Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001941.1 Hibiscus syriacus cultivar Beakdansim tig00003934_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: 155000
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:4009 original size:89 final size:91
Alignment explanation
Indices: 3808--4006 Score: 271
Period size: 89 Copynumber: 2.2 Consensus size: 91
3798 ATACCCATGC
* *
3808 TATATTATTATATACAATAAAGCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCAGGCTT
1 TATA-TATTATATACAATAAAGCTTAAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCAGACTT
3873 TATGGATAATATTCAGCTAGCCTATAT
65 TATGGATAATATTCAGCTAGCCTATAT
* * * *
3900 TAT-TA-TATATACAATAAAGCTTAAGTTCTCCCCCTAAAGCAGTTGGTTAATCGCCCCGACTTT
1 TATATATTATATACAATAAAGCTTAAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCAGACTTT
* *
3963 ATGGATAATTTTCAGCTAG-CT-TGT
66 ATGGATAATATTCAGCTAGCCTATAT
*
3987 TATACTATTATATGCAATAA
1 TATA-TATTATATACAATAA
4007 GCTGTCACTC
Statistics
Matches: 95, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
87 5 0.05
88 2 0.02
89 72 0.76
90 13 0.14
92 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.36
Consensus pattern (91 bp):
TATATATTATATACAATAAAGCTTAAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCAGACTTT
ATGGATAATATTCAGCTAGCCTATAT
Found at i:5388 original size:7 final size:7
Alignment explanation
Indices: 5376--5423 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
5366 ATTTACAATG
5376 AACCCTA
1 AACCCTA
5383 AACCCTA
1 AACCCTA
* *
5390 AATCATA
1 AACCCTA
**
5397 AACTATA
1 AACCCTA
5404 AACCCTA
1 AACCCTA
*
5411 AACTCTA
1 AACCCTA
5418 AACCCT
1 AACCCT
5424 TAATTTGATT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (7 bp):
AACCCTA
Found at i:5407 original size:21 final size:21
Alignment explanation
Indices: 5381--5420 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5371 CAATGAACCC
5381 TAAACCCTAAA-TCATAAACTA
1 TAAACCCTAAACTC-TAAACTA
5402 TAAACCCTAAACTCTAAAC
1 TAAACCCTAAACTCTAAAC
5421 CCTTAATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACCCTAAACTCTAAACTA
Found at i:5422 original size:14 final size:14
Alignment explanation
Indices: 5376--5423 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
5366 ATTTACAATG
*
5376 AACCCTAAACCCTA
1 AACCCTAAACTCTA
* * *
5390 AATCATAAACTATA
1 AACCCTAAACTCTA
5404 AACCCTAAACTCTA
1 AACCCTAAACTCTA
5418 AACCCT
1 AACCCT
5424 TAATTTGATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (14 bp):
AACCCTAAACTCTA
Found at i:6116 original size:16 final size:17
Alignment explanation
Indices: 6080--6121 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
6070 ATTTAATATA
6080 TAAAACCTAATTATAAAC
1 TAAAA-CTAATTATAAAC
*
6098 TAAAACTAA-TATGAAC
1 TAAAACTAATTATAAAC
6114 TAAAACTA
1 TAAAACTA
6122 TCCTCTTCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.61
17 4 0.17
18 5 0.22
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.26
Consensus pattern (17 bp):
TAAAACTAATTATAAAC
Found at i:6756 original size:3 final size:3
Alignment explanation
Indices: 6750--6779 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6740 CTGTTTGTAT
6750 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6780 ATATTTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:8604 original size:11 final size:11
Alignment explanation
Indices: 8586--8625 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
8576 GAGTTTGAGT
8586 TCGAGCTTGAA
1 TCGAGCTTGAA
*
8597 TTGAGCTTGAA
1 TCGAGCTTGAA
*
8608 TCGAGCTTCAA
1 TCGAGCTTGAA
8619 TCGAGCT
1 TCGAGCT
8626 CCTAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:9400 original size:41 final size:43
Alignment explanation
Indices: 9341--9445 Score: 103
Period size: 41 Copynumber: 2.5 Consensus size: 43
9331 TACAATTTAG
* * *
9341 AATGTTG-GGACATCTTAAAGGCCTATTTCA-ACCAGAAAT-A-A
1 AATGTTGAGG-CATTTTAAAGGCCCAATTCATA-CAGAAATGATA
* *
9382 AATGTTGAGGCATTTTAAATGCCCAATTCATACAGAAATGATT
1 AATGTTGAGGCATTTTAAAGGCCCAATTCATACAGAAATGATA
*
9425 CATG-TGAGGCATTTTAAAGGC
1 AATGTTGAGGCATTTTAAAGGC
9446 TCGCATCAGT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
41 30 0.57
42 20 0.38
43 3 0.06
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (43 bp):
AATGTTGAGGCATTTTAAAGGCCCAATTCATACAGAAATGATA
Found at i:11509 original size:42 final size:41
Alignment explanation
Indices: 11444--11540 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 41
11434 TCTTGATTTG
* * * * *
11444 TAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGTATGATGCT
1 TAAATCCTTCGGGCCATCAGTAAGCCTTTCGAGCAAGATG-A
*
11486 TAAATCCTTCGGGCCATCTGTAAGCCTTTCGAGCAAGATGA
1 TAAATCCTTCGGGCCATCAGTAAGCCTTTCGAGCAAGATGA
*
11527 TAAGTCCTTCGGGC
1 TAAATCCTTCGGGC
11541 AATCCATAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 13 0.27
42 35 0.73
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (41 bp):
TAAATCCTTCGGGCCATCAGTAAGCCTTTCGAGCAAGATGA
Found at i:11780 original size:274 final size:274
Alignment explanation
Indices: 11284--12121 Score: 1381
Period size: 274 Copynumber: 3.1 Consensus size: 274
11274 AAGTCCCTCG
*
11284 GGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGATTA
1 GGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTA
* *
11349 TCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAATTTTAAGGGGTTTCTTGACAACTAAGAAACT
66 TCTCAAAAGAGTTGTTAAAGGAAGTTAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAACT
* *
11414 AAGCTTGATTTTCAAGGGTTTCTTGATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGTA
131 AAACTTGATTTTCAAGGGTTTCTTGATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCA
* * *
11479 TGATGCTTAAATCCTTCGGGCCATCTGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCAAT
196 TGATGCTTAAATCCTTCAGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCAT
*
11544 CCATAAGGCCTTCA
261 CCATAAGACCTTCA
*
11558 GGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTTATGATTA
1 GGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTA
*
11623 TCTCAAAAGAGTTGTTCAAGGAAGTTAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAACT
66 TCTCAAAAGAGTTGTTAAAGGAAGTTAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAACT
*
11688 AAACTTGATTTTCAAGGGTTTCTTGATTTGTAAATCCTTTGGGTCATCAGTAAGTCTTTCGAGCA
131 AAACTTGATTTTCAAGGGTTTCTTGATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCA
**
11753 CAATGCTTAAATCCTTCAGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCAT
196 TGATGCTTAAATCCTTCAGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCAT
* *
11818 CCATAAAACCTTTA
261 CCATAAGACCTTCA
* * * *
11832 GACTGGATGTTTTAAAATGAGATTTTAGAAACTAAGCCTGATTTTCAGGGTTTTCTTGATGATTA
1 GGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTA
* *
11897 TCTCAAAAGAGTTGTTAAAAGAA-TCTAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAAT
66 TCTCAAAAGAGTTGTTAAAGGAAGT-TAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAAC
11961 TAAACTTGATTTTCAAGGGTTTCTTGATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGC
130 TAAACTTGATTTTCAAGGGTTTCTTGATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGC
* * * * * *
12026 ATGATGCTTAAATCTTTCTGGTCATCTATAAGCCTTTCGAGCAAAATTATAAGTCATTCGGGCCA
195 ATGATGCTTAAATCCTTCAGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCA
*
12091 TCCATAAGACCTTCG
260 TCCATAAGACCTTCA
* *
12106 GGTAGAATGTTTTCAA
1 GGCAGGATGTTTTCAA
12122 CATTTTCGTT
Statistics
Matches: 522, Mismatches: 41, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
273 1 0.00
274 521 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (274 bp):
GGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTA
TCTCAAAAGAGTTGTTAAAGGAAGTTAAGCCTAATTTTAAGGGGTTCCTTGACAACTAAGAAACT
AAACTTGATTTTCAAGGGTTTCTTGATTTGTAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCA
TGATGCTTAAATCCTTCAGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCAT
CCATAAGACCTTCA
Found at i:12221 original size:36 final size:36
Alignment explanation
Indices: 12169--12255 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 36
12159 GATGTCTTAT
**
12169 TTAAAACAGAAATTTTATCTCA-CTCGAGATAGTTTTTC
1 TTAAAAC--AAATTTTATCTCACCT-GAGATAGTTCCTC
12207 TTAAAACAAATTTTATCTCACCTGAGATAGTTCCTC
1 TTAAAACAAATTTTATCTCACCTGAGATAGTTCCTC
*
12243 TTCAAACAAATTT
1 TTAAAACAAATTT
12256 CTTTTCGTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
36 36 0.80
37 2 0.04
38 7 0.16
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (36 bp):
TTAAAACAAATTTTATCTCACCTGAGATAGTTCCTC
Found at i:15319 original size:21 final size:20
Alignment explanation
Indices: 15291--15329 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
15281 TTAAAAAATT
15291 TGATATTTAGATACTAAAAC
1 TGATATTTAGATACTAAAAC
*
15311 TGATAATTTAGTTACTAAA
1 TGAT-ATTTAGATACTAAA
15330 TACATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (20 bp):
TGATATTTAGATACTAAAAC
Found at i:17566 original size:13 final size:14
Alignment explanation
Indices: 17537--17566 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17527 GCTTTACGGG
*
17537 AAATGAATGGAAAA
1 AAATCAATGGAAAA
17551 AAATCAATGGAAAA
1 AAATCAATGGAAAA
17565 AA
1 AA
17567 GGTTGATATT
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:0.67, C:0.03, G:0.17, T:0.13
Consensus pattern (14 bp):
AAATCAATGGAAAA
Found at i:19225 original size:248 final size:242
Alignment explanation
Indices: 18832--19326 Score: 762
Period size: 248 Copynumber: 2.0 Consensus size: 242
18822 AGAAAGTAAC
* * * *
18832 TCATCATCGTCAGCCAATTTGGACGCAATAACCATAGGCATAGCACATGGTGCATAACTCTTCAT
1 TCATCATCGTCAGCCAATTTGGACGCAAGAACCATAGGCATAACACATGGTGAAGAACTCTTCAT
* *
18897 GTTTGCCTTCTCAAAAATATGAACTTGTTTTGACTGAGCATCAATGAACCATTAAATCATTTCGC
66 GTTCGCCTTCTCAAAAATATGAACTTGTTTTGACTGAGAATCAATGAACCATTAAATCATTTCGC
*
18962 TTCAATCCCTAAGAAATAAC-GTAGAGATCCTAAATCCTTAAGGGAAAACATGTTGTGCAACAAG
131 TTCAATCCCTAAGAAATAACTG-AGAGATCCTAAATCCTTAAGGGAAAACATGTTGCGCAACAAG
*
19026 AGCACAACACCAACAATTGCAGAAGATGATGAACTGGTAATAACAATA
195 AGCACAACACCAACAATTGCAGAAGATGATGAACTAGTAATAACAATA
19074 TCATCATTC-TCAGCCAATTTGGACGCAAGAACCAT-GGCATAACACATGGTGAAGAACTCTTCA
1 TCATCA-TCGTCAGCCAATTTGGACGCAAGAACCATAGGCATAACACATGGTGAAGAACTCTTCA
