Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007508.1 Hibiscus syriacus cultivar Beakdansim tig00020837_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: 109732
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:356 original size:18 final size:18
Alignment explanation
Indices: 333--409 Score: 74
Period size: 18 Copynumber: 4.6 Consensus size: 18
323 GTCATAAACC
333 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
*
351 GACCCGACCCGACTC--T
1 GACCCGACCCGACCCGTT
* *
367 --CCTGACCCGA-TCGTT
1 GACCCGACCCGACCCGTT
* *
382 GACCCGACCCGACCTGCT
1 GACCCGACCCGACCCGTT
400 GACCCGACCC
1 GACCCGACCC
410 ATTGACCGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
13 2 0.04
14 9 0.19
15 1 0.02
16 1 0.02
17 9 0.19
18 26 0.54
ACGTcount: A:0.17, C:0.49, G:0.21, T:0.13
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:384 original size:31 final size:31
Alignment explanation
Indices: 338--416 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 31
328 AAACCGACCC
338 GACCCGACCCGTTGACCCGACCCGACTCTCCT
1 GACCCGACCCGTTGACCCGACCCGAC-CTCCT
* *
370 GACCCGA-TCGTTGACCCGACCCGACCTGCT
1 GACCCGACCCGTTGACCCGACCCGACCTCCT
*
400 GACCCGACCCATTGACC
1 GACCCGACCCGTTGACC
417 GTTGACCGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
30 11 0.26
31 24 0.57
32 7 0.17
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.15
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCTCCT
Found at i:1274 original size:18 final size:18
Alignment explanation
Indices: 1248--1282 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1238 TCGAAAGGAC
*
1248 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1266 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
1283 CCGGATGGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:3615 original size:22 final size:22
Alignment explanation
Indices: 3590--3644 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
3580 ATTTTTACAG
* * *
3590 TGTGACGCTCTGGTGGCCCTAA
1 TGTGACACTCCGGTGACCCTAA
3612 TGTGACACTCCGGTGACCCTAA
1 TGTGACACTCCGGTGACCCTAA
3634 TGTGACACTCC
1 TGTGACACTCC
3645 AAAGCGGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.18, C:0.31, G:0.25, T:0.25
Consensus pattern (22 bp):
TGTGACACTCCGGTGACCCTAA
Found at i:11228 original size:16 final size:16
Alignment explanation
Indices: 11204--11235 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11194 TATCGCCGAC
*
11204 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
11220 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
11236 TGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:18456 original size:16 final size:16
Alignment explanation
Indices: 18435--18476 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
18425 GTACTCAATT
18435 TAACTCGAATAGAAA-A
1 TAACTCGAATA-AAACA
*
18451 TAACTCAAATAAAACA
1 TAACTCGAATAAAACA
*
18467 TAACTTGAAT
1 TAACTCGAAT
18477 CTAAAGCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.24
Consensus pattern (16 bp):
TAACTCGAATAAAACA
Found at i:18758 original size:48 final size:48
Alignment explanation
Indices: 18687--18785 Score: 135
Period size: 48 Copynumber: 2.1 Consensus size: 48
18677 TCTAAACTCG
* * ** * *
18687 AAATGACCCGATTGAAATCGAACTTAAACTGAATACAATTCAAACTTA
1 AAATGACCCGATTGAAATAGAACTCAAACCAAATACAATCCAAACTAA
*
18735 AAATGACCCGATTGAACTAGAACTCAAACCAAATACAATCCAAACTAA
1 AAATGACCCGATTGAAATAGAACTCAAACCAAATACAATCCAAACTAA
18783 AAA
1 AAA
18786 AATGACCTGA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.49, C:0.21, G:0.09, T:0.20
Consensus pattern (48 bp):
AAATGACCCGATTGAAATAGAACTCAAACCAAATACAATCCAAACTAA
Found at i:33449 original size:33 final size:33
Alignment explanation
Indices: 33407--33470 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
33397 GTGACATATA
33407 TCACTATTTAATTGAAGATTAAATTTATTAATG
1 TCACTATTTAATTGAAGATTAAATTTATTAATG
33440 TCACTATTTAATTGAAGATTAAATTTATTAA
1 TCACTATTTAATTGAAGATTAAATTTATTAA
33471 ATTGAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (33 bp):
TCACTATTTAATTGAAGATTAAATTTATTAATG
Found at i:33481 original size:20 final size:21
Alignment explanation
Indices: 33444--33484 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33434 TTAATGTCAC
*
33444 TATTTAATTGAAGATTAAATT
1 TATTAAATTGAAGATTAAATT
*
33465 TATTAAATTGAA-TTTAAATT
1 TATTAAATTGAAGATTAAATT
33485 ATGGTCAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (21 bp):
TATTAAATTGAAGATTAAATT
Found at i:37663 original size:10 final size:11
Alignment explanation
Indices: 37648--37679 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
37638 TAAATAATTC
37648 ATTATAT-TAT
1 ATTATATATAT
37658 ATTATATATAT
1 ATTATATATAT
37669 A-TATATATAT
1 ATTATATATAT
37679 A
1 A
37680 AACTAACCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 17 0.81
11 4 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTATATATAT
Found at i:49336 original size:14 final size:15
Alignment explanation
Indices: 49304--49336 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
49294 TAAACTAAGT
49304 TAAAACTAATAATAA
1 TAAAACTAATAATAA
49319 -AAAACTAATAA-AA
1 TAAAACTAATAATAA
49332 TAAAA
1 TAAAA
49337 AAACGAACGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.12
14 15 0.88
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAAACTAATAATAA
Found at i:50694 original size:26 final size:27
Alignment explanation
Indices: 50664--50716 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
50654 ATTTTTGTTC
50664 GGTAATATAATTA-TTTTTTTATAAAA
1 GGTAATATAATTATTTTTTTTATAAAA
*
50690 GGTAATATGATTATTTTTTTTATAAAA
1 GGTAATATAATTATTTTTTTTATAAAA
50717 AATGAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (27 bp):
GGTAATATAATTATTTTTTTTATAAAA
Found at i:53376 original size:11 final size:11
Alignment explanation
Indices: 53360--53416 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
53350 ATATATATAT
53360 AATTATTAAAA
1 AATTATTAAAA
** *
53371 AATTATTTTAT
1 AATTATTAAAA
*
53382 GATTATT-AAA
1 AATTATTAAAA
53392 AATT-TTAAAAA
1 AATTATT-AAAA
53403 AATTATTAAAA
1 AATTATTAAAA
53414 AAT
1 AAT
53417 AACTATTGTA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
9 2 0.06
10 4 0.11
11 28 0.78
12 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
AATTATTAAAA
Found at i:61018 original size:20 final size:21
Alignment explanation
Indices: 60993--61044 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
60983 TTTTCCCAAT
*
60993 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
61013 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
61034 TCGCAATGCGA
1 TCGCAATGCGA
61045 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:61057 original size:41 final size:41
Alignment explanation
Indices: 61030--61107 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
61020 GCGAATTGGG
* * *
61030 AAAATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
*
61071 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATA
61108 CTGACTTTCG
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:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
Found at i:61058 original size:20 final size:20
Alignment explanation
Indices: 61033--61126 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
61023 AATTGGGAAA
*
61033 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
61053 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
61074 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
61094 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
61114 TTCGCAACGCGAT
1 ATCGCAACGCGAT
61127 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:61705 original size:19 final size:19
Alignment explanation
Indices: 61645--61725 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
61635 TTCGAGAATG
61645 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
61665 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
61681 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
61698 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
61717 AAAATCGCA
1 AAAATCGCA
61726 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:61772 original size:33 final size:33
Alignment explanation
Indices: 61735--61822 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
61725 ATTGCGATTT
* *
61735 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
61768 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
61801 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
61823 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:61824 original size:20 final size:20
Alignment explanation
Indices: 61790--61847 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
61780 GCGATTCTCT
**
61790 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
61810 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
61830 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
61848 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:63909 original size:42 final size:42
Alignment explanation
Indices: 63849--63971 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
63839 GTCCGACTCG
* * *
63849 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
63891 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
63933 ACTGTCATCATTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
63972 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:65347 original size:14 final size:14
Alignment explanation
Indices: 65328--65363 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
65318 ATTGTTTAAT
65328 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
65342 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
65356 TGATTTGT
1 TGATTTGT
