Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008364.1 Hibiscus syriacus cultivar Beakdansim tig00111105_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: 5892847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 27
Found at i:194994 original size:2 final size:2
Alignment explanation
Indices: 194987--195012 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
194977 TGCATGTATG
194987 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
195013 CGCTTTTATA
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:203386 original size:3 final size:3
Alignment explanation
Indices: 203378--203426 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
203368 TATATAAATC
* *
203378 AAT AAT AAT ACT AAT AAT AAT AAGT AAT TAT AAT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT
203423 AAT A
1 AAT A
203427 TATTTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:203414 original size:22 final size:22
Alignment explanation
Indices: 203380--203421 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
203370 TATAAATCAA
*
203380 TAATAATACTAATAATAATAAG
1 TAATAATAATAATAATAATAAG
*
203402 TAATTATAATAATAATAATA
1 TAATAATAATAATAATAATA
203422 TAATATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
TAATAATAATAATAATAATAAG
Found at i:203428 original size:19 final size:20
Alignment explanation
Indices: 203382--203428 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
203372 TAAATCAATA
203382 ATAATACTAATAATAATAAGT
1 ATAATA-TAATAATAATAAGT
*
203403 A-ATTATAATAATAATAA-T
1 ATAATATAATAATAATAAGT
203421 ATAATATA
1 ATAATATA
203429 TTTTTTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 17 0.74
20 3 0.13
21 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
ATAATATAATAATAATAAGT
Found at i:203867 original size:85 final size:84
Alignment explanation
Indices: 203654--203899 Score: 243
Period size: 85 Copynumber: 3.0 Consensus size: 84
203644 TGGTTGATAG
* * * * *
203654 GCCCTCGAGCTGAACG-AACTCGAACTCGAAAGGTC---T-TTGGCAGATAGCCCTTCTCGACTT
1 GCCCTAGAGCTGAGCGTAA-TCGAACTCG-AAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTT
* *
203714 AAGCTAT-ACTGCAAATGATGT
64 GAGTTATGA-TGCAAATGATGT
* * * * **
203735 GCCTTAGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGA
1 GCCCTAGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGA
* *
203800 GTTATGTTGTAAATGATGT
66 GTTATGATGCAAATGATGT
* * **
203819 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTG
1 GCCCTAG-AGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTG
203884 AGTTATGATGCAAATG
65 AGTTATGATGCAAATG
203900 TTGTCTAAAA
Statistics
Matches: 131, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
80 6 0.05
81 21 0.16
82 1 0.01
83 1 0.01
84 39 0.30
85 63 0.48
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (84 bp):
GCCCTAGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGA
GTTATGATGCAAATGATGT
Found at i:204400 original size:105 final size:105
Alignment explanation
Indices: 204091--205132 Score: 1654
Period size: 105 Copynumber: 10.0 Consensus size: 105
204081 GCATTGTTCC
* ** * * * *
204091 GAGTCCAATATCCTCCACTGTGAAGTTGGAATTGACTCTG-AA-T--GAAAT-TTTGTTGACAAT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
* * * * *
204151 CAGCCGCCCCTTCGTCATGAAGTTGAGCTTGTGTTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * *
204192 GA-TTCAAGATCCTTCGTTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAA
* *
204256 CCAGCGGTCCATTCGTCGTGAAGTTGAACTTGTGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
204297 GAGTCCAATATCCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
204362 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
204401 G-GTCCAATATCCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
204465 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
204505 GAGTCCAATATCCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
204570 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
204610 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
* *
204675 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
204715 GAGT-CAAGATCCTTCGTTGAGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
*
204779 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
204819 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
204884 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
204924 GAGTCCAATATCCTTCGTGGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TGTTTATTGACAA
*
204989 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * **
205030 GAGT-CAAGATCCTTCGTTGAGAAGTTGAAATTGGCTCTGAAATTGAAAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
205094 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
205133 AGAGCGACCC
Statistics
Matches: 883, Mismatches: 47, Indels: 19
0.93 0.05 0.02
Matches are distributed among these distances:
100 29 0.03
101 4 0.00
102 1 0.00
103 102 0.12
104 156 0.18
105 449 0.51
106 142 0.16
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:204767 original size:314 final size:314
Alignment explanation
