Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002431.1 Hibiscus syriacus cultivar Beakdansim tig00004971_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: 77092
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:11071 original size:52 final size:52
Alignment explanation
Indices: 10940--11405 Score: 734
Period size: 52 Copynumber: 9.1 Consensus size: 52
10930 ATTTGCCAAT
*
10940 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAATT-AGACAGAATCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGA-ACAGAATCA
*
10992 A-CATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATTGAACAGAATCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGAACAGAATCA
* *
11043 AGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTAATT-AGACAGAAT--
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGA-ACAGAATCA
11093 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT-AGACAGAATCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGA-ACAGAATCA
*
11145 AGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATTGAACAGAATCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGAACAGAATCA
*
11197 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAATT-AGACAGAAT--
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGA-ACAGAATCA
*
11247 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGAACAGAATCA
* *
11299 AGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGAACAGAATCA
* *
11351 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGAACAGAATCA
11403 AGC
1 AGC
11406 CTTAAATGGA
Statistics
Matches: 389, Mismatches: 15, Indels: 20
0.92 0.04 0.05
Matches are distributed among these distances:
50 95 0.24
51 49 0.13
52 244 0.63
53 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (52 bp):
AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGAACAGAATCA
Found at i:11146 original size:102 final size:103
Alignment explanation
Indices: 10940--11402 Score: 738
Period size: 102 Copynumber: 4.5 Consensus size: 103
10930 ATTTGCCAAT
*
10940 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAATTAGACAGAATCAACATCTTCTGGAA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAATTAGACAGAATCAGCATCTTCTGGAA
11005 ATGTTCTTTGAGTTATCTGATCTGATT-GAACAGAATCA
66 ATGTTCTTTGAGTTATCTGATCTGATTAG-ACAGAATCA
*
11043 AGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTAATTAGACAGAAT-AGCATCTTCTGGAA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAATTAGACAGAATCAGCATCTTCTGGAA
*
11107 GTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCA
66 ATGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCA
* *
11145 AGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATT-GAACAGAATCAAGCATCTTCTGG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAATTAG-ACAGAATC-AGCATCTTCTGG
* *
11209 AAGTGTTCTTTGAGTTATCTGATCTAATTAGACAGAAT--
64 AAATGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCA
* *
11247 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATCTTCTGGA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAATTAGACAGAATC-AGCATCTTCTGGA
*
11312 AATGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
65 AATGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCA
** *
11351 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAATTAGACAGAATCA
11403 AGCCTTAAAT
Statistics
Matches: 341, Mismatches: 12, Indels: 14
0.93 0.03 0.04
Matches are distributed among these distances:
101 1 0.00
102 189 0.55
103 52 0.15
104 99 0.29
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (103 bp):
AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAATTAGACAGAATCAGCATCTTCTGGAA
ATGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCA
Found at i:11400 original size:154 final size:154
Alignment explanation
Indices: 10937--11387 Score: 859
Period size: 154 Copynumber: 2.9 Consensus size: 154
10927 TGAATTTGCC
*
10937 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAATTAGACAGAATCAA-CATCTTCT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCAAGCATCTTCT
11001 GGAAATGTTCTTTGAGTTATCTGATCTGATTGAACAGAATCAAGCATCTTCTGGAAGTGTTCTTT
66 GGAAATGTTCTTTGAGTTATCTGATCTGATTGAACAGAATCAAGCATCTTCTGGAAGTGTTCTTT
*
11066 AAGTTATCTGATCTAATTAGACAG
131 GAGTTATCTGATCTAATTAGACAG
11090 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCAAGCATCTTCT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCAAGCATCTTCT
11155 GGAAATGTTCTTTGAGTTATCTGATCTGATTGAACAGAATCAAGCATCTTCTGGAAGTGTTCTTT
66 GGAAATGTTCTTTGAGTTATCTGATCTGATTGAACAGAATCAAGCATCTTCTGGAAGTGTTCTTT
11220 GAGTTATCTGATCTAATTAGACAG
131 GAGTTATCTGATCTAATTAGACAG
*
11244 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATCTTCT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCAAGCATCTTCT
*
11309 GGAAATGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATCTTCTGGAAGTGTTCTTT
66 GGAAATGTTCTTTGAGTTATCTGATCTGATTGAACAGAATCAAGCATCTTCTGGAAGTGTTCTTT
11374 GAGTTATCTGATCT
131 GAGTTATCTGATCT
11388 GGTTGGACAG
Statistics
Matches: 293, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
153 55 0.19
154 238 0.81
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.37
Consensus pattern (154 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCAAGCATCTTCT
GGAAATGTTCTTTGAGTTATCTGATCTGATTGAACAGAATCAAGCATCTTCTGGAAGTGTTCTTT
GAGTTATCTGATCTAATTAGACAG
Found at i:11544 original size:83 final size:83
Alignment explanation
Indices: 11351--11589 Score: 394
Period size: 83 Copynumber: 2.9 Consensus size: 83
11341 GACAGAATCA
* *
11351 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAAGCCTT-AA-ATG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAAGCATTGAATTTG
11414 GAAGATGAATTTGCCAAT
66 GAAGATGAATTTGCCAAT
* **
11432 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTATACAGAATCAAGCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAAGCATTGAATTTG
11497 GAAGATGAATTTGCCAAT
66 GAAGATGAATTTGCCAAT
* *
11515 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTGGACAGAA-CAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAAGCATTGAATTTG
11579 GAAGATGAATT
66 GAAGATGAATT
11590 GCTCATAGTA
Statistics
Matches: 146, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
81 54 0.37
82 27 0.18
83 65 0.45
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.36
Consensus pattern (83 bp):
AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAAGCATTGAATTTG
GAAGATGAATTTGCCAAT
Found at i:12552 original size:113 final size:113
Alignment explanation
Indices: 12210--12856 Score: 1092
Period size: 113 Copynumber: 5.9 Consensus size: 113
12200 TCAAATCCAC
*
12210 TTGATGGATCATTCATTGCCAGATAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-A-
1 TTGATGGATCA-TCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
12272 AAGTTCATAATGAGAAGAACTTGTTCAAC-TTTTGTTTAAATTCATCAT
65 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
12320 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTC-TCT-AAGAA-G--GAAGA
1 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
12380 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
12428 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
