Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001362.1 Hibiscus syriacus cultivar Beakdansim tig00002655_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: 681426
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 1 of 3
Found at i:9852 original size:21 final size:21
Alignment explanation
Indices: 9808--9858 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
9798 CACAGAGTCT
***
9808 GTTCACATTCACTGATTTGGA
1 GTTCACATTCACTGATTCAAA
9829 GTTCACATTCACTGATTCAAA
1 GTTCACATTCACTGATTCAAA
9850 GTTCACATT
1 GTTCACATT
9859 TTCATATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (21 bp):
GTTCACATTCACTGATTCAAA
Found at i:10340 original size:54 final size:54
Alignment explanation
Indices: 10252--10396 Score: 197
Period size: 54 Copynumber: 2.7 Consensus size: 54
10242 GATACTTCCC
*
10252 TTCAAGGGTATCGATACCTCCTCATGGTATCGATACCGATAT-A-ACATTCGATGT
1 TTCAAGGGTATCGATACCTCCTCAAGGTATCGATACC-A-ATCAGACATTCGATGT
* *
10306 TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAATCAGGCATTCGATGT
1 TTCAAGGGTATCGATACCTCCTCAAGGTATCGATACCAATCAGACATTCGATGT
*
10360 TTTAAGGGTATCGATACCATCCTTC-AGGTATCGATAC
1 TTCAAGGGTATCGATACC-TCC-TCAAGGTATCGATAC
10397 TACCCTTACA
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
52 2 0.02
53 2 0.02
54 62 0.76
55 14 0.17
56 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (54 bp):
TTCAAGGGTATCGATACCTCCTCAAGGTATCGATACCAATCAGACATTCGATGT
Found at i:10403 original size:20 final size:21
Alignment explanation
Indices: 10366--10468 Score: 74
Period size: 21 Copynumber: 5.0 Consensus size: 21
10356 ATGTTTTAAG
*
10366 GGTATCGATACCATCCTT-CA
1 GGTATCGATACCACCCTTACA
*
10386 GGTATCGATACTACCCTTACA
1 GGTATCGATACCACCCTTACA
* *
10407 -ATATCGATA-CA-TCTTCAACA
1 GGTATCGATACCACCCTT--ACA
*
10427 GGTATCGATA-C-CTCTTCAACA
1 GGTATCGATACCACCCTT--ACA
*
10448 GGTATCGATACTACCCTTACA
1 GGTATCGATACCACCCTTACA
10469 ACATATTCAT
Statistics
Matches: 68, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
18 3 0.04
19 1 0.01
20 27 0.40
21 33 0.49
23 4 0.06
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (21 bp):
GGTATCGATACCACCCTTACA
Found at i:10434 original size:21 final size:21
Alignment explanation
Indices: 10408--10458 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
10398 ACCCTTACAA
10408 TATCGATACATCTTCAACAGG
1 TATCGATACATCTTCAACAGG
*
10429 TATCGATACCTCTTCAACAGG
1 TATCGATACATCTTCAACAGG
10450 TATCGATAC
1 TATCGATAC
10459 TACCCTTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (21 bp):
TATCGATACATCTTCAACAGG
Found at i:26236 original size:17 final size:17
Alignment explanation
Indices: 26214--26248 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
26204 AATTTCTAAT
*
26214 CATACCTGTGCCGGACA
1 CATACCTGTGCCCGACA
26231 CATACCTGTGCCCGACA
1 CATACCTGTGCCCGACA
26248 C
1 C
26249 TTGCACCCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.20, T:0.17
Consensus pattern (17 bp):
CATACCTGTGCCCGACA
Found at i:27896 original size:59 final size:59
Alignment explanation
Indices: 27833--27954 Score: 181
Period size: 59 Copynumber: 2.1 Consensus size: 59
27823 TAGAGAAATA
* * *
27833 GTATTCTGCAGTCTATATGAATACATTCTCGTGAATTTCTTATTTCCGGCCAGTATCTT
1 GTATTCTGCAGTCTATATGAATACATCCACATGAATTTCTTATTTCCGGCCAGTATCTT
* * **
27892 GTATTCTGCAGTTTATATGAATACATCCACATGAATTTCTTATTTCTGGCTGGTATCTT
1 GTATTCTGCAGTCTATATGAATACATCCACATGAATTTCTTATTTCCGGCCAGTATCTT
27951 GTAT
1 GTAT
27955 CCTACCACAG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (59 bp):
GTATTCTGCAGTCTATATGAATACATCCACATGAATTTCTTATTTCCGGCCAGTATCTT
Found at i:29159 original size:49 final size:49
Alignment explanation
Indices: 29079--29179 Score: 130
Period size: 49 Copynumber: 2.1 Consensus size: 49
29069 AATTCCGGCA
* * * *
29079 TCCTGTACAGCAACTTTTAAGAATTCGGGCCAGATGTACGTTTTTCTTC
1 TCCTGTACAGCAACGTTTAAAAACTCAGGCCAGATGTACGTTTTTCTTC
* * * *
29128 TCCTGTCCGGCAACGTTTAAAAACTCAGGCCAGGTGTTCGTTTTTCTTC
1 TCCTGTACAGCAACGTTTAAAAACTCAGGCCAGATGTACGTTTTTCTTC
29177 TCC
1 TCC
29180 GATCGTCGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.36
Consensus pattern (49 bp):
TCCTGTACAGCAACGTTTAAAAACTCAGGCCAGATGTACGTTTTTCTTC
Found at i:42042 original size:24 final size:24
Alignment explanation
Indices: 42007--42072 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 24
41997 TGGCGGGAAG
*
42007 TTCGTTCATTTATGTTTATTTATA
1 TTCGTTCGTTTATGTTTATTTATA
** *
42031 TTCGTTCGTTTATGTTCGTTTATG
1 TTCGTTCGTTTATGTTTATTTATA
* *
42055 TGCTTTCGTTTATGTTTA
1 TTCGTTCGTTTATGTTTA
42073 GCCTAATATC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.14, C:0.11, G:0.15, T:0.61
Consensus pattern (24 bp):
TTCGTTCGTTTATGTTTATTTATA
Found at i:42253 original size:10 final size:10
Alignment explanation
Indices: 42238--42262 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42228 AATATTTTCA
42238 TTTATGTTTG
1 TTTATGTTTG
42248 TTTATGTTTG
1 TTTATGTTTG
42258 TTTAT
1 TTTAT
42263 TGTGTTCGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.00, G:0.16, T:0.72
Consensus pattern (10 bp):
TTTATGTTTG
Found at i:47133 original size:18 final size:18
Alignment explanation
Indices: 47110--47158 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
47100 GTAATAAAAT
*
47110 ATTAAAATAATAAAAGCG
1 ATTAAAATAATAAAAGCA
47128 ATT-AAATAAGTAAAAGCA
1 ATTAAAATAA-TAAAAGCA
*
47146 ATTAAAGTAATAA
1 ATTAAAATAATAA
47159 TAAGAAGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.22
18 16 0.59
19 5 0.19
ACGTcount: A:0.61, C:0.04, G:0.10, T:0.24
Consensus pattern (18 bp):
ATTAAAATAATAAAAGCA
Found at i:58567 original size:146 final size:146
Alignment explanation
Indices: 58303--58597 Score: 590
Period size: 146 Copynumber: 2.0 Consensus size: 146
58293 AAGATACGTG
58303 CTAATGTAGACTGCTTTTTATTGACATAGAATCCACTTGTCTTCAATGTCATTTTCTCCCTTTCT
1 CTAATGTAGACTGCTTTTTATTGACATAGAATCCACTTGTCTTCAATGTCATTTTCTCCCTTTCT
58368 GATTTCATCTTTTTTCCCCTTTAAAGATGAAAGTTTTATAATTTTATATATGTATCATGTCAATG
66 GATTTCATCTTTTTTCCCCTTTAAAGATGAAAGTTTTATAATTTTATATATGTATCATGTCAATG
58433 CTGTAATTATCATTCT
131 CTGTAATTATCATTCT
58449 CTAATGTAGACTGCTTTTTATTGACATAGAATCCACTTGTCTTCAATGTCATTTTCTCCCTTTCT
1 CTAATGTAGACTGCTTTTTATTGACATAGAATCCACTTGTCTTCAATGTCATTTTCTCCCTTTCT
58514 GATTTCATCTTTTTTCCCCTTTAAAGATGAAAGTTTTATAATTTTATATATGTATCATGTCAATG
66 GATTTCATCTTTTTTCCCCTTTAAAGATGAAAGTTTTATAATTTTATATATGTATCATGTCAATG
58579 CTGTAATTATCATTCT
131 CTGTAATTATCATTCT
58595 CTA
1 CTA
58598 GTGTCTTCTC
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
146 149 1.00
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.46
Consensus pattern (146 bp):
CTAATGTAGACTGCTTTTTATTGACATAGAATCCACTTGTCTTCAATGTCATTTTCTCCCTTTCT
GATTTCATCTTTTTTCCCCTTTAAAGATGAAAGTTTTATAATTTTATATATGTATCATGTCAATG
CTGTAATTATCATTCT
Found at i:61845 original size:21 final size:21
Alignment explanation
Indices: 61802--61846 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
61792 TCAGTAAAAA
* * *
61802 TTTATTTAAAATATTATTATT
1 TTTATCTAAAATATCAATATT
*
61823 TTTATCTAAAATATCAATGTT
1 TTTATCTAAAATATCAATATT
61844 TTT
1 TTT
61847 TTAATATTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTATCTAAAATATCAATATT
Found at i:61899 original size:21 final size:21
Alignment explanation
Indices: 61873--61925 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
61863 AGCGTCCAAT
*
61873 AATAACAAAATCAGTAGAAAA
1 AATAACAAAACCAGTAGAAAA
*
61894 AATAACAAAACCGGTAGAAAA
1 AATAACAAAACCAGTAGAAAA
61915 AATAACAAAAC
1 AATAACAAAAC
61926 TGGTAACGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.66, C:0.13, G:0.09, T:0.11
Consensus pattern (21 bp):
AATAACAAAACCAGTAGAAAA
Found at i:64809 original size:2 final size:2
Alignment explanation
Indices: 64802--64858 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
64792 AGCTTAAAAC
64802 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
64844 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
64859 GTATTTAATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:67284 original size:209 final size:213
Alignment explanation
Indices: 66688--67502 Score: 1155
Period size: 209 Copynumber: 3.8 Consensus size: 213
66678 ATTTAAGAAT
*
66688 TAAATTGAACAAATATGAAATTGCAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACA-T-A-GAG
* *
66753 AGATCAAAACGAAAA-AATTTTAAATTGTGAGGTTGACATTAATACAAAAAAAGTACTAAATTAT
63 AGATCAAATC-AAAATAATTTTAAATTGTGAGGTTGAAATTAATAC-AAAAAAGTACTAAATTAT
* * * *
66817 ACCCATTTAAAAAGTTATGGGACAATTAAAAAAATAGAATTAAGTAATAAGTATGGATCAATTTC
126 ACCCATTTAAAAAGTTATGGGCCAATT-TAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTC
*
66882 ATATGCAAATAAAATTTGGAGGAC
190 AAATGCAAATAAAATTTGGAGGAC
66906 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACA-T-A-GAG
* * *
66971 GGATCAAATCAAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTGTAC
63 AGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
67036 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAAA
128 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAAA
67101 TGCAAATAAAATTTGGAGGAC
193 TGCAAATAAAATTTGGAGGAC
* * * * * *
67122 TAAATTGAACAAATGTTAAATTACAAATAAAACTTTAAATATATTAAACAACGCA-A-A-AGGGA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAGAGAGA
* * *
67184 TCAAATCAAAATAATTTTAAATTTTGAGGTTGAAATTGATAC-AAAAAGTACTAAATTATACCAA
66 TCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCA
**
67248 TTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGGTGC
131 TTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAAATGC
*
67313 AAATAAAATTTGGAGGAT
196 AAATAAAATTTGGAGGAC
* * * *
67331 TAAATTGAATAAATATGAAATAATAAATAAAAATTTAAATATATTAAACAACACA-A-A-AGAGA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAGAGAGA
* * * * * *
67393 TCAAATCGAAATAATTTTAAATTTTGAGATT-AAATTAATATAAAAATGTACTAAATTATACTCA
66 TCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCA
**
67457 TTTAAAAAGTTATGATCCAA-TTAATAAATAGAAATAAGTAATAAGT
131 TTTAAAAAGTTATGGGCCAATTTAA-AAATAGAAATAAGTAATAAGT
67503 TGAGAAAAAA
Statistics
Matches: 553, Mismatches: 41, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
208 12 0.02
209 241 0.44
210 44 0.08
212 1 0.00
215 1 0.00
216 107 0.19
217 47 0.08
218 100 0.18
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (213 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAGAGAGA
TCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCA
TTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAAATGC
AAATAAAATTTGGAGGAC
Found at i:67502 original size:425 final size:427
Alignment explanation
Indices: 66688--67502 Score: 1168
Period size: 425 Copynumber: 1.9 Consensus size: 427
66678 ATTTAAGAAT
*
66688 TAAATTGAACAAATATGAAATTGCAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACA-T-A-GAG
*
66753 AGATCAAAACGAAAAAATTTTAAATTGTGAGGTTGACATTAATACAAAAAAAGTACTAAATTATA
63 AGATCAAAACGAAAAAATTTTAAATTGTGAGGTTGAAATTAATAC-AAAAAAGTACTAAATTATA
* *
66818 CCCATTTAAAAAGTTATGGGACAATTAAAAAAATAGAATTAAGTAATAAGTATGGATCAATTTCA
127 CCAATTTAAAAAGTTATGGGACAATTAAAAAAATAGAAATAAGTAATAAGTATGGATCAATTTCA
* *
66883 TATGCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAA
192 GATGCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATAACAAATAAAAATTTAAATAA
*
66948 ATTAAACAACACACATTGATGAGGGATCAAATCAAAATAATTTTAAATTGTGATGTTGAAATTAA
257 ATTAAACAACACACA-T-A-GAGAGATCAAATCAAAATAATTTTAAATTGTGATGTTGAAATTAA
* *
67013 TACAAAAAAGTACTAAATTGTACCCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGT
319 TACAAAAAAGTACTAAATTATACCCATTTAAAAAGTTATGAGCCAATTTAAAAATAGAAATAAGT
67078 AATAAGTATGGGTCAATTTCAAATGCAAATAAAATTTGGAGGAC
384 AATAAGTATGGGTCAATTTCAAATGCAAATAAAATTTGGAGGAC
* * * * * *
67122 TAAATTGAACAAATGTTAAATTACAAATAAAACTTTAAATATATTAAACAACGCA-A-A-AGGGA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAGAGAGA
* * *
67184 TCAAATC-AAAATAATTTTAAATTTTGAGGTTGAAATTGATAC-AAAAAGTACTAAATTATACCA
66 TCAAAACGAAAA-AATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCA
* * * *
67247 ATTTAAAAAGTTATGGGCCAATT-TAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGGT
130 ATTTAAAAAGTTATGGGACAATTAAAAAAATAGAAATAAGTAATAAGTATGGATCAATTTCAGAT
* * * *
67311 GCAAATAAAATTTGGAGGATTAAATTGAATAAATATGAAATAATAAATAAAAATTTAAATATATT
195 GCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATAACAAATAAAAATTTAAATAAATT
* * *
67376 AAACAACACA-A-A-AGAGATCAAATCGAAATAATTTTAAATTTTGA-GATT-AAATTAATATAA
260 AAACAACACACATAGAGAGATCAAATCAAAATAATTTTAAATTGTGATG-TTGAAATTAATACAA
* * *
67436 AAATGTACTAAATTATACTCATTTAAAAAGTTATGATCCAA-TTAATAAATAGAAATAAGTAATA
324 AAAAGTACTAAATTATACCCATTTAAAAAGTTATGAGCCAATTTAA-AAATAGAAATAAGTAATA
67500 AGT
388 AGT
67503 TGAGAAAAAA
Statistics
Matches: 346, Mismatches: 32, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
417 4 0.01
418 69 0.20
419 31 0.09
421 1 0.00
424 1 0.00
425 106 0.31
426 42 0.12
427 4 0.01
428 37 0.11
430 1 0.00
433 1 0.00
434 49 0.14
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (427 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAGAGAGA
TCAAAACGAAAAAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCAA
TTTAAAAAGTTATGGGACAATTAAAAAAATAGAAATAAGTAATAAGTATGGATCAATTTCAGATG
CAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATAACAAATAAAAATTTAAATAAATTA
AACAACACACATAGAGAGATCAAATCAAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAA
AAGTACTAAATTATACCCATTTAAAAAGTTATGAGCCAATTTAAAAATAGAAATAAGTAATAAGT
ATGGGTCAATTTCAAATGCAAATAAAATTTGGAGGAC
Found at i:67541 original size:2 final size:2
Alignment explanation
Indices: 67528--67578 Score: 50
Period size: 2 Copynumber: 25.0 Consensus size: 2
67518 AAAACAACTA
* * *
67528 AT AT AG AT AT AT AT AT A- AT AT AA ACT AT AT AGT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT
67571 AT AT AT AT
1 AT AT AT AT
67579 TATGTATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:67610 original size:27 final size:28
Alignment explanation
Indices: 67562--67630 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
67552 CTATATAGTT
** *
67562 TATATATA-TATATATATTATGTATAAAG
1 TATA-ATACTATATATACCATGTATAAAC
67590 TATAA-ACTATATATACCATGTATAAAC
1 TATAATACTATATATACCATGTATAAAC
67617 TATAATACTATATA
1 TATAATACTATATA
67631 GTTTATATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.03
27 23 0.64
28 12 0.33
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (28 bp):
TATAATACTATATATACCATGTATAAAC
Found at i:67686 original size:11 final size:11
Alignment explanation
Indices: 67672--67790 Score: 66
Period size: 11 Copynumber: 10.6 Consensus size: 11
67662 ACTACATAGT
67672 TTATATATAAA
1 TTATATATAAA
*
67683 TTATATATGAA
1 TTATATATAAA
67694 TTATATATAAA
1 TTATATATAAA
* * *
67705 --CTATACAAT
1 TTATATATAAA
*
67714 TTATATTTATATA
1 TTATA--TATAAA
*
67727 TTATGTAT-AA
1 TTATATATAAA
*
67737 TTATAAATAATA
1 TTATATATAA-A
*
67749 TATATTGTATAAA
1 T-TA-TATATAAA
**
67762 TTATATAGTTTA
1 TTATATA-TAAA
67774 TTA-ATATAAA
1 TTATATATAAA
67784 TTATATA
1 TTATATA
67791 GTTTATATAT
Statistics
Matches: 78, Mismatches: 20, Indels: 20
0.66 0.17 0.17
Matches are distributed among these distances:
9 6 0.08
10 12 0.15
11 35 0.45
12 9 0.12
13 11 0.14
14 5 0.06
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (11 bp):
TTATATATAAA
Found at i:67717 original size:20 final size:20
Alignment explanation
Indices: 67617--67719 Score: 75
Period size: 20 Copynumber: 5.0 Consensus size: 20
67607 ATGTATAAAC
*
67617 TATAATACTATATAGTTTATA
1 TATAA-ACTATATAATTTATA
* *
67638 TATGAACTAT-TGAA-CTATA
1 TATAAACTATAT-AATTTATA
* * *
67657 TAGAAACTACATAGTTTATA
1 TATAAACTATATAATTTATA
* *
67677 TATAAATTATATATGAATTATA
1 TATAAACTATATA--ATTTATA
*
67699 TATAAACTATACAATTTATA
1 TATAAACTATATAATTTATA
67719 T
1 T
67720 TTATATATTA
Statistics
Matches: 61, Mismatches: 16, Indels: 11
0.69 0.18 0.12
Matches are distributed among these distances:
19 13 0.21
20 28 0.46
21 4 0.07
22 16 0.26
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.42
Consensus pattern (20 bp):
TATAAACTATATAATTTATA
Found at i:67717 original size:42 final size:43
Alignment explanation
Indices: 67648--67746 Score: 103
Period size: 42 Copynumber: 2.3 Consensus size: 43
67638 TATGAACTAT
* * * *
67648 TGAACTATATAGAAACTACATAGTTTATA-TATAAATTATATA
1 TGAATTATATATAAACTACACAATTTATATTATAAATTATATA
* * *
67690 TGAATTATATATAAACTATACAATTTATATTTATATATTATGTA
1 TGAATTATATATAAACTACACAATTTATA-TTATAAATTATATA
*
67734 T-AATTATAAATAA
1 TGAATTATATATAA
67747 TATATATTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 24 0.51
43 11 0.23
44 12 0.26
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (43 bp):
TGAATTATATATAAACTACACAATTTATATTATAAATTATATA
Found at i:67735 original size:17 final size:17
Alignment explanation
Indices: 67715--67768 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
67705 CTATACAATT
* *
67715 TATATTTATATATTATG
1 TATATTTATAAATTATA
* *
67732 TATAATTATAAATAATA
1 TATATTTATAAATTATA
67749 TATATTGTATAAATTATA
1 TATATT-TATAAATTATA
67767 TA
1 TA
67769 GTTTATTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:67810 original size:22 final size:22
Alignment explanation
Indices: 67756--67812 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
67746 ATATATATTG
*
67756 TATAAATTATATAGTTTATTAA
1 TATAAAGTATATAGTTTATTAA
*
67778 TATAAATTATATAGTTTA-TATA
1 TATAAAGTATATAGTTTATTA-A
*
67800 TATATAGTATATA
1 TATAAAGTATATA
67813 TGACTTAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 2 0.06
22 30 0.94
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
TATAAAGTATATAGTTTATTAA
Found at i:68220 original size:29 final size:29
Alignment explanation
Indices: 68186--68244 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
68176 CCTAAATTAA
68186 TTTGATGTCATTACTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
*
68215 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
68244 T
1 T
68245 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTACTTACATCAATTTAGT
Found at i:72870 original size:29 final size:29
Alignment explanation
Indices: 72836--72894 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
72826 CCTAAATTAA
72836 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
72865 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
72894 T
1 T
72895 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:74261 original size:23 final size:23
Alignment explanation
