Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007743.1 Hibiscus syriacus cultivar Beakdansim tig00110006_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: 323463
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:145438 original size:29 final size:29
Alignment explanation
Indices: 145396--145470 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
145386 GCTACGGGTC
*
145396 TTAGATCGAAAAATATAATCTGACTGGTG
1 TTAGATCGGAAAATATAATCTGACTGGTG
145425 TTAGATCGGAAAATATAATCTGACTGGTG
1 TTAGATCGGAAAATATAATCTGACTGGTG
*
145454 TTAGATCGGTAAATATA
1 TTAGATCGGAAAATATA
145471 CCGATCACCG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.32
Consensus pattern (29 bp):
TTAGATCGGAAAATATAATCTGACTGGTG
Found at i:145770 original size:18 final size:18
Alignment explanation
Indices: 145747--145793 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
145737 CGTGCTACAG
145747 GGTATGGGCACTTAGCAA
1 GGTATGGGCACTTAGCAA
145765 GGTATGGGCACTTAGCAA
1 GGTATGGGCACTTAGCAA
*
145783 GGCATGGGCAC
1 GGTATGGGCAC
145794 ACTGGGGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.26, C:0.19, G:0.36, T:0.19
Consensus pattern (18 bp):
GGTATGGGCACTTAGCAA
Found at i:152202 original size:43 final size:43
Alignment explanation
Indices: 152120--152206 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
152110 GAGTGAGTGA
* **
152120 TCATCGGTGGTAATAGTGGTCGACAACGGGATTTCAGGGATAT
1 TCATCGGTGATAATAGTGGTCGACAACGACATTTCAGGGATAT
* * * *
152163 TCATTGGTGATAATGGTGGTCGACAATGACATTTTAGGGATAT
1 TCATCGGTGATAATAGTGGTCGACAACGACATTTCAGGGATAT
152206 T
1 T
152207 TTTAGAGTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.26, C:0.11, G:0.30, T:0.32
Consensus pattern (43 bp):
TCATCGGTGATAATAGTGGTCGACAACGACATTTCAGGGATAT
Found at i:152644 original size:18 final size:18
Alignment explanation
Indices: 152630--152687 Score: 116
Period size: 18 Copynumber: 3.2 Consensus size: 18
152620 ATAGGTACAG
152630 ATACCCAAAGGGGTACCA
1 ATACCCAAAGGGGTACCA
152648 ATACCCAAAGGGGTACCA
1 ATACCCAAAGGGGTACCA
152666 ATACCCAAAGGGGTACCA
1 ATACCCAAAGGGGTACCA
152684 ATAC
1 ATAC
152688 TACTTTACGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.40, C:0.28, G:0.21, T:0.12
Consensus pattern (18 bp):
ATACCCAAAGGGGTACCA
Found at i:154207 original size:18 final size:19
Alignment explanation
Indices: 154171--154206 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
154161 TTGAATCAAT
154171 TTAAAATATATAGTTAAAA
1 TTAAAATATATAGTTAAAA
154190 TTAAAA-ATATA-TTAAAA
1 TTAAAATATATAGTTAAAA
154207 AAGGGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 5 0.29
19 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
TTAAAATATATAGTTAAAA
Found at i:154339 original size:10 final size:10
Alignment explanation
Indices: 154326--154380 Score: 74
Period size: 10 Copynumber: 5.4 Consensus size: 10
154316 TAAAAAGAGC
* *
154326 AAAAAAATTT
1 AAAAAAAATG
*
154336 AAAAAAAATT
1 AAAAAAAATG
154346 AAAAAAAATG
1 AAAAAAAATG
154356 AAAAAAAATG
1 AAAAAAAATG
154366 AAAAAAAAATG
1 -AAAAAAAATG
154377 AAAA
1 AAAA
154381 TGTAAGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
10 32 0.76
11 10 0.24
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:154376 original size:11 final size:11
Alignment explanation
Indices: 154326--154380 Score: 69
Period size: 11 Copynumber: 5.2 Consensus size: 11
154316 TAAAAAGAGC
**
154326 AAAAAAATTTA
1 AAAAAAATGAA
*
154337 AAAAAAAT-TA
1 AAAAAAATGAA
154347 AAAAAAATG-A
1 AAAAAAATGAA
154357 AAAAAAATGAA
1 AAAAAAATGAA
154368 AAAAAAATGAA
1 AAAAAAATGAA
154379 AA
1 AA
154381 TGTAAGAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
10 20 0.48
11 22 0.52
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (11 bp):
AAAAAAATGAA
Found at i:162264 original size:21 final size:21
Alignment explanation
Indices: 162236--162293 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
162226 GAATTGACAC
*
162236 CATT-TGCATTTTCATCATTG
1 CATTATGCATTTGCATCATTG
162256 CATTATGCATTTGCATCATTG
1 CATTATGCATTTGCATCATTG
*
162277 CATTATGCAATTGCATC
1 CATTATGCATTTGCATC
162294 GTATTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 4 0.11
21 31 0.89
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (21 bp):
CATTATGCATTTGCATCATTG
Found at i:164909 original size:39 final size:38
Alignment explanation
Indices: 164837--164991 Score: 127
Period size: 38 Copynumber: 4.1 Consensus size: 38
164827 ATTTTTCTTA
* * * *
164837 AAACTTCAACTTTGTCTCCATTGA-AGTAGTTTCCCTTG
1 AAACATCAAATTTATCTCCCTTGAGA-TAGTTTCCCTTG
* *
164875 AAACATCAAATTTATCTCCCTTGGGATTGTTTTCCCTTG
1 AAACATCAAATTTATCTCCCTTGAGATAG-TTTCCCTTG
* * *
164914 AAACA-CTAGTTTGTCTCCCTTGAGATAGTTTCCCTTG
1 AAACATCAAATTTATCTCCCTTGAGATAGTTTCCCTTG
** ** * *
164951 AAACATTGAATTCT-TCTAACTCGAGATAGATTCCCTTG
1 AAACATCAAATT-TATCTCCCTTGAGATAGTTTCCCTTG
164989 AAA
1 AAA
164992 TTAAAATTAT
Statistics
Matches: 95, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
37 14 0.15
38 65 0.68
39 16 0.17
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (38 bp):
AAACATCAAATTTATCTCCCTTGAGATAGTTTCCCTTG
Found at i:165784 original size:113 final size:114
Alignment explanation
Indices: 165541--165870 Score: 278
Period size: 113 Copynumber: 2.9 Consensus size: 114
165531 CTCGTCTGAC
* * *
165541 CATTCCATATAGGATGAAGCAATCAAAGAATAATAAGTTCATATAGGAA-AGCTTGTTCGACCTC
1 CATTCCATATAGGAAGAAGCAATCAAAG--GAAGAAGTTCATATA-GAAGAGCTTGTTCGACCTC
* * * * * * * *
165605 AACATGGCCTTTGT-GAGATAATAAAGAGCTTATATAGGAGAATTCATATACT
63 AACATGACCTTTATGGA-AGAATAGAGGGCTTATATAAGAGAACTCACATACT
* * *
165657 CTTTCTAAATAGGAAGAAGCAATC-AAGGAAGAAGTTCATATAGAAGAGCTTGTTCGACCTCAAC
1 CATTCCATATAGGAAGAAGCAATCAAAGGAAGAAGTTCATATAGAAGAGCTTGTTCGACCTCAAC
* * * * * *
165721 ATGCCCTTTATGGAAGAATAGAGGGCTTATATAAGATAGCTCGCCTAGT
66 ATGACCTTTATGGAAGAATAGAGGGCTTATATAAGAGAACTCACATACT
* * ** * * * * * *
165770 CATTCCATAGAGGAAAAATG--ATCTTA-GAAGAAATTCATATAGGAGAGTTTTTTTGACGTCAA
1 CATTCCATATAGGAAGAA-GCAATCAAAGGAAGAAGTTCATATAGAAGAGCTTGTTCGACCTCAA
*
165832 CATGACCTTTATGGAAGAATAG-GGAGCTTATATAGGAGA
65 CATGACCTTTATGGAAGAATAGAGG-GCTTATATAAGAGA
165871 GCCAACCCAC
Statistics
Matches: 175, Mismatches: 34, Indels: 14
0.78 0.15 0.06
Matches are distributed among these distances:
111 2 0.01
112 69 0.39
113 78 0.45
114 3 0.02
115 3 0.02
116 20 0.11
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (114 bp):
CATTCCATATAGGAAGAAGCAATCAAAGGAAGAAGTTCATATAGAAGAGCTTGTTCGACCTCAAC
ATGACCTTTATGGAAGAATAGAGGGCTTATATAAGAGAACTCACATACT
Found at i:165912 original size:112 final size:112
Alignment explanation
Indices: 165678--165942 Score: 295
Period size: 112 Copynumber: 2.3 Consensus size: 112
165668 GGAAGAAGCA
* * *
165678 ATCAAGGAAGAAGTTCATATAGAAGAGCTTGTTCGACCTCAACATGCCCTTTATGGAAGAATAGA
1 ATCAAGGAAGAAATTCATATAGGAGAGCTTGTTCGACCTCAACATGACCTTTATGGAAGAATAGA
* * * * * *
165743 GGGCTTATATAAGATAGCTCGCCTAGTCATTCCATAGAGGAAAAATG
66 GGGCTTATATAAGAGAGCTCACCCACTAATTCCATAGAGAAAAAATG
* * * * *
165790 ATCTTA-GAAGAAATTCATATAGGAGAGTTTTTTTGACGTCAACATGACCTTTATGGAAGAATAG
1 ATC-AAGGAAGAAATTCATATAGGAGAGCTTGTTCGACCTCAACATGACCTTTATGGAAGAATAG
*
165854 -GGAGCTTATATAGGAGAGC-CAACCCACTAATTCCATAGAGAAAAAATG
65 AGG-GCTTATATAAGAGAGCTC-ACCCACTAATTCCATAGAGAAAAAATG
* *
165902 ATCAAGGAAGAAGAAGTTCATATAGGA-AACTTGTTCAACCT
1 ATCAAGGAAG-A-AA-TTCATATAGGAGAGCTTGTTCGACCT
165943 AAAAAGTTGT
Statistics
Matches: 124, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
111 4 0.03
112 97 0.78
113 2 0.02
114 10 0.08
115 11 0.09
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (112 bp):
ATCAAGGAAGAAATTCATATAGGAGAGCTTGTTCGACCTCAACATGACCTTTATGGAAGAATAGA
GGGCTTATATAAGAGAGCTCACCCACTAATTCCATAGAGAAAAAATG
Found at i:166122 original size:3 final size:3
Alignment explanation
Indices: 166114--166169 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
166104 TTACCTGACC
166114 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
166162 TAT TAT TA
1 TAT TAT TA
166170 AAGTAAAGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:167482 original size:2 final size:2
Alignment explanation
Indices: 167475--167502 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
167465 AATACGTAAC
167475 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
167503 GCGTGAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:170464 original size:22 final size:25
Alignment explanation
Indices: 170438--170483 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
170428 GGTTTTTTCC
170438 TTTTC-TTT-TACTTTCTC-CTTTT
1 TTTTCTTTTGTACTTTCTCTCTTTT
170460 TTTTCTTTTGTACTTTCTCTCTTT
1 TTTTCTTTTGTACTTTCTCTCTTT
170484 CCAACATGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 3 0.14
24 9 0.43
25 4 0.19
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.72
Consensus pattern (25 bp):
TTTTCTTTTGTACTTTCTCTCTTTT
Found at i:170899 original size:33 final size:33
Alignment explanation
Indices: 170852--170919 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
170842 GGCACATTTT
170852 ACAGAGTTTCTTTTTACGTCAGAAGAGTTTCTA
1 ACAGAGTTTCTTTTTACGTCAGAAGAGTTTCTA
*
170885 ACAGCGTTTCTTTTTACGTCAGAAGAGTTTCTA
1 ACAGAGTTTCTTTTTACGTCAGAAGAGTTTCTA
170918 AC
1 AC
170920 GGCACATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (33 bp):
ACAGAGTTTCTTTTTACGTCAGAAGAGTTTCTA
Found at i:172939 original size:21 final size:21
Alignment explanation
Indices: 172913--172987 Score: 132
Period size: 21 Copynumber: 3.6 Consensus size: 21
172903 GCGTTGCATT
*
172913 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
172934 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
172955 TCGTGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
172976 TCGCGTTGCGAT
1 TCGCGTTGCGAT
172988 TTTCCATTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.31
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:173001 original size:20 final size:20
Alignment explanation
Indices: 172976--173149 Score: 153
Period size: 20 Copynumber: 8.6 Consensus size: 20
172966 TAGTTGAAAA
*
172976 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
* *
172996 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
* *
173018 T-GTCGTTGTGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
* *
