Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004840.1 Hibiscus syriacus cultivar Beakdansim tig00010911_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: 102151
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2314 original size:22 final size:21
Alignment explanation
Indices: 2250--2331 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 21
2240 CAAATCAAAG
2250 AAAAGAGAAAAAACAAAGAAATAA
1 AAAAG-GAAAAAA-AAAGAAA-AA
* * *
2274 AAAAGGGCAAAGAAAAGAAACA
1 AAAA-GGAAAAAAAAAGAAAAA
2296 AAAAGGAAAAAAAAGAGAAAAA
1 AAAAGGAAAAAAAA-AGAAAAA
*
2318 AACAAAGAAAAAAA
1 AA-AAGGAAAAAAA
2332 GAAAAGAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
21 8 0.17
22 13 0.27
23 17 0.35
24 9 0.19
25 1 0.02
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.01
Consensus pattern (21 bp):
AAAAGGAAAAAAAAAGAAAAA
Found at i:2345 original size:9 final size:9
Alignment explanation
Indices: 2286--2348 Score: 56
Period size: 9 Copynumber: 6.8 Consensus size: 9
2276 AAGGGCAAAG
2286 AAAAGAAACA
1 AAAAGAAA-A
2296 AAAAGGAAAA
1 AAAA-GAAAA
2306 AAAAGAGAAA
1 AAAAGA-AAA
* *
2316 AAAACAAAG
1 AAAAGAAAA
*
2325 AAAA-AAAG
1 AAAAGAAAA
*
2333 AAAAGAAAT
1 AAAAGAAAA
2342 AAAAGAA
1 AAAAGAA
2349 GACAAGATGC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
8 8 0.17
9 18 0.38
10 17 0.36
11 4 0.09
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.02
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:2346 original size:22 final size:21
Alignment explanation
Indices: 2282--2348 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 21
2272 AAAAAAGGGC
2282 AAAGAAAAGAAACAAAAAGGAAAAA
1 AAAGAAAAG-AA-AAAAA-G-AAAA
2307 AAAGAGAAA-AAAACAAAGAAAA
1 AAAGA-AAAGAAAA-AAAGAAAA
2329 AAAGAAAAGAAATAAAAGAA
1 AAAGAAAAGAAA-AAAAGAA
2349 GACAAGATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
21 3 0.08
22 18 0.47
23 4 0.11
24 5 0.13
25 5 0.13
26 3 0.08
ACGTcount: A:0.81, C:0.03, G:0.15, T:0.01
Consensus pattern (21 bp):
AAAGAAAAGAAAAAAAGAAAA
Found at i:5987 original size:20 final size:19
Alignment explanation
Indices: 5955--5993 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
5945 GCACTGAATA
*
5955 TTTTTCCCGAAGGACCACT
1 TTTTTCCCAAAGGACCACT
5974 TTTTATCCCAAAGGACCACT
1 TTTT-TCCCAAAGGACCACT
5994 GATAATCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.31
Consensus pattern (19 bp):
TTTTTCCCAAAGGACCACT
Found at i:6001 original size:20 final size:20
Alignment explanation
Indices: 5959--6002 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
5949 TGAATATTTT
* ** *
5959 TCCCGAAGGACCACTTTTTA
1 TCCCAAAGGACCACTGATAA
5979 TCCCAAAGGACCACTGATAA
1 TCCCAAAGGACCACTGATAA
5999 TCCC
1 TCCC
6003 TCGACTCTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.34, G:0.14, T:0.23
Consensus pattern (20 bp):
TCCCAAAGGACCACTGATAA
Found at i:8356 original size:36 final size:36
Alignment explanation
Indices: 8284--8356 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
8274 GTTTCACTTG
* * * *
8284 AAACAAAGTTGATCTCACTTGAGATTATTTTTCTCA
1 AAACAAAGTTCATCTCACATGAGATTATCTTCCTCA
*
8320 AAACAAATTTCATCTCACATGAGA-TAGTCTTCCTCA
1 AAACAAAGTTCATCTCACATGAGATTA-TCTTCCTCA
8356 A
1 A
8357 GACACGAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 2 0.06
36 29 0.94
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.34
Consensus pattern (36 bp):
AAACAAAGTTCATCTCACATGAGATTATCTTCCTCA
Found at i:8566 original size:67 final size:66
Alignment explanation
Indices: 8468--8663 Score: 261
Period size: 66 Copynumber: 3.0 Consensus size: 66
8458 AAAATTGATA
* * *
8468 AACTTTGAGATTG-TTCCTTTTGAAACCAGTTTTGTGTCTTTTGAGACTA-TTTCTCTTGAAACA
1 AACTTTGAGATTGTTTCC-CTTGAAACAAGTTTTGTCTCTTTTGAGAC-AGTTTCTCTTGAAACA
8531 TAC
64 TAC
* *
8534 AACCTTTAAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTTTGGAGACAGTTTCTCTTGAAACAT
1 AA-CTTTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTTTTGAGACAGTTTCTCTTGAAACAT
8599 AC
65 AC
* * * * *
8601 AACATTGAGATTATTTCCCTTGAAACAAGTTTTGTTTCTCTTGAGACATTTTCTCTTGAAACA
1 AACTTTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTTTTGAGACAGTTTCTCTTGAAACA
8664 AATTATCCCT
Statistics
Matches: 115, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
66 57 0.50
67 54 0.47
68 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (66 bp):
AACTTTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTTTTGAGACAGTTTCTCTTGAAACATA
C
Found at i:8971 original size:137 final size:137
Alignment explanation
Indices: 8708--8971 Score: 327
Period size: 137 Copynumber: 1.9 Consensus size: 137
8698 CGTAAGAATT
* * *
8708 GTGTCATCCACCGACCATATCTCCTCATCACGTAGGAGCCGCGTCATCCTCAGATAGCCAAACTT
1 GTGTCATCCACCGACCAGATCTCCTCATCACATAGGAGCCGCGTCACCCTCAGATAGCCAAACTT
* * * * **
8773 CCTTATCACGTATGAACCATGTTATACGCCTTTATCCCTAAAGATGATCAGATGTCCTCATCACG
