Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003792.1 Hibiscus syriacus cultivar Beakdansim tig00008115_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: 64423
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:185 original size:15 final size:16
Alignment explanation
Indices: 165--197 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
155 ACACAGTTAT
*
165 ATAATA-AATTTTAAA
1 ATAATATAATTGTAAA
180 ATAATATAATTGTAAA
1 ATAATATAATTGTAAA
196 AT
1 AT
198 TGAAGAGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
ATAATATAATTGTAAA
Found at i:8620 original size:17 final size:17
Alignment explanation
Indices: 8586--8629 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
8576 GTCCTTAGGA
*
8586 AGCTAGTTAGGTCACTT
1 AGCTAGCTAGGTCACTT
8603 AGCTAGCTAGGT-ATCTT
1 AGCTAGCTAGGTCA-CTT
*
8620 AGGTAGCTAG
1 AGCTAGCTAG
8630 CTAGGTAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (17 bp):
AGCTAGCTAGGTCACTT
Found at i:8626 original size:21 final size:21
Alignment explanation
Indices: 8602--8657 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
8592 TTAGGTCACT
*
8602 TAGCTAGCTAGGTA-TCTTAGG
1 TAGCTAGCTAGGTAGT-GTAGG
*
8623 TAGCTAGCTAGGTAGTGTATG
1 TAGCTAGCTAGGTAGTGTAGG
8644 TAGCTAGCTAGGTA
1 TAGCTAGCTAGGTA
8658 CCTAGTGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.30, T:0.32
Consensus pattern (21 bp):
TAGCTAGCTAGGTAGTGTAGG
Found at i:9385 original size:23 final size:23
Alignment explanation
Indices: 9336--9387 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
9326 GAAGTGCCAC
*
9336 GTAGAATTGTCCCGAAGGATCGA
1 GTAGAATTGTCCCGAAGGATCCA
9359 GTAGAATTGTCCCGAAGGA-CCA
1 GTAGAATTGTCCCGAAGGATCCA
9381 TGTAGAA
1 -GTAGAA
9388 CCCTCGACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 2 0.07
23 25 0.93
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (23 bp):
GTAGAATTGTCCCGAAGGATCCA
Found at i:9922 original size:22 final size:22
Alignment explanation
Indices: 9897--9972 Score: 143
Period size: 22 Copynumber: 3.5 Consensus size: 22
9887 TCTACACCCA
9897 GTACCGATACTTCCCTTCTATG
1 GTACCGATACTTCCCTTCTATG
*
9919 GTACCAATACTTCCCTTCTATG
1 GTACCGATACTTCCCTTCTATG
9941 GTACCGATACTTCCCTTCTATG
1 GTACCGATACTTCCCTTCTATG
9963 GTACCGATAC
1 GTACCGATAC
9973 CTACCTCAGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (22 bp):
GTACCGATACTTCCCTTCTATG
Found at i:23796 original size:16 final size:16
Alignment explanation
Indices: 23775--23814 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
23765 AATACATGCC
23775 AACAAAACTTCAAAAT
1 AACAAAACTTCAAAAT
23791 AACAAAACTTCAAAAT
1 AACAAAACTTCAAAAT
23807 AACAAAAC
1 AACAAAAC
23815 CACCTACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.65, C:0.20, G:0.00, T:0.15
Consensus pattern (16 bp):
AACAAAACTTCAAAAT
Found at i:24207 original size:23 final size:23
Alignment explanation
Indices: 24181--24233 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
24171 CTAAGTGCCA
* *
24181 CGTAGATTTGTCCCGAAGGATCG
1 CGTAGAATTATCCCGAAGGATCG
*
24204 CGTAGAATTATCCCGAATGATCG