173039 T--CGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
*
173059 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
*
173080 T--CGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
173098 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
173118 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
173138 TCGCGTTGCGAT
1 TCGCGTTGCGAT
173150 AGTCTACAGT
Statistics
Matches: 127, Mismatches: 16, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
18 3 0.02
19 22 0.17
20 69 0.54
21 10 0.08
22 23 0.18
ACGTcount: A:0.14, C:0.22, G:0.23, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:173044 original size:41 final size:41
Alignment explanation
Indices: 172979--173089 Score: 179
Period size: 41 Copynumber: 2.7 Consensus size: 41
172969 TTGAAAATCG
*
172979 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
*
173021 CGTTGTGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
173062 CGTTGCGATTTTCCAAATTCGTTGCGAT
1 CGTTGCGATTTTCCAAATTCGTTGCGAT
173090 TTTCCATTTC
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
41 49 0.75
42 13 0.20
43 3 0.05
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.41
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:173064 original size:22 final size:22
Alignment explanation
Indices: 172999--173070 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
172989 TTCCATTTCG
172999 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * * **
173021 CGTTGTGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
173040 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
173062 CGTTGCGAT
1 CGTTGCGAT
173071 TTTCCAAATT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 9 0.24
20 5 0.14
21 5 0.14
22 18 0.49
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:173173 original size:42 final size:41
Alignment explanation
Indices: 173080--173177 Score: 128
Period size: 40 Copynumber: 2.4 Consensus size: 41
173070 TTTTCCAAAT
* * *
173080 TCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCG
1 TCGTTGCGATTTTCCAGTTCGCGTTGCGATTCTACAGTTCG
173121 -CGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCTACAGTT-G
1 TCGTTGCGATTTTCCAGTTCGCGTTGCGAT--TCTACAGTTCG
*
173162 TCGTTGTGATTTTCCA
1 TCGTTGCGATTTTCCA
173178 AATTCTCACG
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
40 28 0.56
41 1 0.02
42 21 0.42
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.42
Consensus pattern (41 bp):
TCGTTGCGATTTTCCAGTTCGCGTTGCGATTCTACAGTTCG
Found at i:173613 original size:39 final size:38
Alignment explanation
Indices: 173541--173618 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 38
173531 ACTATTTAAG
* *
173541 GCTCAATCCCACATAGTATTGGGAACAAGTATTGGTAAT
1 GCTCAATCCCACATAGTATTGGAAACAACTATTGG-AAT
173580 GCTCAAATCCCACATAGTATTGGAAAC-ACTATTGGAAT
1 GCTC-AATCCCACATAGTATTGGAAACAACTATTGGAAT
173618 G
1 G
173619 GTATTTAAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 4 0.11
39 11 0.31
40 21 0.58
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (38 bp):
GCTCAATCCCACATAGTATTGGAAACAACTATTGGAAT
Found at i:173723 original size:6 final size:6
Alignment explanation
Indices: 173707--173840 Score: 261
Period size: 6 Copynumber: 22.5 Consensus size: 6
173697 GTCCGTCTCG
173707 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
173754 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
173802 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
173841 AATACGTGTC
Statistics
Matches: 128, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.04
6 123 0.96
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:173976 original size:27 final size:28
Alignment explanation
Indices: 173946--174002 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
173936 ACATGTAGAT
173946 TTTGCGA-AATGCGAAAT-GCAATGCGAA
1 TTTGCGACAATG-GAAATCGCAATGCGAA
* *
173973 TTTGCGACAGTGGAGATCGCAATGCGAA
1 TTTGCGACAATGGAAATCGCAATGCGAA
174001 TT
1 TT
174003 AGAGATCGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.25
Consensus pattern (28 bp):
TTTGCGACAATGGAAATCGCAATGCGAA
Found at i:174997 original size:17 final size:17
Alignment explanation
Indices: 174946--175017 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
174936 AATTAAGAGT
* *
174946 TAGTCTAATAAATGAAC
1 TAGTTTAATTAATGAAC
* * *
174963 TAGTTTGATGAATAAAC
1 TAGTTTAATTAATGAAC
174980 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
*
174997 TCGCTTT-ATTCAATGAAC
1 TAG-TTTAATT-AATGAAC
175015 TAG
1 TAG
175018 ATGCATGAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
17 32 0.73
18 12 0.27
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:175509 original size:15 final size:16
Alignment explanation
Indices: 175464--175508 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
175454 CCGAAAAAAA
*
175464 TCAGATATCTGAAAA-T
1 TCAGATATC-CAAAATT
175480 TCAGATATCCAAAATT
1 TCAGATATCCAAAATT
*
175496 TCATATATCCAAA
1 TCAGATATCCAAA
175509 TATCCGGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (16 bp):
TCAGATATCCAAAATT
Found at i:176732 original size:75 final size:75
Alignment explanation
Indices: 176651--176842 Score: 246
Period size: 72 Copynumber: 2.6 Consensus size: 75
176641 TCTTATGGAT
* * *
176651 TTTATTGTTCTAGAGTTAATATTATGGTTTGAATCTTGAGATTTGACATTTTAATATTGTGGTTT
1 TTTATTGTTCTAGACTTAATATTGTGGTTTGAATCTTGAGATTTGACATTTTAATATTGTGGGTT
* *
176716 CTTTATAGAC
66 CTTTATAAAA
* * *
176726 TTTATTGTTATAGACTTAATATTGTGGTTTG-A--TTGACATTTGATATTTTAATATTGTGGGTT
1 TTTATTGTTCTAGACTTAATATTGTGGTTTGAATCTTGAGATTTGACATTTTAATATTGTGGGTT
*
176788 GTTTATAAAA
66 CTTTATAAAA
* * * *
176798 TTTATTGTTCTAAATTTAATATTGTGATTTGAGTCTTGAGATTTG
1 TTTATTGTTCTAGACTTAATATTGTGGTTTGAATCTTGAGATTTG
176843 TTTATGGTTT
Statistics
Matches: 99, Mismatches: 15, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
72 61 0.62
74 1 0.01
75 37 0.37
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.52
Consensus pattern (75 bp):
TTTATTGTTCTAGACTTAATATTGTGGTTTGAATCTTGAGATTTGACATTTTAATATTGTGGGTT
CTTTATAAAA
Found at i:177864 original size:28 final size:29
Alignment explanation
Indices: 177833--177887 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
177823 TAAAAAAAAT
177833 TATATTAAACA-TTTATATTATATAATCA
1 TATATTAAACATTTTATATTATATAATCA
** *
177861 TATATTATTCATTTTATGTTATATAAT
1 TATATTAAACATTTTATATTATATAAT
177888 ACAATATGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (29 bp):
TATATTAAACATTTTATATTATATAATCA
Found at i:180818 original size:7 final size:7
Alignment explanation
Indices: 180808--180833 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
180798 TCAAAAAACA
180808 AAAAATT
1 AAAAATT
180815 AAAAATT
1 AAAAATT
180822 AAAAATT
1 AAAAATT
180829 AAAAA
1 AAAAA
180834 CGATCAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAAATT
Found at i:180818 original size:14 final size:14
Alignment explanation
Indices: 180801--180834 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
180791 AAAAATTTCA
180801 AAAAACAAAAAATT
1 AAAAACAAAAAATT
**
180815 AAAAATTAAAAATT
1 AAAAACAAAAAATT
180829 AAAAAC
1 AAAAAC
180835 GATCAAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAAACAAAAAATT
Found at i:191892 original size:22 final size:21
Alignment explanation
Indices: 191846--191906 Score: 88
Period size: 22 Copynumber: 2.9 Consensus size: 21
191836 TTTTGGTACA
*
191846 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
191866 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
191887 GAAGGGAACCGATTCCCCCC
1 G-AGGGAACCGATTCCCCCC
191907 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 17 0.47
ACGTcount: A:0.21, C:0.36, G:0.25, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:196263 original size:22 final size:22
Alignment explanation
Indices: 196228--196269 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
196218 AAACGTTTTA
196228 TTAAAAATTAAAAAAAATAAGT
1 TTAAAAATTAAAAAAAATAAGT
* * *
196250 TTAAAAGTTTAAAAATATAA
1 TTAAAAATTAAAAAAAATAA
196270 AATATAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (22 bp):
TTAAAAATTAAAAAAAATAAGT
Found at i:196273 original size:7 final size:7
Alignment explanation
Indices: 196261--196288 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
196251 TAAAAGTTTA
196261 AAAATAT
1 AAAATAT
196268 AAAATAT
1 AAAATAT
196275 AAAATAT
1 AAAATAT
196282 AAAATAT
1 AAAATAT
196289 TATAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAATAT
Found at i:196295 original size:24 final size:26
Alignment explanation
Indices: 196265--196320 Score: 80
Period size: 24 Copynumber: 2.2 Consensus size: 26
196255 AGTTTAAAAA
*
196265 TATAAAATATAAAATAT-AAAATA-T
1 TATAAAAAATAAAATATAAAAATATT
*
196289 TATAAAAAATAAAATTTAAAAATATT
1 TATAAAAAATAAAATATAAAAATATT
196315 TATAAA
1 TATAAA
196321 GTATTGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 15 0.54
25 6 0.21
26 7 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (26 bp):
TATAAAAAATAAAATATAAAAATATT
Found at i:196310 original size:14 final size:14
Alignment explanation
Indices: 196251--196310 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 14
196241 AAAATAAGTT
196251 TAAAAGTTTAAAAATA
1 TAAAA-TTTAAAAA-A
* *
196267 TAAAATATAAAATA
1 TAAAATTTAAAAAA
196281 TAAAATATTATAAAAAA
1 T-AAA-ATT-TAAAAAA
196298 TAAAATTTAAAAA
1 TAAAATTTAAAAA
196311 TATTTATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 8 0.22
15 12 0.32
16 10 0.27
17 7 0.19
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (14 bp):
TAAAATTTAAAAAA
Found at i:198770 original size:71 final size:71
Alignment explanation
Indices: 198682--198823 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
198672 CATCATTGTT
198682 CATTTCATTCTTAAATTCTAGCAATAAGGTTGACTCTTCAACATCATGTTGATCTTCAATGAGAT
1 CATTTCATTCTTAAATTCTAGCAATAAGGTTGACTCTTCAACATCATGTTGATCTTCAATGAGAT
198747 TGACCC
66 TGACCC
198753 CATTTCATTCTTAAATTCTAGCAATAAGGTTGACTCTTCAACATCATGTTGATCTTCAATGAGAT
1 CATTTCATTCTTAAATTCTAGCAATAAGGTTGACTCTTCAACATCATGTTGATCTTCAATGAGAT
198818 TGACCC
66 TGACCC
198824 TCTCTTAATT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.37
Consensus pattern (71 bp):
CATTTCATTCTTAAATTCTAGCAATAAGGTTGACTCTTCAACATCATGTTGATCTTCAATGAGAT
TGACCC
Found at i:198821 original size:35 final size:35
