Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004686.1 Hibiscus syriacus cultivar Beakdansim tig00010505_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: 144693
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4510 original size:27 final size:27
Alignment explanation
Indices: 4480--4537 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
4470 TAAAAGTACT
4480 TTTTAAAAATT-ATAACTTTATAATTAA
1 TTTT-AAAATTCATAACTTTATAATTAA
**
4507 TTTTTTAATTCATAACTTTATAATTAA
1 TTTTAAAATTCATAACTTTATAATTAA
4534 TTTT
1 TTTT
4538 TAATATGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTTAAAATTCATAACTTTATAATTAA
Found at i:4541 original size:26 final size:26
Alignment explanation
Indices: 4487--4538 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
4477 ACTTTTTAAA
4487 AATTATAACTTTATAATTAATTTTTT
1 AATTATAACTTTATAATTAATTTTTT
4513 AATTCATAACTTTATAATTAATTTTT
1 AATT-ATAACTTTATAATTAATTTTT
4539 AATATGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (26 bp):
AATTATAACTTTATAATTAATTTTTT
Found at i:5263 original size:19 final size:19
Alignment explanation
Indices: 5223--5264 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
5213 AAAATAACTA
* *
5223 TTTTGATTTTAATCATTAT
1 TTTTAATTTTAATCAATAT
5242 TTTTAATTTTAATCAA-AT
1 TTTTAATTTTAATCAATAT
5260 TTTTA
1 TTTTA
5265 TTAATTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTAATTTTAATCAATAT
Found at i:5967 original size:21 final size:21
Alignment explanation
Indices: 5924--5967 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5914 TATTTTCATG
* **
5924 TTGATATTGTAGTTCGCGGTA
1 TTGATATTGTAGTTCACAATA
5945 TTGATATTGTAGTTCACAATA
1 TTGATATTGTAGTTCACAATA
5966 TT
1 TT
5968 AATGTAACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.09, G:0.20, T:0.45
Consensus pattern (21 bp):
TTGATATTGTAGTTCACAATA
Found at i:7701 original size:34 final size:34
Alignment explanation
Indices: 7653--7725 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
7643 TGGGCTGAAT
*
7653 ATAAACGAACATACACATACATAAATGAACAAAC
1 ATAAACGAACATACACAGACATAAATGAACAAAC
* * *
7687 ATAAACGAATATACACGGACATAGATGAACAAAC
1 ATAAACGAACATACACAGACATAAATGAACAAAC
7721 ATAAA
1 ATAAA
7726 TAGACATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.58, C:0.18, G:0.10, T:0.15
Consensus pattern (34 bp):
ATAAACGAACATACACAGACATAAATGAACAAAC
Found at i:14614 original size:17 final size:17
Alignment explanation
Indices: 14588--14625 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
14578 GATCGACTCA
14588 ATCTCGAATAACTCACG
1 ATCTCGAATAACTCACG
*
14605 ATCTCTAATAACTCACG
1 ATCTCGAATAACTCACG
14622 ATCT
1 ATCT
14626 GTCTCATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29
Consensus pattern (17 bp):
ATCTCGAATAACTCACG
Found at i:17881 original size:25 final size:25
Alignment explanation
Indices: 17862--17912 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
17852 AATTAGAGTC
*
17862 ATAAT-AATAAATAAATATTATAAAA
1 ATAATGAA-AAATAAATATTAGAAAA
17887 ATAATGAAAAATAAATATTAGAAAA
1 ATAATGAAAAATAAATATTAGAAAA
17912 A
1 A
17913 GTGAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (25 bp):
ATAATGAAAAATAAATATTAGAAAA
Found at i:18456 original size:31 final size:29
Alignment explanation
