Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000573.1 Hibiscus syriacus cultivar Beakdansim tig00001121_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: 72020
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1573 original size:84 final size:86
Alignment explanation
Indices: 1411--1579 Score: 245
Period size: 84 Copynumber: 2.0 Consensus size: 86
1401 CCTAACACAC
*
1411 CCTTTTATAACCAAGTTACCCTAATCATATTAGGATTTTTATTATTTCAAATTAATTAATATATT
1 CCTTTTATAACCAAGTTACCCTAATCATATGAGGATTTTTATTA-TTCAAATTAATTAATATATT
*
1476 TAATTAATTGAAATTTAATAAT
65 TAATTAATTGAAATTAAATAAT
* * * *
1498 CCTTTTATATCTAAGTTACCCTAATCAT-TGGGGATTTTTATTA-TCAAATTAATTAAATCTATT
1 CCTTTTATAACCAAGTTACCCTAATCATATGAGGATTTTTATTATTCAAATTAATT-AATATATT
1561 T-ATTAATTGAAATTAAATA
65 TAATTAATTGAAATTAAATA
1580 TTCGGGATTA
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
84 28 0.37
85 8 0.11
86 13 0.17
87 26 0.35
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.46
Consensus pattern (86 bp):
CCTTTTATAACCAAGTTACCCTAATCATATGAGGATTTTTATTATTCAAATTAATTAATATATTT
AATTAATTGAAATTAAATAAT
Found at i:7989 original size:42 final size:42
Alignment explanation
Indices: 7942--8029 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
7932 ATTTACAAAG
** *
7942 TAATTTATAA-TTGAACGGTAATTTTAACGTATAATCATAAGC
1 TAATTTATAATTTG-ACAATAATATTAACGTATAATCATAAGC
* *
7984 TAATTTATAATTTGACAATAATATTAATGTATAATCATAAGG
1 TAATTTATAATTTGACAATAATATTAACGTATAATCATAAGC
8026 TAAT
1 TAAT
8030 ACTTGTTGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 37 0.93
43 3 0.08
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (42 bp):
TAATTTATAATTTGACAATAATATTAACGTATAATCATAAGC
Found at i:9346 original size:22 final size:22
Alignment explanation
Indices: 9321--9367 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
9311 GTGGCATGTG
9321 GAATATGTCCCGAAGGACCTAT
1 GAATATGTCCCGAAGGACCTAT
9343 GAATATGTCCCGAAGGACCTAT
1 GAATATGTCCCGAAGGACCTAT
9365 GAA
1 GAA
9368 ACCCTCGACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (22 bp):
GAATATGTCCCGAAGGACCTAT
Found at i:9585 original size:2 final size:2
Alignment explanation
Indices: 9578--9661 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
9568 TCATACAACC
9578 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
9620 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
9662 CTTACGCATG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10102 original size:20 final size:16
Alignment explanation
Indices: 10058--10123 Score: 71
Period size: 16 Copynumber: 3.9 Consensus size: 16
10048 ATTCGATATT
10058 TCCTGGTATCGATACC
1 TCCTGGTATCGATACC
10074 TCCTGGTATCGATACC
1 TCCTGGTATCGATACC
*
10090 TCCCTTATGGTATCGGTACC
1 T-CC---TGGTATCGATACC
*
10110 T-ATGGTATCGATAC
1 TCCTGGTATCGATAC
10124 TATCTTCCCA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
15 11 0.26
16 17 0.40
17 2 0.05
20 13 0.30
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (16 bp):
TCCTGGTATCGATACC
Found at i:14843 original size:20 final size:20
Alignment explanation
Indices: 14807--14849 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
14797 TCAAAATCAT
* *
14807 TTTCCAAAATTTCATTTTGC
1 TTTCCAAAATCTAATTTTGC
*
14827 TTTCCAAAATCTAATTTTTC
1 TTTCCAAAATCTAATTTTGC
14847 TTT
1 TTT
14850 AAAGAGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTCCAAAATCTAATTTTGC
Found at i:17187 original size:2 final size:2
Alignment explanation
Indices: 17180--17244 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
17170 TATATTTAAT
17180 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17222 TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