Alignment explanation
Indices: 198711--198821 Score: 93
Period size: 35 Copynumber: 3.1 Consensus size: 35
198701 AGCAATAAGG
198711 TTGACTCTTCAACATCATGTTGATCTTCAATGAGA
1 TTGACTCTTCAACATCATGTTGATCTTCAATGAGA
* ** * * * * *
198746 TTGAC-C--CCATTTCATTCTTAAATTCTAGCAATAAGG
1 TTGACTCTTCAACATCA-TGTT-GA-TCT-TCAATGAGA
198782 TTGACTCTTCAACATCATGTTGATCTTCAATGAGA
1 TTGACTCTTCAACATCATGTTGATCTTCAATGAGA
198817 TTGAC
1 TTGAC
198822 CCTCTCTTAA
Statistics
Matches: 53, Mismatches: 16, Indels: 14
0.64 0.19 0.17
Matches are distributed among these distances:
32 5 0.09
33 3 0.06
34 2 0.04
35 19 0.36
36 14 0.26
37 2 0.04
38 3 0.06
39 5 0.09
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (35 bp):
TTGACTCTTCAACATCATGTTGATCTTCAATGAGA
Found at i:201658 original size:59 final size:59
Alignment explanation
Indices: 201566--201685 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
201556 GACGACTTAA
201566 TGAATCAAAGACAACACATTGATACGACTTTGTTAAGGCAATCAAATGAAGCTCGTAGT
1 TGAATCAAAGACAACACATTGATACGACTTTGTTAAGGCAATCAAATGAAGCTCGTAGT
201625 TGAATCAAAGACAACACATTGATACGACTTTGTTAAGGCAATCAAATGAAGCTCGTAGT
1 TGAATCAAAGACAACACATTGATACGACTTTGTTAAGGCAATCAAATGAAGCTCGTAGT
201684 TG
1 TG
201686 TTATCGAATG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (59 bp):
TGAATCAAAGACAACACATTGATACGACTTTGTTAAGGCAATCAAATGAAGCTCGTAGT
Found at i:203592 original size:1 final size:1
Alignment explanation
Indices: 203586--203613 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
203576 CCGAAAATGT
203586 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
203614 CTTAACATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:203779 original size:117 final size:115
Alignment explanation
Indices: 203648--203902 Score: 343
Period size: 117 Copynumber: 2.2 Consensus size: 115
203638 CTAAAATGTT
* * * *
203648 ATTTTTTAATATTTTTGGTTGGCAACCGGAAATGTTA-CATTCTTCATAATATTTTCGATTCAAC
1 ATTTTTTAACATTTTCGGTTGGCAACCGGAAATGTTATC-TTCTTCATAACATTTTCGACTCAAC
* * *
203712 TGTAAATGTT-AAAAATTAACATTTCAGGTTGGGCTCAAGAAAAAATGTCAAG
65 CGAAAATGTTAAAAAATTAACATTTCAGGTTGGGCTCAACAAAAAAT-T-AAG
* *
203764 ATTTTTTGAACATTTTCGGTTGGCAACCGGAAATGTTATCTTCTTCGTAACATTTTCGGCTCAAC
1 ATTTTTT-AACATTTTCGGTTGGCAACCGGAAATGTTATCTTCTTCATAACATTTTCGACTCAAC
*
203829 CGAAAATGTTAAAAAATTAACATTTTAGGTTGGGCTCAACAAAAAATTAAG
65 CGAAAATGTTAAAAAATTAACATTTCAGGTTGGGCTCAACAAAAAATTAAG
*
203880 ATTTTTTTTAACATTGTCGGTTG
1 A--TTTTTTAACATTTTCGGTTG
203903 CGCCTTTCCT
Statistics
Matches: 123, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
116 11 0.09
117 71 0.58
118 41 0.33
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (115 bp):
ATTTTTTAACATTTTCGGTTGGCAACCGGAAATGTTATCTTCTTCATAACATTTTCGACTCAACC
GAAAATGTTAAAAAATTAACATTTCAGGTTGGGCTCAACAAAAAATTAAG
Found at i:204089 original size:21 final size:21
Alignment explanation
Indices: 204065--204104 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
204055 ATTTTATTTA
*
204065 GATACCGTAACTTAAAATTAT
1 GATACCGCAACTTAAAATTAT
*
204086 GATACCGCAATTTAAAATT
1 GATACCGCAACTTAAAATT
204105 CCTAATTCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (21 bp):
GATACCGCAACTTAAAATTAT
Found at i:204154 original size:30 final size:30
Alignment explanation
Indices: 204119--204178 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
204109 ATTCCGCCCC
* *
204119 TGATGATCATACATCTTAAATAATAACAGA
1 TGATGATCATACATCTTAAAGAAAAACAGA
204149 TGATGATCATACATCTTAAAGAAAAACAGA
1 TGATGATCATACATCTTAAAGAAAAACAGA
204179 GAAAACATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (30 bp):
TGATGATCATACATCTTAAAGAAAAACAGA
Found at i:205096 original size:3 final size:3
Alignment explanation
Indices: 205088--205117 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
205078 ATCCCGGCGA
205088 ATT ATT ATT ATT ATT ATT ATT ATT AATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT AT
205118 AATTTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:205501 original size:3 final size:3
Alignment explanation
Indices: 205493--205517 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
205483 TAGATTCAAA
205493 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
205518 CAGGGTATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:206287 original size:2 final size:2
Alignment explanation
Indices: 206280--206315 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
206270 ACAATTAAGC
206280 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
206316 TACTTAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:208055 original size:3 final size:3
Alignment explanation
Indices: 208043--208076 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
208033 CGTCTTTTAA
208043 TAT T-T TAT TAT TAT TAT TAT TAT TAAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT T
208077 GTATTTTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:209751 original size:13 final size:14
Alignment explanation
Indices: 209719--209751 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
209709 TGTATATTGC
209719 ATAT-TAATATTAT
1 ATATATAATATTAT
209732 ATATATAATA-TAT
1 ATATATAATATTAT
209745 ATATATA
1 ATATATA
209752 TGTTATAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATATAATATTAT
Found at i:209758 original size:15 final size:15
Alignment explanation
Indices: 209719--209752 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
209709 TGTATATTGC
209719 ATAT-TAATAT-TAT
1 ATATATAATATATAT
209732 ATATATAATATATAT
1 ATATATAATATATAT
209747 ATATAT
1 ATATAT
209753 GTTATAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 6 0.32
15 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATATAATATATAT
Found at i:216472 original size:17 final size:16
Alignment explanation
Indices: 216434--216472 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
216424 TCCAAAAAGG
216434 AAAAAACAAATAAAAA
1 AAAAAACAAATAAAAA
* *
216450 ATAAAAACAATTAAAGA
1 A-AAAAACAAATAAAAA
216467 AAAAAA
1 AAAAAA
216473 GAAAAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.10
Consensus pattern (16 bp):
AAAAAACAAATAAAAA
Found at i:219142 original size:42 final size:42
Alignment explanation
Indices: 219083--219263 Score: 229
Period size: 42 Copynumber: 4.3 Consensus size: 42
219073 TCAAAATTTA
* *
219083 TAAATCCTTCGGGTCATCAATAAGTCTTCTGAGCATGATGCT
1 TAAATCCTTCGGGTCATCAGTAAGTCTTCTGAGCATGATACT
* *
219125 TAAATCCTCCGGGTCATCAGTAAGTCTT-TCGAGCATAATACT
1 TAAATCCTTCGGGTCATCAGTAAGTCTTCT-GAGCATGATACT
* *
219167 TAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
1 TAAATCCTTCGGGTCATCAGTAAGTCTTCTGAGCATGATACT
* * * * *
219209 TAAATCCTTTGGGTCATCTGTAAGCCTTTTGAGCATGATAAT
1 TAAATCCTTCGGGTCATCAGTAAGTCTTCTGAGCATGATACT
* *
219251 TAAGTCCTCCGGG
1 TAAATCCTTCGGG
219264 CAATCTAAAG
Statistics
Matches: 119, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
41 1 0.01
42 118 0.99
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCAGTAAGTCTTCTGAGCATGATACT
Found at i:219224 original size:84 final size:84
Alignment explanation
Indices: 219083--219263 Score: 263
Period size: 84 Copynumber: 2.2 Consensus size: 84
219073 TCAAAATTTA
*
219083 TAAATCCTTCGGGTCATCAATAAGTCTTCTGAGCATGATGCTTAAATCCTCCGGGTCATCAGTAA
1 TAAATCCTTCGGGTCATCAATAAGTCTTCCGAGCATGATGCTTAAATCCTCCGGGTCATCAGTAA
* *
219148 GTCTTTCGAGCATAATACT
66 GCCTTTCGAGCATAATAAT
* ** *
219167 TAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTTGGGTCATCTGTAA
1 TAAATCCTTCGGGTCATCAATAAGTCTTCCGAGCATGATGCTTAAATCCTCCGGGTCATCAGTAA
* *
219232 GCCTTTTGAGCATGATAAT
66 GCCTTTCGAGCATAATAAT
* *
219251 TAAGTCCTCCGGG
1 TAAATCCTTCGGG
219264 CAATCTAAAG
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (84 bp):
TAAATCCTTCGGGTCATCAATAAGTCTTCCGAGCATGATGCTTAAATCCTCCGGGTCATCAGTAA
GCCTTTCGAGCATAATAAT
Found at i:219533 original size:111 final size:111
Alignment explanation
Indices: 219339--220021 Score: 1021
Period size: 111 Copynumber: 6.2 Consensus size: 111
219329 GAAGCAAATT
* *
219339 CAGATTTGATATTCCCTCAGAGGAAGCGGAACAGATCCCTCTT-TTTCAAGATTTGATATTCCCT
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCT-TTCTTTCAAGATTTGATATTCCCT
*
219403 GAGTGTCAGCGGAACAAATCTACCCCGATTCAATGGATCAACTCTCC
65 GAGTGACAGCGGAACAAATCTACCCCGATTCAATGGATCAACTCTCC
*
219450 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAAATCTCTTTCTTTCAAGATTTGATATTCCCTG
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTTTCTTTCAAGATTTGATATTCCCTG
*
219515 AGTGACAGCGGAACAAATCTACCCTGATTCAATGGATCAACTCTCC
66 AGTGACAGCGGAACAAATCTACCCCGATTCAATGGATCAACTCTCC
* * * * *
219561 CATATATGATATTCCCTCAGAGGAAGCGGAACATATCTCTCTCTTTCAAGATTTGATATTCCATG
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTTTCTTTCAAGATTTGATATTCCCTG
* * ** * *
219626 AGTGACAACGGAACAAATCTGCCCTAATTTAATGGATCAACTCTCA
66 AGTGACAGCGGAACAAATCTACCCCGATTCAATGGATCAACTCTCC
* * * *
219672 CAGATCTGATACTCCCTCAGAAGAAGCGGAACAAATCTCTTTCTTTCAAGATTTGATATTCCCTA
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTTTCTTTCAAGATTTGATATTCCCTG
* *
219737 AGTGACAGCGGAACAAATCTGCCCCGATTTAATGGATCAACTCTCC
66 AGTGACAGCGGAACAAATCTACCCCGATTCAATGGATCAACTCTCC
* * *
219783 CAGATCTGATATTCCCTCATAGGAAGCGGAATAGATCTCTCTCTTTCAAGATTTGATATTCCCTG
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTTTCTTTCAAGATTTGATATTCCCTG
* * *
219848 AGTGACAGCGGAATAAATCTGCCCCGATTCAATGAATCAACTCTCC
66 AGTGACAGCGGAACAAATCTACCCCGATTCAATGGATCAACTCTCC
*
219894 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATC-CTTTTTTTTCAAGATTTGATATTCCCT
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTC-TTTCTTTCAAGATTTGATATTCCCT
* * * *
219958 GAGTGACAGCGGAATAAGTCTACCCTGATTCAATGAATCAACATCT-C
65 GAGTGACAGCGGAACAAATCTACCCCGATTCAATGGATCAAC-TCTCC
220005 CAGATCTGATATTCCCT
1 CAGATCTGATATTCCCT
220022 GAGTGACAGC
Statistics
Matches: 525, Mismatches: 44, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
110 3 0.01
111 519 0.99
112 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (111 bp):
CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTTTCTTTCAAGATTTGATATTCCCTG
AGTGACAGCGGAACAAATCTACCCCGATTCAATGGATCAACTCTCC
Found at i:228807 original size:24 final size:24
Alignment explanation
Indices: 228767--228812 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
228757 AGAATTTTCC
*