12493 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
*
12541 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGA
1 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
12606 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
*
12654 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
12719 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTG-TTGAATTCATCAC
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
* * *
12766 TTGAT---T-ATC-TTTCCGGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
1 TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
12825 AGTTCATAATAAGAAGAACTTGTTCAACTTTT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTT
12857 GGCATAATTC
Statistics
Matches: 517, Mismatches: 11, Indels: 22
0.94 0.02 0.04
Matches are distributed among these distances:
105 1 0.00
106 70 0.14
107 39 0.08
108 72 0.14
109 20 0.04
110 36 0.07
111 1 0.00
112 16 0.03
113 262 0.51
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (113 bp):
TTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
Found at i:13182 original size:3 final size:3
Alignment explanation
Indices: 13176--13248 Score: 112
Period size: 3 Copynumber: 24.7 Consensus size: 3
13166 TTTTTATCCA
* *
13176 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
13224 TAT TAT TAT TAT TAC TA- TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
13249 AATATTAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:13269 original size:26 final size:25
Alignment explanation
Indices: 13240--13291 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
13230 TATTATTACT
* *
13240 ATATTATTAAATATTAAATACAATAA
1 ATATTATTAAA-AATAAATAAAATAA
13266 ATATTATTAAAAATAAATAAAATAA
1 ATATTATTAAAAATAAATAAAATAA
13291 A
1 A
13292 AAATATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
ATATTATTAAAAATAAATAAAATAA
Found at i:14340 original size:28 final size:30
Alignment explanation
Indices: 14309--14366 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
14299 TCACTAAACT
14309 GAATTTAAATATT-TTTAATTTAG-TCTTC
1 GAATTTAAATATTATTTAATTTAGTTCTTC
* * *
14337 GAATTTTAATTTTATTTATTTTAGTTCTTC
1 GAATTTAAATATTATTTAATTTAGTTCTTC
14367 ATATTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.44
29 9 0.36
30 5 0.20
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (30 bp):
GAATTTAAATATTATTTAATTTAGTTCTTC
Found at i:18428 original size:20 final size:21
Alignment explanation
Indices: 18400--18439 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
18390 ATTTTATGAA
18400 TTGGATGAACAA-TATCGATT
1 TTGGATGAACAAGTATCGATT
* *
18420 TTGGTTGAAGAAGTATCGAT
1 TTGGATGAACAAGTATCGAT
18440 ACTGATCTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.35
Consensus pattern (21 bp):
TTGGATGAACAAGTATCGATT
Found at i:19116 original size:15 final size:15
Alignment explanation
Indices: 19098--19130 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19088 GTGAAATATG
*
19098 TATATGAAAATATTA
1 TATATGAAAATAATA
19113 TATATGAAAATAATA
1 TATATGAAAATAATA
19128 TAT
1 TAT
19131 GTGCTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (15 bp):
TATATGAAAATAATA
Found at i:19345 original size:21 final size:23
Alignment explanation
Indices: 19295--19354 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
19285 GCCGAGGGTT
* *
19295 CTATGTGGTCCTTTGGGACAAAA
1 CTATGTGGTACTTCGGGACAAAA
*
19318 CTATGTGGTTCTTCGGGAC-AAA
1 CTATGTGGTACTTCGGGACAAAA
19340 -TATGTGGTACTTCGG
1 CTATGTGGTACTTCGG
19355 TGCAAATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 14 0.41
22 3 0.09
