Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009522.1 Hibiscus syriacus cultivar Beakdansim tig00115799_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: 63537
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:4899 original size:24 final size:23
Alignment explanation
Indices: 4848--4892 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
4838 ACATGATTTG
*
4848 TCTGCTCTTGTGGTATGCGATTCC
1 TCTGCTCTTGTGGCA-GCGATTCC
4872 TCTGCTCTTGTGGCA-CGATTC
1 TCTGCTCTTGTGGCAGCGATTC
4893 TGCTCTGGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
24 14 0.70
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (23 bp):
TCTGCTCTTGTGGCAGCGATTCC
Found at i:6348 original size:39 final size:39
Alignment explanation
Indices: 6294--6384 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 39
6284 AAGGACCTAC
* *
6294 GGTAAGGACTTACCCTAAGCAAAAAACT-GAGGAGCTTGA
1 GGTAAGGACTTACCCTAAGC-AAAAACTCGAGAAGCTTAA
* * * *
6333 GGTAACGACTTACCCTGAGCACAAAGTCGAGAAGCTTAA
1 GGTAAGGACTTACCCTAAGCAAAAACTCGAGAAGCTTAA
6372 GGTAAGGACTTAC
1 GGTAAGGACTTAC
6385 AAGTTATAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 5 0.11
39 39 0.89
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (39 bp):
GGTAAGGACTTACCCTAAGCAAAAACTCGAGAAGCTTAA
Found at i:16377 original size:45 final size:45
Alignment explanation
Indices: 16313--16482 Score: 261
Period size: 45 Copynumber: 3.8 Consensus size: 45
16303 GTAACCATGC
* *
16313 AAATAAGCTTATGAGCTTATGGGATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
16358 AAATAAGCTTACGAGCTTATGGAATAAATGGCAAGTGTATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
16403 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
16448 AAATAAGTTTACGAGCTTATAGG-ATAAGTGGTAAG
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAG
16483 AAATTTTATA
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
45 113 0.98
46 2 0.02
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:18757 original size:45 final size:45
Alignment explanation
Indices: 18704--18822 Score: 166
Period size: 45 Copynumber: 2.6 Consensus size: 45
18694 TTATTTAGGG
* * *
18704 CATCCTTTCATGCTTTTAATGCACCTTTATGTATTTCATTTATGA
1 CATCCTTTCATGCCTTTAATGCACCGTTATGTATTTCATGTATGA
* * *
18749 CATTCTTTCATGCCTTTAATGCACAGTTATGTATTTCATGTATGG
1 CATCCTTTCATGCCTTTAATGCACCGTTATGTATTTCATGTATGA
* *
18794 CATCCTTTCACGCCTTTAAAGCACCGTTA
1 CATCCTTTCATGCCTTTAATGCACCGTTA
18823 AGCAAATAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 64 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.43
Consensus pattern (45 bp):
CATCCTTTCATGCCTTTAATGCACCGTTATGTATTTCATGTATGA
Found at i:19063 original size:54 final size:54
Alignment explanation
Indices: 19017--19495 Score: 675
Period size: 54 Copynumber: 8.9 Consensus size: 54
19007 CATATTGTCA
* * *
19017 AAACGGTTGTTCACCAACATATGATGAATTTCGTGAGTTGCACACATAGTGTCA
1 AAACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTGCCG
* * * *
19071 AAATGATTGTTCATCAACATATGATGAATTTCGTGAGTTGTACACATAGTGCCA
1 AAACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTGCCG
*
19125 AAACGGTTGTTCATCAACATATGATGAATTAT-GTGGGTTG-ACACATAGTGCCG
1 AAACGGTTGTTCATCAACATATGATGAATT-TCGTGAGTTGCACACATAGTGCCG
19178 AAAC-G--GTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTGCCG
1 AAACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTGCCG
* * *
19229 AAATGGTTGTTCATCAACATATGATGAATTTCGTGGGTTGCACACATAGTGCTG
1 AAACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTGCCG
* * * *
19283 AAATGATTGTTCATCAACATATGATGAA-TTCTGTGAGTTACACACATAGTACCG
1 AAACGGTTGTTCATCAACATATGATGAATTTC-GTGAGTTGCACACATAGTGCCG
* * * *
19337 AAACGGTTGTTCATCAACATAAGATGAATTAT-GTGGGTTGCACACATAGTGTCA
1 AAACGGTTGTTCATCAACATATGATGAATT-TCGTGAGTTGCACACATAGTGCCG
* * * *
19391 AAACAGTTGTTCATCAACATATGATGAATTTCATGGGTTGCACACATAGTTCCG