** *
19137 TGTTCGCCTTCTCAAAAAGCTCCAAAATGAACTTGTTTTGACTGAGAATCAATGAGTCATTAAGT
65 TGTTCGCCTTCTCAAAAA--T-----ATGAACTTGTTTTGACTGAGAATCAATGAACCATTAAAT
*
19202 CATTTTGCTTCAATCCCTAAGAAATAACTGAGAGATCCTAAATCCTTAAGGGAAAACATGTTGCG
123 CATTTCGCTTCAATCCCTAAGAAATAACTGAGAGATCCTAAATCCTTAAGGGAAAACATGTTGCG
* *
19267 CAACATGAGCACAACACCAACAATTGCAGAAGATGATGATCTAGTAATAACAATA
188 CAACAAGAGCACAACACCAACAATTGCAGAAGATGATGAACTAGTAATAACAATA
19322 TCATC
1 TCATC
19327 GACGTATACC
Statistics
Matches: 230, Mismatches: 14, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
241 42 0.18
242 31 0.13
243 3 0.01
248 153 0.67
249 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (242 bp):
TCATCATCGTCAGCCAATTTGGACGCAAGAACCATAGGCATAACACATGGTGAAGAACTCTTCAT
GTTCGCCTTCTCAAAAATATGAACTTGTTTTGACTGAGAATCAATGAACCATTAAATCATTTCGC
TTCAATCCCTAAGAAATAACTGAGAGATCCTAAATCCTTAAGGGAAAACATGTTGCGCAACAAGA
GCACAACACCAACAATTGCAGAAGATGATGAACTAGTAATAACAATA
Found at i:27580 original size:96 final size:96
Alignment explanation
Indices: 27403--27585 Score: 235
Period size: 96 Copynumber: 1.9 Consensus size: 96
27393 AAGAATTCAC
* * ** * *
27403 GAAACTGATGTGAGGCCTTTTACCAGTAACCACTGCAAGAATATAAGCCATCCTAGAAATGATGG
1 GAAACTGATGTGAGGCCCTTCACCAGTAACCACCACAAGAACATAAGCCATCCTAGAAATGATGA
27468 AACCACGTGATCTCTCTAATAAGCCATCCTT
66 AACCACGTGATCTCTCTAATAAGCCATCCTT
*
27499 GAAA-TGATGTGAGGCCCCTTCACCAGTAATCC-CCACAAGAACATAAGCCATCCTTGAAATGAT
1 GAAACTGATGTGAGG-CCCTTCACCAGTAA-CCACCACAAGAACATAAGCCATCCTAGAAATGAT
* * * *
27562 GAAACCGCTTGTTGTCTCTAATAA
64 GAAACCACGTGATCTCTCTAATAA
27586 TCAATTCCCT
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
95 10 0.14
96 62 0.84
97 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (96 bp):
GAAACTGATGTGAGGCCCTTCACCAGTAACCACCACAAGAACATAAGCCATCCTAGAAATGATGA
AACCACGTGATCTCTCTAATAAGCCATCCTT
Found at i:28949 original size:57 final size:57
Alignment explanation
Indices: 28858--28978 Score: 188
Period size: 57 Copynumber: 2.1 Consensus size: 57
28848 GGATAGCTTC
* ** *
28858 GATTCTGCTGTGGATTCCACTGATTAGGCCTTTCTCGTTGAGAATAACCCTGGTCCT
1 GATTCTGCTGAGGATTCCACTGATTAGGAATTTCTCGTTGAGAATAACCCTGGCCCT
* *
28915 GATTCTGTTGAGGATTCCACTGATTAGGAATTTCTCGTTGAGAATAACCGTGGCCCT
1 GATTCTGCTGAGGATTCCACTGATTAGGAATTTCTCGTTGAGAATAACCCTGGCCCT
28972 GATTCTG
1 GATTCTG
28979 GCGTGTATTC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (57 bp):
GATTCTGCTGAGGATTCCACTGATTAGGAATTTCTCGTTGAGAATAACCCTGGCCCT
Found at i:28989 original size:57 final size:57
Alignment explanation
Indices: 28858--28996 Score: 181
Period size: 57 Copynumber: 2.4 Consensus size: 57
28848 GGATAGCTTC
** *
28858 GATTCT-GCTGTGGATTCCACTGATTAGGCCTTTCTCGTTGAGAATAACCCTGGTCCT
1 GATTCTGGC-GTGGATTCCACTGATTAGGAATTTCTCGTTGAGAATAACCCTGGCCCT
** * *
28915 GATTCTGTTGAGGATTCCACTGATTAGGAATTTCTCGTTGAGAATAACCGTGGCCCT
1 GATTCTGGCGTGGATTCCACTGATTAGGAATTTCTCGTTGAGAATAACCCTGGCCCT
* *
28972 GATTCTGGCGTGTATTCCATTGATT
1 GATTCTGGCGTGGATTCCACTGATT
28997 GTTACCATGA
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
57 69 1.00
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (57 bp):
GATTCTGGCGTGGATTCCACTGATTAGGAATTTCTCGTTGAGAATAACCCTGGCCCT
Found at i:34597 original size:31 final size:31
Alignment explanation
Indices: 34536--34639 Score: 129
Period size: 31 Copynumber: 3.3 Consensus size: 31
34526 GGGCCCGAGA
* **
34536 GCCTACCCAAGAAGGT-TACTCGGGATCGCAGG
1 GCCTACCCAAGAA-ATAT-CTCGGGGCCGCAGG
34568 GCCTACCCAAGAAATATCTCGGGGCCGCAGG
1 GCCTACCCAAGAAATATCTCGGGGCCGCAGG
* * *
34599 GCCTAACCAAGAAAGATCTCGGGGCCTCAGG
1 GCCTACCCAAGAAATATCTCGGGGCCGCAGG
34630 GCCTACCCAA
1 GCCTACCCAA
34640 AGGTCACCTT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
31 50 0.78
32 14 0.22
ACGTcount: A:0.27, C:0.32, G:0.28, T:0.13
Consensus pattern (31 bp):
GCCTACCCAAGAAATATCTCGGGGCCGCAGG
Found at i:36577 original size:27 final size:27
Alignment explanation
Indices: 36547--36600 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
36537 CTATAATATA
*
36547 GTCATTTTATACTTC-AAGGGTATTTTG
1 GTCATTTT-TACCTCAAAGGGTATTTTG
36574 GTCATTTTTACCTCATAAGGGTATTTT
1 GTCATTTTTACCTCA-AAGGGTATTTT
36601 CATAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 5 0.21
27 8 0.33
28 11 0.46
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (27 bp):
GTCATTTTTACCTCAAAGGGTATTTTG
Found at i:39367 original size:23 final size:23
Alignment explanation
Indices: 39341--39385 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
39331 CACCACAGCT
*
39341 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
39364 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
39386 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:40576 original size:18 final size:18
Alignment explanation
Indices: 40555--40589 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40545 TTCCATCTAG
40555 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
40573 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
40590 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:44491 original size:23 final size:23
Alignment explanation
Indices: 44465--44509 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
44455 CACCACAGCT
*
44465 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
44488 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
44510 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:44747 original size:149 final size:149
Alignment explanation
Indices: 44477--44791 Score: 614
Period size: 149 Copynumber: 2.1 Consensus size: 149
44467 TATAATTGCA
44477 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
44541 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
44606 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
44626 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
44691 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
44756 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
44775 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
44792 CCCTCGACTC
Statistics
Matches: 165, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
148 1 0.01
149 164 0.99
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:45695 original size:18 final size:18
Alignment explanation
Indices: 45674--45708 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
45664 TCCCATCTAG
45674 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
45692 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
45709 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:46313 original size:21 final size:21
Alignment explanation
Indices: 46289--46333 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
46279 TATTGTTCGT
* *
46289 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
46310 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
46331 TTG
1 TTG
46334 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:47887 original size:20 final size:20
Alignment explanation
Indices: 47858--47901 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
47848 ATTTTCTTTC
47858 AAAAGCAAAATTGG-ATTTTG
1 AAAAGCAAAA-TGGAATTTTG
*
47878 AAAAGTAAAATGGAATTTTG
1 AAAAGCAAAATGGAATTTTG
47898 AAAA
1 AAAA
47902 ATGATTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.52, C:0.02, G:0.18, T:0.27
Consensus pattern (20 bp):
AAAAGCAAAATGGAATTTTG
Found at i:55575 original size:22 final size:22
Alignment explanation
Indices: 55534--55575 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
55524 TTTCGAACAA
* *
55534 TGCTACTACTGCTATGTAGCAG
1 TGCTACTACTACTATATAGCAG
*
55556 TGCTACTACTATTATATAGC
1 TGCTACTACTACTATATAGC
55576 GATCCTTATT
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:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (22 bp):
TGCTACTACTACTATATAGCAG
Found at i:58095 original size:2 final size:2
Alignment explanation
Indices: 58082--58120 Score: 60
Period size: 2 Copynumber: 18.5 Consensus size: 2
58072 AATCTTGATT
58082 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
58121 TGTCATATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 31 0.89
3 4 0.11
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:59603 original size:78 final size:78
Alignment explanation
Indices: 59521--59671 Score: 196
Period size: 78 Copynumber: 1.9 Consensus size: 78
59511 TATAAAAAAT
* * * * *
59521 AACATTTTAGGTAGCGCCCAATATTAATATTTCCAG-TAAAAAAATAATATTTTAAGTAGTATTT
1 AACATTTTAGATAACGCCCAATATTAATATTT-CAGATAAAAAAATAATATTTTAAATAATATAT
*
59585 TATCGAAAATATTA
65 TATCAAAAATATTA
* * **
59599 AACATTTTAGATAACGTCTAATATTAATATTTTTGATAAAAAAATAATATTTTAAATAATATATT
1 AACATTTTAGATAACGCCCAATATTAATATTTCAGATAAAAAAATAATATTTTAAATAATATATT
59664 ATCAAAAA
66 ATCAAAAA
59672 AAATTAAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
77 1 0.02
78 61 0.98
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.38
Consensus pattern (78 bp):
AACATTTTAGATAACGCCCAATATTAATATTTCAGATAAAAAAATAATATTTTAAATAATATATT
ATCAAAAATATTA
Found at i:60495 original size:22 final size:22
Alignment explanation
Indices: 60467--60517 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
60457 GACACAAAAT
*
60467 AATAAAAAAATTATTTTTATTC
1 AATAAAAAAATTAATTTTATTC
* *
60489 AATAAAAATATTAATTTTATTG
1 AATAAAAAAATTAATTTTATTC
60511 AA-AAAAA
1 AATAAAAA
60518 TATATATAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
AATAAAAAAATTAATTTTATTC
Found at i:60516 original size:21 final size:21
Alignment explanation
Indices: 60470--60520 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
60460 ACAAAATAAT
*
60470 AAAAAA-ATTATTTTTATTCA
1 AAAAAATATTAATTTTATTCA
*
60490 ATAAAAATATTAATTTTATTGA
1 A-AAAAATATTAATTTTATTCA
60512 AAAAAATAT
1 AAAAAATAT
60521 ATATAGATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 13 0.48
22 13 0.48
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAAAATATTAATTTTATTCA
Found at i:60656 original size:38 final size:39
Alignment explanation
Indices: 60608--60684 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 39
60598 TCACCCTAAA
60608 CCCGAACCTGACCCAACCCGAATATCACACTTAAAAAAC
