Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006323.1 Hibiscus syriacus cultivar Beakdansim tig00015109_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: 70052
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:3891 original size:28 final size:28
Alignment explanation
Indices: 3845--3923 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
3835 GAGTCGAGGA
*
3845 TCTACGTGAT-CTTTCGGGACATATATGT
1 TCTACGTGGTCCTTT-GGGACATATATGT
*
3873 TCTACGTGGTCCTTTGGGACATATGTGT
1 TCTACGTGGTCCTTTGGGACATATATGT
** *
3901 TCTATATGGTCCTTCGGGACATA
1 TCTACGTGGTCCTTTGGGACATA
3924 GTGATCATTC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
28 41 0.91
29 4 0.09
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (28 bp):
TCTACGTGGTCCTTTGGGACATATATGT
Found at i:10010 original size:18 final size:18
Alignment explanation
Indices: 9987--10023 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
9977 GAAAATCATC
9987 ACACGCTAAGTATAACTT
1 ACACGCTAAGTATAACTT
10005 ACACGCTAAGTATAACTT
1 ACACGCTAAGTATAACTT
10023 A
1 A
10024 GTGAGGCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.27
Consensus pattern (18 bp):
ACACGCTAAGTATAACTT
Found at i:10375 original size:34 final size:34
Alignment explanation
Indices: 10337--10413 Score: 118
Period size: 34 Copynumber: 2.3 Consensus size: 34
10327 TCACTGTTCC
* *
10337 AATCATAACTGATTATAAAATGCACTCCAAGTGA
1 AATCATAACTAATCATAAAATGCACTCCAAGTGA
* *
10371 AATCATAATTAATCATAAAATGCACTCCAAGTGC
1 AATCATAACTAATCATAAAATGCACTCCAAGTGA
10405 AATCATAAC
1 AATCATAAC
10414 ATCAGCACCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.26
Consensus pattern (34 bp):
AATCATAACTAATCATAAAATGCACTCCAAGTGA
Found at i:12259 original size:23 final size:25
Alignment explanation
Indices: 12233--12278 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12223 AATATAATTT
12233 AATTT-AAAATT-CAATTAATGAGA
1 AATTTCAAAATTGCAATTAATGAGA
*
12256 AATTTCAAAATTGCCATTAATGA
1 AATTTCAAAATTGCAATTAATGA
12279 AACCTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 6 0.30
25 9 0.45
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.35
Consensus pattern (25 bp):
AATTTCAAAATTGCAATTAATGAGA
Found at i:12280 original size:23 final size:22
Alignment explanation
Indices: 12233--12280 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
12223 AATATAATTT
12233 AATTTAAAATTCAATTAATGAGA
1 AATTTAAAATTCAATTAAT-AGA
*
12256 AATTTCAAAATTGCCATTAAT-GA
1 AATTT-AAAATT-CAATTAATAGA
12279 AA
1 AA
12281 CCTGAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 9 0.41
24 6 0.27
25 7 0.32
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (22 bp):
AATTTAAAATTCAATTAATAGA
Found at i:13193 original size:16 final size:16
Alignment explanation
Indices: 13172--13213 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
13162 ATTTTGCTCT
13172 TTATTAATGTACAAAG
1 TTATTAATGTACAAAG
*
13188 TTATTATAT-TACAACG
1 TTATTA-ATGTACAAAG
13204 TT-TTAATGTA
1 TTATTAATGTA
13214 GTGTGTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 2 0.09
15 5 0.22
16 14 0.61
17 2 0.09
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (16 bp):
TTATTAATGTACAAAG
Found at i:16106 original size:12 final size:12
Alignment explanation