1 CGTAGAATTATCCCGAAGGATCG
24227 CGTAGAA
1 CGTAGAA
24234 CCCTCGAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (23 bp):
CGTAGAATTATCCCGAAGGATCG
Found at i:24400 original size:19 final size:20
Alignment explanation
Indices: 24373--24414 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
24363 ATGCTTATAA
* *
24373 AATACAATTTAA-GTAAAAT
1 AATAAAATTTAACATAAAAT
24392 AATAAAATTTAACATAAAAT
1 AATAAAATTTAACATAAAAT
24412 AAT
1 AAT
24415 TCAAATAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (20 bp):
AATAAAATTTAACATAAAAT
Found at i:29660 original size:24 final size:24
Alignment explanation
Indices: 29633--29698 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
29623 ACCTATGTGA
*
29633 TCCTTAGGGATAT-TTCTACGTGG
1 TCCTTAGGGAAATATTCTACGTGG
*
29656 TTCCTCA-GGAAATATTCTACGTGG
1 -TCCTTAGGGAAATATTCTACGTGG
*
29680 TCCTTCGGGACAA-ATTCTA
1 TCCTTAGGGA-AATATTCTA
29699 TGTGACACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 9 0.26
24 24 0.69
25 2 0.06
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (24 bp):
TCCTTAGGGAAATATTCTACGTGG
Found at i:30784 original size:21 final size:21
Alignment explanation
Indices: 30760--30801 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
30750 ACTTCAAGTT
30760 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
30781 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
30802 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:33834 original size:9 final size:9
Alignment explanation
Indices: 33820--33875 Score: 58
Period size: 10 Copynumber: 5.8 Consensus size: 9
33810 GGCTGCTGGA
33820 AACCGGTTT
1 AACCGGTTT
33829 AACCGGTTTT
1 AACCGG-TTT
33839 CAACCGGTTCT
1 -AACCGGTT-T
*
33850 GACCGGTTT
1 AACCGGTTT
33859 CAACCGGTTT
1 -AACCGGTTT
*
33869 GACCGGT
1 AACCGGT
33876 CTGACCCGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 13 0.32
10 20 0.50
11 7 0.17
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:33845 original size:20 final size:20
Alignment explanation
Indices: 33820--33875 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
33810 GGCTGCTGGA
*
33820 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTGACCGGTTTTC
33840 AACCGGTTCTGACCGG-TTTC
1 AACCGGTT-TGACCGGTTTTC
33860 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
33876 CTGACCCGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 7 0.21
20 20 0.61
21 6 0.18
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTTTC
Found at i:33914 original size:22 final size:22
Alignment explanation
Indices: 33889--33950 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
33879 ACCCGACCGA
33889 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
33911 CCGA--C--CCC-ACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
*
33928 CCGACCCGACCGGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
33950 C
1 C
33951 GTTGACTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
17 13 0.38
18 3 0.09
19 1 0.03
20 1 0.03
21 2 0.06
22 14 0.41
ACGTcount: A:0.18, C:0.50, G:0.23, T:0.10