Indices: 204134--205132 Score: 1691
Period size: 314 Copynumber: 3.2 Consensus size: 314
204124 GACTCTGAAT
* * * * * * * *
204134 GAAAT-TTTGTTGACAATCAGCCGCCCCTTCGTCATGAAGTTGAGCTTGTGTTGTCTTGGA-TTC
1 GAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGGAGTCC
* * *
204197 AAGATCCTTCGTTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCG
65 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCG
* * *
204262 GTCCATTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTCGAA
129 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
204327 ATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
194 ATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
* * * *
204392 GCGTTGTCT-G-GTCCAATATCCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGG
259 GCGTTGTCTAGAGT-CAAGATCCTTCGTTGAGAAGTTGAAATTGGCTCTGAAATTGA
204447 GAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 GAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
204512 ATATCCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGT
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGT
204577 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
131 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
* * *
204642 TGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGC
196 TGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
204707 GTTGTCTAGAGTCAAGATCCTTCGTTGAGAAGTTGAAATTGGCTCTGAAATTGA
261 GTTGTCTAGAGTCAAGATCCTTCGTTGAGAAGTTGAAATTGGCTCTGAAATTGA
*
204761 GAAATGTTTATTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 GAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
204826 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGT
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGT
*
204891 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTGGTGAAGTTGAAAT
131 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
204956 TGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
196 TGGCTCTGAAATTGGGAAA-TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
205021 CGTTGTCTAGAGTCAAGATCCTTCGTTGAGAAGTTGAAATTGGCTCTGAAATTGA
260 CGTTGTCTAGAGTCAAGATCCTTCGTTGAGAAGTTGAAATTGGCTCTGAAATTGA
*
205076 AAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
1 GAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
205133 AGAGCGACCC
Statistics
Matches: 649, Mismatches: 32, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
313 161 0.25
314 333 0.51
315 155 0.24
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (314 bp):
GAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGT
CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
TGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
GTTGTCTAGAGTCAAGATCCTTCGTTGAGAAGTTGAAATTGGCTCTGAAATTGA
Found at i:204921 original size:419 final size:417
Alignment explanation
Indices: 204091--205136 Score: 1690
Period size: 419 Copynumber: 2.5 Consensus size: 417
204081 GCATTGTTCC
* ** * * * *
204091 GAGTCCAATATCCTCCACTGTGAAGTTGGAATTGACTCTG-AA-T--GAAAT-TTTGTTGACAAT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
* * * * * *
204151 CAGCCGCCCCTTCGTCATGAAGTTGAGCTTGTGTTGTCTTGGATTCAAGATCCTTCGTTGAGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGGAGTCAAGATCCTTCGTTGAGAAG
* * *
204216 TTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCATTCGTCGTGAAGTT
130 TTGAAATTGGCTCTGAAATTGAGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * * * *
204281 GAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGGGA
194 GAACTTGCGTTGTCTAGAGTCCAAGATCCTTCGTTGAGAAGTCGAAATTGGCTCTGAAATTGAGA
204346 AATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGTCCAATAT
259 AATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGTCCAATAT
*
204411 CCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCCT
324 CCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCT
204476 TCGTCGTGAAGTTGAACTTGCGTTGTCTG
389 TCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
204505 GAGTCCAATATCCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
* *
204570 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT-CAAGATCCTTCGTTGAGAAG
* *
204635 TTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTG
130 TTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
*
204700 AACTTGCGTTGTCTAGAGT-CAAGATCCTTCGTTGAGAAGTTGAAATTGGCTCTGAAATTGAGAA
195 AACTTGCGTTGTCTAGAGTCCAAGATCCTTCGTTGAGAAGTCGAAATTGGCTCTGAAATTGAGAA
*
204764 ATGTTTATTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
260 ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-G-GTCCAATA
* *
204829 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCC
323 TCCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCC
204894 TTCGTCGTGAAGTTGAACTTGCGTTGTCTG
388 TTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
204924 GAGTCCAATATCCTTCGTGGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TGTTTATTGACAA
*
204989 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCAAGATCCTTCGTTGAGAAG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCAAGATCCTTCGTTGAGAAG
*
