Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008407.1 Hibiscus syriacus cultivar Beakdansim tig00111176_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: 88503
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3570 original size:29 final size:29
Alignment explanation
Indices: 3538--3672 Score: 118
Period size: 29 Copynumber: 4.8 Consensus size: 29
3528 TTTACACAAG
*
3538 TAGCACCCTTTTTAAAATAATTACCAAAA
1 TAGCACCCTTTTCAAAATAATTACCAAAA
* *
3567 TAGCACCCTTTTCGAATTAATT-CTCAAAA
1 TAGCACCCTTTTCAAAATAATTAC-CAAAA
* * *
3596 TAGCACCAATTTT-AAATTAATTCCCAAAA
1 TAGCACC-CTTTTCAAAATAATTACCAAAA
* *
3625 TATCA--CTTTTCGAAA-AATTACCAAAA
1 TAGCACCCTTTTCAAAATAATTACCAAAA
* * *
3651 TAGCACCCATTTCGAATTAATT
1 TAGCACCCTTTTCAAAATAATT
3673 CTCAGAATAG
Statistics
Matches: 86, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
26 18 0.21
27 2 0.02
28 9 0.10
29 52 0.60
30 5 0.06
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (29 bp):
TAGCACCCTTTTCAAAATAATTACCAAAA
Found at i:3669 original size:55 final size:57
Alignment explanation
Indices: 3555--3682 Score: 145
Period size: 55 Copynumber: 2.3 Consensus size: 57
3545 CTTTTTAAAA
* * *
3555 TAATTACCAAAATAGCACCCTTTTCGAATTAATTCTCAAAATAGCACCAATTTTAAAT
1 TAATTCCCAAAATAGCA-CCTTTTCGAATAAATTCTCAAAATAGCACCAATTTCAAAT
* * *
3613 TAATTCCCAAAATATCA-CTTTTCGAA-AAATTAC-CAAAATAGCACCCATTTCGAAT
1 TAATTCCCAAAATAGCACCTTTTCGAATAAATT-CTCAAAATAGCACCAATTTCAAAT
* *
3668 TAATTCTCAGAATAG
1 TAATTCCCAAAATAG
3683 TACCAGAACC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
55 35 0.58
56 10 0.17
58 15 0.25
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.31
Consensus pattern (57 bp):
TAATTCCCAAAATAGCACCTTTTCGAATAAATTCTCAAAATAGCACCAATTTCAAAT
Found at i:3681 original size:29 final size:29
Alignment explanation
Indices: 3562--3715 Score: 129
Period size: 29 Copynumber: 5.4 Consensus size: 29
3552 AAATAATTAC
*
3562 CAAAATAGCACCCTTTTCGAATTAATTCT
1 CAAAATAGCACCCATTTCGAATTAATTCT
* ** *
3591 CAAAATAGCACCAATTTTAAATTAATTCC
1 CAAAATAGCACCCATTTCGAATTAATTCT
* * *
3620 CAAAATATCA--CTTTTCGAA-AAATTAC-
1 CAAAATAGCACCCATTTCGAATTAATT-CT
3646 CAAAATAGCACCCATTTCGAATTAATTCT
1 CAAAATAGCACCCATTTCGAATTAATTCT
* * ***
3675 CAGAATAGTA-CCAGAACCGAATTAATTCT
1 CAAAATAGCACCCA-TTTCGAATTAATTCT
*
3704 CAGAATAGCACC
1 CAAAATAGCACC
3716 GGTCAACGGT
Statistics
Matches: 98, Mismatches: 20, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
26 13 0.13
27 6 0.06
28 12 0.12
29 66 0.67
30 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.29
Consensus pattern (29 bp):
CAAAATAGCACCCATTTCGAATTAATTCT
Found at i:3753 original size:18 final size:18
Alignment explanation
Indices: 3723--3769 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
3713 ACCGGTCAAC
3723 GGTCAAC-GGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
3740 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
3758 GGTCAACGGGTC
1 GGTCAACGGGTC
3770 ATGACCGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 7 0.24
18 22 0.76
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:6982 original size:27 final size:27
Alignment explanation
Indices: 6930--6982 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
6920 TCTGTACTTA
*
6930 TTAAAAACATATATTAGTGTTTATTAT
1 TTAAAAACATATATTAGTGTTGATTAT
* *
6957 TTAAAATATATATTTTAG-GTTGATTA
1 TTAAAA-ACATATATTAGTGTTGATTA
6983 ATCAATATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (27 bp):
TTAAAAACATATATTAGTGTTGATTAT
Found at i:14100 original size:27 final size:29
Alignment explanation
Indices: 14042--14100 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
