alignment explanation
Indices: 59211--59264 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
59201 TCAATTATAA
*
59211 TTACAAATATCTTAAAGTGTAAAT
1 TTACAAATATCTTAAAGAGT-AAT
59235 TTACAAATATCTTAAAGAGTAAT
1 TTACAAATATCTTAAAGAGTAAT
*
59258 TAACAAA
1 TTACAAA
59265 GGAATTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.33
Consensus pattern (23 bp):
TTACAAATATCTTAAAGAGTAAT
Found at i:60011 original size:23 final size:23
Alignment explanation
Indices: 59977--60021 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
59967 TTTCAATAAG
* *
59977 TCTACCTGTATGAGACGTTTTCA
1 TCTACCTGTATGACACATTTTCA
*
60000 TCTACCTTTATGACACATTTTC
1 TCTACCTGTATGACACATTTTC
60022 TCATGTCTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.42
Consensus pattern (23 bp):
TCTACCTGTATGACACATTTTCA
Found at i:62545 original size:12 final size:12
Alignment explanation
Indices: 62528--62553 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
62518 ATTAATAGAC
62528 GGGCTGGGACTA
1 GGGCTGGGACTA
62540 GGGCTGGGACTA
1 GGGCTGGGACTA
62552 GG
1 GG
62554 ATTAGGGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.54, T:0.15
Consensus pattern (12 bp):
GGGCTGGGACTA
Found at i:63255 original size:23 final size:26
Alignment explanation
Indices: 63208--63270 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 26
63198 GAAATTATTG
*
63208 TAAATAATATAATATTATTTAATTAA
1 TAAATAATATAATATTATATAATTAA
63234 TAAATAATAT-AT-TTATAT-ATTAA
1 TAAATAATATAATATTATATAATTAA
*
63257 -AAAGTAATAAAATA
1 TAAA-TAATATAATA
63271 ACTCGTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 3 0.09
23 10 0.31
24 7 0.22
25 2 0.06
26 10 0.31
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
TAAATAATATAATATTATATAATTAA
Found at i:63492 original size:17 final size:18
Alignment explanation
Indices: 63460--63493 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
63450 TTCATGGCAC
63460 TTTAATAATATAATTAAA
1 TTTAATAATATAATTAAA
*
63478 TTTAA-AATTTAATTAA
1 TTTAATAATATAATTAA
63494 GGAGAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAATAATATAATTAAA
Found at i:65516 original size:13 final size:13
Alignment explanation
Indices: 65498--65523 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
65488 GACCTACAAT
65498 GATTTGTGTAGGC
1 GATTTGTGTAGGC
65511 GATTTGTGTAGGC
1 GATTTGTGTAGGC
65524 CTGTGGCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.38, T:0.38
Consensus pattern (13 bp):
GATTTGTGTAGGC
Found at i:70061 original size:24 final size:24
Alignment explanation
Indices: 70033--70082 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
70023 ACTGCAATGC
* *
70033 GAAGAACATGTTACTGGACGGATT
1 GAAGAACATGTTACAGGACAGATT
*
70057 GAAGAACATGTTGCAGGACAGATT
1 GAAGAACATGTTACAGGACAGATT
70081 GA
1 GA
70083 TTTCGATCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (24 bp):
GAAGAACATGTTACAGGACAGATT
Found at i:71985 original size:37 final size:37
Alignment explanation
Indices: 71934--72009 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
71924 ATAAAAATTC
*
71934 AAGGTTTTGACATGAAACACAGAATACTCGAGTGCTG