65364 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:65571 original size:33 final size:32
Alignment explanation
Indices: 65526--65652 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
65516 ATTAAATTCG
* *
65526 CGTTGCGCTTTTCATTTTGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
65559 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
65592 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
65625 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
65653 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:65583 original size:19 final size:19
Alignment explanation
Indices: 65561--65652 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
65551 GATTCCCTCG
65561 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
65580 TTGCGA-----AATTAGCG
1 TTGCGATTTTCATTTCGCA
65594 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
65613 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
65627 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
65646 TTGCGAT
1 TTGCGAT
65653 AGTAATTTCC
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
14 17 0.31
16 7 0.13
17 7 0.13
19 24 0.44
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:65605 original size:66 final size:66
Alignment explanation
Indices: 65519--65651 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
65509 ACGCGAAATT
* * *
65519 AAATTCGCGTTGCGCTTTTCATTTTGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
65584 G
66 G
*
65585 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
65650 G
66 G
65651 A
1 A
65652 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:67960 original size:12 final size:12
Alignment explanation
Indices: 67943--67967 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
67933 TCTTCGGGGA
67943 CTTTTTCTTCTT
1 CTTTTTCTTCTT
67955 CTTTTTCTTCTT
1 CTTTTTCTTCTT
67967 C
1 C
67968 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:68176 original size:24 final size:24
Alignment explanation
Indices: 68142--68195 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
68132 CTGAAACATC
* *
68142 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
68166 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
68190 ATCAAA
1 ATCAAA
68196 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:69257 original size:20 final size:20
Alignment explanation
Indices: 69232--69289 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
69222 ATTCATTTGA
69232 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
69252 CTATCGCAACGCAAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
69272 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
69290 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:69349 original size:19 final size:19
Alignment explanation
Indices: 69308--69461 Score: 220
Period size: 19 Copynumber: 8.6 Consensus size: 19
69298 GAAATGAAAA
69308 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
69324 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
69341 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
69360 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
69376 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
69393 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
69412 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
69431 TCGCATTGCGATTTCCATT
1 TCGCATTGCGATTTTCATT
*
69450 TCGCGTTGCGAT
1 TCGCATTGCGAT
69462 AGTCTGTTTT
Statistics
Matches: 126, Mismatches: 2, Indels: 17
0.87 0.01 0.12
Matches are distributed among these distances:
14 22 0.17
16 6 0.05
17 6 0.05
19 92 0.73
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:69364 original size:52 final size:52
Alignment explanation
Indices: 69308--69461 Score: 245
Period size: 52 Copynumber: 2.9 Consensus size: 52
69298 GAAATGAAAA
69308 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
69360 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
* *
69412 TCGCATTGCGATTTTCATTTCGCATTGCGATTTCCATTTCGCGTTGCGAT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATTTCGCATTGCGAT
69462 AGTCTGTTTT
Statistics
Matches: 95, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
52 68 0.72
55 3 0.03
57 24 0.25
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:71488 original size:20 final size:19
Alignment explanation
Indices: 71453--71519 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
71443 GAAACTTAAA
71453 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
71472 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
71492 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
71511 ATCGCAACG
1 ATCGCAACG
71520 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:71527 original size:14 final size:14
Alignment explanation
Indices: 71508--71565 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
71498 ATGCGAAATG