14032 ATTTCTGTAC
*
14042 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
14071 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
14098 TTA
1 TTA
14101 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:16473 original size:27 final size:29
Alignment explanation
Indices: 16415--16473 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
16405 ATTTATGTAC
*
16415 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
16444 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
16471 TTA
1 TTA
16474 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:18851 original size:27 final size:29
Alignment explanation
Indices: 18793--18851 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
18783 ATTTCTGTAC
*
18793 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
18822 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
18849 TTA
1 TTA
18852 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:21233 original size:13 final size:13
Alignment explanation
Indices: 21215--21270 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
21205 TGACCGGTCA
*
21215 CGACCCGTTCACC
1 CGACCCGTTGACC
21228 CGACCC---GACC
1 CGACCCGTTGACC
21238 CGACCCGTTGACC
1 CGACCCGTTGACC
*
21251 CGACTCGTTGACC
1 CGACCCGTTGACC
21264 CGACCCG
1 CGACCCG
21271 ATCGTTGACC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 9 0.24
13 28 0.76
ACGTcount: A:0.16, C:0.50, G:0.21, T:0.12
Consensus pattern (13 bp):
CGACCCGTTGACC
Found at i:21277 original size:17 final size:18
Alignment explanation
Indices: 21247--21280 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
21237 CCGACCCGTT
21247 GACCCGACTCGTTGACCC
1 GACCCGACTCGTTGACCC
21265 GACCCGA-TCGTTGACC
1 GACCCGACTCGTTGACC
21281 GTTGACCGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.18, C:0.41, G:0.24, T:0.18
Consensus pattern (18 bp):
GACCCGACTCGTTGACCC
Found at i:21383 original size:29 final size:29
Alignment explanation
Indices: 21288--21369 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
21278 ACCGTTGACC
21288 GGTGCTATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
21317 GGTGCTATTATGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
* *
21346 GGTGTTATTCTGGTAATTAATTCG
1 GGTGCTATTCTGGTAAATAATTCG
21370 AAATGAGTGC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.45
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:28452 original size:13 final size:13
Alignment explanation
Indices: 28434--28470 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
28424 GACCGGTCAC
28434 GACCCGACCCGTT
1 GACCCGACCCGTT
28447 GACCCGACCCGTT
1 GACCCGACCCGTT
28460 GACCCGACCCG
1 GACCCGACCCG
28471 ATCCGATCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.24, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:28536 original size:29 final size:29
Alignment explanation
Indices: 28494--28574 Score: 144
Period size: 29 Copynumber: 2.8 Consensus size: 29
28484 CGATTGACCA
*
28494 GTGCTATTCTGGTAAATAATTTGGTTTTG
1 GTGCTATTCTGGTAAATAATTCGGTTTTG
28523 GTGCTATTCTGGTAAATAATTCGGTTTTG
1 GTGCTATTCTGGTAAATAATTCGGTTTTG
*
28552 GTGCTATTCTGGTAATTAATTCG
1 GTGCTATTCTGGTAAATAATTCG
28575 AAATGGGTGC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (29 bp):
GTGCTATTCTGGTAAATAATTCGGTTTTG
Found at i:28583 original size:29 final size:29
Alignment explanation
Indices: 28494--28595 Score: 105
Period size: 29 Copynumber: 3.5 Consensus size: 29
28484 CGATTGACCA
* *** *
28494 GTGCTATTCTGGTAAATAATTTGGTTTTG
1 GTGCTATTCTGGTAAATAATTCGAAATGG
*** *
28523 GTGCTATTCTGGTAAATAATTCGGTTTTG
1 GTGCTATTCTGGTAAATAATTCGAAATGG
*
