Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008508.1 Hibiscus syriacus cultivar Beakdansim tig00111360_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: 70385
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1986 original size:16 final size:16
Alignment explanation
Indices: 1965--2013 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
1955 TAAATAAATG
1965 ACATAAACGAACACGA
1 ACATAAACGAACACGA
1981 ACATAAACGAACACGA
1 ACATAAACGAACACGA
*
1997 ACATAAATGAACACGA
1 ACATAAACGAACACGA
2013 A
1 A
2014 AAAAACGTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACATAAACGAACACGA
Found at i:2092 original size:13 final size:13
Alignment explanation
Indices: 2074--2098 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2064 AGTATTGCTG
2074 AGCTCGACTCGAA
1 AGCTCGACTCGAA
2087 AGCTCGACTCGA
1 AGCTCGACTCGA
2099 CTCAAAAACC
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:0.28, C:0.32, G:0.24, T:0.16
Consensus pattern (13 bp):
AGCTCGACTCGAA
Found at i:3134 original size:14 final size:13
Alignment explanation
Indices: 3117--3196 Score: 64
Period size: 14 Copynumber: 6.3 Consensus size: 13
3107 AATTAACATA
3117 AACGAACATAACCG
1 AACGAACATAA-CG
*
3131 AACGAACATAAAG
1 AACGAACATAACG
3144 -A--AACATAATCG
1 AACGAACATAA-CG
*
3155 AACGAACATAAAG
1 AACGAACATAACG
3168 -A--AACATAATCG
1 AACGAACATAA-CG
3179 AACGAACATAACCG
1 AACGAACATAA-CG
3193 AACG
1 AACG
3197 TTCACGAACG
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
10 14 0.26
11 2 0.04
12 4 0.08
13 2 0.04
14 31 0.58
ACGTcount: A:0.55, C:0.21, G:0.14, T:0.10
Consensus pattern (13 bp):
AACGAACATAACG
Found at i:3138 original size:24 final size:24
Alignment explanation
Indices: 3111--3189 Score: 133
Period size: 24 Copynumber: 3.3 Consensus size: 24
3101 TAAATGAATT
*
3111 AACATAAACG-AACATAACCGAACG
1 AACATAAA-GAAACATAATCGAACG
3135 AACATAAAGAAACATAATCGAACG
1 AACATAAAGAAACATAATCGAACG
3159 AACATAAAGAAACATAATCGAACG
1 AACATAAAGAAACATAATCGAACG
3183 AACATAA
1 AACATAA
3190 CCGAACGTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
23 1 0.02
24 52 0.98
ACGTcount: A:0.58, C:0.19, G:0.11, T:0.11
Consensus pattern (24 bp):
AACATAAAGAAACATAATCGAACG
Found at i:17135 original size:41 final size:41
Alignment explanation
Indices: 17078--17155 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
17068 AACTCCCAGG
* *
17078 GAAATAACACGGTTGACGCAGGATCCTAGAGGAAGAAAAGA
1 GAAATAACACGGTTGACACAGGATCCCAGAGGAAGAAAAGA
* *
17119 GAAATAACATGGTTGACACAGTATCCCAGAGGAAGAA
1 GAAATAACACGGTTGACACAGGATCCCAGAGGAAGAA
17156 TAAAGATGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.44, C:0.15, G:0.27, T:0.14
Consensus pattern (41 bp):
GAAATAACACGGTTGACACAGGATCCCAGAGGAAGAAAAGA
Found at i:28219 original size:7 final size:7
Alignment explanation
Indices: 28207--28232 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28197 TTTTTTATGT
28207 TTATGAA
1 TTATGAA
28214 TTATGAA
1 TTATGAA
28221 TTATGAA
1 TTATGAA
28228 TTATG
1 TTATG
28233 TTTGCTTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (7 bp):
TTATGAA
Found at i:31613 original size:11 final size:11
Alignment explanation
Indices: 31597--31643 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 11
31587 AGAAGAATGA
31597 AAATAAAAAAT
1 AAATAAAAAAT
31608 AAATAAAAAAT
1 AAATAAAAAAT
31619 AATAAGTAAAAAAT
1 -A-AA-TAAAAAAT
31633 -AATAGAAAAAT
1 AAATA-AAAAAT
31644 GTTCCTAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 2 0.06
11 19 0.59
12 1 0.03
13 2 0.06
14 8 0.25
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:31628 original size:14 final size:14
Alignment explanation
Indices: 31601--31636 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
31591 GAATGAAAAT
31601 AAAA-AATAAATAA
1 AAAATAATAAATAA
*
31614 AAAATAATAAGTAA
1 AAAATAATAAATAA
31628 AAAATAATA
1 AAAATAATA
31637 GAAAAATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (14 bp):
AAAATAATAAATAA
Found at i:32945 original size:13 final size:13
Alignment explanation
Indices: 32913--32958 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
