Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006916.1 Hibiscus syriacus cultivar Beakdansim tig00017723_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: 68143
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:267 original size:7 final size:7
Alignment explanation
Indices: 252--304 Score: 54
Period size: 7 Copynumber: 7.3 Consensus size: 7
242 ATTATGCTTG
*
252 AAGAGAA
1 AAGAAAA
259 AAGAAAA
1 AAGAAAA
266 AAGAAGAA
1 AAGAA-AA
274 AA-AAAA
1 AAGAAAA
*
280 AGAAAAAA
1 A-AGAAAA
288 AAGAAAA
1 AAGAAAA
295 AAGAAGAA
1 AAGAA-AA
303 AA
1 AA
305 AGGGGGTCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
6 3 0.08
7 24 0.60
8 13 0.32
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:274 original size:10 final size:10
Alignment explanation
Indices: 259--305 Score: 78
Period size: 10 Copynumber: 4.8 Consensus size: 10
249 TTGAAGAGAA
259 AAGAAAAAAG
1 AAGAAAAAAG
*
269 AAGAAAAAAA
1 AAGAAAAAAG
279 AAGAAAAAA-
1 AAGAAAAAAG
288 AAGAAAAAAG
1 AAGAAAAAAG
298 AAGAAAAA
1 AAGAAAAA
306 GGGGGTCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
9 9 0.26
10 26 0.74
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAG
Found at i:285 original size:19 final size:19
Alignment explanation
Indices: 257--306 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
247 GCTTGAAGAG
257 AAAAGAAAAAAGAAGAAAAA
1 AAAAG-AAAAAGAAGAAAAA
*
277 AAAAGAAAAAAAAGAAAAA
1 AAAAGAAAAAGAAGAAAAA
*
296 AGAAGAAAAAG
1 AAAAGAAAAAG
307 GGGGTCAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 22 0.81
20 5 0.19
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAGAAGAAAAA
Found at i:1935 original size:83 final size:83
Alignment explanation
Indices: 1427--2014 Score: 830
Period size: 82 Copynumber: 7.2 Consensus size: 83
1417 GAACAAATGC
1427 AATGT-CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC-AT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1490 CATTGAATTTGAAAGATG
66 CATTGAATTTGAAAGATG
*
1508 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATGTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
*
1573 CATTGAATTTAAAAGATG
66 CATTGAATTTGAAAGATG
1591 -ATGTGCTCATAGCA--TTCTGGAAGTGTTCTTTGAGTTA--TGATCTGGTTTGGTAAAA--AAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
*
1649 CATTGAATTTGGAAGA-G
66 CATTGAATTTGAAAGATG
*
1666 AA--TGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAACCA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG----G------
*
1729 CAAAACCAATCATTGAATTTGAAAGATG
56 TAAAACCAATCATTGAATTTGAAAGATG
*
1757 AATG-G-TCATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC-AT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
*
1819 CATTAAATTTGAAAGATG
66 CATTGAATTTGAAAGATG
* *
1837 AATGTGATCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
* * *
1902 TATTGAATTTGGAAGAGG
66 CATTGAATTTGAAAGATG
* *
1920 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGAAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1985 CATT-AATTTGAAAGATG
66 CATTGAATTTGAAAGATG
* *
2002 AATTTTCTCATAG
1 AATGTGCTCATAG
2015 TAGAAATAAG
Statistics
Matches: 455, Mismatches: 27, Indels: 49
0.86 0.05 0.09
Matches are distributed among these distances:
74 10 0.02
75 1 0.00
76 41 0.09
78 30 0.07
80 46 0.10
81 12 0.03
82 145 0.32
83 98 0.22
87 1 0.00
88 4 0.01
90 18 0.04
91 48 0.11
92 1 0.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (83 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
CATTGAATTTGAAAGATG
Found at i:2215 original size:195 final size:187
Alignment explanation
Indices: 1846--2272 Score: 705
Period size: 195 Copynumber: 2.2 Consensus size: 187
1836 GAATGTGATC
*
1846 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATT
1 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATT
*
1911 TGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGA
66 TGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGA
*
1976 AAAACCAATCATTAATTTGAAAGATGAATTTTCTCATAGTAGAAATAAGGAGACCCA
131 AAAACCAATCATTAATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCA
*
2033 ATAGCATCTT-TGGAAGTATTCTTTGAATTATCTGATCTGGTTTGGTATGAACCACATAACCAGT
1 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGG--T-----A-A-AACCAGT