66 CCTCATCACGTATGAACCATGTTATACGCCTTTA-CCCTAAAAACGACCAGAACTCCTCATCACG
8838 TAGGAGCC
130 TAGGAGCC
* * * *
8846 GTGTCATCCACTGACCAGA-CTCCTCATCACATAGGAGCCGTGTCACCCTTAGATAGCCAGACTT
1 GTGTCATCCACCGACCAGATCTCCTCATCACATAGGAGCCGCGTCACCCTCAGATAGCCAAACTT
* * *
8910 CCTCATCATGTATGAACCATGTTAT-CTCCAAATTTA-CCTAAAAACGACCAGAACTCTTCATC
66 CCTCATCACGTATGAACCATGTTATACGCC---TTTACCCTAAAAACGACCAGAACTCCTCATC
8972 GCGGATGAGC
Statistics
Matches: 107, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
136 3 0.03
137 83 0.78
138 17 0.16
139 4 0.04
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (137 bp):
GTGTCATCCACCGACCAGATCTCCTCATCACATAGGAGCCGCGTCACCCTCAGATAGCCAAACTT
CCTCATCACGTATGAACCATGTTATACGCCTTTACCCTAAAAACGACCAGAACTCCTCATCACGT
AGGAGCC
Found at i:12498 original size:2 final size:2
Alignment explanation
Indices: 12491--12519 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12481 AGTTCAAAAG
12491 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
12520 TGTGTGTGTG
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13339 original size:30 final size:30
Alignment explanation
Indices: 13303--13360 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
13293 TAAATGAATG
13303 TAAATGAACGTAAGTC-AACACAAACAAACT
1 TAAATGAACGTAAG-CGAACACAAACAAACT
*
13333 TAAATGAATGTAAGCGAACACAAACAAA
1 TAAATGAACGTAAGCGAACACAAACAAA
13361 TAAATATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.55, C:0.17, G:0.12, T:0.16
Consensus pattern (30 bp):
TAAATGAACGTAAGCGAACACAAACAAACT
Found at i:24996 original size:15 final size:15
Alignment explanation
Indices: 24972--25003 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
24962 GGTGAAAAAT
*
24972 AAATATATTAAATTA
1 AAATAAATTAAATTA
24987 AAATAAATTAAATTA
1 AAATAAATTAAATTA
25002 AA
1 AA
25004 GTTAGTCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATAAATTAAATTA
Found at i:25294 original size:31 final size:31
Alignment explanation
Indices: 25224--25294 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
25214 GTTAACCTGT
* *
25224 AGTGACCACATCTTAATTAAACAAAAATGAA
1 AGTGACCATATCTTAATTAAACAAAAACGAA
*
25255 AGTGACCATATCTTAATTAAATAAAAACGAA
1 AGTGACCATATCTTAATTAAACAAAAACGAA
25286 AGTGACCAT
1 AGTGACCAT
25295 TTATTATGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.24
Consensus pattern (31 bp):
AGTGACCATATCTTAATTAAACAAAAACGAA
Found at i:25874 original size:23 final size:23
Alignment explanation
Indices: 25821--25906 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
25811 TTATAATATT
25821 ATAA-ATTATTTATTTATTTTTAAA
1 ATAATATTATTTATTTA--TTTAAA
*
25845 ATCATATTATTTATTTATTCT-AA
1 ATAATATTATTTATTTATT-TAAA
** *
25868 ATAATATTAAATATTTATTTGAA
1 ATAATATTATTTATTTATTTAAA
25891 ATAATATTATTT-TTTA
1 ATAATATTATTTATTTA
25907 ATTATCTATT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
22 5 0.09
23 32 0.60
24 4 0.08
25 12 0.23
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (23 bp):
ATAATATTATTTATTTATTTAAA
Found at i:25901 original size:19 final size:18
Alignment explanation
Indices: 25855--25935 Score: 53
Period size: 23 Copynumber: 4.2 Consensus size: 18
25845 ATCATATTAT
25855 TTATTTATTCTAAATAATA
1 TTATTTATT-TAAATAATA
25874 TTAAATATTTATTTGAAATAATA
1 -T---TATTTATTT-AAATAATA
25897 TTATTT-TTT-AAT--TA
1 TTATTTATTTAAATAATA
25911 TCTATTTAATTTTAAATAATA
1 T-TATTT-A-TTTAAATAATA
25932 TTAT
1 TTAT
25936 ATGAAACCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 22
0.69 0.00 0.31
Matches are distributed among these distances:
14 3 0.06
15 5 0.10
16 3 0.06
18 6 0.12
19 8 0.16
20 4 0.08
21 3 0.06
22 2 0.04
23 16 0.32
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (18 bp):
TTATTTATTTAAATAATA
Found at i:26046 original size:23 final size:24
Alignment explanation
Indices: 25999--26046 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
25989 ATTTAAAATT
*
25999 AAATAAATAATTAAAAATATTATTTC
1 AAATAAATAATT--AAATATGATTTC
26025 AAATAAATAATT-AATATGATTT
1 AAATAAATAATTAAATATGATTT
26047 TAAAAATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
26 12 0.57
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
AAATAAATAATTAAATATGATTTC
Found at i:26080 original size:20 final size:20
Alignment explanation
Indices: 26044--26082 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
26034 ATTAATATGA
26044 TTTTAAAAATTCAATAAATGT
1 TTTTAAAAATT-AATAAATGT
26065 TTTTATAAAATT-ATAAAT
1 TTTTA-AAAATTAATAAAT
26083 ATAATTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 5 0.29
22 6 0.35
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (20 bp):
TTTTAAAAATTAATAAATGT
Found at i:28356 original size:2 final size:2
Alignment explanation
Indices: 28338--28374 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
28328 TAGGTGCATG
*
28338 AT AT CAT AT AC 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