1 AAGGTTTTGACATGAAACACAAAATACTCGAGTGCTG
* *
71971 AAGGTTTTGTCATGAAACTCAAAATACTCGAGTGCTG
1 AAGGTTTTGACATGAAACACAAAATACTCGAGTGCTG
72008 AA
1 AA
72010 AAGTATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (37 bp):
AAGGTTTTGACATGAAACACAAAATACTCGAGTGCTG
Found at i:76006 original size:20 final size:20
Alignment explanation
Indices: 75983--76027 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
75973 AATTAGCGTT
* *
75983 GCGAAAATGAAATTTGCAAC
1 GCGAAAATCAAATTCGCAAC
*
76003 GCGAAAGTCAAATTCGCAAC
1 GCGAAAATCAAATTCGCAAC
76023 GCGAA
1 GCGAA
76028 TAGTTAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (20 bp):
GCGAAAATCAAATTCGCAAC
Found at i:76007 original size:48 final size:46
Alignment explanation
Indices: 75912--76007 Score: 104
Period size: 48 Copynumber: 2.0 Consensus size: 46
75902 GCGAATAGTT
* ****
75912 AATTACCTATAGGTAATTAGCGTTGTGAAATGAAATTCGGTTTGCG
1 AATTACCTATAGGTAATTAGCGTTGCGAAATGAAATTCGCAACGCG
*
75958 AATTACCTAAATA-GTAATTAGCGTTGCGAAAATGAAATTTGCAACGCG
1 AATTACCT--ATAGGTAATTAGCGTTGCG-AAATGAAATTCGCAACGCG
76006 AA
1 AA
76008 AGTCAAATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
46 8 0.20
47 14 0.34
48 19 0.46
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (46 bp):
AATTACCTATAGGTAATTAGCGTTGCGAAATGAAATTCGCAACGCG
Found at i:76132 original size:40 final size:39
Alignment explanation
Indices: 76088--76182 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 39
76078 GCGAAAGTCA
* *
76088 AATTCGC-TCGCGAATAGTTTAAATCGCAACGATAATATGT
1 AATTCGCAACGCGAATAG-GTAAATCGCAACGATAATA-GT
*
76128 AATTCTCAACGCGAATAGGTAAATCGCAACGATAATAGT
1 AATTCGCAACGCGAATAGGTAAATCGCAACGATAATAGT
*
76167 AAATCGCAACGCGAAT
1 AATTCGCAACGCGAAT
76183 TCTCCAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
39 16 0.33
40 24 0.49
41 9 0.18
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (39 bp):
AATTCGCAACGCGAATAGGTAAATCGCAACGATAATAGT
Found at i:76144 original size:20 final size:19
Alignment explanation
Indices: 76071--76182 Score: 93
Period size: 20 Copynumber: 5.7 Consensus size: 19
76061 AAAATGAAAT
76071 TCGCAACGCGAA-AGTCAAA
1 TCGCAACGCGAATAGT-AAA
*
76090 TTCGC-TCGCGAATAGTTTAAA
1 -TCGCAACGCGAATAG--TAAA
** *
76111 TCGCAACGATAATATGTAAT
1 TCGCAACGCGAATA-GTAAA
*
76131 TCTCAACGCGAATAGGTAAA
1 TCGCAACGCGAATA-GTAAA
**
76151 TCGCAACGATAATAGTAAA
1 TCGCAACGCGAATAGTAAA
76170 TCGCAACGCGAAT
1 TCGCAACGCGAAT
76183 TCTCCAAATT
Statistics
Matches: 72, Mismatches: 15, Indels: 11
0.73 0.15 0.11
Matches are distributed among these distances:
19 22 0.31
20 39 0.54
21 9 0.12
22 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (19 bp):
TCGCAACGCGAATAGTAAA
Found at i:76508 original size:20 final size:20
Alignment explanation
Indices: 76482--76533 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
76472 TGGAGAATTC
76482 GCGTTGCGATTTATA-TATTA
1 GCGTTGCGATTTA-ACTATTA
* *
76502 TCGTTGCGATTTAACTATTC
1 GCGTTGCGATTTAACTATTA
76522 GCGTTGCGATTT
1 GCGTTGCGATTT
76534 TGGAACCTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.44
Consensus pattern (20 bp):
GCGTTGCGATTTAACTATTA
Done.