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:33950 original size:17 final size:17
Alignment explanation
Indices: 33891--33939 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
33881 CCGACCGACC
33891 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
*
33908 GACCCGACCCCACCGTT
1 GACCCGACCCGACCGTT
33925 GACCCGACCCGACCG
1 GACCCGACCCGACCG
33940 GACCGTTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.18, C:0.51, G:0.22, T:0.08
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:38948 original size:30 final size:30
Alignment explanation
Indices: 38905--38972 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
38895 TTAAAAATAT
38905 GTGCCTAATATTTTATCCGTTACACTTTTAG
1 GTGCCT-ATATTTTATCCGTTACACTTTTAG
* *
38936 GTGCCTATATTTTATTCGTTATACTTTTAG
1 GTGCCTATATTTTATCCGTTACACTTTTAG
*
38966 GTACCTA
1 GTGCCTA
38973 CGCAATAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 28 0.82
31 6 0.18
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (30 bp):
GTGCCTATATTTTATCCGTTACACTTTTAG
Found at i:40559 original size:60 final size:61
Alignment explanation
Indices: 40452--40566 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 61
40442 AAATAATCTA
* * * * *
40452 TTAATTATATGATATTATTTTATTGAATTTTTTTATCTATTGAAAGTTATAAAATGATTTT
1 TTAATTATAAGATATTATTTTATTGAATTATGTGATCTATTAAAAGTTATAAAATGATTTT
* * *
40513 TTAATTATAAGATGTTATTTTTTTTAATTATGTGA-CTATTAAAAGTTATAAAAT
1 TTAATTATAAGATATTATTTTATTGAATTATGTGATCTATTAAAAGTTATAAAAT
40567 AGTCATCTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
60 18 0.39
61 28 0.61
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.53
Consensus pattern (61 bp):
TTAATTATAAGATATTATTTTATTGAATTATGTGATCTATTAAAAGTTATAAAATGATTTT
Found at i:46818 original size:7 final size:7
Alignment explanation
Indices: 46789--46840 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
46779 ATTTGTAATG
46789 AACCCTA
1 AACCCTA
46796 AA-CCTA
1 AACCCTA
*
46802 AA-CATAA
1 AACCCT-A
46809 AACCCTA
1 AACCCTA
46816 AACCCTA
1 AACCCTA
**
46823 AATACTA
1 AACCCTA
46830 AACCCTA
1 AACCCTA
46837 AACC
1 AACC
46841 TAATTATATG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
6 8 0.22
7 27 0.73
8 2 0.05
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (7 bp):
AACCCTA
Found at i:46824 original size:21 final size:21
Alignment explanation
Indices: 46789--46840 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
46779 ATTTGTAATG
46789 AACCCTAAA-CCTAAACA-TAA
1 AACCCTAAACCCTAAACACT-A
*
46809 AACCCTAAACCCTAAATACTA
1 AACCCTAAACCCTAAACACTA
46830 AACCCTAAACC
1 AACCCTAAACC
46841 TAATTATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 9 0.31
21 19 0.66
22 1 0.03
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (21 bp):
AACCCTAAACCCTAAACACTA
Found at i:49461 original size:24 final size:24
Alignment explanation
Indices: 49403--49469 Score: 91
Period size: 23 Copynumber: 2.8 Consensus size: 24
49393 TTAACCCCAC
*
49403 CTCGAGCTTGAATCGAGCTCAAAT
1 CTCGAGCTTCAATCGAGCTCAAAT
* * *
49427 -TTGAGCTTCAATCGAGCTCGAGT