1 AAACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTGCCG
19445 AAACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTG
1 AAACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTG
19496 TCGATAGTAC
Statistics
Matches: 379, Mismatches: 36, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
49 1 0.00
50 29 0.08
51 16 0.04
52 2 0.01
53 20 0.05
54 308 0.81
55 2 0.01
56 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (54 bp):
AAACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTGCCG
Found at i:19275 original size:27 final size:27
Alignment explanation
Indices: 19191--19276 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
19181 CGGTTCATCA
19191 ACATATGATGAATTTCGTGAGTTGCAC
1 ACATATGATGAATTTCGTGAGTTGCAC
** * * *
19218 ACATAGTGCCGAA-ATGGT-TGTT-CATC
1 ACATA-TGATGAATTTCGTGAGTTGCA-C
*
19244 AACATATGATGAATTTCGTGGGTTGCAC
1 -ACATATGATGAATTTCGTGAGTTGCAC
19272 ACATA
1 ACATA
19277 GTGCTGAAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 12
0.66 0.15 0.18
Matches are distributed among these distances:
25 2 0.05
26 9 0.21
27 21 0.49
28 9 0.21
29 2 0.05
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (27 bp):
ACATATGATGAATTTCGTGAGTTGCAC
Found at i:19345 original size:212 final size:215
Alignment explanation
Indices: 19017--19497 Score: 774
Period size: 212 Copynumber: 2.2 Consensus size: 215
19007 CATATTGTCA
*
19017 AAACGGTTGTTCACCAACATATGATGAATTTCGTGAGTTGCACACATAGTGTCAAAATGATTGTT
1 AAACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTGTCAAAATGATTGTT
** * *
19082 CATCAACATATGATGAATTTCGTGAGTTGTACACATAGTGCCAAAACGGTTGTTCATCAACATAT
66 CATCAACATATGATGAATTTCGTGAGTTACACACATAGTACCAAAACGGTTGTTCATCAACATAA
* *
19147 GATGAATTATGTGGGTTG-ACACATAGTGCCGAAAC-G-GTTCATCAACATATGATGAATTTCGT
131 GATGAATTATGTGGGTTGCACACATAGTGCCAAAACAGTGTTCATCAACATATGATGAATTTCAT
19209 GAGTTGCACACATAGTGCCG
196 GAGTTGCACACATAGTGCCG
* * *
19229 AAATGGTTGTTCATCAACATATGATGAATTTCGTGGGTTGCACACATAGTG-CTGAAATGATTGT
1 AAACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTGTC-AAAATGATTGT
*
19293 TCATCAACATATGATGAA-TTCTGTGAGTTACACACATAGTACCGAAACGGTTGTTCATCAACAT
65 TCATCAACATATGATGAATTTC-GTGAGTTACACACATAGTACCAAAACGGTTGTTCATCAACAT
*
19357 AAGATGAATTATGTGGGTTGCACACATAGTGTCAAAACAGTTGTTCATCAACATATGATGAATTT
129 AAGATGAATTATGTGGGTTGCACACATAGTGCCAAAACAG-TGTTCATCAACATATGATGAATTT
* *
19422 CATGGGTTGCACACATAGTTCCG
193 CATGAGTTGCACACATAGTGCCG
19445 AAACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTGTC
1 AAACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTGTC
19498 GATAGTACAC
Statistics
Matches: 246, Mismatches: 16, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
211 4 0.02
212 133 0.54
213 15 0.06
214 1 0.00
216 92 0.37
217 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (215 bp):
AAACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACATAGTGTCAAAATGATTGTT
CATCAACATATGATGAATTTCGTGAGTTACACACATAGTACCAAAACGGTTGTTCATCAACATAA
GATGAATTATGTGGGTTGCACACATAGTGCCAAAACAGTGTTCATCAACATATGATGAATTTCAT
GAGTTGCACACATAGTGCCG
Found at i:19914 original size:42 final size:41
Alignment explanation
Indices: 19842--19934 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 41
19832 CCCTACCATG
* * *
19842 GTATCGATACTTCTATACTATGGTAACGATAACTTTCTCTCA
1 GTATCGATACTACTATACTATAGTAACGAT-ACTTCCTCTCA
* * *
19884 GTATCGATACTACTACT-CTATAGTACCGATACTTCCTTTCG
1 GTATCGATACTACTA-TACTATAGTAACGATACTTCCTCTCA
19925 GTATCGATAC
1 GTATCGATAC
19935 CATTTTGGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 18 0.41
42 25 0.57
43 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.37
Consensus pattern (41 bp):
GTATCGATACTACTATACTATAGTAACGATACTTCCTCTCA
Found at i:22228 original size:29 final size:30
Alignment explanation
Indices: 22180--22290 Score: 106
Period size: 29 Copynumber: 3.8 Consensus size: 30