2097 TATTGAATTTGGAAGAGGAATGT-CTAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
57 TATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
*
2161 TGGTTTGGTAAAACCAATCATTGAATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACC
122 TGGTTTGGAAAAACCAATCATT-AATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACC
2226 CA
186 CA
2228 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTG
1 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTG
2273 AACCACAGAA
Statistics
Matches: 223, Mismatches: 6, Indels: 13
0.92 0.02 0.05
Matches are distributed among these distances:
186 33 0.15
187 10 0.04
188 1 0.00
193 1 0.00
194 62 0.28
195 83 0.37
196 33 0.15
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (187 bp):
ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTTATTGAATT
TGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGA
AAAACCAATCATTAATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCCA
Found at i:2466 original size:299 final size:297
Alignment explanation
Indices: 1928--2469 Score: 921
Period size: 299 Copynumber: 1.8 Consensus size: 297
1918 GGAATGTGCT
* *
1928 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGAAAAACCAATCATTAATT
1 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGAAAAAACCAATCATTAATT
* *
1993 TGAAAGATGAATTTTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTTGGAAGTATTCTTTG
66 TAAAAGATGAATTTGCTCATA-TAGAAATAAGGAGACCCAATAGCATCTTTGGAAGTATTCTTTG
*
2058 AATTATCTGATCTGGTTTGGTATGAACCACATAACCAGTTATTGAATTTGGAAGAGGAATGTCTA
130 AATTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTATTGAATTTGGAAGAGGAATG-CTA
2123 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATT
194 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATT
2188 TGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
259 TGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
2227 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGAACCACAGAACCAATCATT
1 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGAA--A-A-AACCAATCATT
2292 AAATTTAAAAGATGAATTTGCTCAT-TAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTA-T
62 -AATTTAAAAGATGAATTTGCTCATATAGAAATAAGGAGACCCAATAGCATCTT-TGGAAGTATT
*
2355 CTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTATTGAATTTGGAAGAGG-AT
125 CTTTGAATTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTATTGAATTTGGAAGAGGAAT
*
2419 G-TGATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTA
190 GCTAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTA
2470 GGAACTACAG
Statistics
Matches: 230, Mismatches: 7, Indels: 12
0.92 0.03 0.05
Matches are distributed among these distances:
299 95 0.41
301 4 0.02
302 90 0.39
303 19 0.08
304 22 0.10
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.35
Consensus pattern (297 bp):
AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGAAAAAACCAATCATTAATT
TAAAAGATGAATTTGCTCATATAGAAATAAGGAGACCCAATAGCATCTTTGGAAGTATTCTTTGA
ATTATCTGATCTGGTTTGGTATGAACCACAGAACCAGTTATTGAATTTGGAAGAGGAATGCTAAT
AGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTG
AAAGATGAATTTGCTCATAGTAGAAATAAGGAGACCC
Found at i:2890 original size:52 final size:52
Alignment explanation
Indices: 2828--2932 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
2818 TATCGATATC
2828 TGTGAAATCATCTTG-AAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
1 TGTGAAATCATC-TGAAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
*
2880 TGTGAAATCATCTGAAAAGGTCACTTCATAATCAGATGAGTTGTTATCAGAA
1 TGTGAAATCATCTGAAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
2932 T
1 T
2933 TACATGTTGC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 2 0.04
52 49 0.96
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.32
Consensus pattern (52 bp):
TGTGAAATCATCTGAAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
Found at i:3823 original size:113 final size:113
Alignment explanation
Indices: 3219--4440 Score: 1826
Period size: 113 Copynumber: 11.0 Consensus size: 113
3209 GCAAAGATTT
* *
3219 AAATCCATCACTTGATGGATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