1 CTCGAGCTTCAATCGAGCTCAAAT
49450 CTCGAGCTTCAATCGAGCTC
1 CTCGAGCTTCAATCGAGCTC
49470 CTGAAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 19 0.51
24 18 0.49
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (24 bp):
CTCGAGCTTCAATCGAGCTCAAAT
Found at i:52135 original size:21 final size:21
Alignment explanation
Indices: 52078--52183 Score: 53
Period size: 21 Copynumber: 5.3 Consensus size: 21
52068 TATAATAAAA
** *
52078 TATTAATTATAATAATTAAAT
1 TATTAATTATAATTCTTATAT
* * *
52099 TAATAAATAT-A-T-TTATTT
1 TATTAATTATAATTCTTATAT
52117 TATTAATTATAATTCTTATAT
1 TATTAATTATAATTCTTATAT
* * * *
52138 TATGATTTATAAATCTT-TAA
1 TATTAATTATAATTCTTATAT
* *
52158 TA-TAATCATTAATT-TTATTT
1 TATTAATTA-TAATTCTTATAT
52178 TATTAA
1 TATTAA
52184 GTAATTTATG
Statistics
Matches: 61, Mismatches: 18, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
18 12 0.20
19 6 0.10
20 13 0.21
21 30 0.49
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (21 bp):
TATTAATTATAATTCTTATAT
Found at i:52316 original size:18 final size:18
Alignment explanation
Indices: 52293--52377 Score: 88
Period size: 18 Copynumber: 4.9 Consensus size: 18
52283 ATTAATGAAT
52293 TATATAATATATAGTTTA
1 TATATAATATATAGTTTA
* *
52311 TATATACTATATAATTTA
1 TATATAATATATAGTTTA
* *
52329 TATATAGTA-AT-G--AA
1 TATATAATATATAGTTTA
52343 CTATATAATATATAGTTTA
1 -TATATAATATATAGTTTA
*
52362 TATATACTATATAGTT
1 TATATAATATATAGTT
52378 AGAATAAATT
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
14 1 0.02
15 8 0.15
16 2 0.04
17 3 0.06
18 39 0.72
19 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (18 bp):
TATATAATATATAGTTTA
Found at i:52399 original size:51 final size:51
Alignment explanation
Indices: 52285--52385 Score: 150
Period size: 51 Copynumber: 2.0 Consensus size: 51
52275 CATTTAAAAT
* * * *
52285 TAATGAATTATATAATATATAGTTTATATATACTATATAATTTATATATAG
1 TAATGAACTATATAATATATAGTTTATATATACTATATAAGTTAAATAAAG
52336 TAATGAACTATATAATATATAGTTTATATATACTATAT-AGTTAGAATAAA
1 TAATGAACTATATAATATATAGTTTATATATACTATATAAGTTA-AATAAA
52386 TTTATTTTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 4 0.09
51 41 0.91
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.44
Consensus pattern (51 bp):
TAATGAACTATATAATATATAGTTTATATATACTATATAAGTTAAATAAAG
Found at i:54180 original size:18 final size:18
Alignment explanation
Indices: 54127--54460 Score: 250
Period size: 18 Copynumber: 20.2 Consensus size: 18
54117 ATTATTAATT
54127 TATACTAT-TAGTTTATA
1 TATACTATATAGTTTATA
*
54144 TATACTA-AT-G--AACTA
1 TATACTATATAGTTTA-TA
*
54159 TATAATATATAGTTTATA
1 TATACTATATAGTTTATA
54177 TATACTATATAGTTTATA
1 TATACTATATAGTTTATA
54195 TATACTA-AT-G---A-A
1 TATACTATATAGTTTATA
*
54207 TATA-TATATAGTTTGTA
1 TATACTATATAGTTTATA
*
54224 TATACCATATAGTTTATA
1 TATACTATATAGTTTATA
54242 TAT--TATATAGTTTATA
1 TATACTATATAGTTTATA
*
54258 TATACTA-AT-G--AACTA
1 TATACTATATAGTTTA-TA
* * *
54273 TATAATATGTAGTTTTTA
1 TATACTATATAGTTTATA
*
54291 TATAC--CATAGTTTATA
1 TATACTATATAGTTTATA
*
54307 TATACTA-AT-G--AACTA
1 TATACTATATAGTTTA-TA