22170 AATATTTATT
* * *
22180 TTTTTAATTTCAA-ATAAAAATAAAACATA
1 TTTTTAAGTTCAAGATAAGAATAAAATATA
*
22209 TTTTTAA-TTCAAGATGAA-AATGAAATATA
1 TTTTTAAGTTCAAGAT-AAGAATAAAATATA
*
22238 TATTTTAAGTT-AAAATAAGAATAAAATATA
1 T-TTTTAAGTTCAAGATAAGAATAAAATATA
* *
22268 -TTTTAAATTGAAGATAAGAATAA
1 TTTTTAAGTTCAAGATAAGAATAA
22291 TTTTTTTTTA
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
28 13 0.19
29 33 0.47
30 22 0.31
31 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (30 bp):
TTTTTAAGTTCAAGATAAGAATAAAATATA
Found at i:22349 original size:24 final size:23
Alignment explanation
Indices: 22304--22349 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
22294 TTTTTTAAAA
22304 TTAAAATTAAAATAAATTATATTT
1 TTAAAATTAAAATAAA-TATATTT
22328 TTAAAAGTTAAATATAAA-ATAT
1 TTAAAA-TTAAA-ATAAATATAT
22350 CATAGATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
24 10 0.50
25 5 0.25
26 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
TTAAAATTAAAATAAATATATTT
Found at i:25423 original size:14 final size:15
Alignment explanation
Indices: 25382--25423 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
25372 TTCCAGAAAA
*
25382 TAAATTACTGCAATT
1 TAAATTACTGGAATT
25397 TAAATTACTGGAATT
1 TAAATTACTGGAATT
*
25412 TGAATT-CTGGAA
1 TAAATTACTGGAA
25424 AATGAATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (15 bp):
TAAATTACTGGAATT
Found at i:25439 original size:20 final size:20
Alignment explanation
Indices: 25416--25485 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
25406 GGAATTTGAA
25416 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
25436 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
25456 TTCTGGAAAACGAATTACAT
1 TTCTGGAAAATGAATTACAT
25476 TTCTGGAAAA
1 TTCTGGAAAA
25486 CATCTGGAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:25678 original size:49 final size:50
Alignment explanation
Indices: 25581--25679 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
25571 TACAAATATT
*
25581 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * * *
25631 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
25680 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 9 0.21
49 25 0.60
50 8 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:25853 original size:28 final size:28
Alignment explanation
Indices: 25821--25889 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 28
25811 AAAATATTGT
25821 TTAAATATATAAATAATATTAT-TCATTA
1 TTAAATATATAAATAATATTATAT-ATTA
25849 TTAAATATATAAA-AATATTATATATTA
1 TTAAATATATAAATAATATTATATATTA
*
25876 TTAAA-ATAAAAATA
1 TTAAATATATAAATA
25890 TAATATCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
26 6 0.16
27 18 0.47
28 14 0.37
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
TTAAATATATAAATAATATTATATATTA
Found at i:25867 original size:24 final size:28
Alignment explanation
Indices: 25821--25977 Score: 84
Period size: 26 Copynumber: 5.6 Consensus size: 28
25811 AAAATATTGT
25821 TTAAATATATAAATAATATTATTCAT-TA
1 TTAAATATATAAATAATATTATT-ATATA
25849 TTAAATATATAAA-AATATTA-TATATTA
1 TTAAATATATAAATAATATTATTATA-TA
* *
25876 TTAAA-ATAAAAAT-ATAATATCT-TATA
1 TTAAATATATAAATAATATTAT-TATATA
* *
25902 TTATATTATTATAATATAATTGATTATTTTATA
1 TTA-AATA-TATAA-ATAA-T-ATTATTATATA
25935 -T-AATAT-TAAA-AATATAATATTATAATA
1 TTAAATATATAAATAATAT--TATTAT-ATA
*
25962 TTATAA-ATATTAATAA
1 TTA-AATATATAAATAA
25978 ATATATTTTA
Statistics
Matches: 100, Mismatches: 8, Indels: 39
0.68 0.05 0.27
Matches are distributed among these distances:
24 2 0.02
25 3 0.03
26 24 0.24
27 21 0.21
28 19 0.19
29 7 0.07
30 10 0.10
31 3 0.03
32 3 0.03
33 8 0.08
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
TTAAATATATAAATAATATTATTATATA
Found at i:25875 original size:27 final size:27
Alignment explanation
Indices: 25821--25900 Score: 96