Indices: 18421--18492 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 29
18411 AGTTATGCTC
18421 ATAATAACAAATA-TCGAAAAAAATTAGACCT-
1 ATAATAACAAATACT-G--AAAAATTAGA-CTA
*
18452 ATAATAA-AAGTACTGAAAAATTAGACTA
1 ATAATAACAAATACTGAAAAATTAGACTA
18480 ATAATAACAAATA
1 ATAATAACAAATA
18493 AATATTAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
27 2 0.06
28 17 0.47
29 4 0.11
30 5 0.14
31 8 0.22
ACGTcount: A:0.60, C:0.10, G:0.07, T:0.24
Consensus pattern (29 bp):
ATAATAACAAATACTGAAAAATTAGACTA
Found at i:18652 original size:43 final size:43
Alignment explanation
Indices: 18569--18652 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
18559 TGAGAATAAA
* * *
18569 TATTGAAAAAAATGAACTTTTAATAGCAAATGTTAGAAAAAAG
1 TATTGAAAAAAATGAACATTTAATAGCAAATATTAAAAAAAAG
*
18612 TATTGACAAAAAATTGAACATTT-AT-GTAAATATTAAAAAAA
1 TATTGA-AAAAAA-TGAACATTTAATAGCAAATATTAAAAAAA
18653 TAAATAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
43 19 0.54
44 8 0.23
45 8 0.23
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.30
Consensus pattern (43 bp):
TATTGAAAAAAATGAACATTTAATAGCAAATATTAAAAAAAAG
Found at i:20242 original size:58 final size:58
Alignment explanation
Indices: 20149--20274 Score: 207
Period size: 58 Copynumber: 2.2 Consensus size: 58
20139 GGCAAGATTG
*
20149 AAGAAACTTGGATCACACGTAATTGGATTTCGTACCTGCCAGTTAGAGTTTATATAGA
1 AAGAAACTTGGATCACAAGTAATTGGATTTCGTACCTGCCAGTTAGAGTTTATATAGA
* * * *
20207 AAGAAACTTGGGTTATAAGTAATTGGATTTTGTACCTGCCAGTTAGAGTTTATATAGA
1 AAGAAACTTGGATCACAAGTAATTGGATTTCGTACCTGCCAGTTAGAGTTTATATAGA
20265 AAGAAACTTG
1 AAGAAACTTG
20275 CTTCCAATGT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 63 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (58 bp):
AAGAAACTTGGATCACAAGTAATTGGATTTCGTACCTGCCAGTTAGAGTTTATATAGA
Found at i:25231 original size:114 final size:112
Alignment explanation
Indices: 25025--25583 Score: 593
Period size: 111 Copynumber: 5.0 Consensus size: 112
25015 AGAGGGGCTT
* * ** *
25025 CTGCTGCTGAACCAGATGGCCATTCCAGGCAGGAGTTGTGCCTTGAGTGCATAACTGCTCATATC
1 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCACATGACTGCTCATATC
* ** *
25090 GAGGTGATCCTATGTTTGATATGGTTCCATTTGCTTGAAAATTATGCGG
66 GAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAATT-T-CGG
* * * * *
25139 CTGCTGCTGAACCAGCTGGCCACTCCAGGCAGGACTTGAGCCTTGATCACATGTCTGCTCATAAC
1 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCACATGACTGCTCATATC
* * * *
25204 GAGGTGATCCCATGCTTGACACAGTTCCATTGGCATGAAAATCCTGT-GA
66 GAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAAT--T-TCGG
* ** * * *
25253 CTGCTGCTGAACCAGTTGGCCGCTCCAGGCAGGACTTGTGCCTTGAGAACATGTCTGCTCATAGC
1 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCACATGACTGCTCATATC
* * * *
25318 GAGGTGATCCCAAGTTTGATACAGTTCCATTTCCATGGAAA-TTCTG
66 GAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAATTTCGG
* * * * *
25364 CTGCTGCTGAACCATCTGTCCATTCCAGGAAGGACCTGTGCCTTGAGCATATGACTGCTCATATC
1 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCACATGACTGCTCATATC
* * * * * *
25429 CAGGTGATCCCATGTTTGGTACAGCTCCATTCGCAGGAAAATTT-TG
66 GAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAATTTCGG
** * * * * *
25475 CTGCTGCTGAACCATTTGGCCATTCCAGGCAGGACGTGTACATTGAGCATATGACTGCTCGTATC