3284 -A--ATGAAGAAGTTCATAAT--GAAGAATTTGTTCAACCTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
3327 AAATCTATCACTTGAT-GATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
3391 AAGGATGAAGAAGTTCATAAT--GAAGAATTTGTTCAACCTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
3437 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
3502 AATGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
3550 -AATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
3614 AAGGAAGAATAAGTTCATAATGAG-AGAA-TTGTTC-ACC-TTTGTTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * **
3658 AAATCCATCACTTGATGGATTAGCTTTTCCAG-AAGAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAA
3722 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
3771 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
3836 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
3884 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
3949 AATGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
3997 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
4062 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGCTC
66 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGCTC
* * ** * * *
4111 AAATCCATCACTTGATGGATTAGCTTTTCCAG-AAGAAGTTCAT-ATGAGAAAAACTCATTTAAA
1 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAA
* * *
4174 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAGCTTTTTGCTC
65 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * ****
4223 AAATCCATCACTTGATGGGTCAGT-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCTATCACTTGATGGATTA-TCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
* * *
4287 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAGCTTTTTGCTC
65 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * * * *
4336 AAACCCATCACTTGGTGGGTCAGT-TTTTCCAG--AGAAGTTCATAATGAGAAAAACTCATC---
1 AAATCTATCACTTGATGGATTA-TCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGA
* * ** *
4395 AGGA-GAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
64 AGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
4441 AATGACTCTA
Statistics
Matches: 1047, Mismatches: 48, Indels: 38
0.92 0.04 0.03
Matches are distributed among these distances:
107 47 0.04
108 60 0.06
109 86 0.08
110 68 0.06
111 79 0.08
112 154 0.15
113 507 0.48
114 46 0.04
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.32
Consensus pattern (113 bp):
AAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:4420 original size:20 final size:20
Alignment explanation
Indices: 4368--4423 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
4358 GTTTTTCCAG
4368 AGAAGTTCATAATGAG-A-A
1 AGAAGTTCATAATGAGAAGA
* * *
4386 A-AA-CTCATCAGGAGAAGA
1 AGAAGTTCATAATGAGAAGA
4404 AGAAGTTCATAATGAGAAGA
1 AGAAGTTCATAATGAGAAGA
4424 GCTTATTCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
16 8 0.29
17 3 0.11
18 3 0.11
19 2 0.07
20 12 0.43
ACGTcount: A:0.50, C:0.09, G:0.23, T:0.18
Consensus pattern (20 bp):
AGAAGTTCATAATGAGAAGA
Found at i:4675 original size:3 final size:3
Alignment explanation
Indices: 4667--4730 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
4657 ATGTTATTTA
* *
4667 TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT TA- TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
*
4712 AAT TAT ATAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT
4731 AATATATTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 44 0.85
4 6 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:4686 original size:15 final size:15
Alignment explanation
Indices: 4664--4727 Score: 96
Period size: 15 Copynumber: 4.3 Consensus size: 15
4654 TTAATGTTAT
4664 TTAT-ATTATTATTA
1 TTATAATTATTATTA
4678 TTATAATTATTATTA
1 TTATAATTATTATTA
4693 TTATAATTA-TATATA
1 TTATAATTATTAT-TA
4708 TTATAATTATATATTA
1 TTATAATTAT-TATTA
4724 TTAT
1 TTAT
4728 TATAATATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.15
15 30 0.65
16 6 0.13
17 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATAATTATTATTA
Found at i:9986 original size:23 final size:23
Alignment explanation
Indices: 9960--10009 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