28375 TAGGGTAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:30243 original size:2 final size:2
Alignment explanation
Indices: 30236--30278 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
30226 TCTTATTTCA
30236 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
30278 A
1 A
30279 AGCTTTTACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35003 original size:131 final size:131
Alignment explanation
Indices: 34775--35684 Score: 1640
Period size: 131 Copynumber: 6.9 Consensus size: 131
34765 AGTTATGTCG
34775 TGATACATGTAAAGCTTTATTGTTGCTCTTTTAACCAGTATTTGGGGTATTGTGAGCTTGTCTGC
1 TGATACATGTAAAGCTTTATTGTTGCTCTTTTAACCAGTATTTGGGGTATTGTGAGCTTGTCTGC
* *
34840 TGCCTCAGATGGTGGTATGAACTTGGAAGCACTTGTACGTGTGGGCATTGAATTAATGGTATGTT
66 TGCCTCAGATGGTGGTATGAACTTAGAAGCACTTGTACTTGTGGGCATTGAATTAATGGTATGTT
34905 A
131 A
34906 TGATACATGTAAAGCTTTATTGTTGCTCTTTTAACCAGTATTTGGGGTATTGTGAGCTTGTCTGC
1 TGATACATGTAAAGCTTTATTGTTGCTCTTTTAACCAGTATTTGGGGTATTGTGAGCTTGTCTGC
*
34971 TGCCTCAGATGGTGGTATGAACTTAGATGCACTTGTACTTGTGGGCATTGAATTAATGGTATGTT
66 TGCCTCAGATGGTGGTATGAACTTAGAAGCACTTGTACTTGTGGGCATTGAATTAATGGTATGTT
35036 A
131 A
*
35037 TGATACATGCAAAGCTTTATTGTTGCTCTTTTAACCAGTATTTGGGGTATTGTGAGCTTGTCTGC
1 TGATACATGTAAAGCTTTATTGTTGCTCTTTTAACCAGTATTTGGGGTATTGTGAGCTTGTCTGC
*
35102 TGCCTCAGATGGTGGTATGAACTTAGATGCACTTGTACTTGTGGGCATTGAATTAATGGTATGTT
66 TGCCTCAGATGGTGGTATGAACTTAGAAGCACTTGTACTTGTGGGCATTGAATTAATGGTATGTT
35167 A
131 A
35168 TGATACATGTAAAGCTTTATTGTTGCTCTTTTAACCAGTATTTGGGGTATTGTGAGCTTGTCTGC
1 TGATACATGTAAAGCTTTATTGTTGCTCTTTTAACCAGTATTTGGGGTATTGTGAGCTTGTCTGC
* * *
35233 TGCCTCAGATGGTGGTATGAACTTGGAAGCACTTGTACTTGTGGGCATTGAATTAATAGTATGTC
66 TGCCTCAGATGGTGGTATGAACTTAGAAGCACTTGTACTTGTGGGCATTGAATTAATGGTATGTT
*
35298 G
131 A
35299 TGATACATGTAAAGCTTTATTGTTGCTCTTTTAACCAGTATTTGGGGTATTGTGAGCTTGTCTGC
1 TGATACATGTAAAGCTTTATTGTTGCTCTTTTAACCAGTATTTGGGGTATTGTGAGCTTGTCTGC
*
35364 TGCCTCAGATGGTGGTATGAACTTGGAAGCACTTGTACTTGTGGGCATTGAATTAATGGTATGTT
66 TGCCTCAGATGGTGGTATGAACTTAGAAGCACTTGTACTTGTGGGCATTGAATTAATGGTATGTT
35429 A
131 A
* *
35430 TGATACATGTAAAGCTTTATTGTTGCTCTTTTAACCAGTATTTGAGGTATTGTGAGCTTGTTTGC
1 TGATACATGTAAAGCTTTATTGTTGCTCTTTTAACCAGTATTTGGGGTATTGTGAGCTTGTCTGC
* **
35495 TGCCTCAGATGGTGGTATGAACTTAGAAGCACTTGTATTTGTGGGCATTGAATTAATTATATGTT
66 TGCCTCAGATGGTGGTATGAACTTAGAAGCACTTGTACTTGTGGGCATTGAATTAATGGTATGTT
35560 A
131 A
* *
35561 TGATACATGTAAAGCTTTATTGTTGCTCTTTTAACCAGTATTTGGGGTGTTGTGAGCTTGTTTGC
1 TGATACATGTAAAGCTTTATTGTTGCTCTTTTAACCAGTATTTGGGGTATTGTGAGCTTGTCTGC
* * *
35626 TGCCTGAGATGGTGGTATGAACTTAGAAGCACTTTTATTTGTGGGCATTGAATTAATGG
66 TGCCTCAGATGGTGGTATGAACTTAGAAGCACTTGTACTTGTGGGCATTGAATTAATGG
35685 ATTAGTTTGT
Statistics
Matches: 754, Mismatches: 25, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
131 754 1.00
ACGTcount: A:0.22, C:0.13, G:0.25, T:0.39
Consensus pattern (131 bp):
TGATACATGTAAAGCTTTATTGTTGCTCTTTTAACCAGTATTTGGGGTATTGTGAGCTTGTCTGC
TGCCTCAGATGGTGGTATGAACTTAGAAGCACTTGTACTTGTGGGCATTGAATTAATGGTATGTT
A
Found at i:36325 original size:26 final size:26
Alignment explanation
Indices: 36292--36343 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
36282 TTTTACTCAC
36292 CGAATTCAAAAATGTTAAATTTTGGT
1 CGAATTCAAAAATGTTAAATTTTGGT
36318 CGAATTCAAAAATGTTAAATTTTGGT
1 CGAATTCAAAAATGTTAAATTTTGGT
36344 TCTTACATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (26 bp):
CGAATTCAAAAATGTTAAATTTTGGT
Found at i:38204 original size:23 final size:23
Alignment explanation
Indices: 38176--38236 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
38166 ATGTCACCTG
38176 CCACGTCAGATGCCATGTTATTA
1 CCACGTCAGATGCCATGTTATTA
*
38199 CCACGTCAGATGCCATGTTATTG
1 CCACGTCAGATGCCATGTTATTA
*
38222 CCACGTCAGCTGCCA
1 CCACGTCAGATGCCA
38237 CATCATCGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (23 bp):
CCACGTCAGATGCCATGTTATTA
Found at i:38266 original size:12 final size:12
Alignment explanation
Indices: 38220--38266 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
38210 GCCATGTTAT
38220 TGCCACGTCAGC
1 TGCCACGTCAGC
* *
38232 TGCCACATCATC
1 TGCCACGTCAGC
38244 -GCCACGTCAGC
1 TGCCACGTCAGC
*
38255 TGCCACGCCAGC
1 TGCCACGTCAGC
38267 GATGACTAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.19, C:0.45, G:0.21, T:0.15
Consensus pattern (12 bp):
TGCCACGTCAGC
Found at i:42207 original size:26 final size:26
Alignment explanation
Indices: 42166--42237 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 26
42156 TGATAAATAA
*
42166 TAAAAA-AATTACAATAAAAAAGT-C
1 TAAAAACAAATACAATAAAAAAGTAC
*
42190 TAATAAACAACTACAAT-AAAAAGTAC
1 TAA-AAACAAATACAATAAAAAAGTAC
* *
42216 TAAATACAAATATAATAAAAAA
1 TAAAAACAAATACAATAAAAAA
42238 ACAAAATCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 3 0.08
25 20 0.50
26 17 0.43
ACGTcount: A:0.67, C:0.10, G:0.03, T:0.21