Indices: 16089--16141 Score: 64
Period size: 9 Copynumber: 4.9 Consensus size: 12
16079 AGTCTTATAT
16089 ATTATTTTAAAA
1 ATTATTTTAAAA
16101 ATTA-TTT--AA
1 ATTATTTTAAAA
16110 ATTATTTTAAAA
1 ATTATTTTAAAA
16122 ATTA-TTT--AA
1 ATTATTTTAAAA
16131 ATTATTTTAAA
1 ATTATTTTAAA
16142 TCATACTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
9 12 0.34
10 6 0.17
11 6 0.17
12 11 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTATTTTAAAA
Found at i:16113 original size:21 final size:21
Alignment explanation
Indices: 16089--16141 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
16079 AGTCTTATAT
16089 ATTATTTTAAAAATTATTTAA
1 ATTATTTTAAAAATTATTTAA
16110 ATTATTTTAAAAATTATTTAA
1 ATTATTTTAAAAATTATTTAA
16131 ATTATTTTAAA
1 ATTATTTTAAA
16142 TCATACTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTATTTTAAAAATTATTTAA
Found at i:16489 original size:2 final size:2
Alignment explanation
Indices: 16484--16512 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16474 TATATATATA
16484 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
16513 TTGTATTAAA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:21265 original size:13 final size:14
Alignment explanation
Indices: 21249--21291 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
21239 ATAACAAGCA
21249 TATAA-TATCACCC
1 TATAAGTATCACCC
21262 TATAATGTATCACCC
1 TATAA-GTATCACCC
*
21277 TATCATGTATCACCC
1 TAT-AAGTATCACCC
21292 ATACAACCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 5 0.19
15 20 0.77
16 1 0.04
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.33
Consensus pattern (14 bp):
TATAAGTATCACCC
Found at i:21274 original size:15 final size:15
Alignment explanation
Indices: 21254--21291 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
21244 AAGCATATAA
21254 TATCACCCTATAATG
1 TATCACCCTATAATG
*
21269 TATCACCCTATCATG
1 TATCACCCTATAATG
21284 TATCACCC
1 TATCACCC
21292 ATACAACCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (15 bp):
TATCACCCTATAATG
Found at i:25442 original size:8 final size:8
Alignment explanation
Indices: 25429--25453 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
25419 CGGCGGAATA
25429 GGTTTTGG
1 GGTTTTGG
25437 GGTTTTGG
1 GGTTTTGG
25445 GGTTTTGG
1 GGTTTTGG
25453 G
1 G
25454 TGTTCTTGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (8 bp):
GGTTTTGG
Found at i:35404 original size:24 final size:24
Alignment explanation
Indices: 35376--35422 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
35366 AAGAAAGAAA
*
35376 AAATTAGTGAATTTGTTGGAAAAT
1 AAATTAGTGAATTTATTGGAAAAT
35400 AAATTAGTGAATTTATTGGAAAA
1 AAATTAGTGAATTTATTGGAAAA
35423 CCCTTAGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.36
Consensus pattern (24 bp):
AAATTAGTGAATTTATTGGAAAAT
Found at i:40693 original size:22 final size:22
Alignment explanation
Indices: 40663--40742 Score: 101
Period size: 23 Copynumber: 3.7 Consensus size: 22
40653 TGGTGCAGGA
*
40663 GGAATCGATACCCCCTTGAAGG
1 GGAACCGATACCCCCTTGAAGG
*
40685 GGAACCGATTCCCCCTTTGAAGG
1 GGAACCGATACCCCC-TTGAAGG
*
40708 GGAACCGATTCCCCCTTG-A-G
1 GGAACCGATACCCCCTTGAAGG
*
40728 GGAATCGATACCCCC
1 GGAACCGATACCCCC
40743 CACGGGGTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