228767 AAAAAATTTTAATTTTTCGAAATAA
1 AAAAAATGTTAATTTTTC-AAATAA
228792 AAAAAATGTTAA-TTTTCAAAT
1 AAAAAATGTTAATTTTTCAAAT
228813 TATTGTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 5 0.25
25 11 0.55
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (24 bp):
AAAAAATGTTAATTTTTCAAATAA
Found at i:231262 original size:27 final size:28
Alignment explanation
Indices: 231219--231282 Score: 103
Period size: 27 Copynumber: 2.3 Consensus size: 28
231209 GACTTGACTT
231219 GAAAAAATCTATTTTTTTTACTCGATTAG
1 GAAAAAATCTA-TTTTTTTACTCGATTAG
231248 GAAAAAATCTA-TTTTTTACTCGATTAG
1 GAAAAAATCTATTTTTTTACTCGATTAG
*
231275 AAAAAAAT
1 GAAAAAAT
231283 TCGATTTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 23 0.68
29 11 0.32
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (28 bp):
GAAAAAATCTATTTTTTTACTCGATTAG
Found at i:231289 original size:28 final size:27
Alignment explanation
Indices: 231232--231289 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
231222 AAAATCTATT
* *
231232 TTTTTTACTCGATTAGGAAAAAATCTA
1 TTTTTTACTCGATTAGAAAAAAATCGA
231259 TTTTTTACTCGATTAGAAAAAAATTCGA
1 TTTTTTACTCGATTAGAAAAAAA-TCGA
231287 TTT
1 TTT
231290 GAATTGACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.43
Consensus pattern (27 bp):
TTTTTTACTCGATTAGAAAAAAATCGA
Found at i:239018 original size:126 final size:127
Alignment explanation
Indices: 238749--239121 Score: 667
Period size: 126 Copynumber: 2.9 Consensus size: 127
238739 TTAATACTTC
*
238749 CTTTATTGCTTTAAATTTTTCCTAAAAGATGAATGTAAATTGGGTATATGCGTGATCAATGGTAT
1 CTTTATTGCTTTAAATTTTTCCTAAAAGATGAATGTAAATTTGGTATATGCGTGATCAATGGTAT
*
238814 CAATACTCTTGAGCATGTATCTATATCTTAGATTGAAAATTATAAAATTTGAAACCTTCATTG
66 CAATAC-CTTGAGCATGTATCTATATCTTAGTTTGAAAATTATAAAATTTGAAACCTTCATTG
*
238877 CTTCATTGCTTTAAATTTTTCCTAAAAGATGAATGTAAATTTGGTATATGCGTGATCAATGGTAT
1 CTTTATTGCTTTAAATTTTTCCTAAAAGATGAATGTAAATTTGGTATATGCGTGATCAATGGTAT
*
238942 CAATA-CTAGAGCATGTATCTATATCTTAGTTTGAAAATTATAAAATTTGAAACCTTCATTG
66 CAATACCTTGAGCATGTATCTATATCTTAGTTTGAAAATTATAAAATTTGAAACCTTCATTG
* *
239003 CTTTATTGCTTTAAATTTTTCCTAAAAGATGAATGTAAAATTGGTATATGCGTGATCTATGGTAT
1 CTTTATTGCTTTAAATTTTTCCTAAAAGATGAATGTAAATTTGGTATATGCGTGATCAATGGTAT
239068 CAATACTCTTGAGCATGTATCTATATCTTAGTTTGAAAATTATAAAATTTGAAA
66 CAATAC-CTTGAGCATGTATCTATATCTTAGTTTGAAAATTATAAAATTTGAAA
239122 GAAAGGTTTG
Statistics
Matches: 235, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
126 121 0.51
128 114 0.49
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (127 bp):
CTTTATTGCTTTAAATTTTTCCTAAAAGATGAATGTAAATTTGGTATATGCGTGATCAATGGTAT
CAATACCTTGAGCATGTATCTATATCTTAGTTTGAAAATTATAAAATTTGAAACCTTCATTG
Found at i:240972 original size:130 final size:130
Alignment explanation
Indices: 240690--240965 Score: 394
Period size: 130 Copynumber: 2.1 Consensus size: 130
240680 TTCAACCGTT
* * *
240690 ATTTATTACTCCAACCGAAATGAAGAGATATCACTATTCGTCTTAAAATTCAATATTGATTCGAG
1 ATTTATTACTCCAATCGAAATGAAGAGATATCACCATTCGTCTTAAAAATCAATATTGATTCGAG
* * * ** *
240755 AGGAAGCGATAATATCTAATTATTTCCAATCGAGAATAAGTGACATCTCATGGCTTAAAGCAATC
66 AGGAAACGATAATATATAATTATTTCCAATCGAAAATAAACGACATCTCATGCCTTAAAGCAATC
*
240820 ATTTATTATTCCAATCGAAATGAAGAGATATCACCATTTCGTCTTAAAAATCAATATTGATTCGA
1 ATTTATTACTCCAATCGAAATGAAGAGATATCACCA-TTCGTCTTAAAAATCAATATTGATTCGA
* * **
240885 TA-GAAACTGATAATATATAATTATTT-CAATCGAAAATAAACGACCTCTCATGCCTTAAAGCGG
65 GAGGAAAC-GATAATATATAATTATTTCCAATCGAAAATAAACGACATCTCATGCCTTAAAGCAA
240948 TC
129 TC
240950 ATTTATTACTCCAATC
1 ATTTATTACTCCAATC
240966 AGAATGAGAA
Statistics
Matches: 129, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
130 84 0.65
131 45 0.35
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (130 bp):
ATTTATTACTCCAATCGAAATGAAGAGATATCACCATTCGTCTTAAAAATCAATATTGATTCGAG
AGGAAACGATAATATATAATTATTTCCAATCGAAAATAAACGACATCTCATGCCTTAAAGCAATC
Found at i:241616 original size:28 final size:28
Alignment explanation
Indices: 241584--241654 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
241574 ACAAGAGGTA
*
241584 AAAATAAATAAAACATG-GGGACCAAATT
1 AAAATAAATAAAA-ATGCAGGACCAAATT
* *
241612 AAAATGAAATAAAATTGCATGACCAAATT
1 AAAAT-AAATAAAAATGCAGGACCAAATT
*
241641 AAATTAAATAAAAA
1 AAAATAAATAAAAA
241655 CATATTATCG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 15 0.42
29 21 0.58
ACGTcount: A:0.61, C:0.08, G:0.10, T:0.21
Consensus pattern (28 bp):
AAAATAAATAAAAATGCAGGACCAAATT
Found at i:242023 original size:108 final size:107
Alignment explanation
Indices: 241822--242028 Score: 251
Period size: 107 Copynumber: 1.9 Consensus size: 107
241812 ACAAAATAGT
* *
241822 AAAAACACGCCAAACATAGAGGAATAAGAAGCAAATAACCCTAAAATATAAAACATGCGTAAAAA
1 AAAAACACGCCAAACATAGAGGAATAAAAAGCAAATAACCCTAAAATATAAAACATGCGAAAAAA
*
241887 TAGGTAAATAGCATATTCGATCCTTACAGGTGACTAACATGC
66 TAGGTAAATAGCATATTCGATCCCTACAGGTGACTAACATGC
* * * * * *
241929 AAAAACACGCTAAAC-TATGGGGACTAAAAAGTAAATAACCCTAAAA-ATATATATATGCAGAAA
1 AAAAACACGCCAAACATA-GAGGAATAAAAAGCAAATAACCCTAAAATATA-AAACATGC-GAAA
*
241992 AAAT-GAGTAAATAGCA-AGTTCGGTCCCTACAGGTGAC
63 AAATAG-GTAAATAGCATA-TTCGATCCCTACAGGTGAC
242029 CATTTTGTAA
Statistics
Matches: 85, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
106 5 0.06
107 46 0.54
108 34 0.40
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.19
Consensus pattern (107 bp):
AAAAACACGCCAAACATAGAGGAATAAAAAGCAAATAACCCTAAAATATAAAACATGCGAAAAAA
TAGGTAAATAGCATATTCGATCCCTACAGGTGACTAACATGC
Found at i:242821 original size:34 final size:34
Alignment explanation
Indices: 242777--242844 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
242767 GGAAGCAGTG
242777 GTGGCTGGGGACTGGTGCAGCAAGGAATTGGCAA
1 GTGGCTGGGGACTGGTGCAGCAAGGAATTGGCAA
* * * *
242811 GTGGTTGGGGATTGGTGCCGCAAGGCATTGGCAA
1 GTGGCTGGGGACTGGTGCAGCAAGGAATTGGCAA
242845 ATGACTGGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.21, C:0.15, G:0.44, T:0.21
Consensus pattern (34 bp):
GTGGCTGGGGACTGGTGCAGCAAGGAATTGGCAA
Found at i:242973 original size:24 final size:24
Alignment explanation
Indices: 242928--242974 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
242918 CCTAGTTGGT
*
242928 GATTAATCTCAGCCGTTAGATCTG
1 GATTAATCTCAGCCATTAGATCTG
* *
242952 GATTAATCTCGGCCATTGGATCT
1 GATTAATCTCAGCCATTAGATCT
242975 CTCCCAGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (24 bp):
GATTAATCTCAGCCATTAGATCTG
Found at i:243135 original size:3 final size:3
Alignment explanation
Indices: 243127--243174 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
243117 CTACACAAAA
243127 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
243175 TATTATTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:245451 original size:14 final size:13
Alignment explanation
Indices: 245426--245476 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
245416 TTGGGCCTAA
245426 AATAAAAATAAAG
1 AATAAAAATAAAG
*
245439 AATAAAGAATAAAC
1 AATAAA-AATAAAG
*
245453 AA-AATAAATAAAA
1 AATAA-AAATAAAG
*
245466 AATAAATATAA
1 AATAAAAATAA
245477 TGTAACTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 21 0.66
14 11 0.34
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (13 bp):
AATAAAAATAAAG
Found at i:245524 original size:29 final size:31
Alignment explanation
Indices: 245491--245563 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
245481 ACTATAATAA
245491 TAAAAATTATATAATAC-AAAA-TGTGTTTTC
1 TAAAAATTATATAATACAAAAATTGT-TTTTC
* * * *
245521 -AAAAAGTATCTATTTCAAAAATTGTTTTTC
1 TAAAAATTATATAATACAAAAATTGTTTTTC
245551 TAAAAATTATATA
1 TAAAAATTATATA
245564 TTATATATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
29 12 0.35
30 9 0.26
31 13 0.38
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (31 bp):
TAAAAATTATATAATACAAAAATTGTTTTTC
Found at i:245550 original size:30 final size:31
Alignment explanation
Indices: 245491--245565 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 31
245481 ACTATAATAA
* * *
245491 TAAAAATTATATAATAC-AAAATGTGTTTTC
1 TAAAAAGTATATATTTCAAAAATGTGTTTTC
*
245521 -AAAAAGTATCTATTTCAAAAAT-TGTTTTTC
1 TAAAAAGTATATATTTCAAAAATGTG-TTTTC
*
245551 TAAAAATTATATATT
1 TAAAAAGTATATATT
245566 ATATATTTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
29 14 0.39
30 10 0.28
31 12 0.33
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (31 bp):
TAAAAAGTATATATTTCAAAAATGTGTTTTC
Found at i:245587 original size:38 final size:36
Alignment explanation
Indices: 245553--245962 Score: 258
Period size: 38 Copynumber: 11.5 Consensus size: 36
245543 TGTTTTTCTA
*
245553 AAAATTATATATTATATA-TTTTCAAAAGTAT-TTTTT
1 AAAA-TATATATTATATAGTTTTCAAAAG-ATGTTTTC
* * *
245589 ATAA-CTATATTATATACGCTTTCAAAA-ATGTTTTC
1 AAAATATATATTATATA-GTTTTCAAAAGATGTTTTC
* * *
245624 AAAAT-TATA-TATAT-GTTTTCATAAATGTTTTTTTA
1 AAAATATATATTATATAGTTTTCA-AAA-GATGTTTTC
245659 AAAACTATATATTATATATGTTTTCAAAAGATGTTTTC
1 AAAA-TATATATTATATA-GTTTTCAAAAGATGTTTTC
* * *
245697 AAAACTATATATTACATATGCTTTCAAAAAATGTTTTC
1 AAAA-TATATATTATATA-GTTTTCAAAAGATGTTTTC
*
245735 AAAAATATAAATTATATACGTTTTC-AAA-A------C
1 -AAAATATATATTATATA-GTTTTCAAAAGATGTTTTC
*
245765 ----TATATATTATATATGTTTTCAAAAAATGTTTTC
1 AAAATATATATTATATA-GTTTTCAAAAGATGTTTTC
245798 AAAACTATATATTATATACG-TTT-AAAA-ATGTTTTC
1 AAAA-TATATATTATATA-GTTTTCAAAAGATGTTTTC
* * *
245833 AAAACTATATATTATATACGTTTTTAAAAAATGTTTTT
1 AAAA-TATATATTATATA-GTTTTCAAAAGATGTTTTC
* * *
245871 AAAACTACATATTATATACATTTTCGAAAA-ATATTTTCC
1 AAAA-TATATATTATATA-GTTTTC-AAAAGATGTTTT-C
* * *
245910 AAAACTATATATTAAATA--TTTAAAAAAATGTTTTC
1 AAAA-TATATATTATATAGTTTTCAAAAGATGTTTTC
245945 AAAACTATATATTATATA
1 AAAA-TATATATTATATA
245963 CGTTATATAT
Statistics
Matches: 309, Mismatches: 33, Indels: 65
0.76 0.08 0.16
Matches are distributed among these distances:
25 18 0.06
26 3 0.01
27 1 0.00
30 1 0.00
32 6 0.02
33 4 0.01
34 18 0.06
35 70 0.23
36 29 0.09
37 14 0.05
38 111 0.36
39 27 0.09
40 7 0.02
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (36 bp):
AAAATATATATTATATAGTTTTCAAAAGATGTTTTC
Found at i:245694 original size:13 final size:13
Alignment explanation
Indices: 245676--245700 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
245666 TATATTATAT
245676 ATGTTTTCAAAAG
1 ATGTTTTCAAAAG
245689 ATGTTTTCAAAA
1 ATGTTTTCAAAA