9950 GCCACTACTA
* *
9960 ACTGAATCTTCTAGAAGCTATTG
1 ACTGAACCTTCTAAAAGCTATTG
** *
9983 ACTGGGCCTTCTAAAAGCTGTTG
1 ACTGAACCTTCTAAAAGCTATTG
10006 ACTG
1 ACTG
10010 GGCGCCACAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (23 bp):
ACTGAACCTTCTAAAAGCTATTG
Found at i:10010 original size:23 final size:23
Alignment explanation
Indices: 9967--10012 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
9957 CTAACTGAAT
*
9967 CTTCTAGAAGCTATTGACTGGGC
1 CTTCTAAAAGCTATTGACTGGGC
*
9990 CTTCTAAAAGCTGTTGACTGGGC
1 CTTCTAAAAGCTATTGACTGGGC
10013 GCCACATCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (23 bp):
CTTCTAAAAGCTATTGACTGGGC
Found at i:15170 original size:16 final size:16
Alignment explanation
Indices: 15149--15180 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
15139 TTTATTTGTC
15149 TAAATGTCATGAAAAG
1 TAAATGTCATGAAAAG
*
15165 TAAATGTCATGGAAAG
1 TAAATGTCATGAAAAG
15181 CTTGATTGAA
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:0.47, C:0.06, G:0.22, T:0.25
Consensus pattern (16 bp):
TAAATGTCATGAAAAG
Found at i:18259 original size:242 final size:242
Alignment explanation
Indices: 17834--18311 Score: 929
Period size: 242 Copynumber: 2.0 Consensus size: 242
17824 TCTTAACTTG
17834 TTAAATAGATAGCTCATGGCAGATCCTCCACATTGACCCTGCCAAAAATCCCTAACAGTGGCCAA
1 TTAAATAGATAGCTCATGGCAGATCCTCCACATTGACCCTGCCAAAAATCCCTAACAGTGGCCAA
17899 GAACTTTTCATGGCCAGTCCAACAATTGAAAAACTTAAAAGGCAGAGGATACCTAGTCATAACTC
66 GAACTTTTCATGGCCAGTCCAACAATTGAAAAACTTAAAAGGCAGAGGATACCTAGTCATAACTC
17964 CCTTTTGTGTCCATAATAATCCAAGGCAATGATCAGAAACTCCCTGGGCTTTGAATTCAACAAAA
131 CCTTTTGTGTCCATAATAATCCAAGGCAATGATCAGAAACTCCCTGGGCTTTGAATTCAACAAAA
18029 GATTCAGGATAATCCAGCAGCCGCTGATCATTAACTAAAACTCCTTA
196 GATTCAGGATAATCCAGCAGCCGCTGATCATTAACTAAAACTCCTTA
18076 TTAAATAGATAGCTCATGGCAGATCCTCCACATTGACCCTGCCAAAAATCCCTAACAGTGGCCAA
1 TTAAATAGATAGCTCATGGCAGATCCTCCACATTGACCCTGCCAAAAATCCCTAACAGTGGCCAA
* *
18141 GAACTTTTCATGGCCAGTCCAACAATTGAAAAACTTGAAAGGCAGAGGATACTTAGTCATAACTC
66 GAACTTTTCATGGCCAGTCCAACAATTGAAAAACTTAAAAGGCAGAGGATACCTAGTCATAACTC
*
18206 CCTTTTGTGTCCATAATAATCCAAGGCAATGATCAGAAACTCCCTGGGCTTTGAATTCATCAAAA
131 CCTTTTGTGTCCATAATAATCCAAGGCAATGATCAGAAACTCCCTGGGCTTTGAATTCAACAAAA
18271 GATTCAGGATAATCCAGCAGCCGCTGATCATTAACTAAAAC
196 GATTCAGGATAATCCAGCAGCCGCTGATCATTAACTAAAAC
18312 CCTGTCCAAC
Statistics
Matches: 233, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
242 233 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (242 bp):
TTAAATAGATAGCTCATGGCAGATCCTCCACATTGACCCTGCCAAAAATCCCTAACAGTGGCCAA
GAACTTTTCATGGCCAGTCCAACAATTGAAAAACTTAAAAGGCAGAGGATACCTAGTCATAACTC
CCTTTTGTGTCCATAATAATCCAAGGCAATGATCAGAAACTCCCTGGGCTTTGAATTCAACAAAA
GATTCAGGATAATCCAGCAGCCGCTGATCATTAACTAAAACTCCTTA
Found at i:24822 original size:15 final size:15
Alignment explanation
Indices: 24773--24823 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
24763 TTTTTTTTAA
24773 TTTAATTACT-TAAC
1 TTTAATTACTCTAAC
24787 TTTCAAGTTACTCCTAA-
1 TTT-AA-TTACT-CTAAC
*
24804 TTTAATCACTCTAAC
1 TTTAATTACTCTAAC
24819 TTTAA
1 TTTAA
24824 ATTTATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
14 7 0.23
15 11 0.35
16 7 0.23
17 3 0.10
18 3 0.10
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.45
Consensus pattern (15 bp):
TTTAATTACTCTAAC
Found at i:27671 original size:50 final size:50
Alignment explanation
Indices: 27566--27672 Score: 128
Period size: 50 Copynumber: 2.1 Consensus size: 50
27556 TCACACTTCA
* * * * *
27566 ATTTGCCTTTTCATTGCGACTAGGAGGGTTGGTTAGAGACATATTATCGT
1 ATTTTCCTTTTCATTGCGACTAGGAGGGCTCGATAGAGACATATCATCGT
*
27616 GTTTTCCTTTTCATTGCGACTAGGAGGGCTCGATAG-GACATTATCCATC-T
1 ATTTTCCTTTTCATTGCGACTAGGAGGGCTCGATAGAGACA-TAT-CATCGT
27666 ATTTTCC
1 ATTTTCC
27673 GCAAATCCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
49 4 0.08
50 41 0.85
51 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (50 bp):
ATTTTCCTTTTCATTGCGACTAGGAGGGCTCGATAGAGACATATCATCGT
Found at i:27804 original size:3 final size:3
Alignment explanation
Indices: 27796--27891 Score: 167
Period size: 3 Copynumber: 31.7 Consensus size: 3
27786 TTTCGTCCCG