1 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCACATGACTGCTCATATC
** * * *
25540 GAGGCAATCCCGTGTTTGGTACAGTTCCATTCGCATGAAAATTT
66 GAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAATTT
25584 TGTTGTTGTT
Statistics
Matches: 376, Mismatches: 65, Indels: 11
0.83 0.14 0.02
Matches are distributed among these distances:
110 1 0.00
111 186 0.49
112 2 0.01
114 185 0.49
116 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (112 bp):
CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCACATGACTGCTCATATC
GAGGTGATCCCATGTTTGATACAGTTCCATTTGCATGAAAATTTCGG
Found at i:30232 original size:14 final size:14
Alignment explanation
Indices: 30195--30238 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
30185 ATGTTTTATA
*
30195 TAAT-TTTTATTTT
1 TAATATTTTAATTT
30208 TAGATTATTTTAATTT
1 TA-A-TATTTTAATTT
30224 TAATATTTTAATTT
1 TAATATTTTAATTT
30238 T
1 T
30239 TAGTTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 2 0.07
14 13 0.48
15 2 0.07
16 10 0.37
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (14 bp):
TAATATTTTAATTT
Found at i:41874 original size:14 final size:14
Alignment explanation
Indices: 41835--41875 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
41825 ATGAATTACA
* *
41835 TTTCTGGAAAACGT
1 TTTCCGGAAAATGT
41849 TTTCCGGAAAATGT
1 TTTCCGGAAAATGT
*
41863 TTTCCGTAAAATG
1 TTTCCGGAAAATG
41876 AATTACATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (14 bp):
TTTCCGGAAAATGT
Found at i:42210 original size:23 final size:23
Alignment explanation
Indices: 42166--42236 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
42156 AGTGTTATAT
* *
42166 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAATATATTAATTAA
* *
42189 TATATTTTAAATATCTTTATTAA
1 TATATTTTAAATATATTAATTAA
* * *
42212 AATATTATAAATATA-TAAATAA
1 TATATTTTAAATATATTAATTAA
42234 TAT
1 TAT
42237 TATTCATTAT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
22 7 0.18
23 31 0.82
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (23 bp):
TATATTTTAAATATATTAATTAA
Found at i:42289 original size:54 final size:55
Alignment explanation
Indices: 42226--42365 Score: 143
Period size: 55 Copynumber: 2.6 Consensus size: 55
42216 TTATAAATAT
*
42226 ATAAATAATATTATTCATTATTAAATATATAATT-TT-TTATTATATATTATTAAAA
1 ATAAATAATATTATT-ATTATTAAATATATAATTATTATT-TTATATAATATTAAAA
*
42281 A-AAATAATATCT-TATATTATTATA-ATATAATTGATTATTTTATATAATATTAAAA
1 ATAAATAATAT-TAT-TATTATTAAATATATAATT-ATTATTTTATATAATATTAAAA
*
42336 ATATAAT-ATAATATTATTA-TAAATAT-TAAT
1 ATA-AATAATATTATTATTATTAAATATATAAT
42366 AAATAATATT
Statistics
Matches: 72, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
53 8 0.11
54 25 0.35
55 29 0.40
56 7 0.10
57 3 0.04
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (55 bp):
ATAAATAATATTATTATTATTAAATATATAATTATTATTTTATATAATATTAAAA
Found at i:42332 original size:15 final size:16
Alignment explanation
Indices: 42294--42357 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 16
42284 ATAATATCTT
42294 ATATTATTATAATATA
1 ATATTATTATAATATA
*
42310 ATTGATTATT-TTATATA
1 A-T-ATTATTATAATATA
*
42327 ATATTAAAAATATAATATA
1 ATATT---ATTATAATATA
42346 ATATTATTATAA
1 ATATTATTATAA
42358 ATATTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