245701 CTATATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
ATGTTTTCAAAAG
Found at i:245757 original size:25 final size:25
Alignment explanation
Indices: 245729--245789 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
245719 TTCAAAAAAT
245729 GTTTTCAAAAATATAAATTATATAC
1 GTTTTCAAAAATATAAATTATATAC
* * *
245754 GTTTTCAAAACTATATATTATATAT
1 GTTTTCAAAAATATAAATTATATAC
245779 GTTTTCAAAAA
1 GTTTTCAAAAA
245790 ATGTTTTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (25 bp):
GTTTTCAAAAATATAAATTATATAC
Found at i:245759 original size:63 final size:63
Alignment explanation
Indices: 245691--245820 Score: 224
Period size: 63 Copynumber: 2.1 Consensus size: 63
245681 TTCAAAAGAT
245691 GTTTTCAAAACTATATATTACATATGCTTTCAAAAAATGTTTTCAAAAATATAAATTATATAC
1 GTTTTCAAAACTATATATTACATATGCTTTCAAAAAATGTTTTCAAAAATATAAATTATATAC
* * * *
245754 GTTTTCAAAACTATATATTATATATGTTTTCAAAAAATGTTTTCAAAACTATATATTATATAC
1 GTTTTCAAAACTATATATTACATATGCTTTCAAAAAATGTTTTCAAAAATATAAATTATATAC
245817 GTTT
1 GTTT
245821 AAAAATGTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (63 bp):
GTTTTCAAAACTATATATTACATATGCTTTCAAAAAATGTTTTCAAAAATATAAATTATATAC
Found at i:245785 original size:101 final size:98
Alignment explanation
Indices: 245654--245862 Score: 328
Period size: 101 Copynumber: 2.1 Consensus size: 98
245644 ATAAATGTTT
* *
245654 TTTTAAAAACTATATATTATATATGTTTTCAAAAGATGTTTTCAAAACTATATATTACATATGCT
1 TTTTAAAAACTATATATTATATATGTTTTCAAAAAATGTTTTCAAAACTATATATTACATACG-T
245719 TTCAAAAAATGTTTTCAAAAATATAAATTATATACG
65 TT--AAAAATGTTTTCAAAAATATAAATTATATACG
* *
245755 TTTTCAAAACTATATATTATATATGTTTTCAAAAAATGTTTTCAAAACTATATATTATATACGTT
1 TTTTAAAAACTATATATTATATATGTTTTCAAAAAATGTTTTCAAAACTATATATTACATACGTT
* *
245820 TAAAAATGTTTTCAAAACTATATATTATATACG
66 TAAAAATGTTTTCAAAAATATAAATTATATACG
245853 TTTTTAAAAA
1 -TTTTAAAAA
245863 ATGTTTTTAA
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
98 30 0.30
99 8 0.08
100 3 0.03
101 59 0.59
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (98 bp):
TTTTAAAAACTATATATTATATATGTTTTCAAAAAATGTTTTCAAAACTATATATTACATACGTT
TAAAAATGTTTTCAAAAATATAAATTATATACG
Found at i:245795 original size:13 final size:13
Alignment explanation
Indices: 245777--245801 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
245767 TATATTATAT
245777 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
245790 ATGTTTTCAAAA
1 ATGTTTTCAAAA
245802 CTATATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
ATGTTTTCAAAAA
Found at i:245839 original size:73 final size:74
Alignment explanation
Indices: 245754--245966 Score: 299
Period size: 73 Copynumber: 2.9 Consensus size: 74
245744 AATTATATAC
*
245754 GTTTTCAAAACTATATATTATATATGTTTTCAAAAAATGTTTTCAAAACTATATATTATATACGT
1 GTTTTCAAAACTATATATTATATATGTTTTAAAAAAATGTTTTCAAAACTATATATTATATACGT
245819 TT-AAAAAT
66 TTCAAAAAT
* * * * *
245827 GTTTTCAAAACTATATATTATATACGTTTTTAAAAAATGTTTTTAAAACTACATATTATATACAT
1 GTTTTCAAAACTATATATTATATATGTTTTAAAAAAATGTTTTCAAAACTATATATTATATAC-G
245892 TTTCGAAAAAT
65 TTTC-AAAAAT
* *
245903 ATTTTCCAAAACTATATATTA-A-AT-ATTTAAAAAAATGTTTTCAAAACTATATATTATATACG
1 GTTTT-CAAAACTATATATTATATATGTTTTAAAAAAATGTTTTCAAAACTATATATTATATACG
245965 TT
65 TT
245967 ATATATATAA
Statistics
Matches: 124, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
73 61 0.49
74 36 0.29
75 1 0.01
76 11 0.09
77 15 0.12
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (74 bp):
GTTTTCAAAACTATATATTATATATGTTTTAAAAAAATGTTTTCAAAACTATATATTATATACGT
TTCAAAAAT
Found at i:245955 original size:112 final size:110
Alignment explanation
Indices: 245754--245966 Score: 320
Period size: 112 Copynumber: 1.9 Consensus size: 110
245744 AATTATATAC
* ** * *
245754 GTTTTCAAAACTATATATTATATATGTTTTCAAAAAATGTTTTCAAAACTATATATTATATACGT
1 GTTTTCAAAACTACATATTATATACATTTTCAAAAAATATTTTCAAAACTATATATTAAATAC-T
245819 TTAAAAATGTTTTCAAAACTATATATTATATACGTTTTTAAAAAAT
65 TTAAAAATGTTTTCAAAACTATATATTATATACGTTTTTAAAAAAT
* *
245865 GTTTTTAAAACTACATATTATATACATTTTCGAAAAATATTTTCCAAAACTATATATTAAATA-T
1 GTTTTCAAAACTACATATTATATACATTTTCAAAAAATATTTT-CAAAACTATATATTAAATACT
245929 TTAAAAAAATGTTTTCAAAACTATATATTATATACGTT
65 TT--AAAAATGTTTTCAAAACTATATATTATATACGTT
245967 ATATATATAA
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
110 3 0.03
111 37 0.40
112 52 0.57
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (110 bp):
GTTTTCAAAACTACATATTATATACATTTTCAAAAAATATTTTCAAAACTATATATTAAATACTT
TAAAAATGTTTTCAAAACTATATATTATATACGTTTTTAAAAAAT
Found at i:246709 original size:201 final size:200
Alignment explanation
Indices: 246364--246936 Score: 720
Period size: 201 Copynumber: 2.9 Consensus size: 200
246354 TTTTGTTGGC
* * * * *
246364 AAATCGTAGTCAACCTTGGTTTTCTTCTTGACTTAAAGACCTCGGTTTAAAATTCAATCAAAAAG
1 AAATCGTAGTCAACCTAGGTATTCTTCTAGGCTTAAAGACCTCGGTTTAAAATTCAATCAGAAAG
* * *
246429 TAGTTCCTCGTTGCTACCATGTGGTTGATACACCCTCGAGCTGAATGGAATCAAACTCGAAAGTT
66 TAGTTCCTTG-TGCTACCATGTAGTTGATACGCCCTCGAGCTGAATGGAATCAAACTCGAAAGTT
* * *
246494 TTCATTGACAGATAACCCTTCTCGCATTGAGTTATGCTGTAAATTAGGCTGGGAGATAGTTCCTC
130 TTCATTGACAGATAACCCTTCTCGCATTGAGCTATGCTGTAAATTAGGCTGGGAAATAGTTACTC
*
246559 ATTTCT
195 ATTGCT
* * * * *
246565 AAATCGTAGTTAACCTAGGTATTATTCTAGGCTTAAAGTCCTCGGTTTAAAATTCAACCGGAAAG
1 AAATCGTAGTCAACCTAGGTATTCTTCTAGGCTTAAAGACCTCGGTTTAAAATTCAATCAGAAAG
* * *
246630 TAGTTCCTTGCTGCTACCATGTAGTTGATACGCCCTCGAGTTGAATGGAATCTAACTCGAACGTT
66 TAGTTCCTTG-TGCTACCATGTAGTTGATACGCCCTCGAGCTGAATGGAATCAAACTCGAAAGTT
* * ** * * *
246695 TTCTTTAACAGATAACTTTTCTCG-ACTTAAGCTATGTTGTAAATTCGGCTGGGAAATAGTTACT
130 TTCATTGACAGATAACCCTTCTCGCA-TTGAGCTATGCTGTAAATTAGGCTGGGAAATAGTTACT
**
246759 TGTTGCT
194 CATTGCT
* * * *
246766 AAATCGTAGTCAACCTAGGTATTCTTCTAGGCTTAAAAACCTTGGTTTAGAATTTAATCAGAAAG
1 AAATCGTAGTCAACCTAGGTATTCTTCTAGGCTTAAAGACCTCGGTTTAAAATTCAATCAGAAAG
** *
246831 TAGTT-CTTGTGCTACCATACAGTTGATACGCCCTCGAACTGAATGG-ATCAAACTCGAAAGTTT
66 TAGTTCCTTGTGCTACCATGTAGTTGATACGCCCTCGAGCTGAATGGAATCAAACTCGAAAGTTT
* * * * * *
246894 TCGTTGATAGATAACCCTTCTTGCCTTGAGCTATACTATAAAT
131 TCATTGACAGATAACCCTTCTCGCATTGAGCTATGCTGTAAAT
246937 GGTTTCTATA
Statistics
Matches: 314, Mismatches: 56, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
198 46 0.15
199 33 0.11
200 5 0.02
201 230 0.73
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (200 bp):
AAATCGTAGTCAACCTAGGTATTCTTCTAGGCTTAAAGACCTCGGTTTAAAATTCAATCAGAAAG
TAGTTCCTTGTGCTACCATGTAGTTGATACGCCCTCGAGCTGAATGGAATCAAACTCGAAAGTTT
TCATTGACAGATAACCCTTCTCGCATTGAGCTATGCTGTAAATTAGGCTGGGAAATAGTTACTCA
TTGCT
Found at i:248453 original size:16 final size:16
Alignment explanation
Indices: 248432--248465 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
248422 AACACGGGTG
248432 TTGGAAACATAAGAGA
1 TTGGAAACATAAGAGA
248448 TTGGAAACATAAGAGA
1 TTGGAAACATAAGAGA
248464 TT
1 TT
248466 CAAAACCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.24, T:0.24
Consensus pattern (16 bp):
TTGGAAACATAAGAGA
Found at i:248471 original size:16 final size:16
Alignment explanation
Indices: 248436--248471 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
248426 CGGGTGTTGG
**
248436 AAACATAAGAGATTGG
1 AAACATAAGAGATTCA
248452 AAACATAAGAGATTCA
1 AAACATAAGAGATTCA
248468 AAAC
1 AAAC
248472 CTAGAGATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.17, T:0.17
Consensus pattern (16 bp):
AAACATAAGAGATTCA
Found at i:252152 original size:23 final size:23
Alignment explanation
Indices: 252122--252168 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
252112 ATGGAGTAAG
** *
252122 CATGTCTTTAGTAGCCATGCCAT
1 CATGTCTTTAACAGCCATGACAT
252145 CATGTCTTTAACAGCCATGACAT
1 CATGTCTTTAACAGCCATGACAT
252168 C
1 C
252169 CATACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.32
Consensus pattern (23 bp):
CATGTCTTTAACAGCCATGACAT
Found at i:253447 original size:12 final size:12
Alignment explanation
Indices: 253430--253460 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
253420 AATTAGTAAG
253430 ATAAAAATAATA
1 ATAAAAATAATA
253442 ATAAAAATAATA
1 ATAAAAATAATA
*
253454 ATGAAAA
1 ATAAAAA
253461 GATTCCTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (12 bp):
ATAAAAATAATA
Found at i:256119 original size:38 final size:37
Alignment explanation
Indices: 255993--256422 Score: 512
Period size: 38 Copynumber: 11.4 Consensus size: 37
255983 TGTTTAAAAC
* *
255993 TATATTATACACGTTTTCAAAAATGTTTTCAAAATTA
1 TATATTATATACGTTTTCAAAAATGTTTTCAAAACTA
* *
256030 TATATTATAT--GTTTTTAAAAATGTCTTTTTTAAAAACTA
1 TATATTATATACGTTTTCAAAAATG----TTTTCAAAACTA
*
256069 TATATTATATACGTTTTCAAAAGATGTTTTCAAAAGTA
1 TATATTATATACGTTTTCAAAA-ATGTTTTCAAAACTA
*
256107 TATATTACATACGTTTTCAAAAAATGTTTTCAAAACTA
1 TATATTATATACGTTTTC-AAAAATGTTTTCAAAACTA
256145 TATATTATATACGTTTTCAAACAATG-TTTCGAAAACTA
1 TATATTATATACGTTTTCAAA-AATGTTTTC-AAAACTA
* **
256183 TATATTATATATGTTTTCGAAAAATGTTTTCAAAAAAA
1 TATATTATATACGTTTTC-AAAAATGTTTTCAAAACTA
* * * *
256221 TATATTATAGATG-TTTAAAAAAAGTTTTCAAAACTA
1 TATATTATATACGTTTTCAAAAATGTTTTCAAAACTA
**
256257 TATATTATATAAATTTTCAAAAAATGTTTTCAAAACTA
1 TATATTATATACGTTTTC-AAAAATGTTTTCAAAACTA
256295 TATATTATATACGTTTTCAAAAAATGTTTTCAAAACTA
1 TATATTATATACGTTTTC-AAAAATGTTTTCAAAACTA
* *
256333 TATATTATATACATTTTTGAAAAATGTTTTCCAAAACTA
1 TATATTATATAC-GTTTTCAAAAATGTTTT-CAAAACTA
* * *
256372 TATATCATATA--TTTTCAAAAAATATTTTGAAAACTA
1 TATATTATATACGTTTTC-AAAAATGTTTTCAAAACTA
256408 TATATTATATACGTT
1 TATATTATATACGTT
256423 ATATATATAA
Statistics
Matches: 342, Mismatches: 32, Indels: 37
0.83 0.08 0.09
Matches are distributed among these distances:
35 12 0.04
36 47 0.14
37 32 0.09
38 186 0.54
39 53 0.15
41 9 0.03
42 3 0.01
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (37 bp):
TATATTATATACGTTTTCAAAAATGTTTTCAAAACTA
Found at i:256249 original size:36 final size:38
Alignment explanation
Indices: 255926--256418 Score: 494
Period size: 38 Copynumber: 13.1 Consensus size: 38
255916 TTTAAAAAAT
* * *
255926 TATATG-TTTCAAAAATCATTTTTTTAAAATTATATA-T-
1 TATATGTTTTCAAAAA--ATGTTTTCAAAACTATATATTA
* * *
255963 TATATGTTTCCAAAAGTAT-TTGTTTAAAAC--TATATTA
1 TATATGTTTTCAAAA-AATGTT-TTCAAAACTATATATTA
* * *
256000 TACACGTTTTC-AAAAATGTTTTCAAAATTATATA-T-