17245 AATTTAGTTA
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17897 original size:60 final size:60
Alignment explanation
Indices: 17825--17989 Score: 208
Period size: 59 Copynumber: 2.8 Consensus size: 60
17815 TTTCAACGTA
* * ** *
17825 CATCCTGAAACTATGTCTCTTATTCTAAATTAGTCCCTAAACTTTTGAATATTTTAATTC
1 CATCCTCAAACTATGACTCTTATTCTAAATTAGTCCCTAAACTTTTGAATATTCCAAATC
* * * *
17885 CATCCAT-AAACTATGAATCTCATTCTAAATTGGTCCCTAAAC-TTTGAATATTCCAAATG
1 CATCC-TCAAACTATGACTCTTATTCTAAATTAGTCCCTAAACTTTTGAATATTCCAAATC
* *
17944 CATCCTCAAACTATGACCCTTATTCTAAATTAGTCCCCAAACTTTT
1 CATCCTCAAACTATGACTCTTATTCTAAATTAGTCCCTAAACTTTT
17990 AAACATCTCA
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
58 1 0.01
59 48 0.54
60 39 0.44
61 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.38
Consensus pattern (60 bp):
CATCCTCAAACTATGACTCTTATTCTAAATTAGTCCCTAAACTTTTGAATATTCCAAATC
Found at i:22993 original size:21 final size:21
Alignment explanation
Indices: 22964--23016 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
22954 ATTCTGACTA
22964 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
22985 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
23006 TCGCAATGCGA
1 TCGCATTGCGA
23017 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:23038 original size:20 final size:20
Alignment explanation
Indices: 23006--23099 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
22996 TTTTCCTAAT
*
23006 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
* ** *
23026 TCGTAACGCGAATTTGGAAAA
1 TCGCAACGCGAA-TACGTAAA
*
23047 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
23067 TCGCAACGCGAAT-CTGTAAA
1 TCGCAACGCGAATAC-GTAAA
*
23087 CCGCAACGCGAAT
1 TCGCAACGCGAAT
23100 CTGACTATCG
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
19 1 0.02
20 44 0.73
21 15 0.25
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:23999 original size:24 final size:24
Alignment explanation
Indices: 23941--23987 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
23931 AGTCAGTATT
23941 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
23965 CGAAATTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
23988 TCGGATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACC
Found at i:26388 original size:20 final size:20
Alignment explanation
Indices: 26363--26456 Score: 136
Period size: 20 Copynumber: 4.7 Consensus size: 20
26353 GACATTCATT
26363 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
26383 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* *
26403 TGACTATCGTAACGCGGAAT
1 TGACTATCGCAACGCGGAAA
26423 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
26443 TGACTATCACAACG
1 TGACTATCGCAACG
26457 AGAGAATCGC
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 63 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:26516 original size:34 final size:33
Alignment explanation
Indices: 26428--26523 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
26418 GGAATTGACT
* **
26428 ATCGCAACGCGGAAATGACTATCACAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCACAACGAGAGA
*
26462 ATCGCAATGCGAAATGAAAATCACAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
*
26495 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCACAACG
26524 CGAATTTGTG
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 31 0.55
34 25 0.45
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGAGAGA
Found at i:26680 original size:14 final size:14
Alignment explanation
Indices: 26661--26697 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
26651 CATCAATTAA
26661 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