Consensus pattern (26 bp):
TAAAAACAAATACAATAAAAAAGTAC
Found at i:44445 original size:9 final size:9
Alignment explanation
Indices: 44415--44466 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
44405 ATCTGCAAAA
*
44415 AAATTAATT
1 AAATTAAAT
44424 AAA-TAAA-
1 AAATTAAAT
*
44431 ATATTAAAT
1 AAATTAAAT
44440 AAATTAAAT
1 AAATTAAAT
*
44449 -ACTTAAAT
1 AAATTAAAT
44457 AAATTAAAT
1 AAATTAAAT
44466 A
1 A
44467 CAAAATATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 2 0.06
8 14 0.40
9 19 0.54
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AAATTAAAT
Found at i:44447 original size:17 final size:17
Alignment explanation
Indices: 44412--44464 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
44402 TATATCTGCA
* *
44412 AAAAAATTAATTAAA-T
1 AAAATATTAAATAAATT
44428 AAAATATTAAATAAATT
1 AAAATATTAAATAAATT
44445 -AAATACTTAAATAAATT
1 AAAATA-TTAAATAAATT
44462 AAA
1 AAA
44465 TACAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 18 0.56
17 12 0.38
18 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATATTAAATAAATT
Found at i:44465 original size:17 final size:17
Alignment explanation
Indices: 44418--44467 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
44408 TGCAAAAAAA
* *
44418 TTAATTAAATAAAATA-
1 TTAAATAAATTAAATAC
44434 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
44451 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
44468 AAAATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:44534 original size:10 final size:10
Alignment explanation
Indices: 44521--44549 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
44511 ATAAGAGTAT
44521 TTGAGAGAAG
1 TTGAGAGAAG
44531 TTGAGAGAAG
1 TTGAGAGAAG
44541 TTGAGAGAA
1 TTGAGAGAA
44550 TTTGGTGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (10 bp):
TTGAGAGAAG
Found at i:49373 original size:16 final size:16
Alignment explanation
Indices: 49349--49425 Score: 84
Period size: 16 Copynumber: 4.7 Consensus size: 16
49339 GCTTATGTCC
49349 CTCTCCCTCTCCCTCT
1 CTCTCCCTCTCCCTCT
*
49365 CTTTCCCTCTCCCTCT
1 CTCTCCCTCTCCCTCT
* * *
49381 CCCTCTCTTTCCCTCT
1 CTCTCCCTCTCCCTCT
49397 CTCTCCCTC-CCTCTCCCT
1 CTCTCCCTCTCC-CT--CT
49415 CTCTCCCTCTC
1 CTCTCCCTCTC
49426 TTGTAGTCAC
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
15 2 0.04
16 35 0.71
18 11 0.22
19 1 0.02
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (16 bp):
CTCTCCCTCTCCCTCT
Found at i:49374 original size:22 final size:22
Alignment explanation
Indices: 49346--49417 Score: 112
Period size: 22 Copynumber: 3.4 Consensus size: 22
49336 TAAGCTTATG
49346 TCCCTCTCCCTCTCCCTCTCTT
1 TCCCTCTCCCTCTCCCTCTCTT
49368 TCCCTCTCCCTCTCCCTCTCTT
1 TCCCTCTCCCTCTCCCTCTCTT
* *
49390 TCCCTCT--CTCTCCCTCCCTC
1 TCCCTCTCCCTCTCCCTCTCTT
49410 TCCCTCTC
1 TCCCTCTC
49418 TCCCTCTCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 18 0.38
22 29 0.62
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (22 bp):
TCCCTCTCCCTCTCCCTCTCTT
Found at i:49425 original size:6 final size:6
Alignment explanation
Indices: 49346--49417 Score: 71
Period size: 6 Copynumber: 12.3 Consensus size: 6
49336 TAAGCTTATG
* *
49346 TCCCTC TCCCTC TCCCTC T--CTT TCCCTC TCCCTC TCCCTC T--CTT
1 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC
*
49390 TCCCTC TCTCTCCC TCCCTC TCCCTC TC
1 TCCCTC TC-C-CTC TCCCTC TCCCTC TC
49418 TCCCTCTCTT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
4 6 0.11
6 42 0.78
7 2 0.04
8 4 0.07
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (6 bp):
TCCCTC
Found at i:49426 original size:10 final size:10
Alignment explanation
Indices: 49355--49419 Score: 85
Period size: 10 Copynumber: 6.3 Consensus size: 10
49345 GTCCCTCTCC
49355 CTCTCCCTCT
1 CTCTCCCTCT
*
49365 CTTTCCCTCT
1 CTCTCCCTCT
49375 CCCTCTCCCTCT
1 --CTCTCCCTCT
*
49387 CTTTCCCTCT
1 CTCTCCCTCT
*
49397 CTCTCCCTCC
1 CTCTCCCTCT
49407 CTCTCCCTCT
1 CTCTCCCTCT
49417 CTC
1 CTC
49420 CCTCTCTTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
10 38 0.81
12 9 0.19
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (10 bp):
CTCTCCCTCT
Found at i:49521 original size:28 final size:27
Alignment explanation
Indices: 49464--49560 Score: 119
Period size: 26 Copynumber: 3.6 Consensus size: 27
49454 TTATTTAGTG
* *
49464 TATATATATATA-ATATAGTTTTGAAAA
1 TATATATATATATATA-ATTTTTTAAAA
49491 TATATATA-ATATATAATTTTTTAAAA
1 TATATATATATATATAATTTTTTAAAA
*
49517 TATATATAT-TATATAGTTTTTTAAAGAA
1 TATATATATATATATAATTTTTT-AA-AA
49545 TATATATATATATATA
1 TATATATATATATATA
49561 TATATATATA
Statistics
Matches: 62, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
26 32 0.52
27 13 0.21
28 11 0.18
29 6 0.10
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.48
Consensus pattern (27 bp):
TATATATATATATATAATTTTTTAAAA
Found at i:49549 original size:2 final size:2