15 3 0.08
16 8 0.21
17 8 0.21
18 8 0.21
19 11 0.29
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
ATATTATTATAATATA
Found at i:42359 original size:22 final size:22
Alignment explanation
Indices: 42324--42375 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
42314 ATTATTTTAT
42324 ATAATATTAAAAATA-TAATATA
1 ATAATATTAAAAATATTAATA-A
* *
42346 ATATTATTATAAATATTAATAA
1 ATAATATTAAAAATATTAATAA
42368 ATAATATT
1 ATAATATT
42376 TTGATGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAATATTAAAAATATTAATAA
Found at i:42616 original size:41 final size:42
Alignment explanation
Indices: 42546--42653 Score: 148
Period size: 41 Copynumber: 2.6 Consensus size: 42
42536 CAGGAAAATC
* *
42546 AATTACGTGAAACAAACACTGAAAAATATTTTTCGAAA-AACG
1 AATTACGTGAAACAAACACTGAAATATA-TTTTCGAAAGAACA
* *
42588 AATTACGTGAAATAAACAC-GAAATATATTTTCTAAAGAACA
1 AATTACGTGAAACAAACACTGAAATATATTTTCGAAAGAACA
*
42629 AATTACATGAAACAAACACTGAAAT
1 AATTACGTGAAACAAACACTGAAAT
42654 TTAAAGAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
40 8 0.14
41 27 0.47
42 23 0.40
ACGTcount: A:0.52, C:0.14, G:0.10, T:0.24
Consensus pattern (42 bp):
AATTACGTGAAACAAACACTGAAATATATTTTCGAAAGAACA
Found at i:47185 original size:32 final size:32
Alignment explanation
Indices: 47149--47255 Score: 99
Period size: 32 Copynumber: 3.3 Consensus size: 32
47139 CAATTTTATA
*
47149 TAAAATTATTTAAAATAAAATAAACATCAATT
1 TAAAACTATTTAAAATAAAATAAACATCAATT
* ** * ** *
47181 TAAAACTATTTAGAATATTTATCAAA-TTTTATA
1 TAAAACTATTTAAAATA-AAAT-AAACATCAATT
*
47214 TAAAACTATTTAAAATAAAATAAACATCACTT
1 TAAAACTATTTAAAATAAAATAAACATCAATT
*
47246 TAAAAATATT
1 TAAAACTATT
47256 AATATTATAA
Statistics
Matches: 55, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
31 3 0.05
32 28 0.51
33 21 0.38
34 3 0.05
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.37
Consensus pattern (32 bp):
TAAAACTATTTAAAATAAAATAAACATCAATT
Found at i:47224 original size:65 final size:64
Alignment explanation
Indices: 47134--47255 Score: 208
Period size: 65 Copynumber: 1.9 Consensus size: 64
47124 ATTCTTCAAT
* *
47134 TTTATCAATTTTATATAAAATTATTTAAAATAAAATAAACATCAATTTAAAACTATTTAGAATA
1 TTTATCAATTTTATATAAAACTATTTAAAATAAAATAAACATCAATTTAAAAATATTTAGAATA
*
47198 TTTATCAAATTTTATATAAAACTATTTAAAATAAAATAAACATCACTTTAAAAATATT
1 TTTATC-AATTTTATATAAAACTATTTAAAATAAAATAAACATCAATTTAAAAATATT
47256 AATATTATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
64 6 0.11
65 48 0.89
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.40
Consensus pattern (64 bp):
TTTATCAATTTTATATAAAACTATTTAAAATAAAATAAACATCAATTTAAAAATATTTAGAATA
Found at i:48980 original size:15 final size:15
Alignment explanation
Indices: 48960--48989 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
48950 AGTTACCTAA
48960 TATAAACTTTTAGAT
1 TATAAACTTTTAGAT
48975 TATAAACTTTTAGAT
1 TATAAACTTTTAGAT
48990 AGTTACCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
TATAAACTTTTAGAT
Found at i:49775 original size:66 final size:66
Alignment explanation
Indices: 49733--50037 Score: 412
Period size: 66 Copynumber: 4.8 Consensus size: 66
49723 TGGAGTACAT
* *
49733 GTGAACACCGGGAAAGGAAAACCAGGTGGTGGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGG
1 GTGAACACCGGGAAAGGAAAACCAGGGGGCGGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGG
49798 G
66 G
*
49799 GTGAACACC--G---GG--AA--AGGGGGAGGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGG
1 GTGAACACCGGGAAAGGAAAACCAGGGGGCGGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGG
*
49855 A
66 G
* * * * *
49856 GTGAGCACCGGGAAAGGAAAACCAGGGGGTGGTACTCACGTGAGCGTCGGTAAGGGCGGAGTTGG
1 GTGAACACCGGGAAAGGAAAACCAGGGGGCGGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGG
*
49921 C
66 G
* * *
49922 GTGAACACCGGGAAAGGAAAGCCAGGGGGCGGCACTCATGTGAGCGTCGGAAAGGGCGGAGTTGG
1 GTGAACACCGGGAAAGGAAAACCAGGGGGCGGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGG
49987 G
66 G
* *
49988 GTGAACACCGGGAAAGGAAAACCAGGCGGCGGCACTCACGTGAGCGTCGG
1 GTGAACACCGGGAAAGGAAAACCAGGGGGCGGCACTCACGTGAACGTCGG
50038 CGGCAAAGGC
Statistics
Matches: 211, Mismatches: 19, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
57 48 0.23
59 3 0.01
61 2 0.01
62 2 0.01
64 3 0.01
66 153 0.73
ACGTcount: A:0.27, C:0.19, G:0.43, T:0.11
Consensus pattern (66 bp):
GTGAACACCGGGAAAGGAAAACCAGGGGGCGGCACTCACGTGAACGTCGGAAAGGGCGGAGTTGG
G
Found at i:51487 original size:21 final size:20
Alignment explanation
Indices: 51458--51500 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
51448 TAATTTTAAA
* *
51458 AAAATTATTTAAAAAACTTG
1 AAAATTATTAAAAAAACCTG
51478 AAAATATATTAAAAAAACCTG
1 AAAAT-TATTAAAAAAACCTG
51499 AA
1 AA
51501 GTTTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAATTATTAAAAAAACCTG
Found at i:58225 original size:19 final size:19
Alignment explanation
Indices: 58189--58227 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
58179 TCTCAACTTC
* **
58189 AAATGGTTGAATGTATGCA
1 AAATGCTTGAATAAATGCA
58208 AAATGCTTGAATAAATGCA
1 AAATGCTTGAATAAATGCA
58227 A
1 A
58228 TGTTAATGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.28
Consensus pattern (19 bp):
AAATGCTTGAATAAATGCA
Found at i:58263 original size:26 final size:26
Alignment explanation
Indices: 58232--58291 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
58222 ATGCAATGTT
58232 AATGCAAATGCATGATGTAGGACGCA
1 AATGCAAATGCATGATGTAGGACGCA
58258 AATGCAAATGCATGATGTAGGACGCA
1 AATGCAAATGCATGATGTAGGACGCA
58284 AATGCAAA
1 AATGCAAA
58292 AGATATTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (26 bp):
AATGCAAATGCATGATGTAGGACGCA
Found at i:82045 original size:23 final size:23
Alignment explanation
Indices: 82015--82059 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
82005 TTCCATTAGT
82015 GGGTAATGGTTTAGTCATATGGC
1 GGGTAATGGTTTAGTCATATGGC
82038 GGGTAATGGTTTAGTCATATGG
1 GGGTAATGGTTTAGTCATATGG
82060 TCGGCAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.07, G:0.36, T:0.36
Consensus pattern (23 bp):
GGGTAATGGTTTAGTCATATGGC
Found at i:82198 original size:78 final size:78
Alignment explanation
Indices: 82084--82235 Score: 268
Period size: 78 Copynumber: 1.9 Consensus size: 78
82074 GAACTCGCGG
* * *
82084 TGTCTGAAGTGTATCGAGATAGCCCACTGCTTGCACAAATAGAATATGATCCTTCTGATAAGCAT
1 TGTCTGAAGTGTATCGAGATAGCCCACTGCTTGCACAAATAAAATATAATCCTTCTGATAAGAAT
82149 ATTAGACTCGCAT
66 ATTAGACTCGCAT
82162 TGTCTGAAGTGTATCGAGATAGCCCACTGCTTGCACAAATAAAATATAATCCTTCTGATAAGAAT