27796 TTA TTA TTA GGTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA --TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27843 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27890 TT
1 TT
27892 TAAGATTACT
Statistics
Matches: 90, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.02
3 85 0.94
5 3 0.03
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:28454 original size:2 final size:2
Alignment explanation
Indices: 28447--28501 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
28437 TTTGCATACA
28447 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28489 AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT
28502 GCGAGTCTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:29575 original size:2 final size:2
Alignment explanation
Indices: 29568--29668 Score: 77
Period size: 2 Copynumber: 52.0 Consensus size: 2
29558 ATTAATTTAC
* **
29568 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT TT AT GC AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
29608 AT TT TT AT -T AA AC AT CA- AT CT AT GA- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT -AT AT AT AT AT AT AT AT AT
29649 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
29669 TATTTGGTTG
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
1 5 0.06
2 72 0.91
3 2 0.03
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31187 original size:31 final size:31
Alignment explanation
Indices: 31149--31336 Score: 279
Period size: 31 Copynumber: 6.0 Consensus size: 31
31139 AGGGTCGAGG
31149 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
31180 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
31211 GCTTACCTATGTTTTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
31242 GTTTACCTATGTTCTTCGGGACATATTTGACT
1 GTTTACCTATGTTCTTCGGGACATA-TGGACT
* *
31274 GTTTACCTATGTTCTTTGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
31305 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
31336 G
1 G
31337 GTCCTTCGGG
Statistics
Matches: 142, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
31 112 0.79
32 30 0.21
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:31311 original size:94 final size:93
Alignment explanation
Indices: 31149--31336 Score: 288
Period size: 94 Copynumber: 2.0 Consensus size: 93
31139 AGGGTCGAGG
* *
31149 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGCT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGAACTGAT
* * *
31214 TACCTATGTTTTTCGGGA-CATATGGACT
66 TACCTAGGTTCTTCGGAATC-TATGGACT
* *
31242 GTTTACCTATGTTCTTCGGGACATATTTGACTGTTTACCTATGTTCTTTGGGACATATGAACTGA
1 GTTTACCTATGTTCTTCGGGACATA-TGGACTGTTTACCTATGTTCTTCGGGACATATGAACTGA
31307 TTACCTAGGTTCTTCGGAATCTATGGACT
65 TTACCTAGGTTCTTCGGAATCTATGGACT
31336 G
1 G
31337 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
93 25 0.29
94 60 0.70
95 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (93 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGAACTGAT
TACCTAGGTTCTTCGGAATCTATGGACT
Found at i:34621 original size:21 final size:21
Alignment explanation
Indices: 34596--34636 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
34586 TCTAGGCAAA
* *
34596 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
34617 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
34637 ACGAACAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:35351 original size:31 final size:31
Alignment explanation
Indices: 35312--35498 Score: 313
Period size: 31 Copynumber: 6.0 Consensus size: 31
35302 AGGGTCGAGG
35312 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
35343 ATTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
35374 GTTTACCTATGTTTTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
35405 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
35436 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
35467 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
35498 G
1 G
35499 GTCCTTCGGG
Statistics
Matches: 148, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
31 147 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:47898 original size:26 final size:27
Alignment explanation