205054 TTGAAATTGGCTCTGAAATTGAAAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
130 TTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
205119 AACTTGCGTTGTCTAGAG
195 AACTTGCGTTGTCTAGAG
205137 CGACCCGATA
Statistics
Matches: 584, Mismatches: 39, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
414 34 0.06
415 2 0.00
416 1 0.00
417 94 0.16
418 64 0.11
419 332 0.57
420 57 0.10
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (417 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCAAGATCCTTCGTTGAGAAGT
TGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
ACTTGCGTTGTCTAGAGTCCAAGATCCTTCGTTGAGAAGTCGAAATTGGCTCTGAAATTGAGAAA
TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGTCCAATATCC
TTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTC
GTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:209995 original size:3 final size:3
Alignment explanation
Indices: 209987--210035 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
209977 TATATAAATC
* *
209987 AAT AAT AAT ACT AAT AAT AAT AAGT AAT TAT AAT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT
210032 AAT A
1 AAT A
210036 TATTTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:210023 original size:22 final size:22
Alignment explanation
Indices: 209989--210030 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
209979 TATAAATCAA
*
209989 TAATAATACTAATAATAATAAG
1 TAATAATAATAATAATAATAAG
*
210011 TAATTATAATAATAATAATA
1 TAATAATAATAATAATAATA
210031 TAATATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
TAATAATAATAATAATAATAAG
Found at i:210037 original size:19 final size:20
Alignment explanation
Indices: 209991--210037 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
209981 TAAATCAATA
209991 ATAATACTAATAATAATAAGT
1 ATAATA-TAATAATAATAAGT
*
210012 A-ATTATAATAATAATAA-T
1 ATAATATAATAATAATAAGT
210030 ATAATATA
1 ATAATATA
210038 TTTTTTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 17 0.74
20 3 0.13
21 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
ATAATATAATAATAATAAGT
Found at i:211293 original size:193 final size:193
Alignment explanation
Indices: 210964--211349 Score: 772
Period size: 193 Copynumber: 2.0 Consensus size: 193
210954 CTGAAATGAC
210964 AGATGTCACAATAAGAGAGATGATTCCGTCACGTGTCAGTTAACCAGCAGAACCGGCGTGGAAAG
1 AGATGTCACAATAAGAGAGATGATTCCGTCACGTGTCAGTTAACCAGCAGAACCGGCGTGGAAAG
211029 ATATAACGATTCTGCTGTATGTAATCTTATCTAATTAATAAAATAAAATAATTAAAAGAGGGAAG
66 ATATAACGATTCTGCTGTATGTAATCTTATCTAATTAATAAAATAAAATAATTAAAAGAGGGAAG
211094 CGTGTACCGTGTCTTGTCTCCTGTCCCTCGAGCCGAAGGAGAAGCAAATTTTGACTTTTTTTT
131 CGTGTACCGTGTCTTGTCTCCTGTCCCTCGAGCCGAAGGAGAAGCAAATTTTGACTTTTTTTT
211157 AGATGTCACAATAAGAGAGATGATTCCGTCACGTGTCAGTTAACCAGCAGAACCGGCGTGGAAAG
1 AGATGTCACAATAAGAGAGATGATTCCGTCACGTGTCAGTTAACCAGCAGAACCGGCGTGGAAAG
211222 ATATAACGATTCTGCTGTATGTAATCTTATCTAATTAATAAAATAAAATAATTAAAAGAGGGAAG
66 ATATAACGATTCTGCTGTATGTAATCTTATCTAATTAATAAAATAAAATAATTAAAAGAGGGAAG
211287 CGTGTACCGTGTCTTGTCTCCTGTCCCTCGAGCCGAAGGAGAAGCAAATTTTGACTTTTTTTT
131 CGTGTACCGTGTCTTGTCTCCTGTCCCTCGAGCCGAAGGAGAAGCAAATTTTGACTTTTTTTT
211350 TGCGTAAATT
Statistics
Matches: 193, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
193 193 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (193 bp):
AGATGTCACAATAAGAGAGATGATTCCGTCACGTGTCAGTTAACCAGCAGAACCGGCGTGGAAAG
ATATAACGATTCTGCTGTATGTAATCTTATCTAATTAATAAAATAAAATAATTAAAAGAGGGAAG
CGTGTACCGTGTCTTGTCTCCTGTCCCTCGAGCCGAAGGAGAAGCAAATTTTGACTTTTTTTT
Found at i:213755 original size:3 final size:3
Alignment explanation
Indices: 213749--213779 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
213739 CCTTCTTCGT
213749 CTC CTC CTC CTCC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CT-C CTC CTC CTC CTC CTC CTC
213780 TTCGTTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:216857 original size:16 final size:16
Alignment explanation
Indices: 216836--216873 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
216826 TGGTTTGTTG
216836 AGATTGAAAATAGTTA
1 AGATTGAAAATAGTTA
*
216852 AGATTGAAAATGGTTA
1 AGATTGAAAATAGTTA
216868 AGATTG
1 AGATTG
216874 TACATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.32
Consensus pattern (16 bp):
AGATTGAAAATAGTTA
Found at i:217451 original size:15 final size:15
Alignment explanation
Indices: 217431--217462 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
217421 AACCATTTTT
217431 TTATAATAATCTCCA
1 TTATAATAATCTCCA
217446 TTATAATAATCTCCA
1 TTATAATAATCTCCA
217461 TT
1 TT
217463 TCACGCCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAATCTCCA
Found at i:221230 original size:48 final size:48
Alignment explanation
Indices: 221134--221240 Score: 112
Period size: 48 Copynumber: 2.2 Consensus size: 48
221124 AGTTATTCTA
* * *
221134 TATCTAAATTGCGTTTTATAGTTTATATTAATATTTATAAACTTTTTTT
1 TATCTAAATTGCGTTTAATAGTTTATATT-ATATTTAAAAAATTTTTTT
*
221183 TGTCTAAATTGC-TATTAATA-TTTATATT-TATTTAAAAAATTAATTTTT
1 TATCTAAATTGCGT-TTAATAGTTTATATTATATTTAAAAAATT--TTTTT
*
221231 TATTTAAATT
1 TATCTAAATT