23 17 0.50
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (23 bp):
CTATGTGGTACTTCGGGACAAAA
Found at i:23672 original size:23 final size:23
Alignment explanation
Indices: 23607--23675 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
23597 CACCACAGCT
* *
23607 CATACAATTGCACCGAAGTACCA
1 CATAGAATTGCACCGAAGTGCCA
* * *
23630 CATATAATTGCACCGGAGTGCCG
1 CATAGAATTGCACCGAAGTGCCA
* *
23653 CGTAGAATTGCACCGTAGTGCCA
1 CATAGAATTGCACCGAAGTGCCA
23676 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (23 bp):
CATAGAATTGCACCGAAGTGCCA
Found at i:24248 original size:30 final size:30
Alignment explanation
Indices: 24214--24274 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
24204 TATAATATTC
* *
24214 TCATAT-ATTCATATAATTCAGTATCACATA
1 TCATATGAATCATATAAATCA-TATCACATA
*
24244 TCATATGAATCATATAAATCATGTCACATA
1 TCATATGAATCATATAAATCATATCACATA
24274 T
1 T
24275 ACTCATGCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 15 0.56
31 12 0.44
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (30 bp):
TCATATGAATCATATAAATCATATCACATA
Found at i:29290 original size:23 final size:23
Alignment explanation
Indices: 29264--29350 Score: 111
Period size: 23 Copynumber: 3.7 Consensus size: 23
29254 CAGCTCATAT
29264 AATTGCACCGGAGTGCCGTGTAG
1 AATTGCACCGGAGTGCCGTGTAG
* * * *
29287 AATTGCACCGTAGTGCCATATAAT
1 AATTGCACCGGAGTGCCGTGT-AG
*
29311 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGGAGTGCCGTGTAG
*
29334 AATTGCACCGTAGTGCC
1 AATTGCACCGGAGTGCC
29351 ATATAATAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 35 0.66
24 18 0.34
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (23 bp):
AATTGCACCGGAGTGCCGTGTAG
Found at i:29325 original size:47 final size:47
Alignment explanation
Indices: 29262--29360 Score: 189
Period size: 47 Copynumber: 2.1 Consensus size: 47
29252 CACAGCTCAT
*
29262 ATAATTGCACCGGAGTGCCGTGTAGAATTGCACCGTAGTGCCATATA
1 ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
29309 ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
1 ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
29356 ATAAT
1 ATAAT
29361 GTCCATAAGG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.25
Consensus pattern (47 bp):
ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
Found at i:29542 original size:93 final size:98
Alignment explanation
Indices: 29370--29572 Score: 276
Period size: 93 Copynumber: 2.1 Consensus size: 98
29360 TGTCCATAAG
* *
29370 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATA-ATATACCAGAGATCAAGTA-GTGTCTCACCAGAC
29435 TTCACATGTTCCAAAGAATAC-ATATGTCCC-AAA
64 TTCACATGTTCCAAAGAATACAATATGTCCCGAAA
*
29468 GACCACATATCATTCCTTAAG-ATCATAT-A-ATGCCA-AGATCAAGTA-TGTCTCACCAGACTT
1 GACCACATATCATTCCTTAAGAATCATATAATATACCAGAGATCAAGTAGTGTCTCACCAGACTT
*
29528 CACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 --CACATGTTCCAAAGAATACA-ATATGTCCCGAAA
29564 GACCACATA
1 GACCACATA
29573 GACCCTCGAC
Statistics
Matches: 96, Mismatches: 4, Indels: 12
0.86 0.04 0.11
Matches are distributed among these distances:
91 15 0.16
93 28 0.29
94 4 0.04
95 10 0.10
96 11 0.11
97 7 0.07
98 21 0.22
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (98 bp):
GACCACATATCATTCCTTAAGAATCATATAATATACCAGAGATCAAGTAGTGTCTCACCAGACTT
CACATGTTCCAAAGAATACAATATGTCCCGAAA
Found at i:47301 original size:31 final size:31
Alignment explanation
Indices: 47266--47339 Score: 75
Period size: 30 Copynumber: 2.4 Consensus size: 31
47256 AGTTAGTTAA
*
47266 TTATTTTATTAAT-TATGATCACT-CTAAAATT
1 TTATTTTATTAATATAT-ATCA-TACGAAAATT