54322 TATA--ATATAG-TT-TA
1 TATACTATATAGTTTATA
*
54336 TATACCATATAGTTTATA
1 TATACTATATAGTTTATA
*
54354 TATACTA-AT-G--AACTA
1 TATACTATATAGTTTA-TA
* *
54369 TATAATATATAATTTATA
1 TATACTATATAGTTTATA
*
54387 TATACTATATAGTTTATG
1 TATACTATATAGTTTATA
54405 TATACTATATAG-TT-TA
1 TATACTATATAGTTTATA
54421 TATACTATATAGTTTATA
1 TATACTATATAGTTTATA
*
54439 TAAACTATATAGTTTATA
1 TATACTATATAGTTTATA
54457 TATA
1 TATA
54461 TACGCTAAAT
Statistics
Matches: 250, Mismatches: 30, Indels: 73
0.71 0.08 0.21
Matches are distributed among these distances:
11 2 0.01
12 7 0.03
13 3 0.01
14 12 0.05
15 31 0.12
16 57 0.23
17 29 0.12
18 107 0.43
19 2 0.01
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (18 bp):
TATACTATATAGTTTATA
Found at i:54234 original size:47 final size:50
Alignment explanation
Indices: 54127--54244 Score: 181
Period size: 47 Copynumber: 2.4 Consensus size: 50
54117 ATTATTAATT
54127 TATACTAT-TAGTTTATATATACTAATGAACTATATAATATATAGTTTATA
1 TATACTATATAGTTTATATATACTAATGAAC-ATATAATATATAGTTTATA
*
54177 TATACTATATAGTTTATATATACTAATG-A-ATAT-ATATATAGTTTGTA
1 TATACTATATAGTTTATATATACTAATGAACATATAATATATAGTTTATA
*
54224 TATACCATATAGTTTATATAT
1 TATACTATATAGTTTATATAT
54245 TATATAGTTT
Statistics
Matches: 65, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
47 33 0.51
48 4 0.06
50 9 0.14
51 19 0.29
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.47
Consensus pattern (50 bp):
TATACTATATAGTTTATATATACTAATGAACATATAATATATAGTTTATA
Found at i:54258 original size:47 final size:46
Alignment explanation
Indices: 54175--54462 Score: 199
Period size: 47 Copynumber: 5.9 Consensus size: 46
54165 ATATAGTTTA
** * *
54175 TATATACTATATAGTTTATATATACTA-A-TGAATATATATATAGTTTG
1 TATATACTATATAGTTTATATATA-TATAGTTTATATATATAT-G-ATC
* *
54222 TATATACCATATAGTTTATATATTATATAGTTTATATATACTAATGAAC
1 TATATACTATATAGTTTATATA-TATATAGTTTATATATA-T-ATGATC
* * * * *
54271 TATATAATATGTAGTTTTTATATACCATAGTTTATATATACTAATGAAC
1 TATATACTATATAGTTTATATATA-TATAGTTTATATATA-T-ATGATC
* *
54320 TATATA--ATATAGTTTATATACCATATAGTTTATATATACTAATGAAC
1 TATATACTATATAGTTTATATA-TATATAGTTTATATATA-T-ATGATC
* * *
54367 TATATAATATATAATTTATATATACTATATAGTTTATGTATACTATAT-AGTT
1 TATATACTATAT-AGTT-TATATA-TATATAGTTTA--TATA-TATATGA-TC
54419 TATATACTATATAGTTTATATAAACTATATAGTTTATATATATA
1 TATATACTATATAGTTTATAT--A-TATATAGTTTATATATATA
54463 CGCTAAATAG
Statistics
Matches: 203, Mismatches: 21, Indels: 32
0.79 0.08 0.12
Matches are distributed among these distances:
47 64 0.32
48 6 0.03
49 63 0.31
50 14 0.07
51 23 0.11
52 26 0.13
53 5 0.02
54 2 0.01
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (46 bp):
TATATACTATATAGTTTATATATATATAGTTTATATATATATGATC
Found at i:54261 original size:114 final size:113
Alignment explanation
Indices: 54127--54424 Score: 385
Period size: 114 Copynumber: 2.6 Consensus size: 113
54117 ATTATTAATT
54127 TATACTAT-TAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTATATAGTT
1 TATA-TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTATATAGTT
54191 TATATATACTAATGAA-TATAT-ATATAGTTTGTATATACCATATAGTTTA
65 TATATATACTAATGAACTATATAATATAG-TT-TATATACCATATAGTTTA
* * *
54240 TATATTATATAGTTTATATATACTAATGAACTATATAATATGTAGTTTTTATATAC--CATAGTT
1 TATA-TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTATATAGTT
54303 TATATATACTAATGAACTATATAATATAGTTTATATACCATATAGTTTA
65 TATATATACTAATGAACTATATAATATAGTTTATATACCATATAGTTTA
* * ** * *
54352 TATATACTAATGAACTATATAATATA-TAATTTA-TATATACTATATAGTTTATGTATACTATAT
1 TATATA-T-AT--AGTTTAT-ATATACTAATGAACTATATAATATATAGTTTATATATACTATAT
54415 AGTTTATATA
61 AGTTTATATA
54425 CTATATAGTT
Statistics
Matches: 162, Mismatches: 13, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
111 2 0.01
112 45 0.28
113 16 0.10
114 72 0.44
115 10 0.06
116 17 0.10
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (113 bp):
TATATATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTATATAGTTT
ATATATACTAATGAACTATATAATATAGTTTATATACCATATAGTTTA
Found at i:54287 original size:96 final size:96
Alignment explanation
Indices: 54175--54460 Score: 310
Period size: 96 Copynumber: 2.9 Consensus size: 96
54165 ATATAGTTTA
* * *
54175 TATATACTATATAGTTTATATATACTAATGAATATATATATAGTTTGTATATACCATATAGTTTA
1 TATATAATATATAGTTTATATATACTAATGAGTATATATATAGTTTGTATATACAATATAGTTTA
*
54240 TATATTATATAGTTTATATATACTAATGAAC
66 TATACTATATAGTTTATATATACTAATGAAC
* * * * * * * *
54271 TATATAATATGTAGTTTTTATATAC-CAT-AGTTTATATATACTAATGAACTATATAATATAGTT
1 TATATAATATATAGTTTATATATACTAATGAGTATATATATAGT-TTGTA-TATACAATATAGTT
*
54334 TATATACCATATAGTTTATATATACTAATGAAC
64 TATATACTATATAGTTTATATATACTAATGAAC
* *
54367 TATATAATATATAATTTATATATACTATATAGTTTATGTATACTATATAG-TT-TATATACTATA
1 TATATAATATATAGTTTATATATACTA-AT-G---A-GTATA-TATATAGTTTGTATATACAATA
54430 TAGTTTATATAAACTATATAGTTTATATATA
59 TAGTTTATAT--ACTATATAGTTTATATATA
54461 TACGCTAAAT
Statistics
Matches: 153, Mismatches: 24, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
94 11 0.07
95 5 0.03
96 87 0.57
98 2 0.01
101 17 0.11
102 1 0.01
103 20 0.13
104 4 0.03
105 6 0.04
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (96 bp):
TATATAATATATAGTTTATATATACTAATGAGTATATATATAGTTTGTATATACAATATAGTTTA
TATACTATATAGTTTATATATACTAATGAAC
Found at i:54372 original size:2 final size:2
Alignment explanation
Indices: 54367--54588 Score: 54
Period size: 2 Copynumber: 110.5 Consensus size: 2
54357 ACTAATGAAC
* * *
54367 TA TA TA -A TA TA TA -A TT TA TA TA TA CTA TA TA GTT TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
* * * *
54409 CTA TA TA GTT TA TA TA CTA TA TA GTT TA TA TA AA CTA TA TA GTT
1 -TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA -TA TA TA -TA
** * * * *
54453 TA TA TA TA TA CGC TA AA TA GTT TA TA TA CA -A TA TA -A AA T- TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
54494 TA AA TA TA AA CTA TA TA CA T- TA TA TA -A AA CTA TA AA TA TA AA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
54536 CTA TA TA TG T- TA TA TA TG T- TA TA TA TA TA TA TA TA TA T- TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54576 -A TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA T