Indices: 74215--74264 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
74205 ATGCAGTATA
* *
74215 CTTGCTGAATTGATGCAATGATG
1 CTTGCTGAATTGATACAATAATG
* *
74238 CTTGCTGAATTGGTACATTAATG
1 CTTGCTGAATTGATACAATAATG
74261 CTTG
1 CTTG
74265 TCGGTTGCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (23 bp):
CTTGCTGAATTGATACAATAATG
Found at i:74861 original size:13 final size:13
Alignment explanation
Indices: 74842--74879 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
74832 TAATTTAGTG
74842 ATTATAAATAA-A
1 ATTATAAATAAGA
74854 ATTTATAATATAAGA
1 A-TTATAA-ATAAGA
74869 ATTATAAATAA
1 ATTATAAATAA
74880 TATAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:74889 original size:19 final size:19
Alignment explanation
Indices: 74858--74904 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
74848 AATAAAATTT
*
74858 ATAATAT-AAGAATTATAA
1 ATAATATAAAGAATTAGAA
74876 ATAATATAAAGAATTAGAA
1 ATAATATAAAGAATTAGAA
*
74895 TTAATATAAA
1 ATAATATAAA
74905 AAATCTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (19 bp):
ATAATATAAAGAATTAGAA
Found at i:75134 original size:16 final size:16
Alignment explanation
Indices: 75100--75138 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
75090 AGAGTCAATT
* *
75100 ACAGGTCAGGTTCATA
1 ACAGGTCAGGCTCAAA
*
75116 ACAGGTCAGGCTGAAA
1 ACAGGTCAGGCTCAAA
75132 ACAGGTC
1 ACAGGTC
75139 GGATAATATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (16 bp):
ACAGGTCAGGCTCAAA
Found at i:84005 original size:3 final size:3
Alignment explanation
Indices: 83997--84062 Score: 96
Period size: 3 Copynumber: 22.0 Consensus size: 3
83987 TGTTAAACAC
*
83997 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
84045 GTA ATA GTA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA
84063 GTAGTAGTAG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:84063 original size:6 final size:6
Alignment explanation
Indices: 83998--84089 Score: 76
Period size: 6 Copynumber: 15.3 Consensus size: 6
83988 GTTAAACACA
* * * * * * * *
83998 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAACAG
1 TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG
* * * *
84046 TAATAG TAATAG TAATAG TAGTAG TAGTAG TAGTAG TAGTAG TA
1 TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG TA
84090 GTAATAACAA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 82 1.00
ACGTcount: A:0.53, C:0.01, G:0.13, T:0.33
Consensus pattern (6 bp):
TAATAG
Found at i:84069 original size:3 final size:3
Alignment explanation
Indices: 84044--84092 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
84034 TAATAATAAC
* * *
84044 AGT AAT AGT AAT AGT AAT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT
84092 A
1 A
84093 ATAACAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.33
Consensus pattern (3 bp):
AGT
Found at i:84117 original size:3 final size:3
Alignment explanation
Indices: 84109--84135 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
84099 ATTAATAACA
84109 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
84136 CTTAACATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:84273 original size:36 final size:36
Alignment explanation
Indices: 84226--84297 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
84216 AATTTGTGAT
*
84226 AAATTCTCTAGCCATACTTTATAATTAAAACTAACA
1 AAATTCTCTAGCCATACTTTATAATTAAAACCAACA
84262 AAATTCTCTAGCCATACTTTATAATTAAAACCAACA
1 AAATTCTCTAGCCATACTTTATAATTAAAACCAACA
84298 CTTGAGTCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (36 bp):
AAATTCTCTAGCCATACTTTATAATTAAAACCAACA
Found at i:86415 original size:3 final size:3
Alignment explanation
Indices: 86407--86467 Score: 72
Period size: 3 Copynumber: 21.0 Consensus size: 3
86397 TGTTAAACAC
* *
86407 ATA ATA ATA AT- ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ACA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
86453 ATA GTA ATA GTA ATA
1 ATA ATA ATA ATA ATA
86468 GTAGTAGTAG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:86429 original size:17 final size:17
Alignment explanation
Indices: 86407--86447 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
86397 TGTTAAACAC
86407 ATAATAATAATATAATA
1 ATAATAATAATATAATA
86424 ATAATAATAATATAATA
1 ATAATAATAATATAATA
86441 ATAATAA
1 ATAATAA
86448 CAGTAATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAATAATATAATA
Found at i:86468 original size:6 final size:6
Alignment explanation
Indices: 86408--86488 Score: 58
Period size: 6 Copynumber: 13.3 Consensus size: 6
86398 GTTAAACACA
* * * *
86408 TAATAA TAATA- TAATAA TAATAA TAATA- TAATAA TAATAACAG TAATAG
1 TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG TAAT---AG TAATAG
* * *
86457 TAATAG TAATAG TAGTAG TAGTAG TAGTAG TA
1 TAATAG TAATAG TAATAG TAATAG TAATAG TA
86489 GTAAAACAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
5 10 0.15
6 53 0.78
9 5 0.07
ACGTcount: A:0.53, C:0.01, G:0.12, T:0.33
Consensus pattern (6 bp):
TAATAG
Found at i:86474 original size:3 final size:3
Alignment explanation
Indices: 86449--86491 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
86439 TAATAATAAC
* * *
86449 AGT AAT AGT AAT AGT AAT AGT AGT AGT AGT AGT AGT AGT AGT A
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT A
86492 AAACAATTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.33
Consensus pattern (3 bp):
AGT
Found at i:86515 original size:3 final size:3
Alignment explanation
Indices: 86507--86533 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
86497 ATTAATAACA
86507 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
86534 CTTAACATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:86671 original size:36 final size:36
Alignment explanation
Indices: 86624--86695 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
86614 AATTTGTGAT
*
86624 AAATTCTCTAGCCATACTTTATAATTAAAACTAACA
1 AAATTCTCTAGCCATACTTTATAATTAAAACCAACA
86660 AAATTCTCTAGCCATACTTTATAATTAAAACCAACA
1 AAATTCTCTAGCCATACTTTATAATTAAAACCAACA
86696 CTTGAGTCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (36 bp):
AAATTCTCTAGCCATACTTTATAATTAAAACCAACA
Found at i:88781 original size:23 final size:23
Alignment explanation
Indices: 88746--88789 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
88736 CGAGTTCTAT
*
88746 GCATTATAGAAAATACAATATATC
1 GCATAATAGAAAATA-AATATATC
88770 GCATAATA-AAAATAAATATA
1 GCATAATAGAAAATAAATATA
88790 CCCTATTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 6 0.32
24 7 0.37
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.27
Consensus pattern (23 bp):
GCATAATAGAAAATAAATATATC
Found at i:90211 original size:2 final size:2
Alignment explanation
Indices: 90204--90275 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
90194 CCTTAGCGCG
90204 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
90245 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
90276 GAACGGAGAT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:100716 original size:11 final size:13
Alignment explanation
Indices: 100684--100718 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
100674 AATCATGTGC
100684 ACATGATATTTCAA
1 ACAT-ATATTTCAA
100698 ACATATATTTCAA
1 ACATATATTTCAA
*
100711 AAATATAT
1 ACATATAT
100719 ATGGCACACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (13 bp):
ACATATATTTCAA
Found at i:101198 original size:19 final size:19
Alignment explanation
Indices: 101174--101220 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
101164 TGACTTTTTG
*
101174 GTCAAAGTTGACTGTCAAA
1 GTCAAAGTTGACGGTCAAA
*
101193 GTCAAAGTCGACGGTCAAA
1 GTCAAAGTTGACGGTCAAA
101212 GTCAAAGTT
1 GTCAAAGTT
101221 AACAGGCATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (19 bp):
GTCAAAGTTGACGGTCAAA
Found at i:107298 original size:3 final size:3
Alignment explanation
Indices: 107290--107339 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
107280 TAAATGAAAT
107290 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
107338 TT
1 TT
107340 TTCTAGGAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:107938 original size:3 final size:3
Alignment explanation
Indices: 107924--107959 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
107914 TTTAAAAAAG
107924 AAC AAGC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AA-C AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
107960 AACCCTATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.31, G:0.03, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:112459 original size:21 final size:20
Alignment explanation
Indices: 112417--112460 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
112407 TAAATTGTCT
*
112417 TATATTTTCAATTAATAATA
1 TATATTTTCAATTAACAATA
* *
112437 TATATTTATCATTTAACATTA
1 TATATTT-TCAATTAACAATA
112458 TAT
1 TAT
112461 CATGTATCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (20 bp):
TATATTTTCAATTAACAATA
Found at i:115250 original size:13 final size:13
Alignment explanation
Indices: 115232--115280 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
115222 AATTAAAATA
115232 ATTAAATACAAAC
1 ATTAAATACAAAC
115245 ATTAAATACAAAC