Alignment explanation
Indices: 49544--49593 Score: 70
Period size: 2 Copynumber: 26.0 Consensus size: 2
49534 TTTTTAAAGA
49544 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
49586 -T AT -T AT AT
1 AT AT AT AT AT
49594 TTTTATTCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.07
2 39 0.89
3 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:49594 original size:8 final size:9
Alignment explanation
Indices: 49517--49579 Score: 54
Period size: 10 Copynumber: 6.7 Consensus size: 9
49507 TTTTTTAAAA
49517 TATATATAT
1 TATATATAT
*
49526 TATATAGTTT
1 TATATA-TAT
* * * *
49536 TTTAAAGAA
1 TATATATAT
49545 TATATATAT
1 TATATATAT
49554 ATATATATAT
1 -TATATATAT
49564 ATATATATAT
1 -TATATATAT
49574 TATATA
1 TATATA
49580 GTATATTATT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
9 17 0.40
10 25 0.60
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (9 bp):
TATATATAT
Found at i:50088 original size:85 final size:85
Alignment explanation
Indices: 49897--50093 Score: 262
Period size: 85 Copynumber: 2.3 Consensus size: 85
49887 AAACTCATGT
* * *
49897 TTTAAGATAATATTTTAGG---TATTATATTTTATCTTTATTTTAGGTATTTTAGTTTAAATAGG
1 TTTAAGATATTATTTTAGGAATTATTTTATTTTATCTTTATTTTAGGAATTTTAGTTTAAATAGG
49959 TTTTAGTATTTTAATTAGGA
66 TTTTAGTATTTTAATTAGGA
* * *
49979 TTTAGGATATTATTTTA-AATATTATTTTATTTTATCTTTGTTTTAGGAATTTTAGTTTAAATA-
1 TTTAAGATATTATTTTAGGA-ATTATTTTATTTTATCTTTATTTTAGGAATTTTAGTTTAAATAG
50042 GTTTTAAGTGA-TTTAATTAGGA
65 GTTTT-AGT-ATTTTAATTAGGA
50064 TTTAAGATATTATTTTAGGAATTATCTTTA
1 TTTAAGATATTATTTTAGGAATTAT-TTTA
50094 GTTTGTTTTT
Statistics
Matches: 99, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
82 15 0.15
84 5 0.05
85 73 0.74
86 6 0.06
ACGTcount: A:0.31, C:0.02, G:0.13, T:0.55
Consensus pattern (85 bp):
TTTAAGATATTATTTTAGGAATTATTTTATTTTATCTTTATTTTAGGAATTTTAGTTTAAATAGG
TTTTAGTATTTTAATTAGGA
Found at i:50748 original size:13 final size:12
Alignment explanation
Indices: 50726--50756 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
50716 TAAAATTTAA
50726 TTTTTTTTATTT
1 TTTTTTTTATTT
50738 TTTTGTTTTATTT
1 TTTT-TTTTATTT
50751 TTTTTT
1 TTTTTT
50757 CTCTTTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.06, C:0.00, G:0.03, T:0.90
Consensus pattern (12 bp):
TTTTTTTTATTT
Found at i:59226 original size:2 final size:2
Alignment explanation
Indices: 59221--59280 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
59211 AAAAAAATAA
59221 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
59263 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
59281 CAAAGTATTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59513 original size:16 final size:17
Alignment explanation
Indices: 59482--59531 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
59472 AAAATAATAT
59482 AATAAT-AATGAATAAAA
1 AATAATAAAT-AATAAAA
*
59499 AATGA-AAATAATAAAA
1 AATAATAAATAATAAAA
59515 AATAATAAATATATAAA
1 AATAATAAATA-ATAAA
59532 GTTATAAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 11 0.39
17 12 0.43
18 5 0.18
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (17 bp):
AATAATAAATAATAAAA
Found at i:59521 original size:26 final size:25
Alignment explanation
Indices: 59471--59523 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
59461 TTTTTTTTTT
* *
59471 AAAAATAATATAATAATAATGAATA
1 AAAAATAAAATAATAAAAATGAATA
59496 AAAAATGAAAATAATAAAAAAT-AATA
1 AAAAAT-AAAATAAT-AAAAATGAATA
59522 AA
1 AA
59524 TATATAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.25
26 13 0.54
27 5 0.21
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (25 bp):
AAAAATAAAATAATAAAAATGAATA
Found at i:59804 original size:18 final size:17
Alignment explanation
Indices: 59781--59823 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
59771 ATATATACAT
59781 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
59799 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
59816 ATAA-AATA
1 ATAATAATA
59824 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:59824 original size:58 final size:57
Alignment explanation
Indices: 59705--59824 Score: 145
Period size: 60 Copynumber: 2.0 Consensus size: 57
59695 TATTAAAGAA
* * *
59705 ATATATATATATATATATAATAATAAAATATAGTAAAAAAATAAATGAAAATAATTTAAT
1 ATATATATATATACATATAATAATAAAACATAATAAAAAAATAAATG-AAATAA--TAAT
59765 ATATATATATATACATATAATAATAATAACATGAATAATAAAAATAAATG-AATAA-AAT
1 ATATATATATATACATATAATAATAA-AACAT-AATAA-AAAAATAAATGAAATAATAAT
59823 AT
1 AT
59825 CCATATAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
58 5 0.09
60 25 0.46
61 9 0.17
62 4 0.07
63 11 0.20
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (57 bp):
ATATATATATATACATATAATAATAAAACATAATAAAAAAATAAATGAAATAATAAT
Found at i:60230 original size:37 final size:37
Alignment explanation