28552 GTGCTATTCTGGTAATTAATTCGAAATGG
1 GTGCTATTCTGGTAAATAATTCGAAATGG
*
28581 GTGCTATTTTGGTAA
1 GTGCTATTCTGGTAA
28596 TTATTTTAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.44
Consensus pattern (29 bp):
GTGCTATTCTGGTAAATAATTCGAAATGG
Found at i:28596 original size:29 final size:29
Alignment explanation
Indices: 28494--28617 Score: 104
Period size: 29 Copynumber: 4.3 Consensus size: 29
28484 CGATTGACCA
* * *** *
28494 GTGCTATTCTGGTAAATAATTTGGTTTTG
1 GTGCTATTCTGGTAATTAATTCGAAATGG
* *** *
28523 GTGCTATTCTGGTAAATAATTCGGTTTTG
1 GTGCTATTCTGGTAATTAATTCGAAATGG
28552 GTGCTATTCTGGTAATTAATTCGAAATGG
1 GTGCTATTCTGGTAATTAATTCGAAATGG
* * ** *
28581 GTGCTATTTTGGTAATTATTTTAAAAAGG
1 GTGCTATTCTGGTAATTAATTCGAAATGG
28610 GTGCTATT
1 GTGCTATT
28618 TGTGTAAAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 84 1.00
ACGTcount: A:0.24, C:0.08, G:0.23, T:0.44
Consensus pattern (29 bp):
GTGCTATTCTGGTAATTAATTCGAAATGG
Found at i:31141 original size:29 final size:29
Alignment explanation
Indices: 31117--31234 Score: 150
Period size: 29 Copynumber: 4.1 Consensus size: 29
31107 AAAAATTACT
*
31117 AAAATAGCACCTTTTCGAATTAAATTCCC
1 AAAATAGCACCATTTCGAATTAAATTCCC
*
31146 AAAATAGCAACATTTCGAATTAAATTCCC
1 AAAATAGCACCATTTCGAATTAAATTCCC
* * * *
31175 AATATAGCA-CTTTTTGAATTAAATTCCA
1 AAAATAGCACCATTTCGAATTAAATTCCC
*
31203 AAAATATCACCCATTTCGAATT-AATTCCC
1 AAAATAGCA-CCATTTCGAATTAAATTCCC
31232 AAA
1 AAA
31235 CTGTCACACG
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
28 23 0.30
29 44 0.58
30 9 0.12
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (29 bp):
AAAATAGCACCATTTCGAATTAAATTCCC
Found at i:31196 original size:57 final size:58
Alignment explanation
Indices: 31120--31233 Score: 169
Period size: 57 Copynumber: 2.0 Consensus size: 58
31110 AATTACTAAA
*
31120 ATAGCACCTTTTCGAATTAAATTCCCAAAATAGCA-ACATTTCGAATTAAATTCCCAAT
1 ATAGCACCTTTTCGAATTAAATTCCAAAAATAGCACACATTTCGAATT-AATTCCCAAT
* * *
31178 ATAGCA-CTTTTTGAATTAAATTCCAAAAATATCACCCATTTCGAATTAATTCCCAA
1 ATAGCACCTTTTCGAATTAAATTCCAAAAATAGCACACATTTCGAATTAATTCCCAA
31234 ACTGTCACAC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
57 34 0.67
58 17 0.33
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.32
Consensus pattern (58 bp):
ATAGCACCTTTTCGAATTAAATTCCAAAAATAGCACACATTTCGAATTAATTCCCAAT
Found at i:38916 original size:24 final size:24
Alignment explanation
Indices: 38886--38995 Score: 102
Period size: 24 Copynumber: 4.6 Consensus size: 24
38876 GTAAACAGAG
*
38886 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
38910 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
38934 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
38957 AGGTAAC-G-TATCAGAACAGAATTC
1 A--TATCAGAAATCAGAACAGAATTC
*
38981 A-ATTCGGAAATCAGA
1 ATA-TCAGAAATCAGA
38996 TAAAATATTT
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 16 0.23
24 50 0.71
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.20
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:38917 original size:12 final size:12
Alignment explanation
Indices: 38890--38981 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
38880 ACAGAGATAT
* *
38890 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
38902 CAGAATTCATAT
1 CAGAATTCAGAA
38914 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
38926 CAGAATCCAGAT
1 CAGAATTCAGAA
38938 CAGAA-TCAGAA
1 CAGAATTCAGAA
38949 CAGAATTCAGGTAA
1 CAGAATTCA-G-AA
*
38963 C-GTA-TCAGAA
1 CAGAATTCAGAA
38973 CAGAATTCA
1 CAGAATTCA
38982 ATTCGGAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.05
11 14 0.23
12 37 0.60
13 5 0.08
14 3 0.05