54589 TTTTTAATTT
Statistics
Matches: 158, Mismatches: 37, Indels: 50
0.64 0.15 0.20
Matches are distributed among these distances:
1 12 0.08
2 131 0.83
3 15 0.09
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:54528 original size:32 final size:32
Alignment explanation
Indices: 54475--54551 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 32
54465 CTAAATAGTT
*
54475 TATATACA--ATATAAAATTATAAATATAAAC
1 TATATACATTATATAAAACTATAAATATAAAC
54505 TATATACATTATATAAAACTATAAATATAAAC
1 TATATACATTATATAAAACTATAAATATAAAC
**
54537 TATATATGTTATATA
1 TATATACATTATATA
54552 TGTTATATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
30 8 0.19
32 34 0.81
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (32 bp):
TATATACATTATATAAAACTATAAATATAAAC
Found at i:54549 original size:9 final size:9
Alignment explanation
Indices: 54537--54588 Score: 70
Period size: 9 Copynumber: 5.8 Consensus size: 9
54527 AAATATAAAC
*
54537 TATATATGT
1 TATATATAT
*
54546 TATATATGT
1 TATATATAT
54555 TATATATAT
1 TATATATAT
54564 ATATATATAT
1 -TATATATAT
54574 TA-ATATAT
1 TATATATAT
54582 TATATAT
1 TATATAT
54589 TTTTTAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
8 8 0.20
9 23 0.57
10 9 0.22
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (9 bp):
TATATATAT
Found at i:56245 original size:108 final size:107
Alignment explanation
Indices: 56109--56618 Score: 595
Period size: 108 Copynumber: 4.8 Consensus size: 107
56099 TATTAATACG
* * ** * * *
56109 AGGTTGCACCTAATATGTTATGAGAGTTTAAGTTGATGGAGCCTTAGAAATCTCTCGATAACAAA
1 AGGTTACACCTAAAATGTTAACAAAGTTTAAGCTGATGGAGCCTTAGAAATCTCACGATAACAAA
*
56174 ATAGTTTAATTACTTATTTTATTATAAATATTATTAACATAAT
66 ATAG-TTAATTACTTATTTTATTATAAATATTATTAACATATT
* *
56217 AGGTTACACGTAAAATGTTAACAAAGTTTAAGCTGATGGAGGCTTAGAAAT-TCTACGATAA-AA
1 AGGTTACACCTAAAATGTTAACAAAGTTTAAGCTGATGGAGCCTTAGAAATCTC-ACGATAACAA
*
56280 AAAAGTTAATTACTTATTTTATTATAAATATTATTAACATATT
65 AATAGTTAATTACTTATTTTATTATAAATATTATTAACATATT
* * * * *
56323 AGGTTGCACCTAAAATGTTACCAAAGTTAAAGATGAT-GAGACATTAGAAATCTCAC-AGTAACA
1 AGGTTACACCTAAAATGTTAACAAAGTTTAAGCTGATGGAG-CCTTAGAAATCTCACGA-TAACA
* *
56386 AAATAAG-TAATTAACTTATTTTGTTATAAATTTTATTAACATATT
64 AAAT-AGTTAATT-ACTTATTTTATTATAAATATTATTAACATATT
** * * * * *
56431 AAATTGCGCCTAAAATGTTAACAGAGATTAAGCTGATGGGGCCTTAGAAATCTCACGATAAC-AA
1 AGGTTACACCTAAAATGTTAACAAAGTTTAAGCTGATGGAGCCTTAGAAATCTCACGATAACAAA
*
56495 A-AGTTAATTACTTATTTTGTTATAAATATTATTAACATATT
66 ATAGTTAATTACTTATTTTATTATAAATATTATTAACATATT
* * * *
56536 AGGCTACACCTAAAATGTTACCAAAGTTTAAGCTAATGGGGCCTTAGATAATC-CAACGATAACA
1 AGGTTACACCTAAAATGTTAACAAAGTTTAAGCTGATGGAGCCTTAGA-AATCTC-ACGATAACA
* *
56600 AAATAAATTAATTATTTAT
64 AAAT-AGTTAATTACTTAT
56619 AATGTTATGA
Statistics
Matches: 344, Mismatches: 43, Indels: 29
0.83 0.10 0.07
Matches are distributed among these distances:
105 77 0.22
106 99 0.29
107 25 0.07
108 128 0.37
109 15 0.04
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (107 bp):