1 CCCGAACCTGACCCAACCCGAATATCACACTTAAAAAAC
* *
60647 CCCG-ACCTGACTCGACCCGAATATCACACTTAAAAAAC
1 CCCGAACCTGACCCAACCCGAATATCACACTTAAAAAAC
60685 TCGACCCGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 32 0.89
39 4 0.11
ACGTcount: A:0.39, C:0.38, G:0.09, T:0.14
Consensus pattern (39 bp):
CCCGAACCTGACCCAACCCGAATATCACACTTAAAAAAC
Found at i:62335 original size:37 final size:36
Alignment explanation
Indices: 62260--62335 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
62250 TTTTTATATT
*
62260 TTTAATTTTATAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTATAAAAAAATTATATAAATATTATCAA
* *
62296 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTATAAA-AAAATTATATAAATATTAT-CAA
62333 TTT
1 TTT
62336 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (36 bp):
TTTAATTTTATAAAAAAATTATATAAATATTATCAA
Found at i:62481 original size:15 final size:16
Alignment explanation
Indices: 62461--62491 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
62451 AAAATACAAC
62461 ATTCCC-AGTAATCTT
1 ATTCCCTAGTAATCTT
62476 ATTCCCTAGTAATCTT
1 ATTCCCTAGTAATCTT
62492 TTATTCTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTCCCTAGTAATCTT
Found at i:65662 original size:18 final size:17
Alignment explanation
Indices: 65623--65667 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
65613 AAACCCTTTG
*
65623 TAAATAGTTTGTTTTTA
1 TAAATATTTTGTTTTTA
*
65640 TAAATGTTTTGTTTTTA
1 TAAATATTTTGTTTTTA
65657 TAAAATATTTT
1 T-AAATATTTT
65668 AGGTAGGTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (17 bp):
TAAATATTTTGTTTTTA
Found at i:66499 original size:21 final size:21
Alignment explanation
Indices: 66473--66515 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
66463 TTTTTGGGCT
* *
66473 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
66494 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
66515 A
1 A
66516 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:66566 original size:65 final size:66
Alignment explanation
Indices: 66495--66629 Score: 209
Period size: 66 Copynumber: 2.1 Consensus size: 66
66485 ACCCATTCAA
* *
66495 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGAGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGAGGAATCGATACCCCCA
66559 G
66 G
* * * *
66560 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGAGGAATCGATACCCCCA
66625 G
66 G
66626 GGGG
1 GGGG
66630 GGGGGAACCG
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
65 26 0.41
66 37 0.59
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (66 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGAGGAATCGATACCCCCA
G
Found at i:67302 original size:13 final size:13
Alignment explanation
Indices: 67284--67346 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
67274 TTATATGGCA
67284 CTACGGTGCAATT
1 CTACGGTGCAATT
67297 CTACGG-GC-A--
1 CTACGGTGCAATT
*
67306 CTTCGGTGCAATT
1 CTACGGTGCAATT
67319 CTACGG-GC-A--
1 CTACGGTGCAATT
*
67328 CTTCGGTGCAATT
1 CTACGGTGCAATT
67341 CTACGG
1 CTACGG
67347 GCACTTCGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:67367 original size:22 final size:22
Alignment explanation
Indices: 67280--67359 Score: 151
Period size: 22 Copynumber: 3.6 Consensus size: 22
67270 ATCATTATAT
*
67280 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
67302 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
67324 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
67346 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
67360 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.19, C:0.28, G:0.29, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:73433 original size:21 final size:21
Alignment explanation
Indices: 73407--73449 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
73397 TTTTCGGGCT
* *
73407 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
73428 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
73449 A
1 A
73450 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:73509 original size:66 final size:67
Alignment explanation
Indices: 73429--73577 Score: 221
Period size: 67 Copynumber: 2.2 Consensus size: 67
73419 ACCCATTCAA
* *
73429 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATA-CCCCA
73493 -GG
65 GGG
* * *
73495 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCAG
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCAG
73560 GG
66 GG
*
73562 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
73578 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
66 31 0.41
67 44 0.59
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCAG
GG
Found at i:74318 original size:22 final size:22
Alignment explanation
Indices: 74209--74310 Score: 195
Period size: 22 Copynumber: 4.6 Consensus size: 22
74199 ATCATTATAT
*
74209 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
74231 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
74253 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
74275 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
74297 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
74311 TTTATACGAG
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
22 79 1.00
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:81461 original size:14 final size:14
Alignment explanation
Indices: 81442--81489 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
81432 AAAGTTAACA
**
81442 AGTTGACTCGTACG
1 AGTTGACTCAAACG
81456 AGTTGACTCAAACG
1 AGTTGACTCAAACG
* * *
81470 AGTTTACTCAGATG
1 AGTTGACTCAAACG
81484 AGTTGA
1 AGTTGA
81490 TTCAGTTCGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (14 bp):
AGTTGACTCAAACG
Found at i:86658 original size:39 final size:39
Alignment explanation
Indices: 86604--86678 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
86594 TTATTATTAT
*
86604 CTAATTACTATTATGGCCTTAAAATTTTACAATAAACAA
1 CTAATTACTATTATGGCCTTAAAATTTTAAAATAAACAA
*
86643 CTAATTATTATTATGGCCTTAAAATTTTAAAATAAA
1 CTAATTACTATTATGGCCTTAAAATTTTAAAATAAA
86679 TAAACCATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (39 bp):
CTAATTACTATTATGGCCTTAAAATTTTAAAATAAACAA
Found at i:87473 original size:41 final size:41
Alignment explanation
Indices: 87428--87509 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
87418 ATAATTTCGT
87428 CTCCACACTTTTATAATACTTACATATATATATTAGTATTA
1 CTCCACACTTTTATAATACTTACATATATATATTAGTATTA
*
87469 CTCCACACTTTTATAATATTTACATATATATATTAGTATTA
1 CTCCACACTTTTATAATACTTACATATATATATTAGTATTA
87510 ATTTTATTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.37, C:0.16, G:0.02, T:0.45
Consensus pattern (41 bp):
CTCCACACTTTTATAATACTTACATATATATATTAGTATTA
Found at i:88520 original size:31 final size:29
Alignment explanation
Indices: 88476--88587 Score: 73
Period size: 30 Copynumber: 3.6 Consensus size: 29
88466 TAAAAGGGGT
*
88476 AAACTTCATTTTGGCTCCCTCTGTTTTGAA
1 AAACTTCAATTTGG-TCCCTCTGTTTTGAA
* * **
88506 AAACATTCAATTTGGTCCC-CAAATCGGTTGGGT
1 AAAC-TTCAATTTGGTCCCTC---T-GTTTTGAA
* *
88539 AAACTTCATTTTGGCTCCCTCTGTTTTAAA
1 AAACTTCAATTTGG-TCCCTCTGTTTTGAA
*
88569 AAACATTTAATTTGGTCCC
1 AAAC-TTCAATTTGGTCCC
88588 CAAATCGGTT
Statistics
Matches: 61, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
29 1 0.02
30 19 0.31
31 18 0.30
32 10 0.16
33 12 0.20
34 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.38
Consensus pattern (29 bp):
AAACTTCAATTTGGTCCCTCTGTTTTGAA
Found at i:88571 original size:63 final size:63
Alignment explanation
Indices: 88472--88660 Score: 351
Period size: 63 Copynumber: 3.0 Consensus size: 63
88462 TTGCTAAAAG
* *
88472 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTGAAAAACATTCAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
88535 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
*
88598 GGGTAAACTTTATTTTGGCTCCCTCTGTTTTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
88661 TAATTCCCTT
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 123 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (63 bp):
GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
Found at i:99502 original size:20 final size:20
Alignment explanation
Indices: 99457--99502 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
99447 GTCCTAAGTT
*
99457 GAAAAAAAAAAACAACAACA
1 GAAAAAAAAAAACAAAAACA
*
99477 -ACAAAAAAAAAACAAAAAGA
1 GA-AAAAAAAAAACAAAAACA
99497 GAAAAA
1 GAAAAA
99503 CGTTTAAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.83, C:0.11, G:0.07, T:0.00
Consensus pattern (20 bp):
GAAAAAAAAAAACAAAAACA
Found at i:100593 original size:105 final size:105
Alignment explanation
Indices: 100285--100983 Score: 1132
Period size: 105 Copynumber: 6.7 Consensus size: 105
100275 TTTTACCCAT
100285 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
100350 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
*
100390 AGCCAATTTCAACTTCACAACAAAGGAT-TTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
100454 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTCCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
*
100494 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
100559 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTCCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
* * *
100599 AGTCAAGTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
100664 AAGGGACCGCTGGTTGTCAATAAACATTTCCTC-ATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTT-CTCAATTTCAG
*
100704 AGCCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
100769 AAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
* * *
100809 AACCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * * * *
100874 AAGGGACCGCTGGTTGTCAATAAATAACTTCCCAACTTCAG
66 AAGGGACCGCTGGTTGTCAACAAA-CATTTCTCAATTTCAG
* * **** *
100915 AGCCAATTTCAACTTCACAACGAAGGATATTGGATTCAAGACAGTATAAGTTCAACGTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
100980 AAGG
66 AAGG
100984 AGCTATATAC
Statistics
Matches: 560, Mismatches: 30, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
104 103 0.18
105 382 0.68
106 75 0.13