1 TGTCTGAAGTGTATCGAGATAGCCCACTGCTTGCACAAATAAAATATAATCCTTCTGATAAGAAT
*
82227 ATTGGACTC
66 ATTAGACTC
82236 AGGGTCGTGG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (78 bp):
TGTCTGAAGTGTATCGAGATAGCCCACTGCTTGCACAAATAAAATATAATCCTTCTGATAAGAAT
ATTAGACTCGCAT
Found at i:87296 original size:27 final size:27
Alignment explanation
Indices: 87258--87311 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
87248 GCCAGATCAA
87258 AGTTCCTCTCAACAAGAGTTTCTGCAG
1 AGTTCCTCTCAACAAGAGTTTCTGCAG
87285 AGTTCCTCTCAACAAGAGTTTCTGCAG
1 AGTTCCTCTCAACAAGAGTTTCTGCAG
87312 TCTCACACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (27 bp):
AGTTCCTCTCAACAAGAGTTTCTGCAG
Found at i:87304 original size:16 final size:16
Alignment explanation
Indices: 87258--87304 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
87248 GCCAGATCAA
87258 AGTTCCTCTCAACAAG
1 AGTTCCTCTCAACAAG
*
87274 AGTT--TCT--GC-AG
1 AGTTCCTCTCAACAAG
87285 AGTTCCTCTCAACAAG
1 AGTTCCTCTCAACAAG
87301 AGTT
1 AGTT
87305 TCTGCAGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 10
0.67 0.06 0.28
Matches are distributed among these distances:
11 6 0.25
12 1 0.04
13 3 0.12
14 3 0.12
15 1 0.04
16 10 0.42
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (16 bp):
AGTTCCTCTCAACAAG
Found at i:100525 original size:20 final size:20
Alignment explanation
Indices: 100476--100518 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
100466 CTAAACCTTA
* *
100476 AAATCAAAATTTTAAATCCT
1 AAATCATAATTTTAAACCCT
100496 AAATCATAATTTTAAACCCT
1 AAATCATAATTTTAAACCCT
100516 AAA
1 AAA
100519 CAATAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATCATAATTTTAAACCCT
Found at i:101030 original size:23 final size:23
Alignment explanation
Indices: 100980--101054 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
100970 AAAAATGTGT
* * *
100980 CACAAAGACAAAGATAAACGTAC
1 CACAAAGTCAAAAATAAACGTGC
* *
101003 TACAAAGTCAAAAATACACGTGC
1 CACAAAGTCAAAAATAAACGTGC
* *
101026 CACAAA-TGCAAAAAAAAACGTGT
1 CACAAAGT-CAAAAATAAACGTGC
101049 CACAAA
1 CACAAA
101055 AGCATAGATA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
22 1 0.02
23 41 0.98
ACGTcount: A:0.55, C:0.21, G:0.12, T:0.12
Consensus pattern (23 bp):
CACAAAGTCAAAAATAAACGTGC
Found at i:103560 original size:31 final size:31
Alignment explanation
Indices: 103522--103738 Score: 312
Period size: 31 Copynumber: 7.0 Consensus size: 31
103512 AGTCAAGGGA
* *
103522 TTACCTATGTTCTTTGGGACATATGGACATT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
103553 TTACCTATGTTCTTCGGGACATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
103584 TTACCTATGTTCTTCGGGACATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
* *
103615 TTACATATG-TCTTACGGGACATATGGACAAGA
1 TTACCTATGTTCTT-CGGGACATATGGAC-AGT
* *
103647 TTACCTATG-TCTTATGGGACATATGGATAGT
1 TTACCTATGTTCTT-CGGGACATATGGACAGT
* *
103678 TTACCTATGTTCTTTGGGATATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
*
103709 TTACCTATGTTATTCGGGACATATGGACAG
1 TTACCTATGTTCTTCGGGACATATGGACAG
103739 ATTATTATAC
Statistics
Matches: 170, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.02
31 135 0.79
32 31 0.18
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.36