47297 TTA-TTTA-TATATATATATCATACGAAAATT
1 TTATTTTATTA-ATATATATCATACGAAAATT
*
47327 TTATATTATTAAT
1 TTATTTTATTAAT
47340 GCATATGTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
29 3 0.08
30 20 0.56
31 11 0.31
32 2 0.06
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (31 bp):
TTATTTTATTAATATATATCATACGAAAATT
Found at i:52813 original size:20 final size:22
Alignment explanation
Indices: 52762--52819 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 22
52752 TAGTGCAGGA
*
52762 GGAATCGATTCCCCCTTTGAATG
1 GGAATTGATTCCCCCTTT-AATG
*
52785 GGAACTGATTCCCCCTTT-A-G
1 GGAATTGATTCCCCCTTTAATG
*
52805 GGAATTGATACCCCC
1 GGAATTGATTCCCCC
52820 CACGAGGTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 14 0.45
21 1 0.03
23 16 0.52
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (22 bp):
GGAATTGATTCCCCCTTTAATG
Found at i:56928 original size:258 final size:258
Alignment explanation
Indices: 56471--56988 Score: 964
Period size: 258 Copynumber: 2.0 Consensus size: 258
56461 TTATTATTCA
56471 TATTGAACCTGATATGTTGCTGCGTTGATTCTGCTATTCTGTAGTACTACTTTTAAGTCAAATTT
1 TATTGAACCTGATATGTTGCTGCGTTGATTCTGCTATTCTGTAGTACTACTTTTAAGTCAAATTT
* *
56536 TGAAGGTATGCTACTGCGCTAGAGAGAAACCCAGAAGATTATGATGCTCTTTACAACTGGGCATT
66 TGAAGGTATGCTACTGCACTAGAGAGAAACCCAGAAGATTATGATGCTCTTTACAACTGGGAATT
*
56601 GGTTCTTCAAGTTTGAGATGCTGGTTCATTATGATATTGTTATCTTAACATCATTCAAAATGATA
131 GGTTCTTCAAGTTTGAGATGCTGGTTCATTATAATATTGTTATCTTAACATCATTCAAAATGATA
56666 TATCATGTCCAATTCTTATTTTGCTAGAACTTACTGCTTAAGTTTATGAATGTAAACATAATG
196 TATCATGTCCAATTCTTATTTTGCTAGAACTTACTGCTTAAGTTTATGAATGTAAACATAATG
*
56729 TATTGAACCTGATATGTTGCTGCTTTGATTCTGCTATTCTGTAGTACTACTTTTAAGTCAAATTT
1 TATTGAACCTGATATGTTGCTGCGTTGATTCTGCTATTCTGTAGTACTACTTTTAAGTCAAATTT
* *
56794 TGTAGGTATGCTACTGCACTAGAGAGAAACCCATAAGATTATGATGCTCTTTACAACTGGGAATT
66 TGAAGGTATGCTACTGCACTAGAGAGAAACCCAGAAGATTATGATGCTCTTTACAACTGGGAATT
56859 GGTTCTTCAAGTTTGAGATGCTGGTTCATTATAATATTGTTATCTTAACATCATTCAAAATGATA
131 GGTTCTTCAAGTTTGAGATGCTGGTTCATTATAATATTGTTATCTTAACATCATTCAAAATGATA
* *
56924 TATCATGTCCAATTCTTATTTTGCTAGAACTTCCTGCTTAAGTTTATGAATGTAAACATGATG
196 TATCATGTCCAATTCTTATTTTGCTAGAACTTACTGCTTAAGTTTATGAATGTAAACATAATG
56987 TA
1 TA
56989 ATCTTTGCAA
Statistics
Matches: 252, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
258 252 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (258 bp):
TATTGAACCTGATATGTTGCTGCGTTGATTCTGCTATTCTGTAGTACTACTTTTAAGTCAAATTT
TGAAGGTATGCTACTGCACTAGAGAGAAACCCAGAAGATTATGATGCTCTTTACAACTGGGAATT
GGTTCTTCAAGTTTGAGATGCTGGTTCATTATAATATTGTTATCTTAACATCATTCAAAATGATA
TATCATGTCCAATTCTTATTTTGCTAGAACTTACTGCTTAAGTTTATGAATGTAAACATAATG
Found at i:57311 original size:57 final size:57
Alignment explanation
Indices: 57242--57366 Score: 196
Period size: 57 Copynumber: 2.2 Consensus size: 57
57232 GATGACTTCT
* * *
57242 CAGAATGCATAAGCCATATAAGAAGTTGGATAGACAAAAAAAATAAGTGTGGAGATG
1 CAGAATGCATAAGCCATATAAAAAGCTGGATAGACAAAAAAAATAAGTGTAGAGATG
* *
57299 CAGAATGCATAAGCTATATAAAAAGCTGGATAGACAAGAAAAATAAGTGTAGAGATG
1 CAGAATGCATAAGCCATATAAAAAGCTGGATAGACAAAAAAAATAAGTGTAGAGATG
*
57356 CATAATGCATA
1 CAGAATGCATA
57367 GATGTTCCCA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.48, C:0.10, G:0.22, T:0.20
Consensus pattern (57 bp):
CAGAATGCATAAGCCATATAAAAAGCTGGATAGACAAAAAAAATAAGTGTAGAGATG
Found at i:59064 original size:15 final size:15
Alignment explanation
Indices: 59044--59074 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
59034 CAACAAATAG