26675 ACAAATCATCTTTT
1 ACAAATCAACATTT
26689 ACAAATCAA
1 ACAAATCAA
26698 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:28699 original size:20 final size:20
Alignment explanation
Indices: 28676--28784 Score: 173
Period size: 20 Copynumber: 5.5 Consensus size: 20
28666 GAAACTTAAA
28676 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
28696 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
28716 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
28736 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
28756 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
28776 ATCGCAACG
1 ATCGCAACG
28785 AAAGAATCGC
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:28820 original size:20 final size:20
Alignment explanation
Indices: 28791--28972 Score: 149
Period size: 20 Copynumber: 9.8 Consensus size: 20
28781 AACGAAAGAA
*
28791 TCGCAATGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
28811 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
*
28831 TCGTATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
*
28851 TTGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
*
28871 TCGCGTTGC-A-A-T--TTT
1 TCGCATTGCGATAGTCATTT
* **
28886 GTTG--TTGCGATTTTCA-TT
1 -TCGCATTGCGATAGTCATTT
* *
28904 TCGCATCGCGAT--TC--TC
1 TCGCATTGCGATAGTCATTT
*
28920 TCG--TTACGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
* *
28938 TCGCGTTGCGATAGACATTT
1 TCGCATTGCGATAGTCATTT
28958 TCGCATTGCGATAGT
1 TCGCATTGCGATAGT
28973 AAACTATTCT
Statistics
Matches: 130, Mismatches: 18, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
14 9 0.07
15 4 0.03
16 8 0.06
17 6 0.05
18 7 0.05
19 7 0.05
20 89 0.68
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATAGTCATTT
Found at i:30873 original size:20 final size:19
Alignment explanation
Indices: 30834--30903 Score: 104
Period size: 19 Copynumber: 3.6 Consensus size: 19
30824 TCTGAAACTT
30834 AAAATCGCAACACGAAATG
1 AAAATCGCAACACGAAATG
30853 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACG-AAATG
** *
30873 ACTATCGCAACGCGAAATG
1 AAAATCGCAACACGAAATG
30892 AAAATCGCAACA
1 AAAATCGCAACA
30904 ACATAATCGC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
19 28 0.64
20 16 0.36
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACACGAAATG
Found at i:31269 original size:22 final size:22
Alignment explanation
Indices: 31239--31312 Score: 94
Period size: 22 Copynumber: 3.4 Consensus size: 22
31229 TGACCGTGAA
* *
31239 TGATTTCGTCGGAGATGGAGAC
1 TGATATCGTCGGAGATGGGGAC
**
31261 TGATATCGTCGGCTATGGGGAC
1 TGATATCGTCGGAGATGGGGAC
*
31283 TGATTTCGTCGGAGATGGGGAC
1 TGATATCGTCGGAGATGGGGAC
*
31305 AGATATCG
1 TGATATCG
31313 CCTTAGAGAG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.22, C:0.15, G:0.36, T:0.27
Consensus pattern (22 bp):
TGATATCGTCGGAGATGGGGAC
Found at i:31513 original size:20 final size:20
Alignment explanation
Indices: 31488--31534 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
31478 GTAAATCGCA
31488 TTGCGATAGTCAGATTTGCG
1 TTGCGATAGTCAGATTTGCG
31508 TTGCGATAGTCAGATTTGCG
1 TTGCGATAGTCAGATTTGCG
31528 TTGCGAT
1 TTGCGAT
31535 TTACATATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.30, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAGATTTGCG
Found at i:31607 original size:21 final size:20
Alignment explanation
Indices: 31528--31654 Score: 191
Period size: 20 Copynumber: 6.3 Consensus size: 20
31518 CAGATTTGCG
* *
31528 TTGCGATTTACATATTCGTA
1 TTGCGATTTACGTATTCGCA
31548 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
31568 TTGTGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* **
31588 TTGCGATTTTCCAAATTCGCA