1 ATTAAATACAAAC
* *
115258 GTTACAATTCAAAC
1 ATTA-AATACAAAC
115272 AATTAAATA
1 -ATTAAATA
115281 ATAACAACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 16 0.53
14 11 0.37
15 3 0.10
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (13 bp):
ATTAAATACAAAC
Found at i:115864 original size:21 final size:21
Alignment explanation
Indices: 115817--115865 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
115807 CTAAAATGGT
*
115817 TGCGGTGCCATCTGAAACGAC
1 TGCGGTGCCATCTGAAACGAA
* * *
115838 TACGGTGCCATTTGAAATGAA
1 TGCGGTGCCATCTGAAACGAA
115859 TGCGGTG
1 TGCGGTG
115866 TACGCATGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (21 bp):
TGCGGTGCCATCTGAAACGAA
Found at i:123675 original size:40 final size:38
Alignment explanation
Indices: 123626--123710 Score: 127
Period size: 40 Copynumber: 2.2 Consensus size: 38
123616 ACATCATACC
123626 TAAAA-TTTAGTTTTTGTTTCATTTTAGTATCCCGCCGTT
1 TAAAACTTTAGTTTTTGTTTCATTTTAGTA-CCC-CCGTT
*
123665 TAAAACTTTAGTTTTTGTTTCATTTTGGTACCCCCGTT
1 TAAAACTTTAGTTTTTGTTTCATTTTAGTACCCCCGTT
*
123703 CAAAACTT
1 TAAAACTT
123711 AACGTTAAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
38 12 0.28
39 8 0.19
40 23 0.53
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.48
Consensus pattern (38 bp):
TAAAACTTTAGTTTTTGTTTCATTTTAGTACCCCCGTT
Found at i:124203 original size:19 final size:18
Alignment explanation
Indices: 124179--124258 Score: 67
Period size: 19 Copynumber: 4.4 Consensus size: 18
124169 GAATACGAAC
124179 TTAAATAATTTTCAACAAT
1 TTAAATAA-TTTCAACAAT
* *
124198 TTAAAT-ATTTAAATAATT
1 TTAAATAATTTCAACAA-T
* *
124216 TTCAACAATTT-AA-ATAT
1 TTAAATAATTTCAACA-AT
124233 TTAAATAATTTTCAACAAT
1 TTAAATAA-TTTCAACAAT
124252 TTAAATA
1 TTAAATA
124259 TTTAAATAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
17 15 0.31
18 12 0.24
19 21 0.43
20 1 0.02
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAATAATTTCAACAAT
Found at i:124209 original size:8 final size:8
Alignment explanation
Indices: 124196--124266 Score: 56
Period size: 8 Copynumber: 8.1 Consensus size: 8
124186 ATTTTCAACA
124196 ATTTAAAT
1 ATTTAAAT
124204 ATTTAAAT
1 ATTTAAAT
124212 AATTTTCAACA-
1 -A-TTT-AA-AT
124223 ATTTAAAT
1 ATTTAAAT
124231 ATTTAAAT
1 ATTTAAAT
124239 AATTTTCAACA-
1 -A-TTT-AA-AT
124250 ATTTAAAT
1 ATTTAAAT
124258 ATTTAAAT
1 ATTTAAAT
124266 A
1 A
124267 ATTTTCAACG
Statistics
Matches: 53, Mismatches: 0, Indels: 20
0.73 0.00 0.27
Matches are distributed among these distances:
7 2 0.04
8 29 0.55
9 8 0.15
10 8 0.15
11 4 0.08
12 2 0.04
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (8 bp):
ATTTAAAT
Found at i:124211 original size:27 final size:27
Alignment explanation
Indices: 124179--124280 Score: 195
Period size: 27 Copynumber: 3.8 Consensus size: 27
124169 GAATACGAAC
124179 TTAAATAATTTTCAACAATTTAAATAT
1 TTAAATAATTTTCAACAATTTAAATAT
124206 TTAAATAATTTTCAACAATTTAAATAT
1 TTAAATAATTTTCAACAATTTAAATAT
124233 TTAAATAATTTTCAACAATTTAAATAT
1 TTAAATAATTTTCAACAATTTAAATAT
*
124260 TTAAATAATTTTCAACGATTT
1 TTAAATAATTTTCAACAATTT
124281 GAACAGAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.45
Consensus pattern (27 bp):
TTAAATAATTTTCAACAATTTAAATAT
Found at i:132973 original size:23 final size:23
Alignment explanation
Indices: 132920--132978 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
132910 AAAATTTTAA
* *
132920 ATAAAATTCTAAAAAAGAAAATT
1 ATAAATTTCTAAAAAAGAAAATC
* *
132943 ATATATTTTTAAAAAAGTAAAA-C
1 ATAAATTTCTAAAAAAG-AAAATC
132966 ATAAATTTC-AAAA
1 ATAAATTTCTAAAA
132979 TAACCCCTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 4 0.14
23 21 0.72
24 4 0.14
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (23 bp):
ATAAATTTCTAAAAAAGAAAATC
Found at i:133900 original size:19 final size:19
Alignment explanation
Indices: 133887--133929 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
133877 TTAAAGGAAT
133887 ATTCCGCTACTAAAAGAAC
1 ATTCCGCTACTAAAAGAAC
133906 ATTCCGCTACTAAAAGAAC
1 ATTCCGCTACTAAAAGAAC
133925 ATTCC
1 ATTCC
133930 CTTTGGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.40, C:0.28, G:0.09, T:0.23
Consensus pattern (19 bp):
ATTCCGCTACTAAAAGAAC
Found at i:139493 original size:14 final size:14
Alignment explanation
Indices: 139474--139504 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
139464 ATGGCGGCTG
139474 AGGAAATTAGGGTT
1 AGGAAATTAGGGTT
139488 AGGAAATTAGGGTT
1 AGGAAATTAGGGTT
139502 AGG
1 AGG
139505 TTTAATCTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.39, T:0.26
Consensus pattern (14 bp):
AGGAAATTAGGGTT
Found at i:139596 original size:11 final size:11
Alignment explanation
Indices: 139573--139604 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
139563 TGTAATTATT
139573 TATTTATATATA
1 TATTTA-ATATA
139585 TATTTAATATA
1 TATTTAATATA
139596 TATTTAATA
1 TATTTAATA
139605 ATAATGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:139608 original size:3 final size:3
Alignment explanation
Indices: 139600--139700 Score: 168
Period size: 3 Copynumber: 33.7 Consensus size: 3
139590 AATATATATT
*
139600 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA -AA GTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
*
139645 TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
139693 TAA TAA TA
1 TAA TAA TA
139701 TGGATTAAAA
Statistics
Matches: 92, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.02
3 88 0.96
4 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:140824 original size:113 final size:113
Alignment explanation
Indices: 139950--140802 Score: 1265
Period size: 113 Copynumber: 7.5 Consensus size: 113
139940 TCTTGATGAG
*
139950 TTCTTCTCATTATGAACCTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
140015 GAAAGGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAGGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
* *
140063 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGACGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
140128 GAAAAGCTGATCCATCAATTGATGAATTCAGGTAAAAGGTTGAAAAAA
66 GAAAGGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
*
140176 TTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
140241 GAAAGGTTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAGGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
*
140289 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
140354 GAAAGGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAGGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
*
140402 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*** * * * ***
140467 GAAACAATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
66 GAAAGGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
* *
140515 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACCTCCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTATGAACTTTCT
* *** * * * ***
140580 CTGGCAACAATAATCCATCAAGTGATGAATTCAAACAAAAAGGTTGAACAAA
63 CTGGAAAGGCTGATCCATCAAATGATGGATTC-AGGTAAAAGGTTGAACAAA
****
140632 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*** * * * * *
140697 GAAAAATTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAATAAA
66 GAAAGGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
*
140745 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
140803 CGAACTGACA
Statistics
Matches: 688, Mismatches: 48, Indels: 8
0.92 0.06 0.01
Matches are distributed among these distances:
113 530 0.77
114 49 0.07
115 2 0.00
116 57 0.08
117 50 0.07
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAGGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
Found at i:141498 original size:84 final size:84
Alignment explanation
Indices: 141352--141763 Score: 779
Period size: 84 Copynumber: 4.9 Consensus size: 84
141342 ATTTTTACCA
*
141352 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCCTCTAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAAT
*
141417 TCAATGATTAGTTCCGTCC
66 TCAATGATTGGTTCCGTCC
141436 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAAT
*
141501 TCAATGATTGGTTCTGTCC
66 TCAATGATTGGTTCCGTCC
141520 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAAT
*
141585 TCAATGATTGGTTCTGTCC
66 TCAATGATTGGTTCCGTCC
141604 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAAT
*
141669 TCAATGATTGGTTCCGCCC
66 TCAATGATTGGTTCCGTCC
141688 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAAT
141753 TCAATGATTGG
66 TCAATGATTGG
141764 ACCAGGATAT
Statistics
Matches: 323, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 323 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.27
Consensus pattern (84 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAAT
TCAATGATTGGTTCCGTCC
Found at i:142892 original size:1 final size:1
Alignment explanation
Indices: 142888--142948 Score: 68
Period size: 1 Copynumber: 61.0 Consensus size: 1
142878 TTGACCCCCC
* * * * * *
142888 TTTTTCTTTTTTTTTCTTTTTCTTTTTTTTTCTTTTTTTTCTTTTTTTTTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
142949 CAAGCATAAT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:142901 original size:10 final size:10