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
Found at i:101415 original size:41 final size:41
Alignment explanation
Indices: 101358--101439 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
101348 ATAATTTCGT
101358 CTCCACACTTTTATAATACTTACATATATATATTAGTATTA
1 CTCCACACTTTTATAATACTTACATATATATATTAGTATTA
*
101399 CTCCACACTTTTATAATATTTACATATATATATTAGTATTA
1 CTCCACACTTTTATAATACTTACATATATATATTAGTATTA
101440 ATTTTATTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.37, C:0.16, G:0.02, T:0.45
Consensus pattern (41 bp):
CTCCACACTTTTATAATACTTACATATATATATTAGTATTA
Found at i:102338 original size:63 final size:63
Alignment explanation
Indices: 102239--102427 Score: 351
Period size: 63 Copynumber: 3.0 Consensus size: 63
102229 TTGCTAAAAG
* *
102239 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTGAAAAACATTCAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
*
102302 GGGTAAACTTCATTTTGTCTCCCTCTGTTTTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
102365 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
102428 TAATTCCCTT
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 122 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (63 bp):
GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTTAATTTGGTCCCCAAATCGGTT
Found at i:102743 original size:8 final size:8
Alignment explanation
Indices: 102730--102756 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
102720 TACCTATCTA
102730 TTTATATT
1 TTTATATT
102738 TTTATATT
1 TTTATATT
102746 TTTATATT
1 TTTATATT
102754 TTT
1 TTT
102757 TTCTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTATATT
Found at i:109234 original size:22 final size:22
Alignment explanation
Indices: 109204--109248 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
109194 ATTAACAATA
* *
109204 AGTTGATCTTGTGAGATAAGAC
1 AGTTAATCTAGTGAGATAAGAC
109226 AGTTAATCTAGTGAGATAAGAC
1 AGTTAATCTAGTGAGATAAGAC
109248 A
1 A
109249 TTAGATCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (22 bp):
AGTTAATCTAGTGAGATAAGAC
Found at i:115866 original size:37 final size:37
Alignment explanation
Indices: 115816--115968 Score: 306
Period size: 37 Copynumber: 4.1 Consensus size: 37
115806 ATATCCTCGG
115816 GTCAAATTTAATAATATTCTGAGTACTATAAACTTTA
1 GTCAAATTTAATAATATTCTGAGTACTATAAACTTTA
115853 GTCAAATTTAATAATATTCTGAGTACTATAAACTTTA
1 GTCAAATTTAATAATATTCTGAGTACTATAAACTTTA
115890 GTCAAATTTAATAATATTCTGAGTACTATAAACTTTA
1 GTCAAATTTAATAATATTCTGAGTACTATAAACTTTA
115927 GTCAAATTTAATAATATTCTGAGTACTATAAACTTTA
1 GTCAAATTTAATAATATTCTGAGTACTATAAACTTTA
115964 GTCAA
1 GTCAA
115969 TATCATCGTA
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 116 1.00
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (37 bp):
GTCAAATTTAATAATATTCTGAGTACTATAAACTTTA
Found at i:117801 original size:18 final size:19
Alignment explanation
Indices: 117778--117841 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 19
117768 TTTATTGAAA
*
117778 AACCGATAAA-CCGAACCG
1 AACCGAAAAACCCGAACCG
117796 AACCGAAAAACCCGAACCG
1 AACCGAAAAACCCGAACCG
117815 TTAA---AAAAA-CCGAACCG
1 --AACCGAAAAACCCGAACCG
117832 AACCGAAAAA
1 AACCGAAAAA
117842 ACCGGTTTCG
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
15 2 0.05
17 8 0.21
18 19 0.49
19 8 0.21
21 2 0.05
ACGTcount: A:0.52, C:0.30, G:0.14, T:0.05
Consensus pattern (19 bp):
AACCGAAAAACCCGAACCG
Found at i:117842 original size:19 final size:19
Alignment explanation
Indices: 117785--117845 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
117775 AAAAACCGAT
117785 AAACCGAACCGAACCGAAA
1 AAACCGAACCGAACCGAAA
* *
117804 AACCCGAACCGTTA---AAA
1 AAACCGAACCG-AACCGAAA
117821 AAACCGAACCGAACCGAAA
1 AAACCGAACCGAACCGAAA
117840 AAACCG
1 AAACCG
117846 GTTTCGGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.38
19 19 0.56
20 1 0.03
ACGTcount: A:0.51, C:0.31, G:0.15, T:0.03
Consensus pattern (19 bp):
AAACCGAACCGAACCGAAA
Found at i:119577 original size:28 final size:29
Alignment explanation
Indices: 119523--119577 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
119513 CAGTGAATAG
*
119523 TATATTTTTTGATCTAACACCGGTTAGAT
1 TATATTTTTTGATCTAACACCGCTTAGAT
119552 TATATTTTTTGATCTAACACC-CTTAG
1 TATATTTTTTGATCTAACACCGCTTAG
119578 CAGTAAAGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.45
Consensus pattern (29 bp):
TATATTTTTTGATCTAACACCGCTTAGAT
Found at i:119823 original size:12 final size:10
Alignment explanation
Indices: 119782--119822 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
119772 TTTATCGCAC
119782 CAAATTCTCT
1 CAAATTCTCT
119792 CAAATTCTCT
1 CAAATTCTCT
119802 -AAATTTCTCT
1 CAAA-TTCTCT
*
119812 CAAATACTCT
1 CAAATTCTCT
119822 C
1 C
119823 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:120085 original size:110 final size:111
Alignment explanation
Indices: 119946--120166 Score: 381
Period size: 110 Copynumber: 2.0 Consensus size: 111
119936 TGGAAATCAT
* * *
119946 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTCGTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
120011 TAATTAGTT-TTTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
120056 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
120121 TAATTAGTTGATTCATTTAATGCATGCTTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
120167 TTTTTGTAAT
Statistics
Matches: 104, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 71 0.68
111 33 0.32
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:122250 original size:26 final size:24
Alignment explanation
Indices: 122177--122250 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
122167 TTATATTTGT
122177 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
** *
122202 ATTTTTTTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
122226 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
122251 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
24 4 0.11
25 17 0.46
26 16 0.43
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.64
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:125873 original size:51 final size:51
Alignment explanation
Indices: 125797--125921 Score: 214
Period size: 51 Copynumber: 2.5 Consensus size: 51
125787 TTATACAAAA
* * *
125797 CGCGGTACCTGCCCCGCACTCTATAAAATTATGTTAGGAGTAAAGGTATGT
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
125848 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
*
125899 CGCGGTACCTGTCCCGCGCTATA
1 CGCGGTACCTGCCCCGCGCTATA
125922 CCCCTATGTG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 70 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (51 bp):
CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
Found at i:126009 original size:51 final size:51
Alignment explanation
Indices: 125933--126056 Score: 160
Period size: 51 Copynumber: 2.4 Consensus size: 51
125923 CCCTATGTGA
* * * * * *
125933 CGTATAGCGCGTTGTAGGGGCCGCGCTATA-CCCACGTGTATCTCAGATCAC
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGAGC-CAAATCAC
* *
125984 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCAT
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGAGCCAAATCAC
126035 CGTATAGCGCGGTGCAGGGGGC
1 CGTATAGCGCGGTGCAGGGGGC
126057 ACACTTTACT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 55 0.86
52 9 0.14
ACGTcount: A:0.19, C:0.29, G:0.34, T:0.19
Consensus pattern (51 bp):
CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGAGCCAAATCAC
Found at i:126557 original size:16 final size:15
Alignment explanation
Indices: 126536--126571 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
126526 TCCGAAAAAT
126536 AAATTACATTTCTTGA
1 AAATTA-ATTTCTTGA
126552 AAATT-ATTTCTTGA
1 AAATTAATTTCTTGA
126566 AAATTA
1 AAATTA
126572 TTTTATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 14 0.74
16 5 0.26
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (15 bp):
AAATTAATTTCTTGA
Found at i:126562 original size:14 final size:14
Alignment explanation
Indices: 126543--126574 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
126533 AATAAATTAC
126543 ATTTCTTGAAAATT
1 ATTTCTTGAAAATT
126557 ATTTCTTGAAAATT
1 ATTTCTTGAAAATT
126571 ATTT
1 ATTT
126575 TATAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (14 bp):
ATTTCTTGAAAATT
Found at i:126740 original size:14 final size:13
Alignment explanation
Indices: 126721--126773 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
126711 TAATTTATCT
126721 AATATTATTATTAA
1 AATATTA-TATTAA
126735 AATATTATATCTAA
1 AATATTATAT-TAA
* *
126749 AAT-TTAAATAAA
1 AATATTATATTAA
126761 AATATTAATATTA
1 AATATT-ATATTA
126774 TTATACTCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
12 5 0.16
13 10 0.31
14 17 0.53
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
AATATTATATTAA
Found at i:132742 original size:216 final size:216
Alignment explanation
Indices: 132252--133181 Score: 1604
Period size: 214 Copynumber: 4.3 Consensus size: 216
132242 ATTTTATGAA
* * * **
132252 AAATATAAATTTAAGAACTAAATTGAATAAATATGAAATTACAAATTTAAATTTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
*
132317 AC-ACATCACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACA
66 ACAACA-CACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATACA
132381 AAAAAGTACTAAATTATACCCATTT-AAAAGTTATGGGCTAATT-AAAAATATAAATAAGTAATA
130 AAAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCTAATTAAAAAATATAAATAAGTAATA
132444 AGTATGGGCCAATTTCAAATGC
195 AGTATGGGCCAATTTCAAATGC
132466 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
*
132531 ACAACACATATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATACAA
66 ACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATACAA
132596 AAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCTAATTAAAAAATATAAATAAGTAATAA
131 AAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCTAATTAAAAAATATAAATAAGTAATAA
132661 GTATGGGCCAATTTCAAATGC
196 GTATGGGCCAATTTCAAATGC
132682 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
* *
132747 ACAACACATATTGATGAGGGATCAAATTGAAATAATTTTAAATTGTGAGGTTTAAATTAATACAA
66 ACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATACAA
* * *
132812 AAAAGTACTAAATTATATCGATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGTAATAA
131 AAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCTAATTAAAAAATATAAATAAGTAATAA
* *
132877 GTATGGGCCAATTTCATATTC
196 GTATGGGCCAATTTCAAATGC
132898 AAATATAATTTTAA-GACTAAATTGAACAAATATGAAATTACAAAT-AAAATTTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
* *
132961 ACAACACACATTGATGAGGGATCAAATCAAAATAATTTTAAATTGTGAGTTTTAAATTAATACAA
66 ACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATACAA
* *
133026 AAAAGTACTAAATTATACCCA-TTAAAAAGTTATGGG-TCAATTTAAAAATATAAATAAGTAAAA
131 AAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCT-AATTAAAAAATATAAATAAGTAATA
*
133089 AGTATGGGCCAATTTCAGATGC
195 AGTATGGGCCAATTTCAAATGC
* *
133111 TAATATAATTTTAAGGACTAAATTGAACAAATATAAAATTACAAATAAAAATTTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
133176 ACAACA
66 ACAACA
133182 AAAAGGGATC
Statistics
Matches: 684, Mismatches: 26, Indels: 11
0.95 0.04 0.02
Matches are distributed among these distances:
213 71 0.10
214 271 0.40
215 76 0.11
216 266 0.39
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (216 bp):
AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
ACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATACAA
AAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCTAATTAAAAAATATAAATAAGTAATAA
GTATGGGCCAATTTCAAATGC
Found at i:133073 original size:430 final size:430
Alignment explanation
Indices: 132252--133181 Score: 1593
Period size: 430 Copynumber: 2.2 Consensus size: 430
132242 ATTTTATGAA
* * * **
132252 AAATATAAATTTAAGAACTAAATTGAATAAATATGAAATTACAAATTTAAATTTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
132317 AC-ACATCACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACA
66 ACAACATCACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACA
*
132381 AAAAAGTACTAAATTATACCCATTTAAAAGTTATGGGCTAATTAAAAATATAAATAAGTAATAAG
131 AAAAAGTACTAAATTATACCCATTTAAAAGTTATGGGCCAATTAAAAATATAAATAAGTAATAAG
132446 TATGGGCCAATTTCAAATGCAAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAA
196 TATGGGCCAATTTCAAATGCAAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAA
* *
132511 TAAAAATTTAAATAAATTAAACAACACATATTGATGAGGGATCAAATCGAAATAATTTTAAATTG
261 TAAAAATTTAAATAAATTAAACAACACACATTGATGAGGGATCAAATCAAAATAATTTTAAATTG
132576 TGAGGTTTAAATTAATACAAAAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCTAATTAA
326 TGAGGTTTAAATTAATACAAAAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCTAATT-A
*
132641 AAAATATAAATAAGTAATAAGTATGGGCCAATTTCAAATGC
390 AAAATATAAATAAGTAAAAAGTATGGGCCAATTTCAAATGC
132682 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
* * *
132747 ACAACA-CATATTGATGAGGGATCAAATTGAAATAATTTTAAATTGTGAGGTTTAAATTAATACA
66 ACAACATCACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACA
* *
132811 AAAAAGTACTAAATTATATCGATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGTAATA
131 AAAAAGTACTAAATTATACCCATTT-AAAAGTTATGGGCCAATT-AAAAATATAAATAAGTAATA
* *
132876 AGTATGGGCCAATTTCATATTCAAATATAATTTTAA-GACTAAATTGAACAAATATGAAATTACA
194 AGTATGGGCCAATTTCAAATGCAAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACA
132940 AAT-AAAATTTAAATAAATTAAACAACACACATTGATGAGGGATCAAATCAAAATAATTTTAAAT
259 AATAAAAATTTAAATAAATTAAACAACACACATTGATGAGGGATCAAATCAAAATAATTTTAAAT
*
133004 TGTGAGTTTTAAATTAATACAAAAAAGTACTAAATTATACCCA-TTAAAAAGTTATGGG-TCAAT
324 TGTGAGGTTTAAATTAATACAAAAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCT-AA-
*
133067 TTAAAAATATAAATAAGTAAAAAGTATGGGCCAATTTCAGATGC
387 TTAAAAATATAAATAAGTAAAAAGTATGGGCCAATTTCAAATGC
* *
133111 TAATATAATTTTAAGGACTAAATTGAACAAATATAAAATTACAAATAAAAATTTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
133176 ACAACA
66 ACAACA
133182 AAAAGGGATC
Statistics
Matches: 475, Mismatches: 20, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
428 1 0.00
429 126 0.27
430 243 0.51
431 51 0.11
432 54 0.11
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (430 bp):
AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
ACAACATCACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACA
AAAAAGTACTAAATTATACCCATTTAAAAGTTATGGGCCAATTAAAAATATAAATAAGTAATAAG
TATGGGCCAATTTCAAATGCAAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAA
TAAAAATTTAAATAAATTAAACAACACACATTGATGAGGGATCAAATCAAAATAATTTTAAATTG
TGAGGTTTAAATTAATACAAAAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCTAATTAA
AAATATAAATAAGTAAAAAGTATGGGCCAATTTCAAATGC
Found at i:133292 original size:2 final size:2
Alignment explanation
Indices: 133281--133443 Score: 151
Period size: 2 Copynumber: 82.0 Consensus size: 2
133271 TTAAAACAAC
133281 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
133322 TA TA TA TA -A TA TA TA TT TA TA TA AA GTA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * *
133363 AA CTA TA TA GTT TA TA TT TA TA T- TA T- TA TA TA CTA TA TA TA
1 TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * *
133404 AA CTA TA TA TA T- TA TA TA TA T- TA TG TA TA AA CTA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
133444 CCATGTATAA
Statistics
Matches: 132, Mismatches: 16, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
1 7 0.05
2 118 0.89
3 7 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:133449 original size:20 final size:20
Alignment explanation
Indices: 133416--133466 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
133406 CTATATATAT
**
133416 TATATATATTATGTATAAAC
1 TATATATACCATGTATAAAC
133436 TATATATACCATGTATAAAC
1 TATATATACCATGTATAAAC
133456 TATA-ATACCAT
1 TATATATACCAT
133467 ATAGTTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 7 0.24
20 22 0.76
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (20 bp):
TATATATACCATGTATAAAC
Found at i:133452 original size:29 final size:29
Alignment explanation
Indices: 133293--133486 Score: 50
Period size: 29 Copynumber: 6.8 Consensus size: 29
133283 TAATATATAT
* *
133293 ATATATA-TATATATATA-TATATATA-T
1 ATATATACTATATATAAACTATATATACC
* * *
133319 ATATATA-TATAATATATA-TTTATATA-A
1 ATATATACTAT-ATATAAACTATATATACC
* **
133346 AGTATATATTATATATAAACTATATAGT-TT
1 A-TATATACTATATATAAACTATATA-TACC
* * *
133376 ATATTTA-TATTATTATATACTATATATAAACT
1 ATATATACTA-TA-TATAAACTATATAT--ACC
* * * * *
133408 ATATATATTATATATATTA-TGTATAAACT
1 ATATATACTATATATA-AACTATATATACC
* *
133437 ATATATACCATGTATAAACTATA-ATACC
1 ATATATACTATATATAAACTATATATACC
* *
133465 ATATAGT-TTATATATGAACTAT
1 ATATA-TACTATATATAAACTAT
133487 TGAACTATAT
Statistics
Matches: 131, Mismatches: 22, Indels: 28
0.72 0.12 0.15
Matches are distributed among these distances:
26 10 0.08
27 15 0.11
28 34 0.26
29 36 0.27
30 14 0.11
31 9 0.07
32 11 0.08
33 2 0.02
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (29 bp):
ATATATACTATATATAAACTATATATACC
Found at i:133550 original size:13 final size:11
Alignment explanation
Indices: 133513--133570 Score: 61
Period size: 11 Copynumber: 5.5 Consensus size: 11
133503 TACATAGTTT
133513 ATTA-ATATAA
1 ATTATATATAA
133523 ATTATATAGT--
1 ATTATATA-TAA
133533 -TTATATATAA
1 ATTATATATAA
*
133543 ATTATATATGA
1 ATTATATATAA
133554 ATTATATATAA
1 ATTATATATAA
*
133565 ACTATA
1 ATTATA
133571 CAATTTATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
8 1 0.03
9 7 0.17
10 4 0.10
11 27 0.68
12 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (11 bp):
ATTATATATAA
Found at i:133570 original size:22 final size:22
Alignment explanation
Indices: 133472--133570 Score: 75
Period size: 22 Copynumber: 4.7 Consensus size: 22
133462 ACCATATAGT
*
133472 TTATATATGAAC--TAT-TGAA
1 TTATATATAAACTATATATGAA
* * **
133491 CTATATATAAACTACATAGTTTA
1 TTATATATAAACTATATA-TGAA
* *
133514 TTA-ATATAAATTATATA-G-T
1 TTATATATAAACTATATATGAA
*
133533 TTATATATAAATTATATATGAA
1 TTATATATAAACTATATATGAA
133555 TTATATATAAACTATA
1 TTATATATAAACTATA
133571 CAATTTATAT
Statistics
Matches: 61, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
19 13 0.21
20 14 0.23
21 3 0.05
22 27 0.44
23 4 0.07
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (22 bp):
TTATATATAAACTATATATGAA
Found at i:133596 original size:17 final size:17
Alignment explanation
Indices: 133576--133635 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
133566 CTATACAATT
* *
133576 TATATTTATATATTATG
1 TATATTTATAAATTATA
* *
133593 TATAATTATAAATAATA
1 TATATTTATAAATTATA
133610 TATATTGTATAAATTATA
1 TATATT-TATAAATTATA
133628 TA-ATTTAT
1 TATATTTAT
133636 TAATATAAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
16 3 0.08
17 21 0.58
18 12 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:133657 original size:22 final size:22
Alignment explanation
Indices: 133495--133570 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
133485 ATTGAACTAT
*
133495 ATATAAACTACATAGTTTATTA
1 ATATAAACTATATAGTTTATTA
*
133517 ATATAAATTATATAGTTTA-T-
1 ATATAAACTATATAGTTTATTA
* **
133537 ATATAAATTATATA-TGAATTA
1 ATATAAACTATATAGTTTATTA
133558 TATATAAACTATA
1 -ATATAAACTATA
133571 CAATTTATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
19 2 0.04
20 15 0.33
21 1 0.02
22 28 0.61
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATAAACTATATAGTTTATTA
Found at i:133801 original size:20 final size:20
Alignment explanation
Indices: 133776--133847 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
133766 TATACTAACT
133776 TATACTATATGTAAACTATA
1 TATACTATATGTAAACTATA
**
133796 TATACTATATAGTTTAC-ATA
1 TATACTATAT-GTAAACTATA
133816 TGA-ACTATATGTATAAACTATA
1 T-ATACTATATG--TAAACTATA
*
133838 TAAACTATAT
1 TATACTATAT
133848 AGTTTACATA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 1 0.02
20 21 0.50
21 9 0.21
22 11 0.26
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (20 bp):
TATACTATATGTAAACTATA
Found at i:133845 original size:42 final size:42
Alignment explanation
Indices: 133779--133872 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
133769 ACTAACTTAT
*
133779 ACTATATG--TAAACTATATATACTATATAGTTTACATATGA
1 ACTATATGTATAAACTATATAAACTATATAGTTTACATATGA