1 TTGCGA-TTTACGTATTCGCA
31609 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
31629 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
31649 TTGCGA
1 TTGCGA
31655 ATTAGGAAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
20 79 0.82
21 17 0.18
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:31622 original size:61 final size:60
Alignment explanation
Indices: 31528--31654 Score: 209
Period size: 61 Copynumber: 2.1 Consensus size: 60
31518 CAGATTTGCG
* * *
31528 TTGCGATTTACATATTCGTATTGCGATTTACGTATTCGCATTGTGATTTACGTATTCGCA
1 TTGCGATTTACAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
*
31588 TTGCGATTTTCCAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGA-TTTACAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
31649 TTGCGA
1 TTGCGA
31655 ATTAGGAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
60 6 0.10
61 56 0.90
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (60 bp):
TTGCGATTTACAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
Found at i:31677 original size:21 final size:21
Alignment explanation
Indices: 31651--31696 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
31641 TATTCGCATT
31651 GCGAATTAGGAAAATAGCAAC
1 GCGAATTAGGAAAATAGCAAC
* * *
31672 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATAGCAAC
31693 GCGA
1 GCGA
31697 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATAGCAAC
Found at i:31872 original size:2 final size:2
Alignment explanation
Indices: 31865--31890 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31855 TTTTCTATTC
31865 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
31891 ACGGGCGAAT
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):
TA
Found at i:32449 original size:33 final size:34
Alignment explanation
Indices: 32397--32466 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 34
32387 ATAAGTTATT
* *
32397 ATAAAATATATTATTTTAATAATTTAAAATA-TA
1 ATAAAATATAGTATATTAATAATTTAAAATACTA
* *
32430 ATAAAATGTAGTATATTAATTATTTAAAATACTA
1 ATAAAATATAGTATATTAATAATTTAAAATACTA
32464 ATA
1 ATA
32467 TATTTGGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 27 0.84
34 5 0.16
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (34 bp):
ATAAAATATAGTATATTAATAATTTAAAATACTA
Found at i:35889 original size:33 final size:33
Alignment explanation
Indices: 35852--35951 Score: 91
Period size: 33 Copynumber: 2.9 Consensus size: 33
35842 TATATTTCAT
35852 TAAAATTAAAATTTTATTAATTATTTATTA-AAA
1 TAAAATTAAAATTTTATTAA-TATTTATTATAAA
* *
35885 TAAAATTAGTATATTATATTCTAA-ATTTATTAATAAA
1 TAAAATTA--AAATTTTA-T-TAATATTTATT-ATAAA
35922 TAAAATT--AATTTTATTAATAATTTATTATA
1 TAAAATTAAAATTTTATTAAT-ATTTATTATA
35952 TATTATTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
31 3 0.05
32 4 0.07
33 20 0.36
35 13 0.24
36 2 0.04
37 13 0.24
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (33 bp):
TAAAATTAAAATTTTATTAATATTTATTATAAA
Found at i:35904 original size:28 final size:27
Alignment explanation
Indices: 35839--35891 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
35829 ATATTAAGAC
35839 TATTATATTTCATTAAAATTAAAATTT
1 TATTATATTTCATTAAAATTAAAATTT
35866 TATTAATTATTT-ATTAAAA-TAAAATT
1 TATT-A-TATTTCATTAAAATTAAAATT
35892 AGTATATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 11 0.46
28 8 0.33
29 5 0.21
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (27 bp):
TATTATATTTCATTAAAATTAAAATTT
Found at i:35992 original size:18 final size:18
Alignment explanation
Indices: 35969--36010 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
35959 AAAATAAAAA
* *
35969 TATAATGTCATATATTAT
1 TATAATGTAATATATAAT
*