Alignment explanation
Indices: 142887--142949 Score: 83
Period size: 11 Copynumber: 6.1 Consensus size: 10
142877 CTTGACCCCC
142887 CTTTTTCTTTT
1 CTTTTT-TTTT
*
142898 TTTTTCTTTTT
1 CTTTT-TTTTT
142909 CTTTTTTTTT
1 CTTTTTTTTT
142919 C-TTTTTTTT
1 CTTTTTTTTT
142928 CTTTTTTTTTT
1 C-TTTTTTTTT
142939 CTTTTTTTTT
1 CTTTTTTTTT
142949 C
1 C
142950 AAGCATAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
9 9 0.19
10 16 0.34
11 21 0.45
12 1 0.02
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:142908 original size:16 final size:16
Alignment explanation
Indices: 142887--142949 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
142877 CTTGACCCCC
142887 CTTTTTCTTTTTTTTT
1 CTTTTTCTTTTTTTTT
142903 CTTTTTCTTTTTTTTT
1 CTTTTTCTTTTTTTTT
*
142919 CTTTTT-TTTCTTTTT
1 CTTTTTCTTTTTTTTT
142934 -TTTTTCTTTTTTTTT
1 CTTTTTCTTTTTTTTT
142949 C
1 C
142950 AAGCATAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.12
15 16 0.37
16 22 0.51
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (16 bp):
CTTTTTCTTTTTTTTT
Found at i:153611 original size:22 final size:23
Alignment explanation
Indices: 153572--153614 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
153562 ATAATTACAA
*
153572 ATAAAATAAAACATATAAATATT
1 ATAAAATAAAACAAATAAATATT
*
153595 ATAAAA-AAAATAAATAAATA
1 ATAAAATAAAACAAATAAATA
153615 AAAAATTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (23 bp):
ATAAAATAAAACAAATAAATATT
Found at i:155652 original size:14 final size:14
Alignment explanation
Indices: 155633--155663 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
155623 ATGGCGGCTG
155633 AGGAAATTAGGGTT
1 AGGAAATTAGGGTT
155647 AGGAAATTAGGGTT
1 AGGAAATTAGGGTT
155661 AGG
1 AGG
155664 TTTAATCTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.39, T:0.26
Consensus pattern (14 bp):
AGGAAATTAGGGTT
Found at i:155764 original size:3 final size:3
Alignment explanation
Indices: 155748--155847 Score: 175
Period size: 3 Copynumber: 33.7 Consensus size: 3
155738 TATATATATT
*
155748 TAA TAA T-A TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
155795 TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
155843 TAA TA
1 TAA TA
155848 TGGATAAAAA
Statistics
Matches: 93, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
2 2 0.02
3 91 0.98
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:156674 original size:22 final size:22
Alignment explanation
Indices: 156649--156700 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
156639 GCTTAATGAC
156649 CTTGTACCTCGTGCTTTGAACT
1 CTTGTACCTCGTGCTTTGAACT
156671 CTTGTACCTCGTGCTTTGAACT
1 CTTGTACCTCGTGCTTTGAACT
156693 CTTGTACC
1 CTTGTACC
156701 ATATCTTCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.13, C:0.29, G:0.17, T:0.40
Consensus pattern (22 bp):
CTTGTACCTCGTGCTTTGAACT
Found at i:161503 original size:30 final size:30
Alignment explanation
Indices: 161457--161515 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
161447 AAAAACTTAA
161457 TTATAAAATAAGTGTTTAAATTATATTTTTT
1 TTATAAAATAAGTGTTTAAATTAT-TTTTTT
*
161488 TTAT-AAATTAGTGTTTAAATTATTTTTT
1 TTATAAAATAAGTGTTTAAATTATTTTTT
161516 GAATAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 5 0.19
30 18 0.67
31 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (30 bp):
TTATAAAATAAGTGTTTAAATTATTTTTTT
Found at i:161521 original size:28 final size:30
Alignment explanation
Indices: 161462--161530 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 30
161452 CTTAATTATA
* **
161462 AAATAAGTGTTTAAATTATATTTTTTTTAT
1 AAATTAGTGTTTAAATTATATTTTTTGAAT
161492 AAATTAGTGTTTAAA-T-TATTTTTTGAAT
1 AAATTAGTGTTTAAATTATATTTTTTGAAT
*
161520 AATTTAAGTGT
1 AAATT-AGTGT
161531 CTAATGTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.41
29 6 0.18
30 14 0.41
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (30 bp):
AAATTAGTGTTTAAATTATATTTTTTGAAT
Found at i:161618 original size:23 final size:23
Alignment explanation
Indices: 161572--161619 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
161562 TTGGACTGTC
** *
161572 AACGACATTAATTTTCTTCGTTA
1 AACGACATTAATTTAATTAGTTA
*
161595 AACGACATTAATTTAATTATTTA
1 AACGACATTAATTTAATTAGTTA
161618 AA
1 AA
161620 ATTAATAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (23 bp):
AACGACATTAATTTAATTAGTTA
Found at i:162763 original size:21 final size:21
Alignment explanation
Indices: 162717--162764 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
162707 GATTTTGACT
*
162717 ATCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTACAAA
* * *
162738 TTCGCGTTGCGATTTTAGAAA
1 ATCGCATTGCGATTTTACAAA
162759 ATCGCA
1 ATCGCA
162765 ATGCAAATAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
ATCGCATTGCGATTTTACAAA
Found at i:162802 original size:20 final size:20
Alignment explanation
Indices: 162779--162832 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
162769 AAATATGTAA
162779 ATCGCAACGCGATTCTAACT
1 ATCGCAACGCGATTCTAACT
162799 ATCGCAACGCGATTCTAACT
1 ATCGCAACGCGATTCTAACT
*
162819 ATCGCAATGCGATT
1 ATCGCAACGCGATT
162833 TTCAAAGCGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTAACT
Found at i:163426 original size:20 final size:20
Alignment explanation
Indices: 163401--163453 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
163391 CGATTTTAGT
163401 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
**
163421 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
163441 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
163454 TTTCATTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:163459 original size:20 final size:20
Alignment explanation
Indices: 163390--163476 Score: 86
Period size: 20 Copynumber: 4.4 Consensus size: 20
163380 AAATCGCAAC
*
163390 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
** **
163409 GCGATAGTCAAATTCGCGTT
1 GCGATTTTCATTTTCGCGTT
**
163429 GCGATAGTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
**
163449 GCGATTTTCATTTTCATGTT
1 GCGATTTTCATTTTCGCGTT
163469 GCGATTTT
1 GCGATTTT
163477 AAGTTTCAGA
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
19 6 0.11
20 51 0.89
ACGTcount: A:0.16, C:0.17, G:0.23, T:0.44
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:163483 original size:20 final size:20
Alignment explanation
Indices: 163446--163484 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
163436 TCATTTTCGC
* *
163446 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTAAGTTTCAT
163466 GTTGCGATTTTAAGTTTCA
1 GTTGCGATTTTAAGTTTCA
163485 GAAACTATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTAAGTTTCAT
Found at i:165411 original size:20 final size:20
Alignment explanation
Indices: 165388--165476 Score: 115
Period size: 20 Copynumber: 4.5 Consensus size: 20
165378 GAAACTTAAA
165388 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
165408 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
165428 ATCGTAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* * **
165448 ATCGCAATGAGAATTTGACT
1 ATCGCAACGCGAAAATGACT
165468 ATCGCAACG
1 ATCGCAACG
165477 GGATAATCGC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:165509 original size:33 final size:34
Alignment explanation
Indices: 165468--165543 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 34
165458 GAATTTGACT
* *
165468 ATCGCAACGGGATAATCGCAATGCG-AAATAAAA
1 ATCGCAACGGGAAAATCACAATGCGAAAATAAAA
* * *
165501 ATCGCAACGTGAAAATCACAATGTGAAAATGAAA
1 ATCGCAACGGGAAAATCACAATGCGAAAATAAAA
165535 ATCGCAACG
1 ATCGCAACG
165544 CGAATTTAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 21 0.57
34 16 0.43
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (34 bp):
ATCGCAACGGGAAAATCACAATGCGAAAATAAAA
Found at i:165575 original size:14 final size:14
Alignment explanation
Indices: 165553--165583 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
165543 GCGAATTTAG
165553 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
*
165567 TTTCTCATTGCGAT
1 TTTCGCATTGCGAT
165581 TTT
1 TTT
165584 TATTTCGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.19, G:0.16, T:0.52
Consensus pattern (14 bp):
TTTCGCATTGCGAT
Found at i:165611 original size:33 final size:34
Alignment explanation
Indices: 165548--165613 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
165538 GCAACGCGAA
* *
165548 TTTAGTTTCGCATTGCGATTTTCTCATTGCGATT
1 TTTAGTTTCGCATTGCGATTATCCCATTGCGATT
*
165582 TTTA-TTTCGCATTGCGATTATCCCGTTGCGAT
1 TTTAGTTTCGCATTGCGATTATCCCATTGCGAT
165614 AGTCAAATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (34 bp):
TTTAGTTTCGCATTGCGATTATCCCATTGCGATT
Found at i:165630 original size:20 final size:20
Alignment explanation
Indices: 165605--165653 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
165595 GCGATTATCC
*
165605 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAATCAAATTCA
** *
165625 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAATCAAATTCA
165645 CGTTGCGAT
1 CGTTGCGAT
165654 TTTAAGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAATCAAATTCA
Found at i:166206 original size:42 final size:42
Alignment explanation