20 14 0.26
21 1 0.02
22 16 0.30
23 22 0.42
ACGTcount: A:0.24, C:0.33, G:0.25, T:0.19
Consensus pattern (22 bp):
GGAACCGATACCCCCTTGAAGG
Found at i:47365 original size:23 final size:24
Alignment explanation
Indices: 47325--47370 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
47315 TAATTCTACC
**
47325 ATTATATATTTTAATAAT-TATTT
1 ATTATATATGATAATAATATATTT
*
47348 ATTATATATGATATTAATATATT
1 ATTATATATGATAATAATATATT
47371 AAGTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTATATATGATAATAATATATTT
Found at i:49268 original size:26 final size:24
Alignment explanation
Indices: 49238--49286 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
49228 TTATGTAAGA
49238 GGGTACA-AACTTAATAAATATTTTAT
1 GGGTACAGAA-TT-ATAAA-ATTTTAT
49264 GGGTACAGAATTATAAAATTTTA
1 GGGTACAGAATTATAAAATTTTA
49287 GATATGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.27
25 5 0.23
26 9 0.41
27 2 0.09
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (24 bp):
GGGTACAGAATTATAAAATTTTAT
Found at i:49567 original size:35 final size:35
Alignment explanation
Indices: 49528--49596 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
49518 CGTGTCGTGG
49528 TAAATTACTATCTAAGAAATAAATCCGTCCCATAA
1 TAAATTACTATCTAAGAAATAAATCCGTCCCATAA
49563 TAAATTACTATCTAAGAAATAAATCCGTCCCATA
1 TAAATTACTATCTAAGAAATAAATCCGTCCCATA
49597 TTTGTAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.29
Consensus pattern (35 bp):
TAAATTACTATCTAAGAAATAAATCCGTCCCATAA
Found at i:52107 original size:60 final size:60
Alignment explanation
Indices: 52026--52140 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
52016 AGTTGGGTGA
*
52026 TCATTTTGTAACTCTTAATAGTCGAGAGG-CTCAACAAGGCAATGCCTTATAGTCGGAGCG
1 TCATTTTGTAACTCTTAATAGT-GAGAGGACTCAACAAAGCAATGCCTTATAGTCGGAGCG
* * * * *
52086 TCATTTTGTAACTTTTAATAGTTAGAGGATTCAATAAAGCAATGTCTTATAGTCG
1 TCATTTTGTAACTCTTAATAGTGAGAGGACTCAACAAAGCAATGCCTTATAGTCG
52141 AGAGACCAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 5 0.10
60 43 0.90
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (60 bp):
TCATTTTGTAACTCTTAATAGTGAGAGGACTCAACAAAGCAATGCCTTATAGTCGGAGCG
Found at i:58052 original size:43 final size:43
Alignment explanation
Indices: 58005--58206 Score: 273
Period size: 43 Copynumber: 4.7 Consensus size: 43
57995 CGTATTTTGT
58005 GGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGC
1 GGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGC
* * *
58048 GGCGTTTGTGGGAAAAACACCTCTAAATCTCAAAACCTATTGC
1 GGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGC
*** *
58091 AATGTTTGTGGG-AAAACGCCGCTAAATCTCAACACCTATTAC
1 GGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGC
* *
58133 GGCGTTTGTGGGACAAATGCCGCTAAATCTCAACACCTATTGC
1 GGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGC
** *
58176 GGCGTTTGT-CTAACAAACGCCGCTATATCTC
1 GGCGTTTGTGGGAA-AAACGCCGCTAAATCTC
58207 GTTACCTATT
Statistics
Matches: 136, Mismatches: 21, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
42 36 0.26
43 100 0.74
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (43 bp):
GGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGC
Found at i:58121 original size:85 final size:86
Alignment explanation