133819 ACTATATGTATAAACTATATAAACTATATAGTTTACATATGA
1 ACTATATGTATAAACTATATAAACTATATAGTTTACATATGA
* *
133861 CCTATATATATA
1 ACTATATGTATA
133873 GTTTATTAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
40 8 0.16
42 41 0.84
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (42 bp):
ACTATATGTATAAACTATATAAACTATATAGTTTACATATGA
Found at i:133865 original size:20 final size:20
Alignment explanation
Indices: 133799--133868 Score: 79
Period size: 20 Copynumber: 3.4 Consensus size: 20
133789 AACTATATAT
133799 ACTATATAGTTTACATATGA
1 ACTATATAGTTTACATATGA
* *
133819 ACTATAT-GTATAAACTATATAA
1 ACTATATAGT-T-TAC-ATATGA
133841 ACTATATAGTTTACATATGA
1 ACTATATAGTTTACATATGA
*
133861 CCTATATA
1 ACTATATA
133869 TATAGTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 2 0.05
20 20 0.49
21 4 0.10
22 13 0.32
23 2 0.05
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (20 bp):
ACTATATAGTTTACATATGA
Found at i:133868 original size:22 final size:22
Alignment explanation
Indices: 133801--133892 Score: 66
Period size: 22 Copynumber: 4.2 Consensus size: 22
133791 CTATATATAC
133801 TATATAGTTTACATATGAACTA
1 TATATAGTTTACATATGAACTA
* ** *
133823 TATGTA-TAAACTATATAAAC--
1 TATATAGTTTAC-ATATGAACTA
*
133843 TATATAGTTTACATATGACCTATA
1 TATATAGTTTACATATGAAC--TA
*
133867 TATATAGTTTA-TTAGTGAACTA
1 TATATAGTTTACATA-TGAACTA
133889 TATA
1 TATA
133893 AACTATTTAT
Statistics
Matches: 52, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
20 11 0.21
21 6 0.12
22 18 0.35
23 2 0.04
24 15 0.29
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (22 bp):
TATATAGTTTACATATGAACTA
Found at i:133889 original size:24 final size:24
Alignment explanation
Indices: 133843--133923 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 24
133833 CTATATAAAC
* *
133843 TATATAGTTTACATA-TGACCTATA
1 TATATAGTTTA-TTAGTGAACTATA
133867 TATATAGTTTATTAGTGAACTATA
1 TATATAGTTTATTAGTGAACTATA
* *
133891 TAAACTA-TTTATATAGTATATACTATA
1 TATA-TAGTTTAT-TAGT-GA-ACTATA
133918 TATATA
1 TATATA
133924 AACTATAGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
23 2 0.04
24 27 0.57
25 6 0.13
26 3 0.06
27 9 0.19
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (24 bp):
TATATAGTTTATTAGTGAACTATA
Found at i:133915 original size:18 final size:18
Alignment explanation
Indices: 133889--133923 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
133879 TAGTGAACTA
*
133889 TATAAACTATTTATATAG
1 TATAAACTATATATATAG
*
133907 TATATACTATATATATA
1 TATAAACTATATATATA
133924 AACTATAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (18 bp):
TATAAACTATATATATAG
Found at i:133930 original size:20 final size:20
Alignment explanation
Indices: 133907--133957 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
133897 ATTTATATAG
133907 TATATACTATATATATAAAC
1 TATATACTATATATATAAAC
* * *
133927 TATAGT-TTATATTTATATAC
1 TATA-TACTATATATATAAAC
*
133947 TACATACTATA
1 TATATACTATA
133958 GTTGATGTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
19 1 0.04
20 22 0.92
21 1 0.04
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (20 bp):
TATATACTATATATATAAAC
Found at i:133937 original size:27 final size:27
Alignment explanation
Indices: 133902--133960 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
133892 AAACTATTTA
* *
133902 TATAGTATATA-CTATATA-TATAAAC
1 TATAGTTTATATCTATATACTACAAAC
* *
133927 TATAGTTTATATTTATATACTACATAC
1 TATAGTTTATATCTATATACTACAAAC
133954 TATAGTT
1 TATAGTT
133961 GATGTAACAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 10 0.36
26 6 0.21
27 12 0.43
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (27 bp):
TATAGTTTATATCTATATACTACAAAC
Found at i:134597 original size:21 final size:21
Alignment explanation
Indices: 134571--134633 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
134561 ATATAAAATT
* * *
134571 TGTCCCAAAGGACCTTATGTA
1 TGTCCCGAAGGACCTCATATA
*
134592 TGTCCCGAAGGACCTCGTATA
1 TGTCCCGAAGGACCTCATATA
*
134613 TGTCCCGAAGGACTTCATATA
1 TGTCCCGAAGGACCTCATATA
134634 ACCATCGACT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (21 bp):
TGTCCCGAAGGACCTCATATA
Found at i:135417 original size:36 final size:35
Alignment explanation
Indices: 135348--135417 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 35
135338 TATTTCAAAA
** *
135348 TGGTATCGATACATGCCTTATGGTATCGGTACCCT
1 TGGTATCGATACACCCCTTATGGTATCGATACCCT
135383 TGGTATCGATACTACCCCTT-TAGGTATCGATACCC
1 TGGTATCGATAC-ACCCCTTAT-GGTATCGATACCC
135418 CTTTAATAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 13 0.43
36 17 0.57
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.33
Consensus pattern (35 bp):
TGGTATCGATACACCCCTTATGGTATCGATACCCT
Found at i:136017 original size:3 final size:3
Alignment explanation
Indices: 136009--136040 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
135999 CTCACGGCTG
136009 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
136041 GTTCTCTCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:136766 original size:44 final size:44
Alignment explanation
Indices: 136716--136809 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
136706 CAAGGAGATA
* * * * *
136716 CTTTTAGGAACATTTTATCTCTACTTTGAAACTCAATCTCTTTC
1 CTTTTAGAAACACTTTATCTCCAATTTAAAACTCAATCTCTTTC
136760 CTTTTAGAAACACTTTATCTCCAATTTAAAACTCAATCTCTTTC
1 CTTTTAGAAACACTTTATCTCCAATTTAAAACTCAATCTCTTTC
136804 CTTTTA
1 CTTTTA
136810 AGATCAATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.45
Consensus pattern (44 bp):
CTTTTAGAAACACTTTATCTCCAATTTAAAACTCAATCTCTTTC
Found at i:136769 original size:23 final size:23
Alignment explanation
Indices: 136743--136809 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
136733 TCTCTACTTT
136743 GAAACTCAATCTCTTTCCTTTTA
1 GAAACTCAATCTCTTTCCTTTTA
* * * * *
136766 GAAA--CACTTTATCTCCAATTTA
1 GAAACTCAATCTCTTTCC-TTTTA
136788 -AAACTCAATCTCTTTCCTTTTA
1 GAAACTCAATCTCTTTCCTTTTA
136810 AGATCAATTT
Statistics
Matches: 31, Mismatches: 10, Indels: 7
0.65 0.21 0.15
Matches are distributed among these distances:
21 11 0.35
22 8 0.26
23 12 0.39
ACGTcount: A:0.30, C:0.25, G:0.03, T:0.42
Consensus pattern (23 bp):
GAAACTCAATCTCTTTCCTTTTA
Found at i:141628 original size:21 final size:21
Alignment explanation
Indices: 141597--141680 Score: 114
Period size: 21 Copynumber: 4.0 Consensus size: 21
141587 ATATAAAATT
* *
141597 TGTCCCAAAGGACCTCATGTA
1 TGTCCCGAAGGACCTCATATA
* *
141618 TATCCCGAAGGACCTCGTATA
1 TGTCCCGAAGGACCTCATATA
*
141639 TGTCCCGAAGGACCTCGTATA
1 TGTCCCGAAGGACCTCATATA
*
141660 TGTCCCGAAGGACTTCATATA
1 TGTCCCGAAGGACCTCATATA
141681 ACCCTCGACT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (21 bp):
TGTCCCGAAGGACCTCATATA
Found at i:143344 original size:20 final size:20
Alignment explanation
Indices: 143316--143367 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
143306 GTTACAGTTG
* *
143316 ATATTTATATACTATATATT
1 ATATATATATACTATATAGT
* *
143336 ATATATATAAACTATGTAGT
1 ATATATATATACTATATAGT
143356 ATATATAGTATA
1 ATATATA-TATA
143368 ATTTACATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (20 bp):
ATATATATATACTATATAGT
Found at i:143429 original size:18 final size:18
Alignment explanation
Indices: 143408--143584 Score: 67
Period size: 18 Copynumber: 10.2 Consensus size: 18
143398 TTATAAAAAC
143408 TATATAAACTATAGTTTA
1 TATATAAACTATAGTTTA
143426 TATATAAACTATA---TA
1 TATATAAACTATAGTTTA
* *
143441 CTATA-ATA-GATA-TTTA
1 -TATATAAACTATAGTTTA
143457 TATATAAACTATA---TA
1 TATATAAACTATAGTTTA
* *
143472 -A-AT-TA-TATAGTTGA
1 TATATAAACTATAGTTTA
* *
143486 TATATGAATTATAGTTTA
1 TATATAAACTATAGTTTA
* * *
143504 CATATGAACTATA-TATAAA
1 TATATAAACTATAGT-T-TA
143523 CTATAGTAAAACTATATAGTTTA
1 -TATA-T-AAAC--TATAGTTTA
**
143546 TATACGAACTATAGTTTA
1 TATATAAACTATAGTTTA
* *
143564 CATATAAACTATAGTTGA
1 TATATAAACTATAGTTTA
143582 TAT
1 TAT
143585 TTATATATGA
Statistics
Matches: 118, Mismatches: 21, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
11 4 0.03
12 1 0.01
13 2 0.02
14 5 0.04
15 11 0.09
16 10 0.08
17 5 0.04
18 58 0.49
19 1 0.01
20 6 0.05
21 1 0.01
22 7 0.06
23 1 0.01
24 5 0.04
25 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (18 bp):
TATATAAACTATAGTTTA
Found at i:143471 original size:13 final size:13
Alignment explanation
Indices: 143374--143471 Score: 61
Period size: 13 Copynumber: 7.1 Consensus size: 13
143364 TATAATTTAC
*
143374 ATATGAACTATAT
1 ATATAAACTATAT
* *
143387 ATAAAAACTATTT
1 ATATAAACTATAT
*
143400 ATAAAAACTATAT
1 ATATAAACTATAT
* * * *
143413 AAACTATAGTTTAT
1 ATA-TAAACTATAT
143427 ATATAAACTATAT
1 ATATAAACTATAT
*
143440 ACTATAATAGATATTTAT
1 A-TATAA-A-CTA--TAT
143458 ATATAAACTATAT
1 ATATAAACTATAT
143471 A
1 A
143472 AATTATATAG
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
13 36 0.56
14 13 0.20
15 3 0.05
16 3 0.05
17 5 0.08
18 4 0.06
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (13 bp):
ATATAAACTATAT
Found at i:143481 original size:60 final size:60
Alignment explanation
Indices: 143321--143558 Score: 178
Period size: 60 Copynumber: 4.0 Consensus size: 60
143311 AGTTGATATT
* * * * *
143321 TATATACTATATATTATATATATAAACTATGTAGTATATATAGTATAATTTACATATGAACTATA
1 TATATAATAGATATT-TATATATAAACTA--TAGTAAAT-TA-TATAGTTTATATATGAACTATA
* *
143386 TATA-AA-A-ACTATTTATA-A-AAACTATA-TAAA--CTATAGTTTATATATAAACTATA
1 TATATAATAGA-TATTTATATATAAACTATAGTAAATTATATAGTTTATATATGAACTATA
*
143439 TACTATAATAGATATTTATATATAAACTATA-TAAATTATATAGTTGATATATGAA-T-TA
1 TA-TATAATAGATATTTATATATAAACTATAGTAAATTATATAGTTTATATATGAACTATA
* * * *
143497 TAGTTTACATATGA-A-CTATATATAAACTATAGTAAAACTATATAGTTTATATACGAACTATA
1 TA-TATA-ATA-GATATTTATATATAAACTATAGT-AAATTATATAGTTTATATATGAACTATA
143559 GTTTACATAT
Statistics
Matches: 143, Mismatches: 15, Indels: 33
0.75 0.08 0.17
Matches are distributed among these distances:
53 21 0.15
54 2 0.01
55 2 0.01
56 9 0.06
57 5 0.03
58 36 0.25
59 6 0.04
60 43 0.30
61 2 0.01
62 7 0.05
63 5 0.03
64 1 0.01
65 4 0.03
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.40
Consensus pattern (60 bp):
TATATAATAGATATTTATATATAAACTATAGTAAATTATATAGTTTATATATGAACTATA