1 TATATGTTTTCAAAAAATGTTTTCAAAACTATATATTA
* *
256035 TATATGTTTT-TAAAAATGTCTTTTTTAAAAACTATATATTA
1 TATATGTTTTCAAAAAATG----TTTTCAAAACTATATATTA
* * *
256076 TATACGTTTTCAAAAGATGTTTTCAAAAGTATATATTA
1 TATATGTTTTCAAAAAATGTTTTCAAAACTATATATTA
* *
256114 CATACGTTTTCAAAAAATGTTTTCAAAACTATATATTA
1 TATATGTTTTCAAAAAATGTTTTCAAAACTATATATTA
* *
256152 TATACGTTTTCAAACAATG-TTTCGAAAACTATATATTA
1 TATATGTTTTCAAAAAATGTTTTC-AAAACTATATATTA
* **
256190 TATATGTTTTCGAAAAATGTTTTCAAAAAAATATATTA
1 TATATGTTTTCAAAAAATGTTTTCAAAACTATATATTA
* *
256228 TAGATG-TTT-AAAAAAAGTTTTCAAAACTATATATTA
1 TATATGTTTTCAAAAAATGTTTTCAAAACTATATATTA
**
256264 TATAAATTTTCAAAAAATGTTTTCAAAACTATATATTA
1 TATATGTTTTCAAAAAATGTTTTCAAAACTATATATTA
*
256302 TATACGTTTTCAAAAAATGTTTTCAAAACTATATATTA
1 TATATGTTTTCAAAAAATGTTTTCAAAACTATATATTA
** ** *
256340 TATACATTTTTGAAAAATGTTTTCCAAAACTATATATCA
1 TATATGTTTTCAAAAAATGTTTT-CAAAACTATATATTA
* *
256379 TATA--TTTTCAAAAAATATTTTGAAAACTATATATTA
1 TATATGTTTTCAAAAAATGTTTTCAAAACTATATATTA
256415 TATA
1 TATA
256419 CGTTATATAT
Statistics
Matches: 387, Mismatches: 48, Indels: 43
0.81 0.10 0.09
Matches are distributed among these distances:
35 27 0.07
36 52 0.13
37 51 0.13
38 205 0.53
39 36 0.09
40 1 0.00
41 9 0.02
42 6 0.02
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (38 bp):
TATATGTTTTCAAAAAATGTTTTCAAAACTATATATTA
Found at i:256275 original size:150 final size:149
Alignment explanation
Indices: 255993--256418 Score: 542
Period size: 150 Copynumber: 2.8 Consensus size: 149
255983 TGTTTAAAAC
* * *
255993 TATATTATACACGTTTTCAAAAATGTTTTCAAAATTATATA-T-TATATGTTTTTAAAAATGTCT
1 TATATTATATACGTTTTCAAAAATGTTTTCAAAACTATATATTATATATGTTTTGAAAAATG---
* * * * * * **
256056 TTTTTAAAAACTATATATTATATACGTTTTCAAAAGATGTTTTCAAAAGTATATATTACATACGT
63 TTTTCAAAAA-TATATATTATATATG-TTTCAAAAAAAGTTTTCAAAACTATATATTATATAAAT
256121 TTTCAAAAAATGTTTTCAAAACTA
126 TTTCAAAAAATGTTTTCAAAACTA
256145 TATATTATATACGTTTTCAAACAATG-TTTCGAAAACTATATATTATATATGTTTTCGAAAAATG
1 TATATTATATACGTTTTCAAA-AATGTTTTC-AAAACTATATATTATATATGTTTT-GAAAAATG
* *
256209 TTTTCAAAAAAATATATTATAGATGTTT-AAAAAAAGTTTTCAAAACTATATATTATATAAATTT
63 TTTTCAAAAATATATATTATATATGTTTCAAAAAAAGTTTTCAAAACTATATATTATATAAATTT
256273 TCAAAAAATGTTTTCAAAACTA
128 TCAAAAAATGTTTTCAAAACTA
256295 TATATTATATACGTTTTCAAAAAATGTTTTCAAAACTATATATTATATACAT-TTTTGAAAAATG
1 TATATTATATACGTTTTC-AAAAATGTTTTCAAAACTATATATTATAT--ATGTTTTGAAAAATG
* * *
256359 TTTTCCAAAACTATATATCATATAT-TTTCAAAAAATA-TTTTGAAAACTATATATTATATA
63 TTTT-CAAAAATATATATTATATATGTTTCAAAAAA-AGTTTTCAAAACTATATATTATATA
256419 CGTTATATAT
Statistics
Matches: 244, Mismatches: 18, Indels: 25
0.85 0.06 0.09
Matches are distributed among these distances:
150 106 0.43
151 58 0.24
152 39 0.16
153 23 0.09
154 1 0.00
155 10 0.04
156 7 0.03
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (149 bp):
TATATTATATACGTTTTCAAAAATGTTTTCAAAACTATATATTATATATGTTTTGAAAAATGTTT
TCAAAAATATATATTATATATGTTTCAAAAAAAGTTTTCAAAACTATATATTATATAAATTTTCA
AAAAATGTTTTCAAAACTA
Found at i:256443 original size:150 final size:148
Alignment explanation
Indices: 255926--256422 Score: 539
Period size: 150 Copynumber: 3.3 Consensus size: 148
255916 TTTAAAAAAT
* * * * *
255926 TATATGTTTCAAAAATCATTTTTTTAAAATTATATATTATAT--GTTTCCAAAAGTATTTGTTT-
1 TATAT-TTTCAAAAA--ATATTTTCAAAACTATATATTATATACGTTTTCAAAA--A-ATGTTTC
* *
255988 AAAAC--TATATTATACACGTTTTC-AAAAATGTTTTCAAAATTATATATTATAT-GTTTTT-AA
60 AAAACTATATATTATATACGTTTTCAAAAAATGTTTTCAAAACTATATATTATATAGTTTTTGAA
*
256048 AAATGTCTTTTTTAAAAACTATATATTA
125 AAATG----TTTTCAAAACTATATATTA
* * * *
256076 TATACGTTTTCAAAAGATGTTTTCAAAAGTATATATTACATACGTTTTCAAAAAATGTTTTCAAA
1 TATA--TTTTCAAAAAATATTTTCAAAACTATATATTATATACGTTTTCAAAAAATG-TTTCAAA
* *
256141 ACTATATATTATATACGTTTTCAAACAATG-TTTCGAAAACTATATATTATATATGTTTTCGAAA
63 ACTATATATTATATACGTTTTCAAAAAATGTTTTC-AAAACTATATATTATATA-GTTTTTGAAA
**
256205 AATGTTTTCAAAAAAATATATTA
126 AATGTTTTCAAAACTATATATTA
* **
256228 TAGATGTTT-AAAAAA-AGTTTTCAAAACTATATATTATATAAATTTTCAAAAAATGTTTTCAAA
1 TATAT-TTTCAAAAAATA-TTTTCAAAACTATATATTATATACGTTTTCAAAAAATG-TTTCAAA
*
256291 ACTATATATTATATACGTTTTCAAAAAATGTTTTCAAAACTATATATTATATACATTTTTGAAAA
63 ACTATATATTATATACGTTTTCAAAAAATGTTTTCAAAACTATATATTATATA-GTTTTTGAAAA
*
256356 ATGTTTTCCAAAACTATATATCA
127 ATGTTTT-CAAAACTATATATTA
*
256379 TATATTTTCAAAAAATATTTTGAAAACTATATATTATATACGTT
1 TATATTTTCAAAAAATATTTTCAAAACTATATATTATATACGTT
256423 ATATATATAA
Statistics
Matches: 296, Mismatches: 32, Indels: 37
0.81 0.09 0.10
Matches are distributed among these distances:
148 2 0.01
149 25 0.08
150 123 0.42
151 70 0.24
152 42 0.14
153 22 0.07
155 5 0.02
156 7 0.02
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (148 bp):
TATATTTTCAAAAAATATTTTCAAAACTATATATTATATACGTTTTCAAAAAATGTTTCAAAACT
ATATATTATATACGTTTTCAAAAAATGTTTTCAAAACTATATATTATATAGTTTTTGAAAAATGT
TTTCAAAACTATATATTA
Found at i:257151 original size:56 final size:55
Alignment explanation
Indices: 257029--257454 Score: 541
Period size: 56 Copynumber: 7.7 Consensus size: 55
257019 CTACCAATAC
* * * * * * **
257029 GAAATTTATACACTTAGTATAAATTTCCT-AGTTTTGCATATATAGTGATCATACA
1 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATA-A
* * * * ** *
257084 GAAA-TCAATCCACTTAGTATTAATCTCTTAAGTTTTACATATATAATTTCCATAT
1 GAAATTC-ATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATAA
*
257139 GTAAATTCATCCATTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATAA
1 G-AAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATAA
* *
257195 GGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACAAATAGTGCCCATAC
1 -GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATAA
* * *
257251 GAAATTCATCTACTTAGTATGAATTTCTTAAGTTTTACACATATGGTGCCCATACG
1 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATA-A
* *
257307 GAAATTCATCCACTTGGTATGAATTTCTGAAGTTTTACACATATAGTGCCCATACA
1 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATA-A
* *
257363 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGACCATAT
1 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATAA
*
257418 GAAAATTCATCCACTTAGTATGAATTTCTTACGTTTT
1 G-AAATTCATCCACTTAGTATGAATTTCTTAAGTTTT
257455 TGTACAATTA
Statistics
Matches: 328, Mismatches: 36, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
54 1 0.00
55 75 0.23
56 249 0.76
57 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (55 bp):
GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATAA
Found at i:257329 original size:167 final size:167
Alignment explanation
Indices: 257025--257454 Score: 580
Period size: 167 Copynumber: 2.6 Consensus size: 167
257015 CCTGCTACCA
* * * * * * *
257025 ATAC-GAAATTTATACACTTAGTATAAATTTCCT-AGTTTTGCATATATAGTGATCATACAGAAA
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGACCATAC-GAAA
* * * ** * *
257088 -TCAATCCACTTAGTATTAATCTCTTAAGTTTTACATATATAATTTCCATATGTAAATTCATCCA
65 TTC-ATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAATGCCCATACGGAAATTCATCCA
* *
257152 TTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCC
129 CTTAGTATGAATTTCTGAAGTTTTACACATATAGTGCCC
* *
257191 ATA-AGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACAAATAGTGCCCATACGAAA
1 ATACA-GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGACCATACGAAA
* **
257255 TTCATCTACTTAGTATGAATTTCTTAAGTTTTACACATATGGTGCCCATACGGAAATTCATCCAC
65 TTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAATGCCCATACGGAAATTCATCCAC
*
257320 TTGGTATGAATTTCTGAAGTTTTACACATATAGTGCCC
130 TTAGTATGAATTTCTGAAGTTTTACACATATAGTGCCC
*
257358 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGACCATATGAAAA
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGACCATACG-AAA
*
257423 TTCATCCACTTAGTATGAATTTCTTACGTTTT
65 TTCATCCACTTAGTATGAATTTCTTAAGTTTT
257455 TGTACAATTA
Statistics
Matches: 231, Mismatches: 27, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
166 3 0.01
167 172 0.74
168 56 0.24
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (167 bp):
ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGACCATACGAAAT
TCATCCACTTAGTATGAATTTCTTAAGTTTTACACATATAATGCCCATACGGAAATTCATCCACT
TAGTATGAATTTCTGAAGTTTTACACATATAGTGCCC
Found at i:257800 original size:22 final size:19
Alignment explanation
Indices: 257754--257822 Score: 75
Period size: 19 Copynumber: 3.4 Consensus size: 19
257744 CTCCTCAGTG
* *
257754 TCGATACCCCTTCCATGGTA
1 TCGATA-CCCTACTATGGTA
257774 TCGATACTACCATACTATGGTA
1 TCGATAC--CC-TACTATGGTA
*
257796 CCGATACCCTACTATGGTA
1 TCGATACCCTACTATGGTA
257815 TCGATACC
1 TCGATACC
257823 ATTTTTACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
19 18 0.43
20 8 0.19
21 2 0.05
22 14 0.33
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.29
Consensus pattern (19 bp):
TCGATACCCTACTATGGTA
Found at i:263968 original size:56 final size:56
Alignment explanation
Indices: 263869--264411 Score: 761
Period size: 56 Copynumber: 9.7 Consensus size: 56
263859 AAAATTTGTA
* * * ** * *
263869 CACTTAGTATAAATTTCCT-A-TTTTTCTACATATAGTGATCATACAGAAATCCATC
1 CACTTAGTATGAATTTCTTAAGTTTTAC-ACATATAGTGCCCATACGGAAATTCATC
* *
263924 CACTTTGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGGAAATCCATC
1 CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGGAAATTCATC
* *
263980 GACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAGAAATTCATC
1 CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGGAAATTCATC
* * * *
264036 TAGTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCGTATGGAAATTCATC
1 CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGGAAATTCATC
* * *
264092 CTGC-TAGTATGAATTTCTTAAGTTTTACACATATATTGCACATACGGAAATTCATC
1 C-ACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGGAAATTCATC
* * * **
264148 CAATTAGTATGATTTTCTTAAGTTTTACACATATAATGCCCATACAAAAATTCATC
1 CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGGAAATTCATC
* *
264204 CATTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATATGGAAATTCATC
1 CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGGAAATTCATC
* *
264260 CACTTAGTATGAATTTCTCAAGTTTTACACATATAGTGCCCATACGAAAATTCATC
1 CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGGAAATTCATC
*
264316 CACTTAGTATGAATTTCTTAAGTTTTACACATAGAGTGCCCATACGGAAATTCATC