Indices: 60180--60284 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
60170 GTGCTTGTGG
* * * *
60180 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
60217 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
60254 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
60285 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:61131 original size:105 final size:105
Alignment explanation
Indices: 60826--61352 Score: 706
Period size: 105 Copynumber: 5.0 Consensus size: 105
60816 AGCATTGTTC
* * * * ** * * *
60826 CGAGTCCAATATCCTCCGTCGTGAAGCTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGATA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACA
* * * * * *
60891 ACCAGCCGTCACTTCATTGTGAAGTTGAACTTGTGTTGTCT
65 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
60932 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-TGA-AA-TT-TTGTTGACAA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAA
*
60992 GCAGTGGTCCCTTCGTCGT-AGAGTTGAACTTGCGTTGTCT
66 GCAGCGGTCCCTTCGTCGTGA-AGTTGAACTTGCGTTGTCT
* * *
61032 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAA
*
61097 GAAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
**
61137 AAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAA
61202 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
61242 GGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACA
* * * * *
61307 ACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
65 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
61348 CGAGT
1 CGAGT
61353 GTCACGATAT
Statistics
Matches: 377, Mismatches: 36, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
99 1 0.00
100 78 0.21
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.01
105 200 0.53
106 86 0.23
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAA
GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:61525 original size:34 final size:35
Alignment explanation
Indices: 61451--61532 Score: 103
Period size: 34 Copynumber: 2.3 Consensus size: 35
61441 AATTGTGCCG
* * *
61451 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCG
1 TTTCAAGGGAAACTATCTCAA-GGAGACAAAATTCA
* *
61487 TTTCAAGGGAAACTATCTCAA-GCGATAAAATTCA
1 TTTCAAGGGAAACTATCTCAAGGAGACAAAATTCA
61521 TTTCAAGGGAAA
1 TTTCAAGGGAAA
61533 TGTTTTCAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
34 22 0.54
36 19 0.46
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (35 bp):
TTTCAAGGGAAACTATCTCAAGGAGACAAAATTCA
Found at i:61656 original size:104 final size:104
Alignment explanation
Indices: 61450--61749 Score: 502
Period size: 104 Copynumber: 2.9 Consensus size: 104
61440 AAATTGTGCC
* *
61450 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGGAAACTATCTC-A-AGC
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGA
*
61510 GATAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
66 GAAAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
61549 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGA
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGA
*
61614 GAAAAAAATCATTTCAAGGGAAATGTTTTCAATGTTTAT
66 GAAAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
*
61653 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAGGAGA
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGA
* *
61718 GAGAAAATTAATTTCAAGGGAAATGTTTTCAA
66 GAAAAAATTCATTTCAAGGGAAATGTTTTCAA
61750 GAGAAACTGT
Statistics
Matches: 188, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
99 33 0.18
101 3 0.02
102 19 0.10
103 1 0.01
104 132 0.70
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (104 bp):
GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGA
GAAAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
Found at i:61706 original size:39 final size:39
Alignment explanation
Indices: 61652--61726 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
61642 TCAATGTTTA
*
61652 TGTTTCAAGAGAAACTGTCTCAAGG-GAGACAAAATTTTC
1 TGTTTCAAGAGAAACTATCTC-AGGAGAGACAAAATTTTC
* * *
61691 TGTTTCGAGGGAAACTATCTCAGGAGAGAGAAAATT
1 TGTTTCAAGAGAAACTATCTCAGGAGAGACAAAATT
61727 AATTTCAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.10
39 28 0.90
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAGGAGAGACAAAATTTTC
Found at i:61905 original size:36 final size:36
Alignment explanation
Indices: 61865--61978 Score: 113
Period size: 36 Copynumber: 3.2 Consensus size: 36
61855 CTTTCGAGTG
* *
61865 AAAACGGTCTCAAGCGAGACAAATCTTGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
* ** * * * **
61901 AAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
*
61937 AAAACAGTCTCAAGTGAGACAAAGT-ATGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAA-TCTTGTTTTAAGA
61973 AAAACA
1 AAAACA
61979 AATTTGAGTG
Statistics
Matches: 58, Mismatches: 19, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
36 57 0.98