Indices: 47847--47898 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
47837 ATTAAAAATG
*
47847 AAAAAGAAAAGGAAAGAAAAATGAGGA
1 AAAAAGAAAAGAAAAGAAAAATGAGGA
* *
47874 AAAAAGAAAATAAAATAAAAA-GAGG
1 AAAAAGAAAAGAAAAGAAAAATGAGG
47899 GTTTAAGATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (27 bp):
AAAAAGAAAAGAAAAGAAAAATGAGGA
Found at i:49326 original size:111 final size:111
Alignment explanation
Indices: 49121--49439 Score: 444
Period size: 111 Copynumber: 2.9 Consensus size: 111
49111 GTGACAGCGG
* *
49121 AATGAATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGAAACAGATCAC-CATATTCCA
1 AATGGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACAGATCACTC-TATTCCA
* *
49185 AGATTTGATATTCCCTGAGTAACAGCAGAACAAGTCTACCCCGATTC
65 AGATTTGATATTCCCTGAGTGACAGTAGAACAAGTCTACCCCGATTC
** *
49232 AATGGATTGACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACATATCACTCTATTCCAA
1 AATGGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACAGATCACTCTATTCCAA
*
49297 GATTTGATATTCCCTGAGTGACAGTAGAACAAGTCTACCCTGATTC
66 GATTTGATATTCCCTGAGTGACAGTAGAACAAGTCTACCCCGATTC
* * * * * *
49343 AATGGATCAACTCCCCCAAATATGATATTCCCTTTAGAAGAAGCGGAACAGATCCCTCTCATCCC
1 AATGGATCAACTCCTCCAGATCTGATATTCCC-TTAGAAGAAGTGGAACAGATCACTCT-ATTCC
* *
49408 CAGATTTGATA-TCCCTTGAGTGACAGTGGAAC
64 AAGATTTGATATTCCC-TGAGTGACAGTAGAAC
49440 TGATCATTTA
Statistics
Matches: 185, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
111 128 0.69
112 28 0.15
113 29 0.16
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (111 bp):
AATGGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACAGATCACTCTATTCCAA
GATTTGATATTCCCTGAGTGACAGTAGAACAAGTCTACCCCGATTC
Found at i:49572 original size:3 final size:3
Alignment explanation
Indices: 49564--49607 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
49554 TTTCGTCCCG
49564 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
49608 TAAGATTACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:50178 original size:2 final size:2
Alignment explanation
Indices: 50171--50196 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50161 TTTGCATACA
50171 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
50197 GCGAGTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51111 original size:2 final size:2
Alignment explanation
Indices: 51104--51367 Score: 180
Period size: 2 Copynumber: 137.5 Consensus size: 2
51094 TTTTGTAAGG
* *
51104 AT AT AT AT AT AT AT AT AT -T AT TT A- AGT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
*
51145 AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * **
51187 AGT AT GT AG A- AT GT AT AT TT AT -T TT AT -T AT CC AT AT -T AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * ** * *
51226 GT A- AT AT AT AT AT AGC AT AT AT A- AC AT GC GT A- AC ACT -T AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * * * * *
51266 GT AT AT AT -T AT A- AT -T AT TT TT AT -T A- AT TT AC AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51303 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51345 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
51368 AAATTTATGC
Statistics
Matches: 205, Mismatches: 38, Indels: 38
0.73 0.14 0.14
Matches are distributed among these distances:
1 15 0.07
2 187 0.91
3 3 0.01
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53222 original size:13 final size:13
Alignment explanation
Indices: 53206--53237 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
53196 CAAAAAAAAA
53206 ACAAAAAAGGCAC
1 ACAAAAAAGGCAC
53219 ACAAAAAAGGCAC
1 ACAAAAAAGGCAC
53232 A-AAAAA
1 ACAAAAA
53238 CAAAAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.69, C:0.19, G:0.12, T:0.00
Consensus pattern (13 bp):
ACAAAAAAGGCAC
Found at i:61057 original size:24 final size:20
Alignment explanation
Indices: 61008--61065 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
60998 TTCCCATTGA
*
61008 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
61028 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
61051 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
61066 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Done.