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:38951 original size:47 final size:47
Alignment explanation
Indices: 38888--38978 Score: 123
Period size: 47 Copynumber: 1.9 Consensus size: 47
38878 AAACAGAGAT
*
38888 ATCAGAAATCAAAACAGAATTCA-TATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGTAAC-G-TATCAGAACAGAATCCAG
*
38936 ATCAG-AATCAGAACAGAATTCAGGTAACGTATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCA-GTAACGTATCAGAACAGAAT
38979 TCAATTCGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
47 30 0.77
48 6 0.15
49 3 0.08
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.19
Consensus pattern (47 bp):
ATCAGAAATCAAAACAGAATTCAGTAACGTATCAGAACAGAATCCAG
Found at i:41422 original size:5 final size:5
Alignment explanation
Indices: 41412--41485 Score: 58
Period size: 5 Copynumber: 13.0 Consensus size: 5
41402 CAACGGTCAA
41412 CGGGT CGGGT CGGGT CAACGGGT CGGGT CGGGT CAACGGGT CGGGT CGGGT
1 CGGGT CGGGT CGGGT ---CGGGT CGGGT CGGGT ---CGGGT CGGGT CGGGT
*
41463 CAGGT CAACGGGT CGGGT CGGGT
1 CGGGT ---CGGGT CGGGT CGGGT
41486 TGTGACCGGT
Statistics
Matches: 58, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
5 44 0.76
8 14 0.24
ACGTcount: A:0.09, C:0.22, G:0.51, T:0.18
Consensus pattern (5 bp):
CGGGT
Found at i:41459 original size:23 final size:23
Alignment explanation
Indices: 41412--41485 Score: 104
Period size: 23 Copynumber: 3.4 Consensus size: 23
41402 CAACGGTCAA
*
41412 CGGGTCGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAGGTCAACGGGT
41435 CGGGTC--G---GGTCAACGGGT
1 CGGGTCGGGTCAGGTCAACGGGT
41453 CGGGTCGGGTCAGGTCAACGGGT
1 CGGGTCGGGTCAGGTCAACGGGT
41476 CGGGTCGGGT
1 CGGGTCGGGT
41486 TGTGACCGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
18 17 0.37
20 1 0.02
21 1 0.02
23 27 0.59
ACGTcount: A:0.09, C:0.22, G:0.51, T:0.18
Consensus pattern (23 bp):
CGGGTCGGGTCAGGTCAACGGGT
Found at i:41481 original size:18 final size:18
Alignment explanation
Indices: 41406--41464 Score: 118
Period size: 18 Copynumber: 3.3 Consensus size: 18
41396 TTTGGTCAAC
41406 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
41424 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
41442 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
41460 GGTCA
1 GGTCA
41465 GGTCAACGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:42318 original size:29 final size:29
Alignment explanation
Indices: 42293--42412 Score: 136
Period size: 29 Copynumber: 4.2 Consensus size: 29
42283 AATAATTACT
42293 AAAATAGCACCTTTTTGAATTAAATTCCC
1 AAAATAGCACCTTTTTGAATTAAATTCCC
* * * *
42322 AAAATAACATCTATTCGAATTAAATTCCC
1 AAAATAGCACCTTTTTGAATTAAATTCCC
* *
42351 AATATAGCA-TTTTTTGAATTAAATTCCC
1 AAAATAGCACCTTTTTGAATTAAATTCCC
* * *
42379 AAAATATCACCCATTTCGAATT-AATTCCC
1 AAAATAGCA-CCTTTTTGAATTAAATTCCC
42408 AAAAT
1 AAAAT
42413 GTCACCCGGT
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
28 23 0.31
29 44 0.59
30 8 0.11
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAATAGCACCTTTTTGAATTAAATTCCC
Found at i:45793 original size:29 final size:29
Alignment explanation
Indices: 45742--45879 Score: 185
Period size: 28 Copynumber: 4.9 Consensus size: 29
45732 ATAGTCCACA
* *
45742 TTCAAAA-ATTT-CCAAAATGTCACCTTT
1 TTCAAAATATTTCCCAGAATGTCACCATT
* *
45769 TTCAAAATAATTCCCAGAATATCA-CATT
1 TTCAAAATATTTCCCAGAATGTCACCATT
*
45797 TTCAAAATATTTCCTAGAATGTCA-CATT
1 TTCAAAATATTTCCCAGAATGTCACCATT
*
45825 TTCAAAATATTTCCCAGAATGTCACCTTT
1 TTCAAAATATTTCCCAGAATGTCACCATT
*
45854 TTCAAAATATTTCCCAAAATGTCACC
1 TTCAAAATATTTCCCAGAATGTCACC
45880 GGGTCAGGTC
Statistics