59044 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
59059 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
59074 A
1 A
59075 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:65833 original size:30 final size:30
Alignment explanation
Indices: 65795--65934 Score: 154
Period size: 30 Copynumber: 4.6 Consensus size: 30
65785 GTCTGCATAT
*
65795 TAATAATTCTGCTCATATTAATTTTGCTTG
1 TAATAATTCTGCTCATATTAATTCTGCTTG
* *
65825 TGATAATTCTGCTCGTATTAATTCTGCTTG
1 TAATAATTCTGCTCATATTAATTCTGCTTG
* **
65855 TAATAATTCTGCTCATATTAATTCTACTCA
1 TAATAATTCTGCTCATATTAATTCTGCTTG
* ** *
65885 TATTAATTCTGCTTGTAATAATTCTGCTTG
1 TAATAATTCTGCTCATATTAATTCTGCTTG
*
65915 TATTGATAATGCTGCTCATA
1 TA---ATAATTCTGCTCATA
65935 ATTTTTTGCC
Statistics
Matches: 88, Mismatches: 19, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
30 77 0.88
33 11 0.12
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.46
Consensus pattern (30 bp):
TAATAATTCTGCTCATATTAATTCTGCTTG
Found at i:65851 original size:45 final size:45
Alignment explanation
Indices: 65798--65918 Score: 154
Period size: 45 Copynumber: 2.7 Consensus size: 45
65788 TGCATATTAA
** * * * *
65798 TAATTCTGCTCATATTAATTTTGCTTGTGA-TAATTCTGCTCGTAT
1 TAATTCTGCTTGTAATAATTCTGCTTGT-ATTAATTCTACTCATAT
**
65843 TAATTCTGCTTGTAATAATTCTGCTCATATTAATTCTACTCATAT
1 TAATTCTGCTTGTAATAATTCTGCTTGTATTAATTCTACTCATAT
65888 TAATTCTGCTTGTAATAATTCTGCTTGTATT
1 TAATTCTGCTTGTAATAATTCTGCTTGTATT
65919 GATAATGCTG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 1 0.02
45 64 0.98
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.49
Consensus pattern (45 bp):
TAATTCTGCTTGTAATAATTCTGCTTGTATTAATTCTACTCATAT
Found at i:65916 original size:15 final size:15
Alignment explanation
Indices: 65795--65912 Score: 119
Period size: 15 Copynumber: 7.9 Consensus size: 15
65785 GTCTGCATAT
*
65795 TAATAATTCTGCTCA
1 TAATAATTCTGCTCG
* * *
65810 TATTAATTTTGCTTG
1 TAATAATTCTGCTCG
*
65825 TGATAATTCTGCTCG
1 TAATAATTCTGCTCG
* *
65840 TATTAATTCTGCTTG
1 TAATAATTCTGCTCG
*
65855 TAATAATTCTGCTCA
1 TAATAATTCTGCTCG
* * *
65870 TATTAATTCTACTCA
1 TAATAATTCTGCTCG
* *
65885 TATTAATTCTGCTTG
1 TAATAATTCTGCTCG
65900 TAATAATTCTGCT
1 TAATAATTCTGCT
65913 TGTATTGATA
Statistics
Matches: 83, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 83 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.47
Consensus pattern (15 bp):
TAATAATTCTGCTCG
Found at i:67219 original size:33 final size:33
Alignment explanation
Indices: 67182--67245 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
67172 TTCACAACTA
*
67182 CTACATCACTACAACCATCTTCATCTCCATCAT
1 CTACATCACTACAACCATCTCCATCTCCATCAT
* *
67215 CTACATCACTACCATCATCTCCATCTCCATC
1 CTACATCACTACAACCATCTCCATCTCCATC
67246 TCCATCTCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.28, C:0.42, G:0.00, T:0.30
Consensus pattern (33 bp):
CTACATCACTACAACCATCTCCATCTCCATCAT
Found at i:67239 original size:6 final size:6
Alignment explanation
Indices: 67230--67404 Score: 140
Period size: 6 Copynumber: 27.7 Consensus size: 6
67220 TCACTACCAT
* * *
67230 CATCTC CATCTC CATCTC CATCTC CATCATC TA-CGTC ACTACCAC CATCTC
1 CATCTC CATCTC CATCTC CATCTC CATC-TC CATC-TC -C-ATCTC CATCTC
* * *
67281 CATCTC CATCTC CATCTC CATCTC CATCATC TA-CGTC ACTACCAC CATCTC
1 CATCTC CATCTC CATCTC CATCTC CATC-TC CATC-TC -C-ATCTC CATCTC
* * *
67332 CATCTC CATCTC CATCTC CATCATC TACATCGC TA-CTAC TATCTC CATCTC
1 CATCTC CATCTC CATCTC CATC-TC --CATCTC CATCT-C CATCTC CATCTC
67383 CATCTC CATCTC CATCTC CATC
1 CATCTC CATCTC CATCTC CATC
67405 ACCACCACCA