Indices: 58008--58175 Score: 275
Period size: 85 Copynumber: 2.0 Consensus size: 86
57998 ATTTTGTGGC
* *
58008 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGGGAAAAACACCTCTA
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTACGGCGTTTGTGGGAAAAACACCGCTA
58073 AATCTCAAAACCTATTGCAAT
66 AATCTCAAAACCTATTGCAAT
* **
58094 GTTTGTGGG-AAAACGCCGCTAAATCTCAACACCTATTACGGCGTTTGTGGGACAAATGCCGCTA
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTACGGCGTTTGTGGGAAAAACACCGCTA
*
58158 AATCTCAACACCTATTGC
66 AATCTCAAAACCTATTGC
58176 GGCGTTTGTC
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
85 67 0.88
86 9 0.12
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (86 bp):
GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTACGGCGTTTGTGGGAAAAACACCGCTA
AATCTCAAAACCTATTGCAAT
Found at i:58183 original size:85 final size:86
Alignment explanation
Indices: 58005--58206 Score: 273
Period size: 85 Copynumber: 2.4 Consensus size: 86
57995 CGTATTTTGT
* *
58005 GGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGGGAAAAACACCT
1 GGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTACGGCGTTTGTGGGAAAAACACCG
58070 CTAAATCTCAAAACCTATTGC
66 CTAAATCTCAAAACCTATTGC
*** * **
58091 AATGTTTGTGGG-AAAACGCCGCTAAATCTCAACACCTATTACGGCGTTTGTGGGACAAATGCCG
1 GGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTACGGCGTTTGTGGGAAAAACACCG
*
58155 CTAAATCTCAACACCTATTGC
66 CTAAATCTCAAAACCTATTGC
** *
58176 GGCGTTTGT-CTAACAAACGCCGCTATATCTC
1 GGCGTTTGTGGGAA-AAACGCCGCTAAATCTC
58207 GTTACCTATT
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
85 74 0.75
86 25 0.25
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (86 bp):
GGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTACGGCGTTTGTGGGAAAAACACCG
CTAAATCTCAAAACCTATTGC
Found at i:60368 original size:3 final size:3
Alignment explanation
Indices: 60360--60409 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
60350 ATCGTATGTT
* * * *
60360 ATA ATA ATA ACA ATA TTA ATA TTA ATA ATA ATA ATA ATA ATT A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
60407 ATA
1 ATA
60410 TTTTTGTAGA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
2 1 0.03
3 37 0.97
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:62931 original size:131 final size:129
Alignment explanation
Indices: 62691--63109 Score: 427
Period size: 126 Copynumber: 3.2 Consensus size: 129
62681 GGTCGTTTAA
* * *
62691 GGATGACACAGTTCCTACGTGATGAGGACGGT-TGGCTATCTTTAGGGATGGTGATAACACGGTT
1 GGATGACACGGTTCCTATGTGATGAGGACGGTATGGC-ATCTTTAGGGA---TGATAACATGGTT
* * * * * *
62755 CCTATGCGATGAGGACGGATGGTTATCTAGGGGTCACACGGCTCCTACGTGATGAGGAGGTCTAG
62 CCTATGTGATTAGGACGGCTGGTTATCTAAGGGTAACACGACTCCTACGTGATGAGGAGGTCT-G
62820 TCGAG
126 TCG-G
* *
62825 GGATGACACGGTTCCTATATGATGAGGACGGTATGTCATCTTTAGGGATGATAACATGGTTCCTA
1 GGATGACACGGTTCCTATGTGATGAGGACGGTATGGCATCTTTAGGGATGATAACATGGTTCCTA
* * *
62890 TGTGATTAGGACGGCTGGTTATCTAAGGGTGACACGACTCCTA-GTGATAAAGAGGTCTGGTCGG
66 TGTGATTAGGACGGCTGGTTATCTAAGGGTAACACGACTCCTACGTGATGAGGAGGTCT-GTCGG
* * ** * * **
62954 GGATGACATGGTTCCT-T-TGATGAGGATGACA-GGCATCTTTAGTGATGATAACATGATTTATA
1 GGATGACACGGTTCCTATGTGATGAGGACGGTATGGCATCTTTAGGGATGATAACATGGTTCCTA