Matches: 98, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
27 7 0.07
28 54 0.55
29 37 0.38
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.36
Consensus pattern (29 bp):
TTCAAAATATTTCCCAGAATGTCACCATT
Found at i:45861 original size:57 final size:55
Alignment explanation
Indices: 45742--45878 Score: 186
Period size: 57 Copynumber: 2.4 Consensus size: 55
45732 ATAGTCCACA
*
45742 TTCAAAA-ATTTCCAAAATGTCACCTTTTTCAAAATAATTCCCAGAATATCACATT
1 TTCAAAATATTTCCAAAATGTCA-CATTTTCAAAATAATTCCCAGAATATCACATT
* * * *
45797 TTCAAAATATTTCCTAGAATGTCACATTTTCAAAATATTTCCCAGAATGTCACCTTT
1 TTCAAAATATTTCC-AAAATGTCACATTTTCAAAATAATTCCCAGAATATCA-CATT
45854 TTCAAAATATTTCCCAAAATGTCAC
1 TTCAAAATATTT-CCAAAATGTCAC
45879 CGGGTCAGGT
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
55 7 0.10
56 31 0.43
57 32 0.44
58 2 0.03
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.36
Consensus pattern (55 bp):
TTCAAAATATTTCCAAAATGTCACATTTTCAAAATAATTCCCAGAATATCACATT
Found at i:53325 original size:28 final size:29
Alignment explanation
Indices: 53272--53366 Score: 156
Period size: 29 Copynumber: 3.3 Consensus size: 29
53262 AAATTTTCAA
*
53272 AATGTCACCTTTTTCAAAATAATTCCCAG
1 AATGTCACCTTTTTCAAAATATTTCCCAG
* *
53301 AATGTCA-CATTTTCAAAATATTTCCTAG
1 AATGTCACCTTTTTCAAAATATTTCCCAG
53329 AATGTCACCTTTTTCAAAATATTTCCCAG
1 AATGTCACCTTTTTCAAAATATTTCCCAG
53358 AATGTCACC
1 AATGTCACC
53367 GGGTCGGGTC
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
28 25 0.42
29 35 0.58
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (29 bp):
AATGTCACCTTTTTCAAAATATTTCCCAG
Found at i:53388 original size:17 final size:18
Alignment explanation
Indices: 53361--53399 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
53351 TTCCCAGAAT
53361 GTCACCGGGTCGGGTCGG
1 GTCACCGGGTCGGGTCGG
53379 GTCA-CGGGTCGGGTCGG
1 GTCACCGGGTCGGGTCGG
53396 GTCA
1 GTCA
53400 GACCGATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.08, C:0.26, G:0.49, T:0.18
Consensus pattern (18 bp):
GTCACCGGGTCGGGTCGG
Found at i:53421 original size:19 final size:19
Alignment explanation
Indices: 53397--53460 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
53387 TCGGGTCGGG
* *
53397 TCAGACCGATCAACCCGGT
1 TCAGACCGGTCAAACCGGT
*
53416 TCAGACCGGTCAAATCGGT
1 TCAGACCGGTCAAACCGGT
*
53435 TCAGGCCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
53454 TAAGACC
1 TCAGACC
53461 CGTTTGGACA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.27, C:0.31, G:0.25, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:53565 original size:12 final size:12
Alignment explanation
Indices: 53548--53572 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53538 CCGCTTCCGG
53548 CCTCCAAAAATT
1 CCTCCAAAAATT
53560 CCTCCAAAAATT
1 CCTCCAAAAATT
53572 C
1 C
53573 TTTTAAGCGA
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:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (12 bp):
CCTCCAAAAATT
Found at i:60440 original size:27 final size:29
Alignment explanation
Indices: 60382--60440 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
60372 ATTTCTGTAC
*
60382 TTATTGAAAACATATATGGTTAGTGTTTA
1 TTATTGAAAACATATATGGTTAGTGTTGA
* * *
60411 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTGAAAACATATATGGTTAGTGTTGA
60438 TTA
1 TTA
60441 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.49
Consensus pattern (29 bp):
TTATTGAAAACATATATGGTTAGTGTTGA
Found at i:62363 original size:9 final size:9
Alignment explanation
Indices: 62349--62416 Score: 55
Period size: 10 Copynumber: 7.0 Consensus size: 9
62339 GGCTGCTGGA
62349 AACCGGTTT
1 AACCGGTTT
62358 AACCGGTTTT