Statistics
Matches: 140, Mismatches: 16, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
5 1 0.01
6 116 0.83
7 12 0.09
8 5 0.04
9 6 0.04
ACGTcount: A:0.21, C:0.46, G:0.02, T:0.31
Consensus pattern (6 bp):
CATCTC
Found at i:67252 original size:45 final size:45
Alignment explanation
Indices: 67196--67398 Score: 282
Period size: 45 Copynumber: 4.4 Consensus size: 45
67186 ATCACTACAA
*
67196 CCATCTTCATCTCCATCATCTACATCACTACCATCATCTCCATCT
1 CCATCTCCATCTCCATCATCTACATCACTACCATCATCTCCATCT
*
67241 CCATCTCCATCTCCATCATCTACGTCACTACCACCATCTCCATCTCCATCT
1 CCATCTCCATCTCCATCATCTACATCACT---ACCA--T-CATCTCCATCT
* *
67292 CCATCTCCATCTCCATCATCTACGTCACTACCACCATCTCCATCT
1 CCATCTCCATCTCCATCATCTACATCACTACCATCATCTCCATCT
* *
67337 CCATCTCCATCTCCATCATCTACATCGCTACTA-CTATCTCCATCT
1 CCATCTCCATCTCCATCATCTACATCACTACCATC-ATCTCCATCT
67382 CCATCTCCATCTCCATC
1 CCATCTCCATCTCCATC
67399 TCCATCACCA
Statistics
Matches: 145, Mismatches: 6, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
44 1 0.01
45 95 0.66
48 8 0.06
50 1 0.01
51 40 0.28
ACGTcount: A:0.22, C:0.45, G:0.01, T:0.31
Consensus pattern (45 bp):
CCATCTCCATCTCCATCATCTACATCACTACCATCATCTCCATCT
Found at i:67285 original size:51 final size:51
Alignment explanation
Indices: 67196--67404 Score: 283
Period size: 51 Copynumber: 4.2 Consensus size: 51
67186 ATCACTACAA
* *
67196 CCATCTTCATCTCCATCATCTACATCACT---ACCA--T-CATCTCCATCT
1 CCATCTCCATCTCCATCATCTACGTCACTACCACCATCTCCATCTCCATCT
67241 CCATCTCCATCTCCATCATCTACGTCACTACCACCATCTCCATCTCCATCT
1 CCATCTCCATCTCCATCATCTACGTCACTACCACCATCTCCATCTCCATCT
67292 CCATCTCCATCTCCATCATCTACGTCACTACCACCATCTCCATCTCCATCT
1 CCATCTCCATCTCCATCATCTACGTCACTACCACCATCTCCATCTCCATCT
* * *
67343 CCATCTCCATCATCTACATC-GCTAC-T-ACTATCTCCATCTCCATCTCCATCT
1 CCATCTCCATC-TC--CATCATCTACGTCACTACCACCATCTCCATCTCCATCT
67394 CCATCTCCATC
1 CCATCTCCATC
67405 ACCACCACCA
Statistics
Matches: 150, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
45 27 0.18
48 4 0.03
50 1 0.01
51 107 0.71
52 3 0.02
53 4 0.03
54 4 0.03
ACGTcount: A:0.22, C:0.45, G:0.01, T:0.31
Consensus pattern (51 bp):
CCATCTCCATCTCCATCATCTACGTCACTACCACCATCTCCATCTCCATCT
Found at i:69236 original size:13 final size:13
Alignment explanation
Indices: 69218--69243 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
69208 AAGCTTGAGC
69218 AGTTGGGCTAGTT
1 AGTTGGGCTAGTT
69231 AGTTGGGCTAGTT
1 AGTTGGGCTAGTT
69244 GTTATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.38, T:0.38
Consensus pattern (13 bp):
AGTTGGGCTAGTT
Found at i:71288 original size:56 final size:54
Alignment explanation
Indices: 71197--71307 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 54
71187 ATTCTACTTA
71197 TCCCTCTGTAAACACCACCTCTTTTCACCCATTTTAACCTCCAAAAATATTTTT
1 TCCCTCTGTAAACACCACCTCTTTTCACCCATTTTAACCTCCAAAAATATTTTT
71251 TCCCTCTGTAAACACCACATCTCTTTTCACCCATTTTAACCTCCAAAAATATTTTT
1 TCCCTCTGTAAACACCAC--CTCTTTTCACCCATTTTAACCTCCAAAAATATTTTT
71307 T
1 T
71308 TTCCATTGGG
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
54 18 0.33
56 37 0.67
ACGTcount: A:0.28, C:0.32, G:0.02, T:0.38
Consensus pattern (54 bp):
TCCCTCTGTAAACACCACCTCTTTTCACCCATTTTAACCTCCAAAAATATTTTT
Found at i:73208 original size:18 final size:18
Alignment explanation
Indices: 73182--73216 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
73172 TTTTCTTTCT
* *
73182 TTTTCTTTTTTATATTTA
1 TTTTATTTTTAATATTTA
73200 TTTTATTTTTAATATTT
1 TTTTATTTTTAATATTT
73217 GAAGTTATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTATTTTTAATATTTA
Done.