32903 AAATTATAAC
*
32913 TAATAATATTAAA
1 TAATTATATTAAA
32926 T-ATTATATTAAA
1 TAATTATATTAAA
32938 TAATTATATTAAA
1 TAATTATATTAAA
32951 TATATTAT
1 TA-ATTAT
32959 GTATTTAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 11 0.37
13 14 0.47
14 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATTATATTAAA
Found at i:35952 original size:8 final size:8
Alignment explanation
Indices: 35939--35979 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
35929 CTCATTTTCA
35939 GAGAATTT
1 GAGAATTT
35947 GAGAATTT
1 GAGAATTT
*
35955 -AGAGTTT
1 GAGAATTT
*
35962 GGGAATTT
1 GAGAATTT
35970 GAGAATTT
1 GAGAATTT
35978 GA
1 GA
35980 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:36494 original size:125 final size:126
Alignment explanation
Indices: 36046--36774 Score: 1399
Period size: 126 Copynumber: 5.8 Consensus size: 126
36036 CTATAATCGG
*
36046 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
36111 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
36172 TTCACAATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
36237 TCATTGACCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
36298 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
36363 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCA-TACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
36423 TTCACAATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
36488 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
36549 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
36614 TCATTGCCCTATTATGTCATTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
36674 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
36739 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
36775 ATACTTAAAT
Statistics
Matches: 593, Mismatches: 8, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
125 248 0.42
126 345 0.58
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:36527 original size:251 final size:252
Alignment explanation
Indices: 36046--36774 Score: 1408
Period size: 251 Copynumber: 2.9 Consensus size: 252
36036 CTATAATCGG
*
36046 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
36111 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
36176 CAATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
131 CAATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
*
36241 TGACCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
196 TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
36298 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
36363 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCA-TACCTATTATTTCA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
36427 CAATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
131 CAATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
36492 TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
196 TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
36549 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
36614 TCATTGCCCTATTATGTCATTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTATTTCA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
*
36678 CTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
131 CAATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
*
36743 TGCCCTATTATGTCACTCATGTCCCTCGGGGA
196 TGCCCTATTATGTCATTCATGTCCCTCGGGGA
36775 ATACTTAAAT
Statistics
Matches: 472, Mismatches: 4, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
250 18 0.04
251 340 0.72
252 114 0.24
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (252 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
CAATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:37219 original size:33 final size:34
Alignment explanation
Indices: 37158--37257 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
37148 AAATTTAATG
*
37158 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
37192 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
37225 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