1 CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGGAAATTCATC
* *
264372 CACTTAGTATAAATTTCTTAAGTTTTTCACA-ATTAGTGCC
1 CACTTAGTATGAATTTCTTAAGTTTTACACATA-TAGTGCC
264412 ATTTGGTAAT
Statistics
Matches: 437, Mismatches: 46, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
55 17 0.04
56 415 0.95
57 5 0.01
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (56 bp):
CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACGGAAATTCATC
Found at i:264803 original size:19 final size:18
Alignment explanation
Indices: 264734--264805 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 18
264724 TGGCTCCTCA
264734 GTATCGATACCCCTATCATG
1 GTATCGATA-CCCTAT-ATG
*
264754 GTATCGATACTACTATACTATG
1 GTATCGATAC--C-CTA-TATG
264776 GTA-CTGATACCCTAGTATG
1 GTATC-GATACCCTA-TATG
264795 GTATCGATACC
1 GTATCGATACC
264806 ATTTTTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
19 16 0.37
20 11 0.26
21 2 0.05
22 13 0.30
23 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Consensus pattern (18 bp):
GTATCGATACCCTATATG
Found at i:264852 original size:20 final size:20
Alignment explanation
Indices: 264827--264879 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
264817 CTATTTTGAA
*
264827 TGGTATCGATACGT-TCCCTT
1 TGGTATCGATAC-TCCCCCTT
*
264847 TGGTATTGATACTCCCCCTT
1 TGGTATCGATACTCCCCCTT
*
264867 CGGTATCGATACT
1 TGGTATCGATACT
264880 GATTGAATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (20 bp):
TGGTATCGATACTCCCCCTT
Found at i:272518 original size:20 final size:20
Alignment explanation
Indices: 272493--272544 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
272483 ACCCGACGGA
*
272493 TGCATCGATGCATGGTTCTG
1 TGCATCGATGCATGGCTCTG
272513 TGCATCGATGCATGGCTCTG
1 TGCATCGATGCATGGCTCTG
272533 TGCATCGATGCA
1 TGCATCGATGCA
272545 CATTCAAGCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.17, C:0.23, G:0.29, T:0.31
Consensus pattern (20 bp):
TGCATCGATGCATGGCTCTG
Found at i:272584 original size:21 final size:21
Alignment explanation
Indices: 272558--272633 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 21
272548 TCAAGCGTGC
272558 ATCGATGCATCTTCATGATGT
1 ATCGATGCATCTTCATGATGT
* *
272579 ATCGATACA-CATTCATAGGGATGA
1 ATCGATGCATC-TTCAT---GATGT
*
272603 ATCGATGCACCTTCAT-AGTGT
1 ATCGATGCATCTTCATGA-TGT
272624 ATCGATGCAT
1 ATCGATGCAT
272634 TATGCACAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
20 2 0.05
21 24 0.55
24 17 0.39
25 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (21 bp):
ATCGATGCATCTTCATGATGT
Found at i:272606 original size:24 final size:24
Alignment explanation
Indices: 272574--272620 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
272564 GCATCTTCAT
*
272574 GATGTATCGATACACATTCATAGG
1 GATGAATCGATACACATTCATAGG
* *
272598 GATGAATCGATGCACCTTCATAG
1 GATGAATCGATACACATTCATAG
272621 TGTATCGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (24 bp):
GATGAATCGATACACATTCATAGG
Found at i:272617 original size:45 final size:43
Alignment explanation
Indices: 272536--272629 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 43
272526 GGCTCTGTGC
* * *
272536 ATCGATGCACATTCAAGCGTGCATCGATGCATCTTCAT-GATGT
1 ATCGATACACATTCAAGCGTGAATCGATGCACCTTCATAG-TGT
*
272579 ATCGATACACATTCATAGGGATGAATCGATGCACCTTCATAGTGT
1 ATCGATACACATTCA-AGCG-TGAATCGATGCACCTTCATAGTGT
272624 ATCGAT
1 ATCGAT
272630 GCATTATGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
43 14 0.32
44 3 0.07
45 26 0.59
46 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (43 bp):
ATCGATACACATTCAAGCGTGAATCGATGCACCTTCATAGTGT
Found at i:276199 original size:22 final size:21
Alignment explanation
Indices: 276157--276196 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
276147 GAGATTATTT
*
276157 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
276178 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
276197 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:278930 original size:14 final size:14
Alignment explanation
Indices: 278913--278942 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
278903 AACGAATATA
278913 AATGAACATAAACG
1 AATGAACATAAACG
*
278927 AATGAATATAAACG
1 AATGAACATAAACG
278941 AA
1 AA
278943 CATAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.10, G:0.13, T:0.17
Consensus pattern (14 bp):
AATGAACATAAACG
Found at i:278957 original size:24 final size:24
Alignment explanation
Indices: 278903--278967 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
278893 AATATAGATG
* **
278903 AACGAATATAAATGAACATAAACG
1 AACGAATATAAACGAACATAAAAA
*
278927 AATGAATATAAACGAACATAAAAA
1 AACGAATATAAACGAACATAAAAA
*
278951 AACGAATATAAGCGAAC
1 AACGAATATAAACGAAC
278968 GAATTATCGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.15
Consensus pattern (24 bp):
AACGAATATAAACGAACATAAAAA
Found at i:279328 original size:20 final size:20
Alignment explanation
Indices: 279298--279358 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
279288 TATTAAAATG
*
279298 ATAAAAGAATGTAAATGAAC
1 ATAAACGAATGTAAATGAAC
*
279318 ATAAACTAATGTAAACT-AAC
1 ATAAACGAATGTAAA-TGAAC
* *
279338 ATAAACGAACGTACATGAAC
1 ATAAACGAATGTAAATGAAC
279358 A
1 A
279359 CAAATGAACA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.56, C:0.13, G:0.11, T:0.20
Consensus pattern (20 bp):
ATAAACGAATGTAAATGAAC
Found at i:280556 original size:74 final size:75
Alignment explanation
Indices: 280412--280600 Score: 197
Period size: 74 Copynumber: 2.5 Consensus size: 75
280402 TGAATAAATG
* * *
280412 ACATTGAAAGAAAACTCAAGCAATTTCATTTTATA-CTAGGTGGAAAAAATGACATAAATTACAA
1 ACATTAAAAGAAAATTCAAGCAATTTCATTTTATACCTAGGTAGAAAAAATGACATAAATTACAA
*
280476 TAAAATAATG
66 TAAAATAATA
* * ** * * *
280486 TCATTAAAATAAAACTT-AATTAATTTCATTTTATACCT-GGTAGAGATAATGACATTAATTGA-
1 ACATTAAAAGAAAA-TTCAAGCAATTTCATTTTATACCTAGGTAGAAAAAATGACATAAATT-AC
* *
280548 ACTTAAATAATA
64 AATAAAATAATA
* *
280560 ACATTAAAAGAAAATTCAAGCAATTTAATTTTATACTTAGG
1 ACATTAAAAGAAAATTCAAGCAATTTCATTTTATACCTAGG
280601 ATCTAAATGA
Statistics
Matches: 91, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
73 2 0.02
74 83 0.91
75 6 0.07
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (75 bp):
ACATTAAAAGAAAATTCAAGCAATTTCATTTTATACCTAGGTAGAAAAAATGACATAAATTACAA
TAAAATAATA
Found at i:281420 original size:59 final size:59
Alignment explanation
Indices: 281328--281445 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
281318 CCTTTGTCTC
281328 AATGTTCCACACTTTTAGACACTTGAAAAGTGAATCATAGATACAAACTCCATAATATG
1 AATGTTCCACACTTTTAGACACTTGAAAAGTGAATCATAGATACAAACTCCATAATATG
281387 AATGTTCCACACTTTTAGACACTTGAAAAGTGAATCATAGATACAAACTCCATAATATG
1 AATGTTCCACACTTTTAGACACTTGAAAAGTGAATCATAGATACAAACTCCATAATATG
281446 GTGAAGGCAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.29
Consensus pattern (59 bp):
AATGTTCCACACTTTTAGACACTTGAAAAGTGAATCATAGATACAAACTCCATAATATG
Found at i:285782 original size:131 final size:129
Alignment explanation
Indices: 285583--285931 Score: 430
Period size: 131 Copynumber: 2.7 Consensus size: 129
285573 AAGAAACAAC
* * * * * * * *
285583 CTCTCATGCCTTAAAGTAGTGATTTCTTACTCCAATCAAAATAAAGAAATATTATTATTTACTTC
1 CTCTCATGCCTTAAAGCAGTAATTTATTACTCCAATCGAAATGAAGAGATATTACTATTT-CTAC
** * *
285648 TAAAATTTGATATTAATTCGAGAAAAAATGATAATATCTAATTATTTCCAATTC-AGAATAAATG
65 TAAAATTAAATATTAATTCGAGAAAAAACGATAATATCCAATTATTTCCAA-TCGAGAATAAATG
285712 A
129 A
* *
285713 TCTCTCATGCCTTAAAGCAATAATTTATTACTCCAATCGAAATGAAGAGATATTACTATTTCGTC
1 -CTCTCATGCCTTAAAGCAGTAATTTATTACTCCAATCGAAATGAAGAGATATTACTATTTC-TA
* * * *
285778 CTAAAATTAAATATTAATCCAAGAGAAAACGATAATATCCCATTATTTCCAATCGAGAATAAATG
64 CTAAAATTAAATATTAATTCGAGAAAAAACGATAATATCCAATTATTTCCAATCGAGAATAAATG
285843 A
129 A
* * *
285844 CTTCTCATACCTTAAAACAGTCATTTATTACTCCAATCGAAATGAAGAGATATTACTATTTCATA
1 C-TCTCATGCCTTAAAGCAGTAATTTATTACTCCAATCGAAATGAAGAGATATTACTATTTC-TA
* *
285909 ATAAAATTCAATATTAATTCGAG
64 CTAAAATTAAATATTAATTCGAG
285932 TGTTACTATT
Statistics
Matches: 188, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
130 4 0.02
131 184 0.98
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (129 bp):
CTCTCATGCCTTAAAGCAGTAATTTATTACTCCAATCGAAATGAAGAGATATTACTATTTCTACT
AAAATTAAATATTAATTCGAGAAAAAACGATAATATCCAATTATTTCCAATCGAGAATAAATGA
Found at i:286426 original size:24 final size:24
Alignment explanation
Indices: 286380--286429 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
286370 TGACCAAAAT
* *
286380 AAAATAACATAAAAGCAACATGCA
1 AAAATAAAATAAAAGCAAAATGCA
286404 AAAATTAAAATAAAA-CAAAATGCA
1 AAAA-TAAAATAAAAGCAAAATGCA
286428 AA
1 AA
286430 TAGGACTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.68, C:0.12, G:0.06, T:0.14
Consensus pattern (24 bp):
AAAATAAAATAAAAGCAAAATGCA
Found at i:289225 original size:23 final size:23
Alignment explanation
Indices: 289195--289252 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
289185 TAAGAGTGTT
289195 GAATTTATAAAATTATAGATGAG
1 GAATTTATAAAATTATAGATGAG
*
289218 GAATTTATAAAATTATAGATGAT
1 GAATTTATAAAATTATAGATGAG
*
289241 GAACTTATAAAA
1 GAATTTATAAAA
289253 CTTTTGGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.34
Consensus pattern (23 bp):
GAATTTATAAAATTATAGATGAG
Found at i:289572 original size:3 final size:3
Alignment explanation
Indices: 289564--289636 Score: 58
Period size: 3 Copynumber: 24.0 Consensus size: 3
289554 TCATTTCATT
* ** ** *
289564 TTA TTA TTA TTA TTT TTA AAA TTA AAA TTA TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
289612 TATA TT- GTA TATA TTA TTA TTA TTA
1 T-TA TTA TTA T-TA TTA TTA TTA TTA
289637 AATAAATAAT
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
2 1 0.02
3 46 0.87
4 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:289598 original size:24 final size:24
Alignment explanation
Indices: 289566--289611 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
289556 ATTTCATTTT
*
289566 ATTATTATTATTTTTAAAATTAAA
1 ATTATTATTATTATTAAAATTAAA
*
289590 ATTATTATTATTATTAATATTA
1 ATTATTATTATTATTAAAATTA
289612 TATATTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTATTATTATTATTAAAATTAAA
Found at i:291139 original size:2 final size:2
Alignment explanation
Indices: 291132--291169 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