Period size: 24 Copynumber: 3.0 Consensus size: 27
25811 AAAATATTGT
25821 TTAAATATATAAATAATATTAT-TCATTA
1 TTAAATATATAAA-AATATTATAT-ATTA
25849 TTAAATATATAAAAATATTATATATTA
1 TTAAATATATAAAAATATTATATATTA
* *
25876 TT-AA-A-ATAAAAATATAATATCTTA
1 TTAAATATATAAAAATATTATATATTA
25900 T
1 T
25901 ATTATATTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
24 18 0.37
25 1 0.02
26 2 0.04
27 14 0.29
28 14 0.29
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (27 bp):
TTAAATATATAAAAATATTATATATTA
Found at i:25951 original size:14 final size:14
Alignment explanation
Indices: 25932--25982 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
25922 TGATTATTTT
25932 ATATAATATTAAAA
1 ATATAATATTAAAA
25946 ATATAATATTATAATA
1 ATATAATATTA-AA-A
*
25962 TTATAAATATTAATAA
1 ATAT-AATATTAA-AA
25978 ATATA
1 ATATA
25983 TTTTAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 11 0.35
15 3 0.10
16 9 0.29
17 8 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATAATATTAAAA
Found at i:25958 original size:22 final size:23
Alignment explanation
Indices: 25933--25976 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
25923 GATTATTTTA
25933 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
*
25955 TATAATATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
25977 AATATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:25960 original size:8 final size:8
Alignment explanation
Indices: 25899--25973 Score: 52
Period size: 8 Copynumber: 9.8 Consensus size: 8
25889 ATAATATCTT
25899 ATATTATA
1 ATATTATA
*
25907 TTATTATA
1 ATATTATA
25915 ATA-TA-A
1 ATATTATA
* *
25921 TTGATTATT
1 AT-ATTATA
*
25930 TTA-TATA
1 ATATTATA
25937 ATATTA-A
1 ATATTATA
*
25944 A-AATATA
1 ATATTATA
25951 ATATTATA
1 ATATTATA
25959 ATATTATAA
1 ATATTAT-A
25968 ATATTA
1 ATATTA
25974 ATAAATATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
6 5 0.10
7 12 0.23
8 26 0.50
9 9 0.17
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (8 bp):
ATATTATA
Found at i:25979 original size:10 final size:9
Alignment explanation
Indices: 25930--25981 Score: 51
Period size: 8 Copynumber: 6.1 Consensus size: 9
25920 ATTGATTATT
25930 TTATATAATA
1 TTATA-AATA
25940 TTA-AAA-A
1 TTATAAATA
25947 -TAT-AATA
1 TTATAAATA
25954 TTAT-AATA
1 TTATAAATA
25962 TTATAAATA
1 TTATAAATA
25971 TTAATAAATA
1 TT-ATAAATA
25981 T
1 T
25982 ATTTTAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
6 4 0.11
7 2 0.05
8 13 0.35
9 7 0.19
10 11 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTATAAATA
Found at i:25992 original size:30 final size:31
Alignment explanation
Indices: 25862--25998 Score: 105
Period size: 31 Copynumber: 4.6 Consensus size: 31
25852 AATATATAAA
25862 AATATTAT-ATATTATTAAA-A-TAAAAATAT
1 AATATTATAATATTA-TAAATATTAAAAATAT
* *
25891 AATATCT-T-ATATTAT-ATTATT-ATAATAT
1 AATAT-TATAATATTATAAATATTAAAAATAT
* * *
25919 AAT-TGATTATTTTATATAATATTAAAAATAT
1 AATATTATAATATTATA-AATATTAAAAATAT
25950 AATATTATAATATTATAAATATTAATAAATAT
1 AATATTATAATATTATAAATATTAA-AAATAT
* *
25982 -ATTTTA-AATATTTTAAA
1 AATATTATAATATTATAAA
25999 AAATAATATT
Statistics
Matches: 87, Mismatches: 11, Indels: 19
0.74 0.09 0.16
Matches are distributed among these distances:
27 3 0.03
28 17 0.20
29 13 0.15
30 16 0.18
31 22 0.25
32 16 0.18
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (31 bp):
AATATTATAATATTATAAATATTAAAAATAT
Found at i:25997 original size:23 final size:22
Alignment explanation
Indices: 25956--26010 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
25946 ATATAATATT
* *
25956 ATAATATTATAAATATTAATAA
1 ATAATATTTTAAATATTAAAAA
25978 AT-ATATTTTAAATATTTTAAAAA
1 ATAATATTTTAAATA--TTAAAAA
26001 ATAATATTTT
1 ATAATATTTT
26011 GATGAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 11 0.39
22 2 0.07
23 8 0.29
24 7 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAATATTTTAAATATTAAAAA
Found at i:26001 original size:55 final size:52
Alignment explanation
Indices: 25899--26008 Score: 134
Period size: 54 Copynumber: 2.1 Consensus size: 52
25889 ATAATATCTT
* ** *
25899 ATATTATATTATTATAATATAATTGATTATTTTATATAATATTAAAAATATA
1 ATATTATAATATTATAATATAATAAATTATTTTAAATAATATTAAAAATATA
*
25951 ATATTATAATATTATAAATATTAATAAATATATTTTAAAT-ATTTTAAAAA-ATA
1 ATATTATAATATTAT-AATA-TAATAAAT-TATTTTAAATAATATTAAAAATATA
26004 ATATT
1 ATATT
26009 TTGATGAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
52 14 0.28
53 12 0.24
54 15 0.30
55 9 0.18
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (52 bp):
ATATTATAATATTATAATATAATAAATTATTTTAAATAATATTAAAAATATA
Found at i:26006 original size:30 final size:32
Alignment explanation
Indices: 25944--26006 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 32
25934 ATAATATTAA
* *
25944 AAATATAATATTATAATATTATAAATATTAAT
1 AAATATAATATTATAATATTATAAAAAATAAT
* *
25976 AAATAT-ATTTTA-AATATTTTAAAAAATAAT
1 AAATATAATATTATAATATTATAAAAAATAAT
26006 A
1 A
26007 TTTTGATGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 16 0.59
31 5 0.19
32 6 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
AAATATAATATTATAATATTATAAAAAATAAT
Found at i:26240 original size:42 final size:42
Alignment explanation
Indices: 26182--26297 Score: 187
Period size: 42 Copynumber: 2.8 Consensus size: 42
26172 ATGAATTACA
* *
26182 TTCCGGAAAATAAATTATGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAATGAATTACGTGAAACAAACACGGGAAAACATT
*
26224 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAATGAATTACGTGAAACAAACACGGGAAAACATT
* *
26266 TTCCGGAAAATGAATTACATTAAACAAACACG
1 TTCCGGAAAATGAATTACGTGAAACAAACACG
26298 AGATTTCGGG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.20
Consensus pattern (42 bp):
TTCCGGAAAATGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:26590 original size:18 final size:18
Alignment explanation
Indices: 26567--26619 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 18
26557 ATTATAAAAA
26567 ATAATTTTTATATTTAAT
1 ATAATTTTTATATTTAAT
26585 ATAATTTATTA-A-TTAAT
1 ATAATTT-TTATATTTAAT
*
26602 -TAATATTT-TATTTAAT
1 ATAATTTTTATATTTAAT
26618 AT
1 AT
26620 TTTATTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
15 3 0.10
16 10 0.33
17 6 0.20
18 8 0.27
19 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATAATTTTTATATTTAAT
Found at i:26616 original size:12 final size:12
Alignment explanation
Indices: 26601--26625 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26591 TATTAATTAA
26601 TTAATATTTTAT
1 TTAATATTTTAT
26613 TTAATATTTTAT
1 TTAATATTTTAT
26625 T
1 T
26626 ATTTTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTAATATTTTAT
Found at i:30597 original size:27 final size:27
Alignment explanation
Indices: 30495--30580 Score: 154
Period size: 27 Copynumber: 3.2 Consensus size: 27
30485 TTTATTATTT
*
30495 TTTAGAGTTTTTAGTTAGATTTTGTGG
1 TTTAGAGTTTTTAGTTAGAATTTGTGG
*
30522 TTTAGAGTTTTTAGTTAGACTTTGTGG
1 TTTAGAGTTTTTAGTTAGAATTTGTGG
30549 TTTAGAGTTTTTAGTTAGAATTTGTGG
1 TTTAGAGTTTTTAGTTAGAATTTGTGG
30576 TTTAG
1 TTTAG
30581 GGTTCTAAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.20, C:0.01, G:0.26, T:0.53
Consensus pattern (27 bp):
TTTAGAGTTTTTAGTTAGAATTTGTGG
Found at i:33856 original size:2 final size:2
Alignment explanation
Indices: 33849--33883 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
33839 CTTTTAATTG
33849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33884 ATTTGGAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34651 original size:20 final size:20
Alignment explanation
Indices: 34626--34673 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
34616 TTCATAGAGT
34626 ATCGATACTG-AAGAGTTAGC
1 ATCGATACTGAAAG-GTTAGC
34646 ATCGATACTGAAAGGTTAGC