Found at i:143548 original size:31 final size:30
Alignment explanation
Indices: 143399--143560 Score: 108
Period size: 31 Copynumber: 5.5 Consensus size: 30
143389 AAAAACTATT
*
143399 TATAAAAACTATA-TAAAC--TATAGTTTA
1 TATATAAACTATAGTAAACTATATAGTTTA
143426 TATATAAACTATA-T--ACTATAATAGATATTTA
1 TATATAAACTATAGTAAACTAT-ATAG---TTTA
* *
143457 TATATAAACTATA-TAAATTATATAGTTGA
1 TATATAAACTATAGTAAACTATATAGTTTA
* * ** **
143486 TATATGAATTATAGTTTAC-ATAT-GAACTA
1 TATATAAACTATAGTAAACTATATAG-TTTA
143515 TATATAAACTATAGTAAAACTATATAGTTTA
1 TATATAAACTATAGT-AAACTATATAGTTTA
**
143546 TATACGAACTATAGT
1 TATATAAACTATAGT
143561 TTACATATAA
Statistics
Matches: 103, Mismatches: 19, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
25 2 0.02
27 14 0.14
28 5 0.05
29 32 0.31
30 4 0.04
31 37 0.36
32 5 0.05
33 4 0.04
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (30 bp):
TATATAAACTATAGTAAACTATATAGTTTA
Found at i:143559 original size:60 final size:58
Alignment explanation
Indices: 143455--143576 Score: 181
Period size: 60 Copynumber: 2.1 Consensus size: 58
143445 AATAGATATT
* * * *
143455 TATATATAAACTATATAAATTATATAGTTGATATATGAATTATAGTTTACATATGAAC
1 TATATATAAACTATATAAACTATATAGTTGATATACGAACTATAGTTTACATATAAAC
*
143513 TATATATAAACTATAGTAAAACTATATAGTTTATATACGAACTATAGTTTACATATAAAC
1 TATATATAAACTATA-T-AAACTATATAGTTGATATACGAACTATAGTTTACATATAAAC
143573 TATA
1 TATA
143577 GTTGATATTT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 15 0.26
59 1 0.02
60 41 0.72
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (58 bp):
TATATATAAACTATATAAACTATATAGTTGATATACGAACTATAGTTTACATATAAAC
Found at i:143655 original size:24 final size:24
Alignment explanation
Indices: 143628--143677 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
143618 ATATATAAAC
143628 TATATAGTTTACATA-TGAACTATA
1 TATATAGTTTA-ATAGTGAACTATA
*
143652 TATATAGTTTATTAGTGAACTATA
1 TATATAGTTTAATAGTGAACTATA
143676 TA
1 TA
143678 AACTATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (24 bp):
TATATAGTTTAATAGTGAACTATA
Found at i:143737 original size:24 final size:22
Alignment explanation
Indices: 143703--143761 Score: 82
Period size: 24 Copynumber: 2.6 Consensus size: 22
143693 ATATACTACA
143703 TATATAAACTATAGTTTATATT
1 TATATAAACTATAGTTTATATT
*
143725 TATATACATACTATAGTTTATATA
1 TATATA-A-ACTATAGTTTATATT
*
143749 AATATAAACTATA
1 TATATAAACTATA
143762 TATACTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 12 0.36
23 2 0.06
24 19 0.58
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (22 bp):
TATATAAACTATAGTTTATATT
Found at i:143770 original size:22 final size:22
Alignment explanation
Indices: 143702--143772 Score: 72
Period size: 24 Copynumber: 3.1 Consensus size: 22
143692 TATATACTAC
*
143702 ATATATAAACTATAGTTTATAT
1 ATATATAAACTATAGTATATAT
* *
143724 TTATATACATACTATAGTTTATAT
1 ATATATA-A-ACTATAGTATATAT
*
143748 AAATATAAACTATA-TATACTAT
1 ATATATAAACTATAGTATA-TAT
143770 ATA
1 ATA
143773 GTAATTTACA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
21 3 0.07
22 17 0.41
23 2 0.05
24 19 0.46
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (22 bp):
ATATATAAACTATAGTATATAT
Found at i:143822 original size:27 final size:25
Alignment explanation
Indices: 143792--143848 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 25
143782 ATATGAACTA
143792 TATATAAAAACTATATAAACTATAGTT
1 TATATAAAAACTATAT--ACTATAGTT
*
143819 TATATATAAACTATATACTATAGTT
1 TATATAAAAACTATATACTATAGTT
*
143844 GATAT
1 TATAT
143849 TTATATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 13 0.46
27 15 0.54
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (25 bp):
TATATAAAAACTATATACTATAGTT
Found at i:143853 original size:27 final size:26
Alignment explanation
Indices: 143792--143864 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 26
143782 ATATGAACTA
*
143792 TATATAAAAACTATATAAACTATAGTT
1 TATATATAAACTATAT-AACTATAGTT
143819 TATATATAAACTATAT-ACTATAGTT
1 TATATATAAACTATATAACTATAGTT
* * *
143844 GATATTTATA-TATA-AACTATA
1 TATATATAAACTATATAACTATA
143865 TAAATTATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 10 0.24
25 16 0.39
27 15 0.37
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (26 bp):
TATATATAAACTATATAACTATAGTT
Found at i:143903 original size:18 final size:18
Alignment explanation
Indices: 143872--144058 Score: 79
Period size: 18 Copynumber: 9.2 Consensus size: 18
143862 ATATAAATTA
* *
143872 TATAGTTGATATATGAAC
1 TATAGTTTACATATGAAC
143890 TATAGTTTACATATGATAAGAAC
1 TATAGTTTAC--AT-AT--GAAC
* *
143913 TATAGTTAAACTATAGTTAAAC
1 TATAGTT-TAC-ATA--TGAAC
* *
143935 TATATAGTTTATATACGAAC
1 TAT--AGTTTACATATGAAC
* *
143955 TATAGTCTACATATAAAC
1 TATAGTTTACATATGAAC
143973 TATAGTTGATATTTACATATGAAC
1 TATA---G-T--TTACATATGAAC
143997 TATAGTTTACATATGAAC
1 TATAGTTTACATATGAAC
* *
144015 TATA-TATAAACTATATAAAC
1 TATAGT-T-TAC-ATATGAAC
144035 TATATAGTTTACATATGAAC
1 --TATAGTTTACATATGAAC
144055 TATA
1 TATA
144059 TATATAGTTT
Statistics
Matches: 129, Mismatches: 18, Indels: 44
0.68 0.09 0.23
Matches are distributed among these distances:
17 1 0.01
18 44 0.34
19 2 0.02
20 23 0.18
21 6 0.05
22 16 0.12
23 16 0.12
24 21 0.16
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (18 bp):
TATAGTTTACATATGAAC
Found at i:143943 original size:13 final size:11
Alignment explanation
Indices: 143910--143938 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
143900 ATATGATAAG
143910 AACTATAGTTA
1 AACTATAGTTA
143921 AACTATAGTTA
1 AACTATAGTTA
143932 AACTATA
1 AACTATA
143939 TAGTTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (11 bp):
AACTATAGTTA
Found at i:144059 original size:20 final size:20
Alignment explanation
Indices: 143932--144060 Score: 106
Period size: 20 Copynumber: 6.5 Consensus size: 20
143922 ACTATAGTTA
* *
143932 AACTATATAGTTTATATACG
1 AACTATATAGTTTACATATG
* *
143952 AAC--TATAGTCTACATATA
1 AACTATATAGTTTACATATG
*
143970 AACTATAGTTGATATTTACATATG
1 AACTATA--T-A-GTTTACATATG
143994 AAC--TATAGTTTACATATG
1 AACTATATAGTTTACATATG
** *
144012 AACTATATA-TAAACTATATA
1 AACTATATAGTTTAC-ATATG
144032 AACTATATAGTTTACATATG
1 AACTATATAGTTTACATATG
144052 AACTATATA
1 AACTATATA
144061 TATAGTTTAT
Statistics
Matches: 85, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
18 27 0.32
19 4 0.05
20 36 0.42
21 3 0.04
22 3 0.04
23 1 0.01
24 11 0.13
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (20 bp):
AACTATATAGTTTACATATG
Found at i:144077 original size:24 final size:24
Alignment explanation
Indices: 144035--144115 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 24
144025 CTATATAAAC
*
144035 TATATAGTTTACATA-TGAACTATA
1 TATATAGTTTA-TTAGTGAACTATA
*
144059 TATATAGTTTATTAGTGAACTAAA
1 TATATAGTTTATTAGTGAACTATA
* *
144083 TAAACTA-TTTATATAGTATATACTATA
1 TATA-TAGTTTAT-TAGT-GA-ACTATA
144110 TATATA
1 TATATA
144116 AACTATAGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
23 2 0.04
24 27 0.59
25 6 0.13
26 3 0.07
27 8 0.17
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.43
Consensus pattern (24 bp):
TATATAGTTTATTAGTGAACTATA
Found at i:144129 original size:27 final size:27
Alignment explanation
Indices: 144094--144167 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
144084 AAACTATTTA
* *
144094 TATAGTATATA-CTATATA-TATAAAC
1 TATAGTTTATATCTATATACTACAAAC
* *
144119 TATAGTTTATATTTATATACTACATAC
1 TATAGTTTATATCTATATACTACAAAC
*
144146 TATAGTTTATATTTATATACTA
1 TATAGTTTATATCTATATACTA
144168 TATATTATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.23
26 6 0.14
27 27 0.63
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (27 bp):
TATAGTTTATATCTATATACTACAAAC
Found at i:144175 original size:20 final size:20
Alignment explanation
Indices: 144088--144211 Score: 92
Period size: 20 Copynumber: 6.2 Consensus size: 20
144078 CTAAATAAAC
*
144088 TATTTATATAGTATATACTA
1 TATTTATATACTATATACTA
* * *
144108 TATATATAAACTATAGT-TTA
1 TATTTATATACTATA-TACTA
*
144128 TATTTATATACTACATACTA
1 TATTTATATACTATATACTA
*
144148 TAGTTTATAT-TTATATACTA
1 TA-TTTATATACTATATACTA
* *
144168 TATATTATATAATATA-ATTTA
1 TAT-TTATATACTATATA-CTA
* * *
144189 TACTTATATAATTTATACTA
1 TATTTATATACTATATACTA
144209 TAT
1 TAT
144212 AAATTCAAAA
Statistics
Matches: 81, Mismatches: 16, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
19 2 0.02
20 62 0.77
21 17 0.21
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.50
Consensus pattern (20 bp):
TATTTATATACTATATACTA
Found at i:144176 original size:27 final size:27
Alignment explanation
Indices: 144106--144176 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
144096 TAGTATATAC
*
144106 TATATA-TATAAACTATAGTTTATATT
1 TATATACTATATACTATAGTTTATATT
*
144132 TATATACTACATACTATAGTTTATATT
1 TATATACTATATACTATAGTTTATATT
*
144159 TATATACTATATATTATA
1 TATATACTATATACTATA
144177 TAATATAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 6 0.15
27 34 0.85
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (27 bp):
TATATACTATATACTATAGTTTATATT
Found at i:144183 original size:27 final size:27
Alignment explanation
Indices: 144126--144211 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 27
144116 AACTATAGTT
* * *
144126 TATATTTATATACTACATACTATAGT-T
1 TATATTTATATACTATATATTATA-TAA
144153 TATATTTATATACTATATATTATATAA
1 TATATTTATATACTATATATTATATAA
* *
144180 TATAATT-TATACTTATATAATT-TATAC
1 TATATTTATATAC-TATAT-ATTATATAA
144207 TATAT
1 TATAT
144212 AAATTCAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
26 6 0.12
27 41 0.82
28 3 0.06
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (27 bp):
TATATTTATATACTATATATTATATAA
Found at i:144189 original size:34 final size:34
Alignment explanation
Indices: 144088--144213 Score: 130
Period size: 34 Copynumber: 3.7 Consensus size: 34
144078 CTAAATAAAC
* **
144088 TATTTATATAGTATATACTATAT-ATATAAACTA
1 TATTTATATAATATATACTATATAATATAATTTA
* * * *
144121 TAGTTTATAT-TTATATACTACATACTATAGTTTA
1 TA-TTTATATAATATATACTATATAATATAATTTA
* *
144155 TATTTATATACTATATATTATATAATATAATTTA
1 TATTTATATAATATATACTATATAATATAATTTA