37 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (36 bp):
AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
Found at i:61957 original size:72 final size:74
Alignment explanation
Indices: 61820--61994 Score: 216
Period size: 72 Copynumber: 2.4 Consensus size: 74
61810 TAAAATCTTC
** * *
61820 TTAA-AAAAACAGCCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGA
1 TTAAGAAAAACAATCTTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGA
*
61884 CAAA-TCTTGTT
64 CAAAGT-ATGTT
*
61895 TTAAGAAAAACAATCTTGAGTGAAATAAAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACA
1 TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACA
61958 AAGTATGTT
66 AAGTATGTT
*
61967 TTAAGAAAAACAAAT-TTGAGTGAGATAA
1 TTAAGAAAAAC-AATCTTGAGTGAAATAA
61995 TCATCTGCAT
Statistics
Matches: 90, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
72 48 0.53
73 15 0.17
75 8 0.09
76 19 0.21
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (74 bp):
TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACA
AAGTATGTT
Found at i:63443 original size:183 final size:183
Alignment explanation
Indices: 63135--63854 Score: 1298
Period size: 183 Copynumber: 3.9 Consensus size: 183
63125 ATCAGGTTTA
* *
63135 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGGGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* * **
63200 GCCAAGTGTCCAAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
*
63264 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGAACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* *
63318 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAACAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
63383 TCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
63448 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
63501 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
63566 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
63631 TCCTCTATAACTAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* *
63684 ACTGAAGGTTTCATCTCATCACAAAGTCTTTGGCTTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
63749 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATATATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
63814 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
63855 CATATTTAAT
Statistics
Matches: 518, Mismatches: 18, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
183 517 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:68594 original size:18 final size:17
Alignment explanation
Indices: 68571--68613 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
68561 ATATATACAT
68571 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
68589 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
68606 ATAA-AATA
1 ATAATAATA
68614 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:68621 original size:58 final size:61
Alignment explanation
Indices: 68505--68621 Score: 134
Period size: 64 Copynumber: 1.9 Consensus size: 61
68495 AAATATATTT
*
68505 ATATAATAATAATAAAATATAGTAAAAAAAATAAATGAAAATAATTTAATATATATATATATAC
1 ATATAATAATAATAAAATATAGTAAAAAAAATAAATG-AAATAA--TAATATACATATATATAC
* * *
68569 ATATAATAATAATAACATGA-A-TAATAAAAATAAATG-AATAA-AATATCCATATA
1 ATATAATAATAATAAAAT-ATAGTAAAAAAAATAAATGAAATAATAATATACATATA
68622 ATAAATAAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
58 10 0.21
61 5 0.10
63 14 0.29
64 18 0.38
65 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (61 bp):
ATATAATAATAATAAAATATAGTAAAAAAAATAAATGAAATAATAATATACATATATATAC
Found at i:69020 original size:37 final size:37
Alignment explanation
Indices: 68970--69073 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
68960 GTGCTTGTGG
* * * *
68970 ATCCTATCTTTAGGAATTTAAATCTTAGTATAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAAAACTCT
* * * *
69007 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAAAACTCT
69044 ATCCTATTTTTAGGAGTTTAAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTA
69074 GGACGAAAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAAAACTCT
Found at i:77632 original size:11 final size:12
Alignment explanation
Indices: 77603--77634 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
77593 CTGTAAATGA
77603 ATTGAA-CGTTC
1 ATTGAACCGTTC
77614 ATTGAACCGTTC
1 ATTGAACCGTTC
77626 A-TGAACCGT
1 ATTGAACCGT
77635 GCGACGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (12 bp):
ATTGAACCGTTC
Found at i:82586 original size:10 final size:10
Alignment explanation
Indices: 82571--82645 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
82561 GGGTCTCCAA
82571 CGTTTATGTT
1 CGTTTATGTT
82581 CGTTTATGTT
1 CGTTTATGTT
*
82591 TGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
82602 ATGTTCGTGTT
1 -CGTTTATGTT
82613 CGTTTATGTT
1 CGTTTATGTT
82623 CG----TGTT
1 CGTTTATGTT
82629 CGTTTATGTT