71508 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
71522 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
71538 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
71554 AAAATCGCAACG
1 AAAATCGCAACG
71566 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:71550 original size:32 final size:33
Alignment explanation
Indices: 71492--71570 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
71482 GGAAATGGCT
*
71492 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
71525 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
71557 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
71571 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:71616 original size:14 final size:14
Alignment explanation
Indices: 71593--71656 Score: 67
Period size: 14 Copynumber: 4.4 Consensus size: 14
71583 TGCGATTTTC
71593 ATTTTG-CGTTGCG
1 ATTTTGTCGTTGCG
71606 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
*
71620 ATTTCATTTCGCATTGCG
1 ATTT--TGTCG--TTGCG
*
71638 ATTTTGTCGTTGCA
1 ATTTTGTCGTTGCG
71652 ATTTT
1 ATTTT
71657 CATTTCGCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
13 6 0.14
14 20 0.47
16 8 0.19
18 9 0.21
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.50
Consensus pattern (14 bp):
ATTTTGTCGTTGCG
Found at i:71663 original size:33 final size:33
Alignment explanation
Indices: 71582--71672 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
71572 ACAAATCGCA
* *
71582 TTGCGATTTTCATTTTGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
71615 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
71647 TTGCAATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
71673 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 29 0.54
33 25 0.46
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:71709 original size:19 final size:19
Alignment explanation
Indices: 71656--71710 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
71646 GTTGCAATTT
*
71656 TCATTTCGCATTGCGATAG
1 TCATTTCGCGTTGCGATAG
*
71675 CCATTTCCGCGTTGCGATAG
1 TCATTT-CGCGTTGCGATAG
*
71695 TCATTTCGTGTTGCGA
1 TCATTTCGCGTTGCGA
71711 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATAG
Found at i:72211 original size:18 final size:18
Alignment explanation
Indices: 72188--72226 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
72178 CAGACGATGA
* *
72188 CTCTGGGTGGGGTGATAG
1 CTCTGGGCGAGGTGATAG
*
72206 CTCTGGGCGAGGTGATGG
1 CTCTGGGCGAGGTGATAG
72224 CTC
1 CTC
72227 CCGAAGTGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.10, C:0.18, G:0.46, T:0.26
Consensus pattern (18 bp):
CTCTGGGCGAGGTGATAG
Found at i:73769 original size:22 final size:22
Alignment explanation
Indices: 73744--73787 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
73734 GATTTAGATA
73744 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
73766 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
73788 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:74060 original size:20 final size:20
Alignment explanation
Indices: 73955--74068 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
73945 CGCTTTGAAA
73955 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
73975 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
73995 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * * * *
74015 ATCTCGTTGTGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
74036 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
74056 ATCGCATTGCGAT
1 ATCGCATTGCGAT
74069 TTTCCCAATT
Statistics
Matches: 75, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 55 0.73
21 11 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:74070 original size:41 final size:41
Alignment explanation
Indices: 73994--74071 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
73984 CGAAAGTCAG
* * * *
73994 TATCGCGTTGCGAAAGTAAGTATCTCGTTGTGATTTTGTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
*
74035 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
74072 CCCAATTCGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
Found at i:74105 original size:41 final size:41
Alignment explanation
Indices: 74060--74149 Score: 153
Period size: 41 Copynumber: 2.2 Consensus size: 41
74050 GTAAGTATCG
* *
74060 CATTGCGATTTTCCCAATTCGTGTTGTGATTTACTTATTCA
1 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCA
*
74101 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
1 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCA
74142 CATTGCGA
1 CATTGCGA
74150 ATTGGGAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (41 bp):
CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCA
Found at i:74127 original size:21 final size:21
Alignment explanation
Indices: 74057--74149 Score: 73
Period size: 20 Copynumber: 4.5 Consensus size: 21
74047 ATAGTAAGTA