AGGTTACACCTAAAATGTTAACAAAGTTTAAGCTGATGGAGCCTTAGAAATCTCACGATAACAAA
ATAGTTAATTACTTATTTTATTATAAATATTATTAACATATT
Found at i:56479 original size:214 final size:212
Alignment explanation
Indices: 56109--56618 Score: 618
Period size: 214 Copynumber: 2.4 Consensus size: 212
56099 TATTAATACG
* ** * * * * *
56109 AGGTTGCACCTAATATGTTATGAGAGTTTAAGTTGATGGAGCCTTAGAAATCTCTCGATAACAAA
1 AGGTTGCACCTAAAATGTTACCAAAGTTAAAGATGATGGAGCATTAGAAATCTCACGATAACAAA
** *
56174 ATAGTTTAATTACTTATTTTATTATAAATATTATTAACATAATAGGTTACACGTAAAATGTTAAC
66 ATAG-TTAATTACTTATTTTATTATAAATATTATTAACATAATAAATTACACCTAAAATGTTAAC
*
56239 AAAGTTTAAGCTGATGGAGGCTTAGAAAT-TCTACGATAAAAAAAAGTTAATTACTTATTTTATT
130 AAAGATTAAGCTGATGGAGGCTTAGAAATCTC-ACGAT-AAAAAAAGTTAATTACTTATTTTATT
56303 ATAAATATTATTAACATATT
193 ATAAATATTATTAACATATT
56323 AGGTTGCACCTAAAATGTTACCAAAGTTAAAGATGAT-GAGACATTAGAAATCTCAC-AGTAACA
1 AGGTTGCACCTAAAATGTTACCAAAGTTAAAGATGATGGAG-CATTAGAAATCTCACGA-TAACA
* * * * *
56386 AAATAAG-TAATTAACTTATTTTGTTATAAATTTTATTAACATATTAAATTGCGCCTAAAATGTT
64 AAAT-AGTTAATT-ACTTATTTTATTATAAATATTATTAACATAATAAATTACACCTAAAATGTT
* * *
56450 AACAGAGATTAAGCTGATGG-GGCCTTAGAAATCTCACGATAACAAAAGTTAATTACTTATTTTG
127 AACAAAGATTAAGCTGATGGAGG-CTTAGAAATCTCACGATAAAAAAAGTTAATTACTTATTTTA
56514 TTATAAATATTATTAACATATT
191 TTATAAATATTATTAACATATT
* * * * * * *
56536 AGGCTACACCTAAAATGTTACCAAAGTTTAAGCTAATGGGGCCTTAGATAATC-CAACGATAACA
1 AGGTTGCACCTAAAATGTTACCAAAGTTAAAGATGATGGAGCATTAGA-AATCTC-ACGATAACA
* *
56600 AAATAAATTAATTATTTAT
64 AAAT-AGTTAATTACTTAT
56619 AATGTTATGA
Statistics
Matches: 256, Mismatches: 29, Indels: 22
0.83 0.09 0.07
Matches are distributed among these distances:
213 94 0.37
214 152 0.59
215 10 0.04
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (212 bp):
AGGTTGCACCTAAAATGTTACCAAAGTTAAAGATGATGGAGCATTAGAAATCTCACGATAACAAA
ATAGTTAATTACTTATTTTATTATAAATATTATTAACATAATAAATTACACCTAAAATGTTAACA
AAGATTAAGCTGATGGAGGCTTAGAAATCTCACGATAAAAAAAGTTAATTACTTATTTTATTATA
AATATTATTAACATATT
Found at i:62988 original size:20 final size:20
Alignment explanation
Indices: 62907--62998 Score: 71
Period size: 20 Copynumber: 4.5 Consensus size: 20
62897 CTCTTTCTAG
*
62907 GTATCGATACTAC-TAGCATA
1 GTATCGATACTACTTA-AATA
*
62927 GTATCGATACTACTTGAATGA
1 GTATCGATACTACTTAAAT-A
* * *
62948 GTATTGATACT-GTTCATATA
1 GTATCGATACTACTT-AAATA
*
62968 GTACCGATACTACTTAAATA
1 GTATCGATACTACTTAAATA
*
62988 GGCATCGATAC
1 -GTATCGATAC
62999 CTATGTATCG
Statistics
Matches: 55, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
20 31 0.56
21 24 0.44
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (20 bp):
GTATCGATACTACTTAAATA
Found at i:63049 original size:18 final size:19
Alignment explanation
Indices: 63026--63063 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
63016 TCGAAATATG
*
63026 CCTTGA-AGTATCGATACT
1 CCTTGAGAGTACCGATACT
63044 CCTTGAGGAGTACCGATACT
1 CCTTGA-GAGTACCGATACT
63064 ACTCATCGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (19 bp):
CCTTGAGAGTACCGATACT
Done.