35987 TATAATTTAATATATAAT
1 TATAATGTAATATATAAT
36005 TATAAT
1 TATAAT
36011 ACTAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
TATAATGTAATATATAAT
Found at i:36306 original size:23 final size:23
Alignment explanation
Indices: 36276--36328 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
36266 ACCAAACACT
36276 GGAAAATG-AGTAAAACATTTTCC
1 GGAAAATGAAG-AAAACATTTTCC
36299 GGAAAATGAAGAAAACATTTTCC
1 GGAAAATGAAGAAAACATTTTCC
36322 GGAAAAT
1 GGAAAAT
36329 CAATTACAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 27 0.93
24 2 0.07
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (23 bp):
GGAAAATGAAGAAAACATTTTCC
Found at i:37968 original size:24 final size:24
Alignment explanation
Indices: 37941--37988 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
37931 TCAATTAATA
* *
37941 TTATTCATATACGATTGAGTCCTC
1 TTATTCATATACAATAGAGTCCTC
37965 TTATTCATATACAATAGAGTCCTC
1 TTATTCATATACAATAGAGTCCTC
37989 AAACTTCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (24 bp):
TTATTCATATACAATAGAGTCCTC
Found at i:38847 original size:43 final size:41
Alignment explanation
Indices: 38761--38848 Score: 104
Period size: 43 Copynumber: 2.1 Consensus size: 41
38751 AAGGCCCATG
* ** ** *
38761 TTTTTTATTTTATTTTTATTTTTATAATTGAGTTCTTTCAT
1 TTTTTTATTTTATTTTTATATTTATAATTGAGACCCATAAT
38802 TTTTTTGATTTTATTTTTTATATTTATAATTGAGACCCATAAT
1 TTTTTT-ATTTTA-TTTTTATATTTATAATTGAGACCCATAAT
38845 TTTT
1 TTTT
38849 GCAATCCTAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 6 0.15
42 6 0.15
43 27 0.69
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.66
Consensus pattern (41 bp):
TTTTTTATTTTATTTTTATATTTATAATTGAGACCCATAAT
Found at i:38963 original size:46 final size:47
Alignment explanation
Indices: 38886--38983 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 47
38876 GGGGCCTTTA
* * * *
38886 TTTTTTTTCAATCAAACTTTTTTATAATTATAATTGATGATTCTAAT
1 TTTTTTTTCAATCAAACTTTTTTACAATTATAACTGAGGATCCTAAT
** ** *
38933 TTTTTTTTCAATCTCAC-TTTTTACCTTTATAACTGAGGCTCCTAAT
1 TTTTTTTTCAATCAAACTTTTTTACAATTATAACTGAGGATCCTAAT
38979 TTTTT
1 TTTTT
38984 CAGTATCATT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
46 27 0.64
47 15 0.36
ACGTcount: A:0.26, C:0.14, G:0.05, T:0.55
Consensus pattern (47 bp):
TTTTTTTTCAATCAAACTTTTTTACAATTATAACTGAGGATCCTAAT
Found at i:38997 original size:43 final size:44
Alignment explanation
Indices: 38935--39027 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
38925 ATTCTAATTT
* *
38935 TTTTTTCAATCTCA-CTTTTTACCTTTATAACTGAGGCTC-CTAA
1 TTTTTTCAATATCATCTTTTTACCTTTAAAACTGAGGC-CACTAA
* * *
38978 TTTTTTCAGTATCATTTTTTTACCTTTAAAATTGAGGCCACTAA
1 TTTTTTCAATATCATCTTTTTACCTTTAAAACTGAGGCCACTAA
39022 TTTTTT
1 TTTTTT
39028 AACCTCTCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 13 0.30
44 30 0.70
ACGTcount: A:0.24, C:0.18, G:0.08, T:0.51
Consensus pattern (44 bp):
TTTTTTCAATATCATCTTTTTACCTTTAAAACTGAGGCCACTAA
Found at i:41770 original size:21 final size:21
Alignment explanation
Indices: 41729--41771 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
41719 AACAAATATA
* *
41729 TTATTTTTCAATATATTAAAT
1 TTATTTTTCAATAAATAAAAT
41750 TTATTTTT-AATAAATCAAAAT
1 TTATTTTTCAATAAAT-AAAAT
41771 T
1 T
41772 AAAAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (21 bp):
TTATTTTTCAATAAATAAAAT
Found at i:52720 original size:30 final size:29
Alignment explanation
Indices: 52656--52720 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
52646 GTTTTGTGTG
52656 AGCTGTTATGTCTCCCAAATGCTCCACCA
1 AGCTGTTATGTCTCCCAAATGCTCCACCA
* * *
52685 GGCTGTGTATGTCTTCCAAATGCTCCACTA
1 AGCTGT-TATGTCTCCCAAATGCTCCACCA
52715 AGCTGT
1 AGCTGT