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACAGT
Found at i:103687 original size:94 final size:93
Alignment explanation
Indices: 103537--103742 Score: 299
Period size: 94 Copynumber: 2.2 Consensus size: 93
103527 TATGTTCTTT
**
103537 GGGACATATGGACATTTTACCTATGTTCTTCGGGACATATGGACAGTTTACCTATGTTCTTCGGG
1 GGGACATATGGACAGATTACCTATGTTCTTCGGGACATATGGACAGTTTACCTATGTTCTTCGGG
103602 ACATATGGACAGTTTACATATGTCT-TAC
66 ACATATGGACAGTTTACATATGT-TATAC
* * *
103630 GGGACATATGGACAAGATTACCTATG-TCTTATGGGACATATGGATAGTTTACCTATGTTCTTTG
1 GGGACATATGGAC-AGATTACCTATGTTCTT-CGGGACATATGGACAGTTTACCTATGTTCTTCG
* * *
103694 GGATATATGGACAGTTTACCTATGTTATTC
64 GGACATATGGACAGTTTACATATGTTATAC
103724 GGGACATATGGACAGATTA
1 GGGACATATGGACAGATTA
103743 TTATACGAGC
Statistics
Matches: 102, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
93 24 0.24
94 78 0.76
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.35
Consensus pattern (93 bp):
GGGACATATGGACAGATTACCTATGTTCTTCGGGACATATGGACAGTTTACCTATGTTCTTCGGG
ACATATGGACAGTTTACATATGTTATAC
Found at i:104492 original size:21 final size:21
Alignment explanation
Indices: 104451--104492 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
104441 CGATGTTTTT
* *
104451 GTGCATCGGTACACTGTAGCA
1 GTGCATCGGTACAATGCAGCA
104472 GTGCATCGGTACAATGCAGCA
1 GTGCATCGGTACAATGCAGCA
104493 CTGTTCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (21 bp):
GTGCATCGGTACAATGCAGCA
Found at i:109922 original size:30 final size:31
Alignment explanation
Indices: 109886--109968 Score: 114
Period size: 33 Copynumber: 2.6 Consensus size: 31
109876 CTTTATTTTG
*
109886 TTCGGGTAGGGTCGGGTTTTTTAA-GTGATA
1 TTCGGGTCGGGTCGGGTTTTTTAAGGTGATA
109916 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGG-TTTTTTAAG-GTGATA
*
109949 TTCAGGTCGGGTTCGGGTTT
1 TTCGGGTCGGG-TCGGGTTT
109969 AGGGTGAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
30 15 0.32
31 8 0.17
33 19 0.40
34 5 0.11
ACGTcount: A:0.12, C:0.10, G:0.37, T:0.41
Consensus pattern (31 bp):
TTCGGGTCGGGTCGGGTTTTTTAAGGTGATA
Found at i:110121 original size:180 final size:181
Alignment explanation
Indices: 109922--110263 Score: 578
Period size: 180 Copynumber: 1.9 Consensus size: 181
109912 GATATTCGGG
* * **
109922 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGGGTTCGGGTTTAGGGTGAAAAAGCCCGGA
1 TCGGGTCGGGTTCTTTTAAGTGTGATATTCAGGTCGGGTTCGGGTTTAAGGTGAAAAAAACCGGA
* * *
109987 CCGACTCGAAAATATATATAATTCGGGTCGGGTCGGATTAAGTTACTGTTTTTATTAAATAAAAA
66 CCGACCCGAAAATATATATAATTCGGGTAGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAA
*
110052 TAATTTTTTATTATTTCGGGTCGGGTTGGGTCGGATGAAATTTTATTTTGT
131 TAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATGAAATTTTATTTTGT
* *
110103 TCGGGTCGGG-TCTTTTAAGTGTGATATTCGGGTCGGGTTTGGGTTTAAGGTGAAAAAAACCGGA
1 TCGGGTCGGGTTCTTTTAAGTGTGATATTCAGGTCGGGTTCGGGTTTAAGGTGAAAAAAACCGGA
110167 CCGACCCGAAAATATATATAATTCGGGTAGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAA
66 CCGACCCGAAAATATATATAATTCGGGTAGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAA
*
110232 TAATTTTTTATTATTTTGGGTCGGGTCGGGTC
131 TAATTTTTTATTATTTCGGGTCGGGTCGGGTC
110264 AAATTTCTAA
Statistics
Matches: 150, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
180 140 0.93