1 AACCGG-TTT
*
62368 CAACCAGTTCT
1 -AACCGGTT-T
*
62379 GACCGGTTT
1 AACCGGTTT
*
62388 GACCGGTTT
1 AACCGGTTT
*
62397 CAACCGGTTCG
1 -AACCGGTT-T
62408 AACCGGTTT
1 AACCGGTTT
62417 GATCGGTCTG
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
9 16 0.33
10 26 0.54
11 6 0.12
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (9 bp):
AACCGGTTT
Found at i:62404 original size:10 final size:10
Alignment explanation
Indices: 62349--62416 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 10
62339 GGCTGCTGGA
62349 AACCGGTTT-
1 AACCGGTTTC
62358 AACCGGTTTTC
1 AACCGG-TTTC
*
62369 AACCAG-TTC
1 AACCGGTTTC
*
62378 TGACCGGTTT-
1 -AACCGGTTTC
*
62388 GACCGGTTTC
1 AACCGGTTTC
62398 AACCGG-TTC
1 AACCGGTTTC
62407 GAACCGGTTT
1 -AACCGGTTT
62417 GATCGGTCTG
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
9 21 0.44
10 18 0.38
11 9 0.19
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (10 bp):
AACCGGTTTC
Found at i:62412 original size:29 final size:30
Alignment explanation
Indices: 62349--62423 Score: 100
Period size: 29 Copynumber: 2.5 Consensus size: 30
62339 GGCTGCTGGA
*
62349 AACCGGTTTAACCGGTTTTCAACCAGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCAGTTCTG
*
62380 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCAGTTCTG
*
62408 AACCGGTTTGATCGGT
1 AACCGGTTTGACCGGT
62424 CTGAGACCGG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 1 0.03
29 26 0.65
30 13 0.32
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCAGTTCTG
Found at i:62462 original size:5 final size:5
Alignment explanation
Indices: 62454--62494 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
62444 TCCGACCGTT
*
62454 GACCC GACCC GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC
62495 GTTGACCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.20, C:0.54, G:0.22, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:62463 original size:22 final size:22
Alignment explanation
Indices: 62437--62501 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
62427 AGACCGGTCT
*
62437 GACCCGATCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
62459 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
62481 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
62502 GTTGACCGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:62503 original size:7 final size:7
Alignment explanation
Indices: 62491--62535 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
62481 GACCCGACCC
62491 GACCGTT
1 GACCGTT
62498 GACCGTT
1 GACCGTT
62505 GACCGTT
1 GACCGTT
62512 GACCGTT
1 GACCGTT
62519 GACCGTT
1 GACCGTT
62526 GACCGTT
1 GACCGTT
62533 GAC
1 GAC
62536 TTTCTTTGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:69681 original size:9 final size:9
Alignment explanation
Indices: 69667--69760 Score: 62
Period size: 10 Copynumber: 9.8 Consensus size: 9
69657 GGCTGCTGGA
69667 AACCGGTTT
1 AACCGGTTT
69676 AACCGGTTTT
1 AACCGG-TTT
69686 CAACCGGTTCT
1 -AACCGGTT-T
*
69697 GACCGGTTT
1 AACCGGTTT
*
69706 GACCGGTTT
1 AACCGGTTT
* *
69715 CAACCAGTTCG
1 -AACCGGTT-T
69726 AACCGGTTT
1 AACCGGTTT
* *
69735 GACCGGTCTG
1 AACCGGT-TT
*
69745 AATCGGTTT
1 AACCGGTTT
*
69754 GACCGGT
1 AACCGGT
69761 CTGACCCGAT
Statistics
Matches: 66, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
9 28 0.42
10 31 0.47
11 7 0.11
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:69692 original size:20 final size:21
Alignment explanation
Indices: 69667--69705 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
69657 GGCTGCTGGA
69667 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