37258 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:37864 original size:21 final size:21
Alignment explanation
Indices: 37776--37869 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
37766 TATGGTATAA
*
37776 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
37797 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
37818 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
37839 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
37860 AACCCTGCGG
1 AACCCTGCGG
37870 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:39658 original size:15 final size:16
Alignment explanation
Indices: 39638--39709 Score: 53
Period size: 15 Copynumber: 4.7 Consensus size: 16
39628 ATAATTCTAA
39638 ATAAATAATAATT-AT
1 ATAAATAATAATTAAT
* *
39653 ATAAATATTATTTTAAT
1 ATAAATAATA-ATTAAT
* * *
39670 AAAAATAAT-ATTTAC
1 ATAAATAATAATTAAT
39685 ATAAAT-AT-ATTAAT
1 ATAAATAATAATTAAT
*
39699 ATAAAAAATAA
1 ATAAATAATAA
39710 CTATTTAAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
14 11 0.26
15 19 0.45
16 3 0.07
17 9 0.21
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAAATAATAATTAAT
Found at i:39688 original size:17 final size:16
Alignment explanation
Indices: 39640--39724 Score: 54
Period size: 17 Copynumber: 5.3 Consensus size: 16
39630 AATTCTAAAT
* *
39640 AAATAATAATT-ATAT
1 AAATAATATTTAATAA
*
39655 AAATATTATTTTAATAA
1 AAATAATA-TTTAATAA
39672 AAATAATATTTACAT--
1 AAATAATATTTA-ATAA
*
39687 AAAT-ATATTAATATAAA
1 AAATAATATTTA-AT-AA
39704 AAATAACTATTTAA-AA
1 AAATAA-TATTTAATAA
39720 AAATA
1 AAATA
39725 CTAACATAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
14 8 0.15
15 11 0.20
16 13 0.24
17 16 0.29
18 2 0.04
19 5 0.09
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATAATATTTAATAA
Found at i:39706 original size:32 final size:32
Alignment explanation
Indices: 39635--39716 Score: 87
Period size: 32 Copynumber: 2.5 Consensus size: 32
39625 TTAATAATTC
* * *
39635 TAAATAAATAATAATTATATAAATATTATTTTA
1 TAAA-AAATAATATTTACATAAATATTATTATA
39668 -ATAAAAATAATATTTACATAAATA-TATTAATA
1 TA-AAAAATAATATTTACATAAATATTATT-ATA
39700 TAAAAAATAACTATTTA
1 TAAAAAATAA-TATTTA
39717 AAAAAATACT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
31 4 0.10
32 29 0.69
33 9 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (32 bp):
TAAAAAATAATATTTACATAAATATTATTATA
Found at i:39734 original size:31 final size:32
Alignment explanation
Indices: 39670--39743 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
39660 TTATTTTAAT
* * *
39670 AAAAATAATATTTACATAAATATATTAATATA
1 AAAAATAATATTTACATAAAAATACTAACATA
39702 AAAAATAACTATTTA-A-AAAAATACTAACAT-
1 AAAAATAA-TATTTACATAAAAATACTAACATA
39732 AAAAATAA-ATTT
1 AAAAATAATATTT
39744 CTTACCACTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 4 0.11
30 8 0.21
31 11 0.29
32 9 0.24
33 6 0.16
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (32 bp):
AAAAATAATATTTACATAAAAATACTAACATA
Found at i:41559 original size:7 final size:7
Alignment explanation
Indices: 41547--41606 Score: 57
Period size: 7 Copynumber: 7.9 Consensus size: 7
41537 AATGGGGCTT
41547 ATAAAAA
1 ATAAAAA
41554 ATAAAAA
1 ATAAAAA
41561 ATAAAAATA
1 AT-AAAA-A
41570 ATAATAATA
1 ATAA-AA-A
*
41579 ATAATAA
1 ATAAAAA
41586 ATAAATAA
1 ATAAA-AA
*
41594 ATAAATA
1 ATAAAAA
41601 ATAAAA
1 ATAAAA
41607 TTATTTTGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
7 20 0.44
8 14 0.31
9 11 0.24
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
ATAAAAA
Found at i:41566 original size:6 final size:6
Alignment explanation
Indices: 41550--41606 Score: 51
Period size: 6 Copynumber: 8.7 Consensus size: 6
41540 GGGGCTTATA
* *
41550 AAAAAT AAAAAAT AAAAAT AATAAT AATAAT AATAAAT AAATAAAT AAATAAT
1 AAAAAT -AAAAAT AAAAAT AAAAAT AAAAAT AA-AAAT -AA-AAAT AAA-AAT
41603 AAAA
1 AAAA
41607 TTATTTTGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
6 21 0.47
7 17 0.38
8 7 0.16
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (6 bp):
AAAAAT
Found at i:41575 original size:12 final size:13