1 CGTTTATGTT
82639 CGTTTAT
1 CGTTTAT
82646 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 33 0.65
11 7 0.14
12 5 0.10
ACGTcount: A:0.09, C:0.11, G:0.21, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:82596 original size:16 final size:16
Alignment explanation
Indices: 82577--82641 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
82567 CCAACGTTTA
*
82577 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
*
82593 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
82609 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
82625 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
82641 T
1 T
82642 TTATTTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:82617 original size:26 final size:26
Alignment explanation
Indices: 82573--82623 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
82563 GTCTCCAACG
* *
82573 TTTATGTTCGTTTATGTTTGTGTTCA
1 TTTATGTTCGTTTACGTTTATGTTCA
82599 TTTATGTTCGTGTT-CGTTTATGTTC
1 TTTATGTTCGT-TTACGTTTATGTTC
82624 GTGTTCGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.61
Consensus pattern (26 bp):
TTTATGTTCGTTTACGTTTATGTTCA
Found at i:85539 original size:20 final size:20
Alignment explanation
Indices: 85496--85540 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
85486 ATTACATTCA
* *
85496 TTATCTTTATTTTTATTTTG
1 TTATCTTTATTTATATTATG
85516 TTATCTTTATTCTATATTAT-
1 TTATCTTTATT-TATATTATG
85536 TTATC
1 TTATC
85541 ATCAACTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.69
Consensus pattern (20 bp):
TTATCTTTATTTATATTATG
Found at i:86719 original size:26 final size:26
Alignment explanation
Indices: 86682--86741 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
86672 AGAATCAAGT
*
86682 TTTTCTTTTACCAAAATCCTCTTATA
1 TTTTCTTCTACCAAAATCCTCTTATA
*
86708 TTTTCTTCTACCAAAATCCTCTTGTA
1 TTTTCTTCTACCAAAATCCTCTTATA
86734 TTTTCTTC
1 TTTTCTTC
86742 CTTCATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.22, C:0.25, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTTCTTCTACCAAAATCCTCTTATA
Found at i:88103 original size:139 final size:137
Alignment explanation
Indices: 87730--88162 Score: 490
Period size: 134 Copynumber: 3.2 Consensus size: 137
87720 TGAATCAAAT
* * *
87730 AATTAATTAGGATTAATATTAGATCCTCCATCTTAGGCCTAATTTCATATTTAGTCCTTAAATTA
1 AATTAATTATGATTAATATTAGA-CCTCCATCTTAGGCCTAATTTTATATTTAATCCTTAAATTA
* ** * *
87795 GGAGAATTCTTAATTTGGTAATTGCTTATGCTCGAGGTTCCGAATTAATTATTCGGTAGTCCATA
65 -GAAAATTCTTAATTTGGTCCTAGCTTATGCTCGAGGTTCCCAATTAATTATTCGGTAGTCCATA
87860 ATTAATTAA
129 ATTAATTAA
* *
87869 AATTAATTATGATT--TAGT-G-CCTCCATTTTAGGCCTAATTTTATATTTAGA-CCTTAAATTA
1 AATTAATTATGATTAATATTAGACCTCCATCTTAGGCCTAATTTTATATTTA-ATCCTTAAATTA
* * *
87929 GGAAATTTCTTAATTTGATCCTCA-CTTATGCTCGAGGTTCCCAATTAATTATTTGGTAGTCCAT
65 -GAAAATTCTTAATTTGGTCCT-AGCTTATGCTCGAGGTTCCCAATTAATTATTCGGTAGTCCAT
87993 AATTAATTAA
128 AATTAATTAA
* **
88003 AATTAATTATGATTAATATTAGAACCTCCATCTTAGTCCTAATTTTACCTTTAATCCTTAAATTA
1 AATTAATTATGATTAATATTAG-ACCTCCATCTTAGGCCTAATTTTATATTTAATCCTTAAATTA
* * * * * * *
88068 GAATAATTCTTAATTTGGTCCTAGCTTTTGCTCGAGATT-CTACTTTAATTATTC-GAATTACA-
65 GAA-AATTCTTAATTTGGTCCTAGCTTATGCTCGAGGTTCCCA-ATTAATTATTCGGTAGTCCAT
88130 ATATTAATTAA
128 A-ATTAATTAA
*
88141 AATTAATT-TAAGTTAATATTAG
1 AATTAATTATGA-TTAATATTAG
88163 GGCCTACTTT
Statistics
Matches: 252, Mismatches: 29, Indels: 27
0.82 0.09 0.09
Matches are distributed among these distances:
134 116 0.46
136 4 0.02
137 7 0.03
138 39 0.15
139 86 0.34
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (137 bp):
AATTAATTATGATTAATATTAGACCTCCATCTTAGGCCTAATTTTATATTTAATCCTTAAATTAG
AAAATTCTTAATTTGGTCCTAGCTTATGCTCGAGGTTCCCAATTAATTATTCGGTAGTCCATAAT
TAATTAA
Found at i:89633 original size:20 final size:22
Alignment explanation
Indices: 89596--89635 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
89586 TTTATTTTAA
89596 TAAAAATAATACATTAAATATT
1 TAAAAATAATACATTAAATATT
89618 TAAAAA-AATA-ATTAAATA
1 TAAAAATAATACATTAAATA
89636 ACTTTAGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAAATAATACATTAAATATT
Found at i:95625 original size:17 final size:17
Alignment explanation
Indices: 95603--95642 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
95593 TATATTATCA
95603 ATAAATAGAATTTTTAT
1 ATAAATAGAATTTTTAT
95620 ATAAAT--AATTTTTAT
1 ATAAATAGAATTTTTAT
*
95635 TTAAATAG
1 ATAAATAG
95643 TTAAAATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 14 0.70
17 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
ATAAATAGAATTTTTAT
Found at i:100876 original size:2 final size:2
Alignment explanation
Indices: 100869--100898 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
100859 ATATCTTATC
100869 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
100899 TAATCAAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.