Indices: 166160--166251 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
166150 TATCCTATCG
*
166160 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCT
1 TTCAAGAGGCCCCTATCATCCCTCAAGAGGT-CCCTCCCACCA
* ** *
166202 TTCAAGAGGCCCCTGTCATCGTTGAAGAGGTCCCTCCCACCA
1 TTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCACCA
166244 TTCAAGAG
1 TTCAAGAG
166252 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 42 0.95
43 2 0.05
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.22
Consensus pattern (42 bp):
TTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCACCA
Found at i:166229 original size:21 final size:21
Alignment explanation
Indices: 166133--166236 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
166123 GACTAACCTG
166133 TCATCGTTCAAGAGG--CCTA
1 TCATCGTTCAAGAGGCCCCTA
166152 TCCTATCGTTCAAGAGGCCCCTA
1 T-C-ATCGTTCAAGAGGCCCCTA
** * *
166175 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTA
* * * *
166196 CCACCTTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTA
* *
166217 TCATCGTTGAAGAGGTCCCT
1 TCATCGTTCAAGAGGCCCCT
166237 CCCACCATTC
Statistics
Matches: 66, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 58 0.88
22 1 0.02
23 5 0.08
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.25
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTA
Found at i:166250 original size:21 final size:21
Alignment explanation
Indices: 166182--166251 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
166172 CTATCATCCC
*
166182 TCAAGA-GTCCCCTCCCACCTT
1 TCAAGAGGT-CCCTCCCACCAT
* ** * *
166203 TCAAGAGGCCCCTGTCATCGT
1 TCAAGAGGTCCCTCCCACCAT
*
166224 TGAAGAGGTCCCTCCCACCAT
1 TCAAGAGGTCCCTCCCACCAT
166245 TCAAGAG
1 TCAAGAG
166252 CCCGATTCAC
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
21 35 0.97
22 1 0.03
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
TCAAGAGGTCCCTCCCACCAT
Found at i:167663 original size:14 final size:14
Alignment explanation
Indices: 167644--167682 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
167634 TTGCTTGTTT
167644 AATTGATTTGTAAA
1 AATTGATTTGTAAA
167658 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
167672 AGTTGATTTGT
1 AATTGATTTGT
167683 TTAATTGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:167841 original size:20 final size:20
Alignment explanation
Indices: 167816--167879 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
167806 AACGCTAAAC
* *
167816 TCAAAATCACAATTTGAAAG
1 TCAAAATCGCAATGTGAAAG
*
167836 TCAAAATCGCAATGCGAAAG
1 TCAAAATCGCAATGTGAAAG
* *
167856 CCAAAATCGCAACGTGAAAG
1 TCAAAATCGCAATGTGAAAG
167876 TCAA
1 TCAA
167880 TTCGCATTGC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.17
Consensus pattern (20 bp):
TCAAAATCGCAATGTGAAAG
Found at i:167846 original size:40 final size:40
Alignment explanation
Indices: 167802--167879 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
167792 AGGTACACTT
* **
167802 TCGCAACGCTAAA-CTCAAAATCACAATTTGAAAGTCAAAA
1 TCGCAACGCGAAAGC-CAAAATCACAACGTGAAAGTCAAAA
* *
167842 TCGCAATGCGAAAGCCAAAATCGCAACGTGAAAGTCAA
1 TCGCAACGCGAAAGCCAAAATCACAACGTGAAAGTCAA
167880 TTCGCATTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 31 0.97
41 1 0.03
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.17
Consensus pattern (40 bp):
TCGCAACGCGAAAGCCAAAATCACAACGTGAAAGTCAAAA
Found at i:167943 original size:20 final size:20
Alignment explanation
Indices: 167918--167994 Score: 118
Period size: 20 Copynumber: 3.9 Consensus size: 20
167908 GCGATTTTCT
*
167918 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCA
*
167938 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
167958 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
*
167978 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
167995 GAATGTGTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:167973 original size:40 final size:40
Alignment explanation
Indices: 167918--167994 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
167908 GCGATTTTCT
167918 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCA
* *
167958 CGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAAT
167995 GAATGTGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (40 bp):
CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCA
Found at i:171176 original size:17 final size:17
Alignment explanation
Indices: 171154--171191 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
171144 CGGATGGGAA
171154 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
171171 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
171188 AGGA
1 AGGA
171192 ACGGATGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.37, T:0.32
Consensus pattern (17 bp):
AGGATGTCGTTGGATAT
Found at i:171200 original size:22 final size:20
Alignment explanation
Indices: 171153--171206 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 20
171143 CCGGATGGGA
171153 AAGGATGTCGTTGGATAT--
1 AAGGATGTCGTTGGATATGG
171171 -AGGATGTCGTTGGATATAGG
1 AAGGATGTCGTTGGATAT-GG
*
171191 AACGGATGTCGCTGGA
1 AA-GGATGTCGTTGGA
171207 GAGAGTGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 17 0.57
21 1 0.03
22 12 0.40
ACGTcount: A:0.26, C:0.09, G:0.37, T:0.28
Consensus pattern (20 bp):
AAGGATGTCGTTGGATATGG
Found at i:171363 original size:20 final size:20
Alignment explanation
Indices: 171338--171406 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
171328 GAAATTCAGT
171338 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* ** *
171358 GTTGCGATTTTGT-ATTATCAC
1 GTTGCGA--TAGTCAGAATCGC
171379 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
171399 ATTGCGAT
1 GTTGCGAT
171407 TTACATATTC
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 3 0.08
20 19 0.51
21 12 0.32
22 3 0.08
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:171944 original size:47 final size:47
Alignment explanation
Indices: 171893--171989 Score: 167
Period size: 47 Copynumber: 2.1 Consensus size: 47
171883 ATTAGTCAAC
* *
171893 ACAGATTAAAGCTTCAAAATAGGAATCGTTTTAGCCTTTGTTATCCA
1 ACAGATTAAAGCTTCAAAATAGGAATCGTTTTAGCATTTGTCATCCA
*
171940 ACAGATTAAAGCTTCAAAATAGGAATTGTTTTAGCATTTGTCATCCA
1 ACAGATTAAAGCTTCAAAATAGGAATCGTTTTAGCATTTGTCATCCA
171987 ACA
1 ACA
171990 ACATCTAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (47 bp):
ACAGATTAAAGCTTCAAAATAGGAATCGTTTTAGCATTTGTCATCCA
Found at i:176876 original size:14 final size:15
Alignment explanation
Indices: 176857--176890 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
176847 TGGAAAAGTG
*
176857 TTAAAAAAT-TATTT
1 TTAAAAAATATAGTT
176871 TTAAAAAATATAGTT
1 TTAAAAAATATAGTT
176886 TTAAA
1 TTAAA
176891 TTTAACTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
TTAAAAAATATAGTT
Found at i:184333 original size:21 final size:21
Alignment explanation
Indices: 184289--184332 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
184279 AAACTACGTA
184289 TTTAATATCTAAATAATTTAT
1 TTTAATATCTAAATAATTTAT
* *
184310 TTTAATATTTAAAT-TTTTAT
1 TTTAATATCTAAATAATTTAT
184330 TTT
1 TTT
184333 TTTAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTAATATCTAAATAATTTAT
Found at i:184995 original size:26 final size:26
Alignment explanation
Indices: 184959--185022 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
184949 ATGATTTATG
184959 ACATGTTCAAGTGGTCCAATCTAGAA
1 ACATGTTCAAGTGGTCCAATCTAGAA
184985 ACATGTTCAAGTGGTCCAATCTAGAA
1 ACATGTTCAAGTGGTCCAATCTAGAA
185011 ACATGTTCAAGT
1 ACATGTTCAAGT
185023 AAATAAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (26 bp):
ACATGTTCAAGTGGTCCAATCTAGAA
Found at i:195228 original size:136 final size:133
Alignment explanation
Indices: 194991--195254 Score: 465
Period size: 136 Copynumber: 2.0 Consensus size: 133
194981 GGAGACAAGT
* *
194991 ATAGACCAAAGCCTCAGCCCAAAATTCTTTGCTTAACCCAGCATTAGACAACATACACCGAACCT
1 ATAGACCAAAGCCTCAGCCCAAAATTCTTTGCCTAACCCAACATTAGACAACATACACCGAACCT
* *
195056 TCTCCACTAATGTTCGATTCATACGCTCTGCTACCCCATTCTGTTGTGGTGTACTTTTGACAGTG
66 TCTCCACTAATGTTCGATTCATACGCTCTGCCACCCCATTCTG-T-T-GTGTACTTATGACAGTG
195121 ACAAAC
128 ACAAAC
195127 ATAGACCAAAGCCTCAGCCCAAAATTCTTTGCCTAACCCAACATTAGACAACATACACCGAACCT
1 ATAGACCAAAGCCTCAGCCCAAAATTCTTTGCCTAACCCAACATTAGACAACATACACCGAACCT
195192 TCTCCACTAATGTTCGATTCATACGCTCTGCCACCCCATTCTGTTGTGTACTTATGACAGTGA
66 TCTCCACTAATGTTCGATTCATACGCTCTGCCACCCCATTCTGTTGTGTACTTATGACAGTGA
195255 AGTGCCTGAC
Statistics
Matches: 124, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
133 17 0.14
134 1 0.01
135 1 0.01
136 105 0.85
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.27
Consensus pattern (133 bp):
ATAGACCAAAGCCTCAGCCCAAAATTCTTTGCCTAACCCAACATTAGACAACATACACCGAACCT
TCTCCACTAATGTTCGATTCATACGCTCTGCCACCCCATTCTGTTGTGTACTTATGACAGTGACA
AAC
Found at i:196825 original size:39 final size:39
Alignment explanation
Indices: 196771--196850 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
196761 GAAAGACACG
196771 ATCGAATAGTACCACATGCCAATCTATTGATCCTCTTTC
1 ATCGAATAGTACCACATGCCAATCTATTGATCCTCTTTC
196810 ATCGAATAGTACCACATGCCAATCTATTGATCCTCTTTC
1 ATCGAATAGTACCACATGCCAATCTATTGATCCTCTTTC
196849 AT
1 AT