181 10 0.07
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.37
Consensus pattern (181 bp):
TCGGGTCGGGTTCTTTTAAGTGTGATATTCAGGTCGGGTTCGGGTTTAAGGTGAAAAAAACCGGA
CCGACCCGAAAATATATATAATTCGGGTAGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAA
TAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATGAAATTTTATTTTGT
Found at i:110995 original size:18 final size:18
Alignment explanation
Indices: 110959--111022 Score: 105
Period size: 18 Copynumber: 3.7 Consensus size: 18
110949 TATGGAATTG
110959 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
110975 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
110993 GATTCCAATTCCTTCGCA
1 GATTCCAATTCCTTCACA
111011 GATTCCAATTCC
1 GATTCCAATTCC
111023 CTCATAAACA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
16 12 0.27
17 1 0.02
18 32 0.71
ACGTcount: A:0.27, C:0.33, G:0.08, T:0.33
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:127730 original size:2 final size:2
Alignment explanation
Indices: 127725--127753 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
127715 TTACACACAC
127725 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
127754 CCCAACCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:127937 original size:17 final size:17
Alignment explanation
Indices: 127915--127948 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
127905 GGCACTCAAG
127915 CTGCTGAGAGAGAGCTT
1 CTGCTGAGAGAGAGCTT
127932 CTGCTGAGAGAGAGCTT
1 CTGCTGAGAGAGAGCTT
127949 TGCAAACAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (17 bp):
CTGCTGAGAGAGAGCTT
Found at i:129070 original size:22 final size:22
Alignment explanation
Indices: 129031--129075 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
129021 TGTGTGTGTG
129031 TGTATATATATATATATATGTA
1 TGTATATATATATATATATGTA
* * *
129053 TGTATGTATGTATGTATATGTA
1 TGTATATATATATATATATGTA
129075 T
1 T
129076 ATACCTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (22 bp):
TGTATATATATATATATATGTA
Found at i:130923 original size:21 final size:21
Alignment explanation
Indices: 130867--130915 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
130857 TTTTCAATGC
130867 TGATATGGCGATATCTTATAG
1 TGATATGGCGATATCTTATAG
130888 TGATATGGCGATATCTTATAG
1 TGATATGGCGATATCTTATAG
130909 TGATATG
1 TGATATG
130916 TCAGTATCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (21 bp):
TGATATGGCGATATCTTATAG
Found at i:136071 original size:21 final size:21
Alignment explanation
Indices: 136047--136087 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
136037 TTAAAACTCT
*
136047 AAGTTAGGATTTAAGGTTTAG
1 AAGTTAGGATTCAAGGTTTAG
*
136068 AAGTTATGATTCAAGGTTTA
1 AAGTTAGGATTCAAGGTTTA
136088 TAATTTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.02, G:0.24, T:0.39
Consensus pattern (21 bp):
AAGTTAGGATTCAAGGTTTAG
Found at i:136559 original size:21 final size:21
Alignment explanation
Indices: 136526--136570 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
136516 TTTTGAAGGA
* *
136526 AAAATTGAAAGTTTATGTACT
1 AAAACTGAAAGTTTAAGTACT
* *
136547 AAAACTGATAGTTTAAGTATT
1 AAAACTGAAAGTTTAAGTACT
136568 AAA
1 AAA
136571 CGCGTTATCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (21 bp):
AAAACTGAAAGTTTAAGTACT
Done.