* * * * * * *
63016 CGTG-TTGAGGATGACTAGTTATCTAAAGGTAACACAACTCCTACGTGATGAGGATGTCTGTTCG
66 TGTGATT-AGGACGGCTGGTTATCTAAGGGTAACACGACTCCTACGTGATGAGGAGGTCTG-TC-
63080 GG
128 GG
* *
63082 GGATGACATGGTTCCTATGCGATGAGGA
1 GGATGACACGGTTCCTATGTGATGAGGA
63110 TAGAAGGCCA
Statistics
Matches: 244, Mismatches: 34, Indels: 18
0.82 0.11 0.06
Matches are distributed among these distances:
125 2 0.01
126 60 0.25
127 25 0.10
128 19 0.08
129 17 0.07
130 25 0.10
131 53 0.22
134 40 0.16
135 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (129 bp):
GGATGACACGGTTCCTATGTGATGAGGACGGTATGGCATCTTTAGGGATGATAACATGGTTCCTA
TGTGATTAGGACGGCTGGTTATCTAAGGGTAACACGACTCCTACGTGATGAGGAGGTCTGTCGG
Found at i:63276 original size:21 final size:20
Alignment explanation
Indices: 63234--63276 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
63224 ATTTCTCAAG
*
63234 AAAACTTTCTCAAGAGAGAC
1 AAAACTTTCTCAAGAGAAAC
* *
63254 AAAACTTGTTTCAAGGGAAAC
1 AAAACTT-TCTCAAGAGAAAC
63275 AA
1 AA
63277 TCTCAAAGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (20 bp):
AAAACTTTCTCAAGAGAAAC
Found at i:63524 original size:37 final size:36
Alignment explanation
Indices: 63435--63524 Score: 101
Period size: 36 Copynumber: 2.5 Consensus size: 36
63425 TTTTTGAGAG
* * *
63435 AATTGTCTCAAGCGAAACAAAATTTGTTTTTAGCGA
1 AATTGTCTCAAGCGAGACAAAATTTATTTTTAGCAA
* *
63471 AATTGTCGCAAGCGAGACGAAATTTATTTTTAAG-AA
1 AATTGTCTCAAGCGAGACAAAATTTATTTTT-AGCAA
*
63507 AACTTGTCTCAATCGAGA
1 AA-TTGTCTCAAGCGAGA
63525 TGACCCTTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
36 30 0.67
37 15 0.33
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (36 bp):
AATTGTCTCAAGCGAGACAAAATTTATTTTTAGCAA
Found at i:64544 original size:7 final size:8
Alignment explanation
Indices: 64527--64586 Score: 61
Period size: 8 Copynumber: 7.2 Consensus size: 8
64517 AGAAAGAAAG
64527 AAAATGAA
1 AAAATGAA
64535 AAAATGAA
1 AAAATGAA
64543 AAAATGAA
1 AAAATGAA
*
64551 AAAAAGAGA
1 AAAATGA-A
64560 AAAATAAAGAA
1 AAAAT---GAA
64571 AAAA-GAA
1 AAAATGAA
64578 AAAA-GAA
1 AAAATGAA
64585 AA
1 AA
64587 GAGAATAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
7 12 0.26
8 22 0.48
9 5 0.11
11 5 0.11
12 2 0.04
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (8 bp):
AAAATGAA
Found at i:64555 original size:17 final size:16
Alignment explanation
Indices: 64527--64586 Score: 68
Period size: 16 Copynumber: 3.6 Consensus size: 16
64517 AGAAAGAAAG
*
64527 AAAATGAAAAAATGAA
1 AAAATGAAAAAAAGAA
64543 AAAATGAAAAAAAGAGA
1 AAAATGAAAAAAAGA-A
*
64560 AAAATAAAGAAAAAAGAA
1 AAAAT-GA-AAAAAAGAA
64578 AAAA-GAAAA
1 AAAATGAAAA
64587 GAGAATAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 3 0.08
16 15 0.39
17 6 0.16
18 6 0.16
19 8 0.21
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (16 bp):
AAAATGAAAAAAAGAA
Found at i:65356 original size:14 final size:14
Alignment explanation
Indices: 65332--65399 Score: 70
Period size: 14 Copynumber: 4.9 Consensus size: 14
65322 ATCATCTCTT
65332 TTTTCTTTCTTTTG-
1 TTTT-TTTCTTTTGA
65346 TTCTTTTTC-TTTGA
1 TT-TTTTTCTTTTGA
* *
65360 TTTTTTTTTTTTGC
1 TTTTTTTCTTTTGA
65374 TTTTTTTCTCTTTG-
1 TTTTTTTCT-TTTGA
65388 TTTTTTTCTTTT
1 TTTTTTTCTTTT