196851 TCTTTCTCCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.29, C:0.28, G:0.10, T:0.34
Consensus pattern (39 bp):
ATCGAATAGTACCACATGCCAATCTATTGATCCTCTTTC
Found at i:203727 original size:2 final size:2
Alignment explanation
Indices: 203720--203744 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
203710 ACTAATTTCA
203720 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
203745 GAGATAGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:228115 original size:176 final size:176
Alignment explanation
Indices: 227807--228140 Score: 476
Period size: 176 Copynumber: 1.9 Consensus size: 176
227797 ACGATTAATC
** * * *
227807 GTTATTAACGATTCGGTTACATGTTAACCACATGCAGAGACAGAGTTCACTTAGAGCCCAAGGGG
1 GTTATTAACGATTCAATTACAAGTTAACCACAGGCAGAGACAGAGCTCACTTAGAGCCCAAGGGG
* * *
227872 TCCCGGCCTCTGTTAAAATTTGTATATTCAGTATAATTTTAGTTTAATAATATTTTTGTTTATGT
66 TCCCGACCTCTGTTAAAATTTGTATATTCAGTATAATTTTAGTTTAATAATATTTTGGTTCATGT
227937 AAAAATAAATATTTAAATTTAAAAAATATAAAAATATAAAAATTTT
131 AAAAATAAATATTTAAATTTAAAAAATATAAAAATATAAAAATTTT
* * * *
227983 GTTATTAACGATTCAATTACAAGTTAACCACAGGTAGGGACAGAGCTCCCTTATAGCCCAAGGGG
1 GTTATTAACGATTCAATTACAAGTTAACCACAGGCAGAGACAGAGCTCACTTAGAGCCCAAGGGG
* * * *
228048 TCTCGA-ATCCTGTTAAAATTTTTATATTC-GATATAATTTT-GATTTAATAGTATTTTGGTTCA
66 TCCCGACCT-CTGTTAAAATTTGTATATTCAG-TATAATTTTAG-TTTAATAATATTTTGGTTCA
228110 TGTAAAAATAAATATTTAAATTTAAAAAATA
128 TGTAAAAATAAATATTTAAATTTAAAAAATA
228141 AATATGTATT
Statistics
Matches: 139, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
175 3 0.02
176 136 0.98
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (176 bp):
GTTATTAACGATTCAATTACAAGTTAACCACAGGCAGAGACAGAGCTCACTTAGAGCCCAAGGGG
TCCCGACCTCTGTTAAAATTTGTATATTCAGTATAATTTTAGTTTAATAATATTTTGGTTCATGT
AAAAATAAATATTTAAATTTAAAAAATATAAAAATATAAAAATTTT
Found at i:228708 original size:50 final size:51
Alignment explanation
Indices: 228596--228868 Score: 263
Period size: 50 Copynumber: 5.4 Consensus size: 51
228586 ATAAAAAGAA
* * *
228596 TGTAACACTTAACACATACTTACA-CTGATATAAGTGAATAAAATAAACAAA
1 TGTAACACTTAACACATACTTACACCAG-TGTAAGTGAATAAAATAAACAAG
* *
228647 TATAACACTTAACACATACTTACACCAGTGTAAGTG-ATAAAATAAATAAG
1 TGTAACACTTAACACATACTTACACCAGTGTAAGTGAATAAAATAAACAAG
* * * *
228697 TGTAGCACTTAATACATACATACACCGGTGTAAGTG-ATAAAATAAACAAG
1 TGTAACACTTAACACATACTTACACCAGTGTAAGTGAATAAAATAAACAAG
* * *
228747 TGTAACACTTAATACATACTTATACCAGTGTAAGTGAAT-AAA-AAA-ATG
1 TGTAACACTTAACACATACTTACACCAGTGTAAGTGAATAAAATAAACAAG
* * * ** * * * *
228795 TATATCACTTAACACATAC-TATATTAATGTAAGCGAATAAAATAAAATAAAA
1 TGTAACACTTAACACATACTTACACCAGTGTAAGTGAATAAAAT-AAA-CAAG
* *
228847 TATAATACTTAACACATACTTA
1 TGTAACACTTAACACATACTTA
228869 TAACGGTGTA
Statistics
Matches: 187, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
47 15 0.08
48 21 0.11
49 3 0.02
50 94 0.50
51 32 0.17
52 20 0.11
53 2 0.01
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (51 bp):
TGTAACACTTAACACATACTTACACCAGTGTAAGTGAATAAAATAAACAAG
Found at i:228888 original size:100 final size:99
Alignment explanation
Indices: 228585--228889 Score: 325
Period size: 100 Copynumber: 3.1 Consensus size: 99
228575 TAATTCATAC
* *
228585 TATAAAAAGAATGTA-ACACTTAACACATACTTACACTGATATAAGTGAATAAAATAAACAAATA
1 TATAAAAA-AATGTATACACTTAACACATACATACACTGATGTAAGTGAATAAAATAAACAAATA
*
228649 TAACACTTAACACATACTTACACCAGTGTAAGTGA
65 TAACACTTAACACATACTTATACCAGTGTAAGTGA
* * * * * *
228684 TAAAATAAATAAGTGTA-GCACTTAATACATACATACACCGGTGTAAGTG-ATAAAATAAACAAG
1 TATAA-AAA-AA-TGTATACACTTAACACATACATACACTGATGTAAGTGAATAAAATAAACAAA
* *
228747 TGTAACACTTAATACATACTTATACCAGTGTAAGTGA
63 TATAACACTTAACACATACTTATACCAGTGTAAGTGA
* * * * *
228784 -ATAAAAAAATGTATATCACTTAACACATAC-TATATTAATGTAAGCGAATAAAATAAAATAAAA
1 TATAAAAAAATGTATA-CACTTAACACATACATACACTGATGTAAGTGAATAAAAT-AAA-CAAA
* * * *
228847 TATAATACTTAACACATACTTATAACGGTGTAAAT-A
63 TATAACACTTAACACATACTTATACCAGTGTAAGTGA
228883 TATAAAA
1 TATAAAA
228890 TAAAAAAGTA
Statistics
Matches: 169, Mismatches: 29, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
96 4 0.02
97 12 0.07
98 23 0.14
99 11 0.07
100 89 0.53
101 30 0.18
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (99 bp):
TATAAAAAAATGTATACACTTAACACATACATACACTGATGTAAGTGAATAAAATAAACAAATAT
AACACTTAACACATACTTATACCAGTGTAAGTGA
Found at i:229598 original size:2 final size:2
Alignment explanation
Indices: 229591--229657 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
229581 TACCAAATGT
229591 TA TA TA 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
229633 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
229658 TGAATATGTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:234202 original size:92 final size:92
Alignment explanation
Indices: 234061--234334 Score: 462
Period size: 91 Copynumber: 3.0 Consensus size: 92
234051 GTGGCTCACT
*
234061 CAAGCTTGAGGAT-AAGGCTTCCCAAGCTATCTCTCTTCTCTCTCAAAGAGGCTCTCTAACTCTC
1 CAAGCTTGAGGATAAAGCCTTCCCAAGCTATCTCTCTTCTCTCTCAAAGAGGCTCTCTAACTCTC
234125 TAGTATCTCAAGCTTGGATTTCTTGGA
66 TAGTATCTCAAGCTTGGATTTCTTGGA
* *
234152 CAAGCTTGAGGATAAAGCCTTCCCAAGCTATCTCTATTCTCTCTCAAAGAGACTCTCTAACTCTC
1 CAAGCTTGAGGATAAAGCCTTCCCAAGCTATCTCTCTTCTCTCTCAAAGAGGCTCTCTAACTCTC
*
234217 TAGTATCTCAAGCTTGAATTTCTT-GA
66 TAGTATCTCAAGCTTGGATTTCTTGGA
* * *
234243 TAAACTTGAGGATAAAGCCTTCCCAAACTATCTCTCTTCTCTCTCAAAGAGGCTCTCTAACTCTC
1 CAAGCTTGAGGATAAAGCCTTCCCAAGCTATCTCTCTTCTCTCTCAAAGAGGCTCTCTAACTCTC
*
234308 TAGTTTCTCAAGCTTGGATTTCTTGGA
66 TAGTATCTCAAGCTTGGATTTCTTGGA
234335 TTTTGGATGG
Statistics
Matches: 170, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
91 97 0.57
92 73 0.43
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (92 bp):
CAAGCTTGAGGATAAAGCCTTCCCAAGCTATCTCTCTTCTCTCTCAAAGAGGCTCTCTAACTCTC
TAGTATCTCAAGCTTGGATTTCTTGGA
Found at i:235784 original size:15 final size:16
Alignment explanation
Indices: 235755--235787 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
235745 AAAATAGTTA
235755 GACCCTAATTTTTTTG
1 GACCCTAATTTTTTTG
235771 GACCCTAATTTTTTTG
1 GACCCTAATTTTTTTG
235787 G
1 G
235788 GAAAATGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.48
Consensus pattern (16 bp):
GACCCTAATTTTTTTG
Found at i:244450 original size:2 final size:2
Alignment explanation
Indices: 244443--244476 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
244433 TTGCAGCCGC
244443 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
244477 GCATGCATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:264866 original size:21 final size:21
Alignment explanation
Indices: 264826--264866 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
264816 CTGGAAGGTG
* *
264826 CCAGCTCAGCACGGTTGTTAT
1 CCAGCTCAGCACAGTAGTTAT
*
264847 CCAGCTCAGCATAGTAGTTA
1 CCAGCTCAGCACAGTAGTTA
264867 GCAGACTAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (21 bp):
CCAGCTCAGCACAGTAGTTAT
Found at i:278844 original size:105 final size:104
Alignment explanation
Indices: 278521--278977 Score: 778
Period size: 104 Copynumber: 4.4 Consensus size: 104
278511 GTGTTGTTTC
278521 GAGTCCAAT-TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGGAAATGTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAATGTTGTTGACAAC
*
278585 CAGC-GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* **
278624 GAGTCCAATATCCCTCGTTGTGAAGCAGAAATTGGCTCTGAAATTGAG-AATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTT-GTTGACAAC
* *
278688 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
*
278728 GAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG-TTGTTGACAAC
278793 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
278833 GAGTCCAATATCCTTCGTTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTGTTGACAAC
1 GAGTCCAATATCCTTCG-TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTGTTGACAAC
278898 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
278938 GAGTCC-ATATCCTTCGTTGTGAAGTTGAAATTGGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATT-GGCTCTG
278978 GTAAACGTTG
Statistics
Matches: 336, Mismatches: 11, Indels: 13
0.93 0.03 0.04
Matches are distributed among these distances:
102 6 0.02
103 38 0.11
104 130 0.39
105 125 0.37
106 37 0.11
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (104 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
Found at i:278911 original size:210 final size:208
Alignment explanation
Indices: 278521--278977 Score: 778
Period size: 210 Copynumber: 2.2 Consensus size: 208
278511 GTGTTGTTTC
278521 GAGTCCAAT-TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGGAAATGTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGGAAATGTTGTTGACAAC
*
278585 CAGCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCCTCGTTGTGAAGC
66 CAGCGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCCTCGTTGTGAAGC
*
278650 AGAAATTGGCTCTGAAATTGAGAATGTTCGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAA
131 AGAAATTGGCTCTGAAATTGAGAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
278715 CTTGCGTTGTCTG
196 CTTACGTTGTCTG
*
278728 GAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGA-GAAATGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGGAAATG-TTGTTGACAA