Alignment explanation
Indices: 41550--41606 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
41540 GGGGCTTATA
*
41550 AAAAATAAAAAAT
1 AAAAATAAATAAT
41563 AAAAATAATAATAAT
1 AAAAAT-A-AATAAT
*
41578 AATAATAAATAA-
1 AAAAATAAATAAT
*
41590 ATAAATAAATAAT
1 AAAAATAAATAAT
41603 AAAA
1 AAAA
41607 TTATTTTGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
12 10 0.28
13 14 0.39
14 2 0.06
15 10 0.28
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAATAAATAAT
Found at i:41587 original size:25 final size:25
Alignment explanation
Indices: 41553--41604 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
41543 GCTTATAAAA
41553 AATAAAAAATAAAAATAAT-AATAAT
1 AATAAAAAATAAAAA-AATAAATAAT
* *
41578 AATAATAAATAAATAAATAAATAAT
1 AATAAAAAATAAAAAAATAAATAAT
41603 AA
1 AA
41605 AATTATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (25 bp):
AATAAAAAATAAAAAAATAAATAAT
Found at i:41859 original size:2 final size:2
Alignment explanation
Indices: 41854--41904 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
41844 TAAACGTGTG
41854 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
41896 TA TA TA TA T
1 TA TA TA TA T
41905 TAAATACATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42342 original size:85 final size:86
Alignment explanation
Indices: 42182--42343 Score: 193
Period size: 85 Copynumber: 1.9 Consensus size: 86
42172 ATATCAACAT
* * * *
42182 AATTTAGTCCTTGAACTTTTAATTAGATATTCATTTAACATAATTAATTAGGGTTATTAATTAGA
1 AATTTAGTCATTGAACTTTT-ATTAGATATTCATTTAACATAATTAACTAGGATTAGTAATTAGA
* *
42247 GCTTTAATCTTAAACTCTACAC
65 GCCTCAATCTTAAACTCTACAC
* * * *
42269 AATTTAGTCATTGAAC-TTT-TTAGGTATTCATTTTGATATAATTAACTAGGATTGGTAATTAGA
1 AATTTAGTCATTGAACTTTTATTAGATATTCA-TTTAACATAATTAACTAGGATTAGTAATTAGA
*
42332 GCCTCCATCTTA
65 GCCTCAATCTTA
42344 GTTAAATTTC
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
84 10 0.16
85 35 0.56
86 3 0.05
87 15 0.24
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (86 bp):
AATTTAGTCATTGAACTTTTATTAGATATTCATTTAACATAATTAACTAGGATTAGTAATTAGAG
CCTCAATCTTAAACTCTACAC
Found at i:46552 original size:22 final size:22
Alignment explanation
Indices: 46522--46563 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
46512 AGGGTTCACT
* *
46522 AACCTTTCTATATTCTAAAACC
1 AACCATTCTAGATTCTAAAACC
46544 AACCATTCTAGATTCTAAAA
1 AACCATTCTAGATTCTAAAA
46564 AATACTAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.33
Consensus pattern (22 bp):
AACCATTCTAGATTCTAAAACC
Found at i:47078 original size:2 final size:2
Alignment explanation
Indices: 47073--47097 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47063 TGTTTGTGTG
47073 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
47098 GCACGAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56615 original size:17 final size:17
Alignment explanation
Indices: 56593--56626 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
56583 CTCAATCGTG
56593 AAAATTGAAACTTAAAT
1 AAAATTGAAACTTAAAT
*
56610 AAAATTGAAATTTAAAT
1 AAAATTGAAACTTAAAT
56627 CAATCTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (17 bp):
AAAATTGAAACTTAAAT
Found at i:59900 original size:42 final size:42
Alignment explanation
Indices: 59845--59925 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
59835 TGAACCCTCC
* * *
59845 TTTTTTACCTAGAG-AGTCATTTTCAGGTTTTCACTCTAATTT
1 TTTTTTACATAGAGCA-CCATTTTCAGGTTTTCAATCTAATTT
*
59887 TTTTTTACATAGAGCACCATTTTCGGGTTTTCAATCTAA
1 TTTTTTACATAGAGCACCATTTTCAGGTTTTCAATCTAA
59926 GTTCTTCAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.47
Consensus pattern (42 bp):
TTTTTTACATAGAGCACCATTTTCAGGTTTTCAATCTAATTT
Found at i:62472 original size:21 final size:21
Alignment explanation
Indices: 62443--62485 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
62433 ATGTTCCTTG
62443 GTATCGATACC-CTTCACATAT
1 GTATCGATACCTCTTC-CATAT
*
62464 GTATTGATACCTCTTCCATAT
1 GTATCGATACCTCTTCCATAT
62485 G
1 G
62486 GTACCTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.37
Consensus pattern (21 bp):
GTATCGATACCTCTTCCATAT
Done.