65400 CTTTGTTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
13 12 0.26
14 29 0.62
15 6 0.13
ACGTcount: A:0.01, C:0.12, G:0.06, T:0.81
Consensus pattern (14 bp):
TTTTTTTCTTTTGA
Found at i:65382 original size:41 final size:43
Alignment explanation
Indices: 65332--65422 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 43
65322 ATCATCTCTT
65332 TTTTCTTTCT-TTTGTTCTTTTTCTTTGATTT-TTTTTTTTTGC
1 TTTTCTTTCTCTTTGTT-TTTTTCTTTGATTTGTTTTTTTTTGC
**
65374 TTTT-TTTCTCTTTGTTTTTTTCTTTTCTTTGTTTTTTTTT-C
1 TTTTCTTTCTCTTTGTTTTTTTCTTTGATTTGTTTTTTTTTGC
*
65415 TCTTCTTT
1 TTTTCTTT
65423 GATTTGATCT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
41 21 0.49
42 22 0.51
ACGTcount: A:0.01, C:0.13, G:0.05, T:0.80
Consensus pattern (43 bp):
TTTTCTTTCTCTTTGTTTTTTTCTTTGATTTGTTTTTTTTTGC
Found at i:65385 original size:29 final size:27
Alignment explanation
Indices: 65331--65409 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 27
65321 TATCATCTCT
*
65331 TTTTTCTTTCTTTTG-TTCTTTTTCTTTG
1 TTTTT-TTT-TTTTGCTTTTTTTTCTTTG
65359 ATTTTTTTTTTTTGCTTTTTTTCTCTTTG
1 -TTTTTTTTTTTTGCTTTTTTT-TCTTTG
*
65388 TTTTTTTCTTTT-CTTTGTTTTT
1 TTTTTTTTTTTTGCTTT-TTTTT
65410 TTTTCTCTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
27 10 0.22
28 24 0.53
29 11 0.24
ACGTcount: A:0.01, C:0.11, G:0.06, T:0.81
Consensus pattern (27 bp):
TTTTTTTTTTTTGCTTTTTTTTCTTTG
Found at i:65408 original size:14 final size:15
Alignment explanation
Indices: 65350--65415 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 15
65340 CTTTTGTTCT
65350 TTTTCTTTGATTTTT-
1 TTTTCTTTG-TTTTTC
65365 TTTT-TTTGCTTTTT-
1 TTTTCTTTG-TTTTTC
*
65379 TTCTCTTTGTTTTTTTC
1 TTTTCTTTG--TTTTTC
65396 TTTTCTTTGTTTTT-
1 TTTTCTTTGTTTTTC
65410 TTTTCT
1 TTTTCT
65416 CTTCTTTGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
14 18 0.41
15 13 0.30
16 5 0.11
17 8 0.18
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTTCTTTGTTTTTC
Found at i:65412 original size:19 final size:18
Alignment explanation
Indices: 65330--65422 Score: 71
Period size: 19 Copynumber: 4.8 Consensus size: 18
65320 TTATCATCTC
65330 TTTTTTC-TTTCTTTTGTT
1 TTTTTTCTTTTCTTTT-TT
* *
65348 CTTTTTCTTTGATTTTTTTT
1 TTTTTTCTTT--TCTTTTTT
* *
65368 TTTTGCTTTTTTTCTCTTTGT
1 TTTT--TTCTTTTCT-TTTTT
65389 TTTTTTCTTTTCTTTGTTT
1 TTTTTTCTTTTCTTT-TTT
*
65408 TTTTTTCTCTTCTTT
1 TTTTTTCTTTTCTTT
65423 GATTTGATCT
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
18 8 0.14
19 26 0.44
20 7 0.12
21 13 0.22
22 5 0.08
ACGTcount: A:0.01, C:0.13, G:0.05, T:0.81
Consensus pattern (18 bp):
TTTTTTCTTTTCTTTTTT
Found at i:65416 original size:33 final size:32
Alignment explanation
Indices: 65330--65418 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 32
65320 TTATCATCTC
* *
65330 TTTTTTC-TTTCTTT-TGTTCTTTT-TCTTTG
1 TTTTTTCTTTTCTTTGTCTTTTTTTCTCTTTG
*
65359 ATTTTT-TTTT-TTTG-CTTTTTTTCTCTTTG
1 TTTTTTCTTTTCTTTGTCTTTTTTTCTCTTTG
*
65388 TTTTTTTCTTTTCTTTGTTTTTTTTTCTCTT
1 -TTTTTTCTTTTCTTTGTCTTTTTTTCTCTT
65419 CTTTGATTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
28 9 0.19
29 14 0.29
30 5 0.10
31 4 0.08
32 4 0.08
33 12 0.25
ACGTcount: A:0.01, C:0.12, G:0.06, T:0.81
Consensus pattern (32 bp):
TTTTTTCTTTTCTTTGTCTTTTTTTCTCTTTG
Done.