291122 CATATTAGTC
291132 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
291170 TAATATAGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:291564 original size:160 final size:156
Alignment explanation
Indices: 291178--291604 Score: 439
Period size: 160 Copynumber: 2.7 Consensus size: 156
291168 ATTAATATAG
* * * * *
291178 TATTTATTTATTT-TTTA-ATCAAAGAAAGGGCAATCTTAATA-CAACTATATGTCTATTCTGGT
1 TATTTATTTATTTATTTATATTAAAGAAAGGGCATTCTTAA-AGCAACTAGATGTCTTTTCTGAT
* ** *
291240 A-TTTTAAATAAATAAATATCTTGCTTATAAAA-ACCAAAATATATATACATTGTTTTATTTAAA
65 ATTTTTAAATAAATAAATATCATATTTATAAAACACCAAAATATATATACA-TGTATTATTTAAA
291303 TTATCTTCTTAGGAAAATTATAATATTT
129 TTATCTTCTTAGGAAAATTATAATATTT
* * *
291331 TATTTATTTATTTATTAATATTGAAGAAAGGGGC-TGTCTTAAAGCAACTAGAAGTCTTTTTCTG
1 TATTTATTTATTTATTTATATTAAAGAAA-GGGCAT-TCTTAAAGCAACTAGATGTC-TTTTCTG
* * *
291395 ATATTTTTAAATAAATAAATATCCTATTTATAAAACTCTCTAAAA-ATATTTAC-T-TATTATTT
63 ATATTTTTAAATAAATAAATATCATATTTATAAAACAC-C-AAAATATATATACATGTATTATTT
*
291457 -TATTAT-TT-TTAGGAAAATTATTATATTCTTATTCT
126 AAATTATCTTCTTAGGAAAATTA-TA-A----TATT-T
* *
291492 TATTTATTTTTTTATTTATATTAAAGAAAAGGCATTCTTAAAGCAACTAGATGTCATTTTCTGAT
1 TATTTATTTATTTATTTATATTAAAGAAAGGGCATTCTTAAAGCAACTAGATGTC-TTTTCTGAT
* * *
291557 ATTTTTAAATAAATAAATGTCATATTTACAAAAC-CCTAAATATATATA
65 ATTTTTAAATAAATAAATATCATATTTATAAAACACCAAAATATATATA
291605 TATATATATA
Statistics
Matches: 229, Mismatches: 26, Indels: 33
0.80 0.09 0.11
Matches are distributed among these distances:
153 13 0.06
154 15 0.07
155 13 0.06
156 26 0.11
157 18 0.08
158 36 0.16
159 2 0.01
160 74 0.32
161 32 0.14
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (156 bp):
TATTTATTTATTTATTTATATTAAAGAAAGGGCATTCTTAAAGCAACTAGATGTCTTTTCTGATA
TTTTTAAATAAATAAATATCATATTTATAAAACACCAAAATATATATACATGTATTATTTAAATT
ATCTTCTTAGGAAAATTATAATATTT
Found at i:291603 original size:2 final size:2
Alignment explanation
Indices: 291596--291650 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
291586 AAAACCCTAA
291596 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
291638 AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT
291651 TTTTCCTTAG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:294506 original size:20 final size:19
Alignment explanation
Indices: 294454--294508 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
294444 GCATTCATAT
*
294454 TTTTCATTACATTTTTATG
1 TTTTCATTACATTTTTATA
*
294473 TTTGT-ATTTGCATTTTTATA
1 TTT-TCA-TTACATTTTTATA
294493 TTTTCATGTACATTTT
1 TTTTCAT-TACATTTT
294509 CATTTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.64
Consensus pattern (19 bp):
TTTTCATTACATTTTTATA
Found at i:296730 original size:135 final size:135
Alignment explanation
Indices: 296484--296752 Score: 475
Period size: 135 Copynumber: 2.0 Consensus size: 135
296474 TAAAAAAATG
296484 AAAAAAAGAATCATATATTCAAAGCATGACCTTGATCAGATATTTGGCAGTTCGGTGTTTGCTCC
1 AAAAAAAGAATCATATATTCAAAGCATGACCTTGATCAGATATTTGGCAGTTCGGTGTTTGCTCC
*
296549 ACTGTGATTGTCAAGTCAAAGACATTGTGATGAGTTGAGCCCTTTAATTAGTCCAATAAAGGCTA
66 ACTGTGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCCTTTAATTAGTCCAATAAAGGCTA
296614 ATGTT
131 ATGTT
* * *
296619 AAAAAAAGAGTCATATATTCAAAGCATGACCTTGATCGGGTATTTGGCAGTTCGGTGTTTGCTCC
1 AAAAAAAGAATCATATATTCAAAGCATGACCTTGATCAGATATTTGGCAGTTCGGTGTTTGCTCC
* * *
296684 ACTGTGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCGTTTAATTATTCCAATGAAGGCTA
66 ACTGTGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCCTTTAATTAGTCCAATAAAGGCTA
296749 ATGT
131 ATGT
296753 CAATAAAGGT
Statistics
Matches: 127, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
135 127 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (135 bp):
AAAAAAAGAATCATATATTCAAAGCATGACCTTGATCAGATATTTGGCAGTTCGGTGTTTGCTCC
ACTGTGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCCTTTAATTAGTCCAATAAAGGCTA
ATGTT
Found at i:299802 original size:54 final size:54
Alignment explanation
Indices: 299744--300003 Score: 301
Period size: 54 Copynumber: 4.8 Consensus size: 54
299734 ACATCTGTGT
* *
299744 AGAAGCCACATGAAAGGATGAATGTGTTGTCAAATGTATTACGAACATCTATAC
1 AGAAGCCACATGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTATAC
* * *
299798 AGAAGACACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTGTAC
1 AGAAGCCACATGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTATAC
* * * * * * * * *
299852 AAAAGACACAGGAAATGATTAATCTATTGTCAAATGTTTGACGAACATCTTTGC
1 AGAAGCCACATGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTATAC
* * * * *
299906 ATAAACCATATGAAATGATGAAAT-T-TTGTCAAGTGTTTTACGAACATCTGA-GC
1 AGAAGCCACATGAAATGATG-AATGTGTTGTCAAATGTTTTACGAACATCT-ATAC
*
299959 AGAAGCCACATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAA
1 AGAAGCCACATGAAATGATGAATGTGTTGTCAAATGTTTTACGAA
300004 TCAGTTATGG
Statistics
Matches: 176, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
52 3 0.02
53 41 0.23
54 129 0.73
55 3 0.02
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (54 bp):
AGAAGCCACATGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTATAC
Found at i:300385 original size:22 final size:22
Alignment explanation
Indices: 300331--300390 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
300321 TTTACATCTA
*
300331 CACTCTTCAAAGATGATAGATT
1 CACTCTTCAAAAATGATAGATT
* *
300353 CACTCTCCAAATATGATAGATT
1 CACTCTTCAAAAATGATAGATT
* *
300375 CTCTTTTCAAAAATGA
1 CACTCTTCAAAAATGA
300391 AAGCTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (22 bp):
CACTCTTCAAAAATGATAGATT
Found at i:301181 original size:76 final size:76
Alignment explanation
Indices: 301055--301317 Score: 402
Period size: 76 Copynumber: 3.5 Consensus size: 76
301045 CCATTTCCCA
* *
301055 CATCTGTAAGCCCTTCAGTGCATGATGTTTTGAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTTCAA
301120 AACCTTCAGGT
66 AACCTTCAGGT
* * * *
301131 CATCTATAAGCCCTACAGTACATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTTCAA
*
301196 AACCTTCAAGT
66 AACCTTCAGGT
** *
301207 CATCTGTAA-AACTTGCAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTTCA
1 CATCTGTAAGCCCTT-CAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTTCA
* *
301271 AAGCCTTCGGGT
65 AAACCTTCAGGT
301283 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
301318 GCCTTCGGGT
Statistics
Matches: 165, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
75 2 0.01
76 160 0.97
77 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTTCAA
AACCTTCAGGT
Found at i:301316 original size:45 final size:45
Alignment explanation
Indices: 301260--301497 Score: 359
Period size: 45 Copynumber: 5.3 Consensus size: 45
301250 AGGAGCTTTT
*
301260 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
301305 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAACCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
301350 TGATGTTTTCAAAACCTTTGGGTCATCTATAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
301395 TGATGTTTGCAAAGTCTTCGGGTCATTTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* ** *
301440 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGCCCTACAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
301485 GGATGTTTTCAAA
1 TGATGTTTTCAAA
301498 AAGCTTCGGG
Statistics
Matches: 173, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 173 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:301568 original size:75 final size:74
Alignment explanation
Indices: 301440--301581 Score: 203
Period size: 75 Copynumber: 1.9 Consensus size: 74
301430 CTTCAGTGCA
* * * *
301440 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCTTC
1 TGATATTTTCAAAACCTTCGAGTCATCCATAAGACCTACAGTGCAGGATGTTTTC-AAAACCTTC
301505 GGGAGCTTTT
65 GGGAGCTTTT
** * *
301515 TGATATTTTCAAAACCTTCGAGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATATTTTCAAAACCTTCGAGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAACCTTCG
301580 GG
66 GG
301582 TCATCTGTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
74 11 0.19
75 48 0.81
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (74 bp):
TGATATTTTCAAAACCTTCGAGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAACCTTCG
GGAGCTTTT
Found at i:301585 original size:45 final size:45
Alignment explanation
Indices: 301515--301609 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
301505 GGGAGCTTTT
* *
301515 TGATATTTTCAAAACCTTCGAGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGACCTACAGTGCA
*
301560 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGACCTACAGTGCA
*
301605 AGATG
1 TGATG
301610 ATAAGACCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGACCTACAGTGCA
Found at i:301798 original size:3 final size:3
Alignment explanation
Indices: 301783--301835 Score: 70
Period size: 3 Copynumber: 17.0 Consensus size: 3
301773 TCATTTCATT
* *
301783 TTA TTA ATA TTA TTA TTA TTA TTA TTA ATA TATA TTA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA T-TA TTA TTA
301830 TTA TTA
1 TTA TTA
301836 AATAAATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:303812 original size:2 final size:2
Alignment explanation
Indices: 303805--303846 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
303795 AAAACCCTAA
303805 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
303847 TTTCCTTAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:311638 original size:21 final size:21
Alignment explanation
Indices: 311612--311651 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
311602 CAGAACCCCA
*
311612 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
311633 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
311652 TCAATGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:311673 original size:22 final size:21
Alignment explanation
Indices: 311634--311680 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
311624 TTCCCCTGTG
*
311634 GGGGGAATCGGTTCCCCTTCAAT
1 GGGGGAATCGGCTCCCC-TC-AT
311657 GGGGGAATCGGCT-CCCTCAT
1 GGGGGAATCGGCTCCCCTCAT
311677 GGGG
1 GGGG
311681 ATTGATTCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.26
21 2 0.09
22 3 0.13
23 12 0.52
ACGTcount: A:0.15, C:0.26, G:0.38, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGCTCCCCTCAT
Done.