69687 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
69706 GACCGGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:69712 original size:19 final size:19
Alignment explanation
Indices: 69669--69766 Score: 69
Period size: 19 Copynumber: 5.1 Consensus size: 19
69659 CTGCTGGAAA
* * *
69669 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
69689 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
* *
69708 CCGGTTTCAACCAGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
69728 CCGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
*
69747 TCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
69765 CC
1 CC
69767 CGATCCGACC
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
18 5 0.08
19 37 0.57
20 15 0.23
21 8 0.12
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:69730 original size:29 final size:30
Alignment explanation
Indices: 69667--69741 Score: 109
Period size: 29 Copynumber: 2.5 Consensus size: 30
69657 GGCTGCTGGA
* *
69667 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCAGTTCTG
69698 -ACCGGTTTGACCGGTTTCAACCAGTTC-G
1 AACCGGTTTGACCGGTTTCAACCAGTTCTG
69726 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
69742 CTGAATCGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 1 0.02
29 27 0.66
30 13 0.32
ACGTcount: A:0.19, C:0.27, G:0.25, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCAGTTCTG
Found at i:69788 original size:5 final size:5
Alignment explanation
Indices: 69780--69830 Score: 75
Period size: 5 Copynumber: 9.8 Consensus size: 5
69770 TCCGACCGTT
*
69780 GACCC GACCC GACCC GACCGTT GACCC GACCC GACCC GACCC GACCC GACC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACCC GACCC GACC
69831 GTTGACCGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 38 0.90
7 4 0.10
ACGTcount: A:0.20, C:0.55, G:0.22, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:69789 original size:22 final size:22
Alignment explanation
Indices: 69763--69820 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
69753 TGACCGGTCT
*
69763 GACCCGATCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
69785 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
69807 GACCCGACCCGACC
1 GACCCGACCCGACC
69821 CGACCCGACC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.19, C:0.50, G:0.22, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:69839 original size:7 final size:7
Alignment explanation
Indices: 69827--69857 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
69817 GACCCGACCC
69827 GACCGTT
1 GACCGTT
69834 GACCGTT
1 GACCGTT
69841 GACCGTT
1 GACCGTT
69848 GACCGTT
1 GACCGTT
69855 GAC
1 GAC
69858 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:74920 original size:27 final size:29
Alignment explanation
Indices: 74862--74920 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
74852 ATTTCTGTAC
*
74862 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
74891 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
74918 TTA
1 TTA
74921 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:84294 original size:27 final size:29
Alignment explanation
Indices: 84236--84294 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
84226 ATTTATGTAC
*
84236 TTATTTAAAACATATATGGTTAGTGTTTA
1 TTATTTAAAACATATATGGTTAGTGTTGA
* *
84265 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTTAAAACATATATGGTTAGTGTTGA
84292 TTA
1 TTA
84295 ATCAATATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 7 0.26
28 4 0.15
29 16 0.59
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.51
Consensus pattern (29 bp):
TTATTTAAAACATATATGGTTAGTGTTGA
Done.