*
278792 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTTGTGA
65 CCAGC-GTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCCTCG-TTGTGA
**
278857 AGTTGAAATTGGCTCTGAAATTGAGAAATGTT-GTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
128 AGCAGAAATTGGCTCTGAAATTGAG-AATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
278921 TGAACTTACGTTGTCTG
192 TGAACTTACGTTGTCTG
278938 GAGTCC-ATATCCTTCGTTGTGAAGTTGAAATTGGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATT-GGCTCTG
278978 GTAAACGTTG
Statistics
Matches: 236, Mismatches: 8, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
207 15 0.06
208 51 0.22
209 75 0.32
210 89 0.38
211 6 0.03
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (208 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGGAAATGTTGTTGACAAC
CAGCGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCCTCGTTGTGAAGC
AGAAATTGGCTCTGAAATTGAGAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
CTTACGTTGTCTG
Found at i:279029 original size:54 final size:54
Alignment explanation
Indices: 278928--279031 Score: 192
Period size: 55 Copynumber: 1.9 Consensus size: 54
278918 AGTTGAACTT
278928 ACGTTGTCTGGAGTCCATATCCTTCGTTGTGAAGTTGAAATTGGGCTCTGGTAA
1 ACGTTGTCTGGAGTCCATATCCTTCGTTGTGAAGTTGAAATTGGGCTCTGGTAA
278982 ACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT-GGCTCTG
1 ACGTTGTCTGGAGTCC-ATATCCTTCGTTGTGAAGTTGAAATTGGGCTCTG
279032 AAATTGAGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
54 23 0.47
55 26 0.53
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (54 bp):
ACGTTGTCTGGAGTCCATATCCTTCGTTGTGAAGTTGAAATTGGGCTCTGGTAA
Found at i:279037 original size:158 final size:160
Alignment explanation
Indices: 278823--279141 Score: 608
Period size: 159 Copynumber: 2.0 Consensus size: 160
278813 AGTTGAACTT
278823 ACGTTGTCTGGAGTCCAATATCCTTCGTTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG-
1 ACGTTGTCTGGAGTCCAATATCCTTCGTTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
278887 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCATATCCTT
66 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCATATCCTT
278952 CGTTGTGAAGTTGAAATTGGGCTCT-GGTAA
131 CGTTGTGAAGTTGAAATT-GGCTCTGGGTAA
278982 ACGTTGTCTGGAGTCCAATATCCTTCG-TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
1 ACGTTGTCTGGAGTCCAATATCCTTCGTTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
279046 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCATATCCTT
66 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCATATCCTT
279111 CGTTGTGAAGTTGAAATTGGCTCTGGGTAA
131 CGTTGTGAAGTTGAAATTGGCTCTGGGTAA
279141 A
1 A
279142 ACCTGCAAAG
Statistics
Matches: 158, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
158 42 0.27
159 116 0.73
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (160 bp):
ACGTTGTCTGGAGTCCAATATCCTTCGTTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGT
TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCATATCCTT
CGTTGTGAAGTTGAAATTGGCTCTGGGTAA
Found at i:290533 original size:2 final size:2
Alignment explanation
Indices: 290526--290551 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
290516 ATAAAATACG
290526 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
290552 TAGAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:297947 original size:36 final size:36
Alignment explanation
Indices: 297866--298045 Score: 274
Period size: 36 Copynumber: 5.1 Consensus size: 36
297856 AGATGAACAA
* * *
297866 TTGAATCGAAAGTGTTGATGCTTCCTTCCGTT-TAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC
297901 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC
297937 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC
* * *
297973 TTGAATCGAAAGTGTCGATGTTTCCTTCCGTTC-AC
1 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC
* *
298008 TTGAATCGAAAGTGTTGATGCTTCCTTTTGTTCTTC
1 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC
298044 TT
1 TT
298046 ATTCACCTTC
Statistics
Matches: 132, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
35 60 0.45
36 72 0.55
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (36 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC
Found at i:298011 original size:71 final size:72
Alignment explanation
Indices: 297866--298045 Score: 283
Period size: 71 Copynumber: 2.5 Consensus size: 72
297856 AGATGAACAA
* * *
297866 TTGAATCGAAAGTGTTGATGCTTCCTTCCGTT-TACTTGAATCGAAAGTGTCGATGCTTCCTTTC
1 TTGAATCGAAAGTGTTGATGCTTCCTTTCGTTCTTCTTGAATCGAAAGTGTCGATGCTTCCTTCC
*
297930 GTTCTTC
66 GTTCTAC
* *
297937 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTCTTGAATCGAAAGTGTCGATGTTTCCTTCC
1 TTGAATCGAAAGTGTTGATGCTTCCTTTCGTTCTTCTTGAATCGAAAGTGTCGATGCTTCCTTCC
298002 GTTC-AC
66 GTTCTAC
*
298008 TTGAATCGAAAGTGTTGATGCTTCCTTTTGTTCTTCTT
1 TTGAATCGAAAGTGTTGATGCTTCCTTTCGTTCTTCTT
298046 ATTCACCTTC
Statistics
Matches: 100, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
71 67 0.67
72 33 0.33
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (72 bp):
TTGAATCGAAAGTGTTGATGCTTCCTTTCGTTCTTCTTGAATCGAAAGTGTCGATGCTTCCTTCC
GTTCTAC
Found at i:299882 original size:100 final size:100
Alignment explanation
Indices: 299709--299904 Score: 340
Period size: 100 Copynumber: 2.0 Consensus size: 100
299699 CTCAACTAAT
*
299709 CATTAACAACAATCTTCTAGAATCACTATGCAATATGCACTAGAGCTCGAGTAGTGTAGGAGCAC
1 CATTAACAACAATCTTCTAGAATCACTATGCAACATGCACTAGAGCTCGAGTAGTGTAGGAGCAC
*
299774 GATCGTTGATGCTCACTAACTCCTTATGCTATCAA
66 GATCGTTGATGCTCACTAACTCATTATGCTATCAA
* *
299809 CATTAACAACAATCTTCTAGAATCACTATGCAGCATGCAGTAGAGCTCGA-TCAGTGTAGGAGCA
1 CATTAACAACAATCTTCTAGAATCACTATGCAACATGCACTAGAGCTCGAGT-AGTGTAGGAGCA
299873 CGATCGTTGATGCTCACTAACTCATTATGCTA
65 CGATCGTTGATGCTCACTAACTCATTATGCTA
299905 ACAGAGAGAC
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
99 1 0.01
100 90 0.99
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (100 bp):
CATTAACAACAATCTTCTAGAATCACTATGCAACATGCACTAGAGCTCGAGTAGTGTAGGAGCAC
GATCGTTGATGCTCACTAACTCATTATGCTATCAA
Found at i:306182 original size:42 final size:46
Alignment explanation
Indices: 306084--306185 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 46
306074 TTATTATTTA
306084 AAATAATTAAAATAATATATTTTGTAACAATTATTTATTATATATT
1 AAATAATTAAAATAATATATTTTGTAACAATTATTTATTATATATT
*** *
306130 AAACGGTTAAAATAATATA-TTT-TAA-AA-TATATT-TTATATTTT
1 AAATAATTAAAATAATATATTTTGTAACAATTAT-TTATTATATATT
*
306172 TAATAATTAAAATA
1 AAATAATTAAAATA
306186 TAAAAAAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
42 21 0.45
43 4 0.09
44 3 0.06
45 3 0.06
46 16 0.34
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (46 bp):
AAATAATTAAAATAATATATTTTGTAACAATTATTTATTATATATT
Found at i:310891 original size:60 final size:60
Alignment explanation
Indices: 310783--310917 Score: 180
Period size: 60 Copynumber: 2.2 Consensus size: 60
310773 GTAGTAGGGT
** * *
310783 GAATCAACATACTGCGAGTGGTAGTGTTGGTGAAAGCCAAAATAATAGCTTGGTGGGAGA
1 GAATCAACATACTGAAAGTAGTAGTGTTGGTGAAAGCCAAAATAATAGCCTGGTGGGAGA
* * * * *
310843 GAATCAACATACTGAAAGTAGTAGTGTTGGTGGAAGTCATAATGATAGCCTGGTGGGAGT
1 GAATCAACATACTGAAAGTAGTAGTGTTGGTGAAAGCCAAAATAATAGCCTGGTGGGAGA
*
310903 GAATCAACACACTGA
1 GAATCAACATACTGA
310918 GAGTGAATCA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.24
Consensus pattern (60 bp):
GAATCAACATACTGAAAGTAGTAGTGTTGGTGAAAGCCAAAATAATAGCCTGGTGGGAGA
Found at i:310923 original size:19 final size:19
Alignment explanation
Indices: 310899--310938 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
310889 AGCCTGGTGG
310899 GAGTGAATCAACACACTGA
1 GAGTGAATCAACACACTGA
310918 GAGTGAATCAACACACTGA
1 GAGTGAATCAACACACTGA
310937 GA
1 GA
310939 CTGATAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
GAGTGAATCAACACACTGA
Found at i:314670 original size:30 final size:29
Alignment explanation
Indices: 314632--314716 Score: 88
Period size: 29 Copynumber: 2.9 Consensus size: 29
314622 CTAAAATATA
314632 TAAA-TTTTAAAAATTACTATTTAAGTCCC
1 TAAACTTTTAAAAATTACTATTT-AGTCCC
*
314661 TAAACTTTTAAAAGTTTA-TACTTTAG-CCC
1 TAAACTTTTAAAA-ATTACTA-TTTAGTCCC
*
314690 TAAACTTTCAAAAATTAC-ATTTTAGTC
1 TAAACTTTTAAAAATTACTA-TTTAGTC
314717 AGTAGACAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
28 9 0.19
29 20 0.43
30 12 0.26
31 6 0.13
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (29 bp):
TAAACTTTTAAAAATTACTATTTAGTCCC
Found at i:317730 original size:2 final size:2
Alignment explanation
Indices: 317711--317767 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
317701 GTTATGTATG
* * *
317711 AT AT AT AC AT AG AC 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
* *
317753 AT AT GT CT AT AT AT A
1 AT AT AT AT AT AT AT A
317768 GAAATGCGTG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:319062 original size:2 final size:2
Alignment explanation
Indices: 319057--319087 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
319047 ACACACATAC
319057 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
319088 ACTTTGGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.