1 ATCGATACTGAAAGGTTAGC
*
34666 ATCAATAC
1 ATCGATAC
34674 CAAGAGTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGATACTGAAAGGTTAGC
Found at i:35513 original size:44 final size:46
Alignment explanation
Indices: 35427--35513 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
35417 AAGAGTCATG
*
35427 TTCTACGCGGTCCTTCGGGACAATTCTATGTGGTCCTTTGGGATAT
1 TTCTACGCGGTCCTTCGAGACAATTCTATGTGGTCCTTTGGGATAT
* *
35473 TTCTACGTGGTCCTTCGAGAC-ATT-TATGTGGTCTTTTGGGA
1 TTCTACGCGGTCCTTCGAGACAATTCTATGTGGTCCTTTGGGA
35514 CATTGACGCC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 16 0.42
45 3 0.08
46 19 0.50
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.39
Consensus pattern (46 bp):
TTCTACGCGGTCCTTCGAGACAATTCTATGTGGTCCTTTGGGATAT
Found at i:35515 original size:21 final size:22
Alignment explanation
Indices: 35435--35517 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 22
35425 TGTTCTACGC
*
35435 GGTCCTTCGGGACAATTCTATGT
1 GGTCCTTTGGGAC-ATTCTATGT
* *
35458 GGTCCTTTGGGATATTTCTACGT
1 GGTCCTTTGGGACA-TTCTATGT
* *
35481 GGTCCTTCGAGACATT-TATGT
1 GGTCCTTTGGGACATTCTATGT
*
35502 GGTCTTTTGGGACATT
1 GGTCCTTTGGGACATT
35518 GACGCCAGAC
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
21 17 0.35
22 3 0.06
23 29 0.59
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.40
Consensus pattern (22 bp):
GGTCCTTTGGGACATTCTATGT
Found at i:35724 original size:36 final size:36
Alignment explanation
Indices: 35682--35757 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
35672 TTATAGCTAA
*
35682 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
35718 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
35754 AAAA
1 AAAA
35758 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:40239 original size:15 final size:15
Alignment explanation
Indices: 40221--40250 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40211 CCACGGTGCT
40221 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
40236 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
40251 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:40714 original size:36 final size:36
Alignment explanation
Indices: 40672--40747 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
40662 TTATAGCTAA
*
40672 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
40708 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
40744 AAAA
1 AAAA
40748 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:45675 original size:3 final size:3
Alignment explanation
Indices: 45667--45704 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
45657 TTTTATCTAT
*
45667 TTA TTA TTA TTA TTA TTA TTA -TA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
45705 AATTAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:45695 original size:20 final size:19
Alignment explanation
Indices: 45659--45704 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
45649 GTCACGGTTT
*
45659 TTATCTATTTATTATTATTA
1 TTAT-TATTTATCATTATTA
45679 TTATTATTATATCATTATTA
1 TTATTATT-TATCATTATTA
45699 TTATTA
1 TTATTA
45705 AATTAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATTATTTATCATTATTA
Found at i:61487 original size:13 final size:13
Alignment explanation
Indices: 61469--61493 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61459 TGTAGAATAA
61469 TTAAAAATATTAT
1 TTAAAAATATTAT
61482 TTAAAAATATTA
1 TTAAAAATATTA
61494 AAAGAATGCA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAAAATATTAT
Found at i:62187 original size:16 final size:16
Alignment explanation
Indices: 62166--62197 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
62156 TATGTTCAAG
62166 GCAAATTGGTCATTTT
1 GCAAATTGGTCATTTT
62182 GCAAATTGGTCATTTT
1 GCAAATTGGTCATTTT
62198 TAAGAATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (16 bp):
GCAAATTGGTCATTTT
Done.