* *
144189 TACTTATATAATTTATACTATATAA
1 TATTTATATAATATATACTATATAA
144214 ATTCAAAATA
Statistics
Matches: 75, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
33 20 0.27
34 55 0.73
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.49
Consensus pattern (34 bp):
TATTTATATAATATATACTATATAATATAATTTA
Found at i:144213 original size:14 final size:14
Alignment explanation
Indices: 144161--144213 Score: 67
Period size: 15 Copynumber: 3.9 Consensus size: 14
144151 TTTATATTTA
144161 TATACTATAT-A-T
1 TATACTATATAATT
144173 TATA-TAATATAATT
1 TATACT-ATATAATT
144187 TATACTTATATAATT
1 TATAC-TATATAATT
144202 TATACTATATAA
1 TATACTATATAA
144214 ATTCAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.03
12 8 0.22
13 1 0.03
14 12 0.33
15 13 0.36
16 1 0.03
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (14 bp):
TATACTATATAATT
Found at i:144232 original size:7 final size:7
Alignment explanation
Indices: 144091--144212 Score: 62
Period size: 7 Copynumber: 18.0 Consensus size: 7
144081 AATAAACTAT
144091 TTATATA
1 TTATATA
*
144098 GTATATA
1 TTATATA
*
144105 CTATATA
1 TTATATA
*
144112 -TATAAA
1 TTATATA
*
144118 CTATAGT-
1 TTATA-TA
144125 TTATAT-
1 TTATATA
144131 TTATATA
1 TTATATA
* *
144138 CTACATA
1 TTATATA
*
144145 CTATAGT-
1 TTATA-TA
144152 TTATAT-
1 TTATATA
144158 TTATATA
1 TTATATA
*
144165 CTATATA
1 TTATATA
144172 TTATATA
1 TTATATA
*
144179 ATATA-A
1 TTATATA
144185 TT-TATA
1 TTATATA
144191 CTTATATAA
1 -TTATAT-A
144200 TT-TATA
1 TTATATA
*
144206 CTATATA
1 TTATATA
144213 AATTCAAAAT
Statistics
Matches: 91, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
5 2 0.02
6 24 0.26
7 58 0.64
8 6 0.07
9 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (7 bp):
TTATATA
Found at i:144300 original size:18 final size:16
Alignment explanation
Indices: 144277--144509 Score: 65
Period size: 18 Copynumber: 13.9 Consensus size: 16
144267 ATACACGATT
144277 TATATAGTATATACTAC
1 TATATAGTATATA-TAC
144294 ATATATAGTTTATATATAC
1 -TATATAG--TATATATAC
*
144313 TATATAGTTTACATATGAAC
1 TATATAG--TATATAT--AC
*
144333 TATATA-TA-A-AAAC
1 TATATAGTATATATAC
*
144346 TATATA-TATA-A-AG
1 TATATAGTATATATAC
* *
144359 TATATGGTATATACAAAC
1 TATATAGTATAT--ATAC
* * *
144377 TATTTATTATATAGTTC
1 TATATAGTATATA-TAC
144394 -AT-TAGTATATATAAAC
1 TATATAGTATATAT--AC
* * *
144410 TATACATTATATAGTTC
1 TATATAGTATATA-TAC
144427 -AT-TAGTATATATAAAC
1 TATATAGTATATAT--AC
*
144443 TATATGGTATATATAAAC
1 TATATAGTATATAT--AC
* * *
144461 TATACATTATATATAG
1 TATATAGTATATATAC
144477 T-TCATTAGTATATATAAC
1 TAT-A-TAGTATATAT-AC
144495 TATATAGTATATATA
1 TATATAGTATATATA
144510 AACTATATTT
Statistics
Matches: 165, Mismatches: 26, Indels: 50
0.68 0.11 0.21
Matches are distributed among these distances:
13 16 0.10
14 8 0.05
15 17 0.10
16 12 0.07
17 27 0.16
18 66 0.40
19 5 0.03
20 14 0.08
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (16 bp):
TATATAGTATATATAC
Found at i:144348 original size:13 final size:13
Alignment explanation
Indices: 144330--144363 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
144320 TTTACATATG
144330 AACTATATATAAA
1 AACTATATATAAA
*
144343 AACTATATATATA
1 AACTATATATAAA
*
144356 AAGTATAT
1 AACTATAT
144364 GGTATATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (13 bp):
AACTATATATAAA
Found at i:144447 original size:84 final size:83
Alignment explanation
Indices: 144348--144507 Score: 241
Period size: 84 Copynumber: 1.9 Consensus size: 83
144338 ATAAAAACTA
*
144348 TATATATAAAGTATATGGTATATACAAACTAT-TTATTATATAGTTCATTAGTATATATAAACTA
1 TATATATAAACTATATGGTATATACAAACTATATTA-TATATAGTTCATTAGTATATAT-AACTA
*
144412 TACATTATATAGTTCATTAG
64 TACAGTATATAGTTCATTAG
*
144432 TATATATAAACTATATGGTATATATAAACTATACATTATATATAGTTCATTAGTATATATAACTA
1 TATATATAAACTATATGGTATATACAAACTAT--ATTATATATAGTTCATTAGTATATATAACTA
*
144497 TATAGTATATA
64 TACAGTATATA
144508 TAAACTATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
84 30 0.43
85 14 0.20
86 22 0.32
87 3 0.04
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.42
Consensus pattern (83 bp):
TATATATAAACTATATGGTATATACAAACTATATTATATATAGTTCATTAGTATATATAACTATA
CAGTATATAGTTCATTAG
Found at i:144453 original size:51 final size:51
Alignment explanation
Indices: 144396--144550 Score: 251
Period size: 52 Copynumber: 3.0 Consensus size: 51
144386 TATAGTTCAT
144396 TAGTATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTATA
1 TAGTATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTATA
*
144447 TGGTATATATAAACTATACATTATATATAGTTCATTAGTATATAT-AACTATA
1 TAGTATATATAAACTATACA-T-TATATAGTTCATTAGTATATATAAACTATA
* *
144499 TAGTATATATAAACTATA-TTTATATAGTTCATTAGTATATATAACCTATA
1 TAGTATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTATA
144549 TA
1 TA
144551 TTAATTTATT
Statistics
Matches: 97, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
49 22 0.23
50 9 0.09
51 19 0.20
52 25 0.26
53 22 0.23
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (51 bp):
TAGTATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTATA
Found at i:144454 original size:33 final size:33
Alignment explanation
Indices: 144335--144553 Score: 168
Period size: 33 Copynumber: 6.6 Consensus size: 33
144325 ATATGAACTA
* * *
144335 TATATAAAAACTATATA-TATAAAG-T-ATATGG
1 TATATATAAACTATATATTATATAGTTCAT-TAG
* *
144366 TATATACAAACTATTTATTATATAGTTCATTAG
1 TATATATAAACTATATATTATATAGTTCATTAG
*
144399 TATATATAAACTATACATTATATAGTTCATTAG
1 TATATATAAACTATATATTATATAGTTCATTAG
* *
144432 TATATATAAACTATATGGTATATATAAACTATACATTA-
1 TATATATAAACTATA---TAT-TATATAGT-T-CATTAG
** **
144470 TATATAGTTCA-T-TAGTA-TATATAACT-ATATAG
1 TATATA-TAAACTATA-TATTATATAGTTCAT-TAG
144502 TATATATAAACTATAT-TTATATAGTTCATTAG
1 TATATATAAACTATATATTATATAGTTCATTAG
*
144534 TATATATAACCTATATATTA
1 TATATATAAACTATATATTA
144554 ATTTATTAAT
Statistics
Matches: 151, Mismatches: 20, Indels: 32
0.74 0.10 0.16
Matches are distributed among these distances:
30 2 0.01
31 19 0.13
32 40 0.26
33 60 0.40
34 2 0.01
35 3 0.02
36 2 0.01
37 8 0.05
38 8 0.05
39 7 0.05
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.42
Consensus pattern (33 bp):
TATATATAAACTATATATTATATAGTTCATTAG
Found at i:144490 original size:17 final size:18
Alignment explanation
Indices: 144384--144541 Score: 63
Period size: 17 Copynumber: 9.3 Consensus size: 18
144374 AACTATTTAT
144384 TATATAGTTCAT-TAGTA
1 TATATAGTTCATATAGTA
** *
144401 TATATA-AAC-TATA-CA
1 TATATAGTTCATATAGTA
144416 TTATATAGTTCAT-TAGTA
1 -TATATAGTTCATATAGTA
** *
144434 TATATA-AACTATATGGTA
1 TATATAGTTC-ATATAGTA
** * *
144452 TATATA-AACTATACATTA
1 TATATAGTTC-ATATAGTA
144470 TATATAGTTCAT-TAGTA
1 TATATAGTTCATATAGTA
**
144487 TATATAACT-ATATAGTA
1 TATATAGTTCATATAGTA
** *
144504 TATATA-AAC-TATA-TT
1 TATATAGTTCATATAGTA
144519 TATATAGTTCAT-TAGTA
1 TATATAGTTCATATAGTA
144536 TATATA
1 TATATA
144542 ACCTATATAT
Statistics
Matches: 104, Mismatches: 24, Indels: 26
0.68 0.16 0.17
Matches are distributed among these distances:
15 9 0.09
16 19 0.18
17 46 0.44
18 29 0.28
19 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (18 bp):
TATATAGTTCATATAGTA
Found at i:144515 original size:18 final size:18
Alignment explanation
Indices: 144348--144517 Score: 110
Period size: 18 Copynumber: 9.9 Consensus size: 18
144338 ATAAAAACTA
* *
144348 TATATATAAAGTATATGG
1 TATATATAAACTATATAG
* *
144366 TATATACAAACTATTTA-
1 TATATATAAACTATATAG
**
144383 T-TATAT-AGTTCAT-TAG
1 TATATATAAACT-ATATAG
*
144399 TATATATAAACTATACA-
1 TATATATAAACTATATAG
**
144416 T-TATAT-AGTTCAT-TAG
1 TATATATAAACT-ATATAG
*
144432 TATATATAAACTATATGG
1 TATATATAAACTATATAG
* *
144450 TATATATAAACTATACAT
1 TATATATAAACTATATAG
**
144468 TATATAT-AGTTCAT-TAG
1 TATATATAAACT-ATATAG
144485 TATATAT-AACTATATAG
1 TATATATAAACTATATAG
144502 TATATATAAACTATAT
1 TATATATAAACTATAT
144518 TTATATAGTT
Statistics
Matches: 114, Mismatches: 25, Indels: 26
0.69 0.15 0.16
Matches are distributed among these distances:
15 7 0.06
16 17 0.15
17 38 0.33
18 52 0.46
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (18 bp):
TATATATAAACTATATAG
Found at i:144683 original size:61 final size:61
Alignment explanation
Indices: 144608--144745 Score: 215
Period size: 61 Copynumber: 2.3 Consensus size: 61
144598 ATATAAGGAT
* *
144608 TAAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTG-TAACATTAAATTTGGAC
1 TAAATTGAACAAATTTGAAATATGAAGCTTAAATTAATAAATCGCT-ACATTAAATTTGGAC
* * *
144669 TAAATTGAAGAAATTTGAAATATGAAGCTTAAATTAATATATCGCTTCATTAAATTTGGAC
1 TAAATTGAACAAATTTGAAATATGAAGCTTAAATTAATAAATCGCTACATTAAATTTGGAC
144730 TAAATTGAACAAATTT
1 TAAATTGAACAAATTT
144746 AAAACTAGGA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
61 69 0.99
62 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (61 bp):
TAAATTGAACAAATTTGAAATATGAAGCTTAAATTAATAAATCGCTACATTAAATTTGGAC
Found at i:145361 original size:6 final size:6
Alignment explanation
Indices: 145352--145428 Score: 73
Period size: 6 Copynumber: 12.7 Consensus size: 6
145342 CCCTAACCTT
* * * **
145352 AACCCG AACCCA AACCCA AACCCA AACCCA AACCCG AACCTA AAATCA
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* * *
145400 AATCCTA AACCCA AACCCG AACCCG AACC
1 AA-CCCA AACCCA AACCCA AACCCA AACC
145429 TGAATCTGAA
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
6 55 0.95
7 3 0.05
ACGTcount: A:0.45, C:0.44, G:0.05, T:0.05
Consensus pattern (6 bp):
AACCCA
Found at i:145446 original size:43 final size:42
Alignment explanation
Indices: 145363--145464 Score: 107
Period size: 43 Copynumber: 2.4 Consensus size: 42
145353 ACCCGAACCC
145363 AAACCCAAACCCAAACCCAAACCCGAACCTAAAATCAAATCCT
1 AAACCCAAACCCAAACCCAAACCCGAACCTAAAATCAAAT-CT
* * * * * *
145406 AAACCCAAACCCGAACCCGAACCTGAATCT-GAACCTAAATCT
1 AAACCCAAACCCAAACCCAAACCCGAACCTAAAATC-AAATCT
**
145448 AAACCTGAACCCAAACC
1 AAACCCAAACCCAAACC
145465 TAAATACAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
42 19 0.39
43 30 0.61
ACGTcount: A:0.45, C:0.38, G:0.06, T:0.11
Consensus pattern (42 bp):
AAACCCAAACCCAAACCCAAACCCGAACCTAAAATCAAATCT
Done.