74057 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
** * * **
74078 TCGTGTTGTGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
74098 TCACATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
74119 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
74139 TCGCATTGCGA
1 TCGCATTGCGA
74150 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 19, Indels: 3
0.70 0.26 0.04
Matches are distributed among these distances:
20 29 0.56
21 23 0.44
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:74482 original size:21 final size:21
Alignment explanation
Indices: 74458--74501 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
74448 ATAATCTTTT
*
74458 AAGTAA-AAGTATAAATAAGCG
1 AAGTAATAA-TATAAATAAACG
*
74479 AAGTAATAATATATATAAACG
1 AAGTAATAATATAAATAAACG
74500 AA
1 AA
74502 TTACACTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.59, C:0.05, G:0.14, T:0.23
Consensus pattern (21 bp):
AAGTAATAATATAAATAAACG
Found at i:76020 original size:5 final size:5
Alignment explanation
Indices: 76012--76045 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
76002 CGCCGTTTGT
* *
76012 CTCGT CTCGG CTCGG CTCGG CACGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
76046 TGGTCATGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.03, C:0.41, G:0.35, T:0.21
Consensus pattern (5 bp):
CTCGG
Found at i:82206 original size:22 final size:22
Alignment explanation
Indices: 82181--82235 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
82171 TCAGGAGTTA
* *
82181 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
82203 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
82225 CGGGAGTTATA
1 CAGGAGTTATA
82236 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:89169 original size:2 final size:2
Alignment explanation
Indices: 89162--89186 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
89152 TTAAAATTTA
89162 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 A
89187 ATTTTTATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:92250 original size:75 final size:75
Alignment explanation
Indices: 92104--92253 Score: 210
Period size: 75 Copynumber: 2.0 Consensus size: 75
92094 GTTGAGCATA
* *** * ** *
92104 AATAAAATTTCAGGGTGGACACCATTTGTAAAATATGTGACTAATCGAAGAAAATTTATCTTTGA
1 AATAAAATTTCAGGATGGACACCATCAATAAAATATGTGACTAATCGAAGAAAATTCAGATTTCA
92169 GGGTAGACAC
66 GGGTAGACAC
*
92179 AATAAAATTTCAGGATGGGCACCATCAATAAAATATGTGACTAATCGAAGAAAATTCAGATTTCA
1 AATAAAATTTCAGGATGGACACCATCAATAAAATATGTGACTAATCGAAGAAAATTCAGATTTCA
*
92244 GTGTAGACAC
66 GGGTAGACAC
92254 GTGCCCACCT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (75 bp):
AATAAAATTTCAGGATGGACACCATCAATAAAATATGTGACTAATCGAAGAAAATTCAGATTTCA
GGGTAGACAC
Found at i:93638 original size:17 final size:17
Alignment explanation
Indices: 93598--93645 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
93588 ATGTCCTTTA
93598 ATAATA-ATATTCA-AT
1 ATAATATATATTCACAT
*
93613 ATCATATATATTCACAT
1 ATAATATATATTCACAT
*
93630 TTAATATATATTCACA
1 ATAATATATATTCACA
93646 CTGAATTGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 5 0.18
16 7 0.25
17 16 0.57
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAATATATATTCACAT
Found at i:97649 original size:16 final size:17
Alignment explanation
Indices: 97617--97649 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
97607 TAATTCTAAT
97617 TTTTGGTATCCAAATTC
1 TTTTGGTATCCAAATTC
*
97634 TTTTGGT-TCCATATTC
1 TTTTGGTATCCAAATTC
97650 ATTAGTTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (17 bp):
TTTTGGTATCCAAATTC
Found at i:100166 original size:65 final size:64
Alignment explanation
Indices: 99983--100174 Score: 205
Period size: 65 Copynumber: 3.0 Consensus size: 64
99973 AGTGCATCGG
* * *
99983 TGCATTCGATGTTTCA-AAATAGCCA-GAGTGCATCGATGCATGGCTGGTGCATCGATGCATCAA
1 TGCATTCGATGTTTCATAAA-A-TCATTAGTGCATCGATGCATGGTTGGTGCATCGATGCATCAA
100046 A
64 A
* *
100047 TGCATTCGATGTTTTCATAAAATCCTTAGTGCATCGATGCATGGTAT-GTGCATCGATGCATGAA
1 TGCATTCGATG-TTTCATAAAATCATTAGTGCATCGATGCATGGT-TGGTGCATCGATGCATCAA
100111 A
64 A
* * * *
100112 TGCATTCGATG-TTCAATTTAATTCATT-GTGCATCGATGCATGGATTGGTACATCGGTGCATCA
1 TGCATTCGATGTTTC-A-TAAAATCATTAGTGCATCGATGCATGG-TTGGTGCATCGATGCATCA
100175 CTTTGATAAA
Statistics
Matches: 109, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
63 3 0.03
64 30 0.28
65 72 0.66
66 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (64 bp):
TGCATTCGATGTTTCATAAAATCATTAGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAA
Found at i:107907 original size:2 final size:2
Alignment explanation
Indices: 107902--107926 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
107892 AACGAAACTG
107902 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
107927 CAACTAAGAG
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Done.