52721 CCCAACGTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (29 bp):
AGCTGTTATGTCTCCCAAATGCTCCACCA
Found at i:59843 original size:28 final size:26
Alignment explanation
Indices: 59773--59830 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
59763 TGTCAAGATT
59773 TATATAACATGTATTATTTATTTTGA
1 TATATAACATGTATTATTTATTTTGA
59799 TATATAACATGTATTATTTATTTTGA
1 TATATAACATGTATTATTTATTTTGA
59825 TATATA
1 TATATA
59831 TAACATGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.53
Consensus pattern (26 bp):
TATATAACATGTATTATTTATTTTGA
Found at i:62303 original size:23 final size:23
Alignment explanation
Indices: 62263--62316 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
62253 ATAGTACAAC
62263 AATTAAAATATATCTATAGATTTT
1 AATTAAAATATATCTATA-ATTTT
*
62287 AATTCAAAATAT-T-TATAATTTA
1 AATT-AAAATATATCTATAATTTT
62309 ATATTAAA
1 A-ATTAAA
62317 GTTTAACTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 8 0.30
23 7 0.26
24 5 0.19
25 7 0.26
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (23 bp):
AATTAAAATATATCTATAATTTT
Found at i:63231 original size:19 final size:19
Alignment explanation
Indices: 63204--63257 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
63194 AAAAGATCAC
*
63204 AAAATATAAAAAAATATAAT
1 AAAA-ATAAAAAAATAGAAT
* *
63224 AAAAATAAAAATAAGAGATT
1 AAAAATAAAAA-AATAGAAT
63244 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
63258 TATATCAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 9 0.31
20 20 0.69
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (19 bp):
AAAAATAAAAAAATAGAAT
Found at i:66617 original size:16 final size:16
Alignment explanation
Indices: 66596--66627 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
66586 TGTTTAGTTG
66596 CCTTGAATGCTTGAGA
1 CCTTGAATGCTTGAGA
66612 CCTTGAATGCTTGAGA
1 CCTTGAATGCTTGAGA
66628 ACTTTTCTAT
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:0.19, G:0.25, T:0.31
Consensus pattern (16 bp):
CCTTGAATGCTTGAGA
Found at i:67341 original size:16 final size:17
Alignment explanation
Indices: 67303--67348 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
67293 TGTTTATGAG
*
67303 GGAATTGGAATCTGTGAA
1 GGAATTGAAATCTGT-AA
67321 GGAATTGAAATCTGT-A
1 GGAATTGAAATCTGTAA
67337 GGAATTGAAATC
1 GGAATTGAAATC
67349 CAATTCTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 13 0.48
18 14 0.52
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (17 bp):
GGAATTGAAATCTGTAA
Found at i:67918 original size:38 final size:37
Alignment explanation
Indices: 67866--67947 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 37
67856 TTCACCCTAA
*
67866 ACCCGAACCCGACCCGAATATCACACTTAAAAAACCCCG
1 ACCCG-ACCCGACCCGAATATCAAACTTAAAAAA-CCCG
*
67905 ACCCGACTCGACCCGAATATCAAACTTAAAAAACCCG
1 ACCCGACCCGACCCGAATATCAAACTTAAAAAACCCG
67942 ACCCGA
1 ACCCGA
67948 ACAAAATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
37 10 0.24
38 26 0.63
39 5 0.12
ACGTcount: A:0.39, C:0.39, G:0.11, T:0.11
Consensus pattern (37 bp):
ACCCGACCCGACCCGAATATCAAACTTAAAAAACCCG
Found at i:68136 original size:37 final size:38
Alignment explanation
Indices: 68056--68137 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
68046 TTCACCCTAA
68056 ACCCGAACCCGACCCGAATATCACACTTAAAAAAACCCG
1 ACCCG-ACCCGACCCGAATATCACACTTAAAAAAACCCG
* *
68095 ACCCGACTCGACCCGAATATCACACTT-TAAAAACCCG
1 ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCG
68132 ACCCGA
1 ACCCGA
68138 AATAATAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
37 15 0.37
38 21 0.51
39 5 0.12
ACGTcount: A:0.38, C:0.39, G:0.11, T:0.12
Consensus pattern (38 bp):
ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCG
Found at i:68360 original size:217 final size:223
Alignment explanation
Indices: 68127--68574 Score: 701
Period size: 228 Copynumber: 2.0 Consensus size: 223
68117 CACTTTAAAA
* *
68127 ACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGAC
1 ACCCAACCCAAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGAC
* *
68192 CCGAA-TATATATA-TTTCGGGTCGGTCCGG-TTTTTTCACCCT-AAACCCG-ACCCGACTCGAC
66 CCGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAAACCCGAACCCGACCCAAC
* * *
68252 CTGAATATCACACTT-AAAAAACCTGACCCGACCCAAACAAAATAAAGTTTCATCCGACCCGACC
131 CCGAATATCACACTTAAAAAAACCCGACCCGACCCAAACAAAATAAAGTTTCACCCGACCCGACC
*
68316 CGAATATATGAATTAGAAATCCGACCCG
196 CGAATATATGAATTAGAAACCCGACCCG
68344 ACCCAACCCAAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGAC
1 ACCCAACCCAAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGAC
*
68409 CTGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCAAACCCGAACCCGAC
66 CCGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCT--A---AAACCCGAACCCGAC
* * *
68474 CCAACCCGAATATCACACTTAAAAAAACCCGATCCGACCCGACCAAAATAAAGTTTCACCCGACC
126 CCAACCCGAATATCACACTTAAAAAAACCCGACCCGACCCAAACAAAATAAAGTTTCACCCGACC
68539 CGACCCGAATATATGAATTAGAAACCCGACCCG
191 CGACCCGAATATATGAATTAGAAACCCGACCCG
68572 ACC
1 ACC
68575 GAAATAATAA
Statistics
Matches: 208, Mismatches: 12, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
217 67 0.32
218 8 0.04
219 16 0.08
220 12 0.06
226 7 0.03
227 24 0.12
228 74 0.36
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.23
Consensus pattern (223 bp):
ACCCAACCCAAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGAC
CCGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAAACCCGAACCCGACCCAAC
CCGAATATCACACTTAAAAAAACCCGACCCGACCCAAACAAAATAAAGTTTCACCCGACCCGACC
CGAATATATGAATTAGAAACCCGACCCG
Found at i:69417 original size:44 final size:44
Alignment explanation
Indices: 69319--69417 Score: 100
Period size: 44 Copynumber: 2.2 Consensus size: 44
69309 GTTATAATAT
* *
69319 TTTATATATATTAACTTAAAAAATATTTTTATATTACTTATTAAA
1 TTTAAATATATTAACTTAAAAAATATTTTTATATTAC-AATTAAA
69364 --TAAATTATATTAACTTAATTAAAA-ATATTTTAT-TTA-AATTAAA
1 TTTAAA-TATATTAACTTAA--AAAATAT-TTTTATATTACAATTAAA
69407 TTTAAATATAT
1 TTTAAATATAT
69418 ATTTTATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
43 9 0.20
44 18 0.39
45 9 0.20
46 10 0.22
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.49
Consensus pattern (44 bp):
TTTAAATATATTAACTTAAAAAATATTTTTATATTACAATTAAA
Found at i:71424 original size:39 final size:39
Alignment explanation
Indices: 71378--71452 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
71368 CCAATTTAGC
71378 ACACTTTTATGTCATGTAAGTGGAAGGAGATTTTAGGGT
1 ACACTTTTATGTCATGTAAGTGGAAGGAGATTTTAGGGT
*
71417 ACACTTTTATGTCATGTAAGTGGAAGGAGTTTTTAG
1 ACACTTTTATGTCATGTAAGTGGAAGGAGATTTTAG
71453 AGTATGTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.28, C:0.08, G:0.27, T:0.37
Consensus pattern (39 bp):
ACACTTTTATGTCATGTAAGTGGAAGGAGATTTTAGGGT
Found at i:72007 original size:30 final size:28
Alignment explanation
Indices: 71927--72010 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 28
71917 AATTTTAATA
*
71927 ATTTATTATATATTATTAAAAATAAAATTAT
1 ATTTATTATA-A-TATT-AAAATATAATTAT
71958 ATCTTATTAT-ATATT--AATATAATTGATT
1 AT-TTATTATAATATTAAAATATAATT-A-T
71986 ATTTATTATAATATTAAAATATAAT
1 ATTTATTATAATATTAAAATATAAT
72011 ATTATATTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
26 8 0.17
27 8 0.17
28 8 0.17
29 4 0.09
30 9 0.20
31 2 0.04
32 7 0.15
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (28 bp):
ATTTATTATAATATTAAAATATAATTAT
Done.