221241 TGATTTCGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
46 11 0.22
48 22 0.45
49 16 0.33
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (48 bp):
TATCTAAATTGCGTTTAATAGTTTATATTATATTTAAAAAATTTTTTT
Found at i:222034 original size:17 final size:18
Alignment explanation
Indices: 222002--222036 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
221992 TAAAAACGTG
222002 TTATAAAGACAAAGATAA
1 TTATAAAGACAAAGATAA
*
222020 TTATAAA-ATAAAGATAA
1 TTATAAAGACAAAGATAA
222037 AAATAAACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.63, C:0.03, G:0.09, T:0.26
Consensus pattern (18 bp):
TTATAAAGACAAAGATAA
Found at i:223677 original size:20 final size:20
Alignment explanation
Indices: 223652--223695 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
223642 GAAAATCTGT
223652 TTCA-CCTTCTAGAATTTTAG
1 TTCACCCTT-TAGAATTTTAG
*
223672 TTCACCCTTTGGAATTTTAG
1 TTCACCCTTTAGAATTTTAG
223692 TTCA
1 TTCA
223696 TCCCCATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.45
Consensus pattern (20 bp):
TTCACCCTTTAGAATTTTAG
Found at i:233461 original size:26 final size:28
Alignment explanation
Indices: 233432--233498 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
233422 AACTAACAAC
* *
233432 TTTCTATCAAA-ATATAA-TTAAAATTA
1 TTTCTATCAAATAAAAAATTTAAAATTA
*
233458 TTTCAATCAAATAAAAAATTTAAAATTA
1 TTTCTATCAAATAAAAAATTTAAAATTA
*
233486 TTTATCATCAAAT
1 TTTCT-ATCAAAT
233499 TTACCAGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 10 0.30
27 4 0.12
28 12 0.36
29 7 0.21
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (28 bp):
TTTCTATCAAATAAAAAATTTAAAATTA
Found at i:234870 original size:60 final size:60
Alignment explanation
Indices: 234763--234877 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
234753 ATTATCTTTA
* * * * *
234763 AACCTTAGGCGTTACCATCTTTATTGGACTACATAAACTTATTATCATCATTTTTACCTC
1 AACCTTAGCCATTACCACCTTTATTGGACTACATAAACTCATCATCATCATTTTTACCTC
* * *
234823 AACCTTAGCCATTATCACCTTTATT-GATCTACATAAACTCGTCATCATTATTTTT
1 AACCTTAGCCATTACCACCTTTATTGGA-CTACATAAACTCATCATCATCATTTTT
234878 TTTCTCTCGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 2 0.04
60 44 0.96
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.41
Consensus pattern (60 bp):
AACCTTAGCCATTACCACCTTTATTGGACTACATAAACTCATCATCATCATTTTTACCTC
Found at i:235046 original size:5 final size:5
Alignment explanation
Indices: 235027--235058 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
235017 AAAACAAATA
235027 ATAAT A-AAT -TAAT ATAAT ATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
235059 ATTTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 6 0.24
5 19 0.76
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:235610 original size:2 final size:2
Alignment explanation
Indices: 235603--235636 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
235593 ATCACCTATT
235603 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
235637 CCCTCTTATC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:245157 original size:21 final size:20
Alignment explanation
Indices: 245131--245228 Score: 74
Period size: 21 Copynumber: 4.8 Consensus size: 20
245121 ATCAGTTTCC
245131 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
245152 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
**
245171 ACAAATTCGCATTGCGATTTT-
1 A-AAA-TCGCAACGCGATTTTG
* *
245192 ACAGAATCGCAACGCGAATATG
1 A-A-AATCGCAACGCGATTTTG
245214 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
245229 ACACATAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
19 1 0.02
20 17 0.27
21 42 0.67
22 3 0.05
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:245221 original size:20 final size:20
Alignment explanation
Indices: 245196--245388 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
245186 GATTTTACAG
* ** *
245196 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
245216 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
245236 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
245256 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
245276 AATCGCAACGCATATCCGTA
1 AATCGCAACGCGTATCCGTA
*
245296 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
245316 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
245336 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
245357 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
245377 AATCGCAACGCG
1 AATCGCAACGCG
245389 ATTTTTAAAG
Statistics
Matches: 149, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
19 1 0.01
20 129 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:245804 original size:33 final size:33
Alignment explanation
Indices: 245765--245835 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
245755 TTCACTTAGA
*
245765 TTTCATTTCGCGTTACGATTCTCTTGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
245798 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
245831 TTTCA
1 TTTCA
245836 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:245942 original size:21 final size:20
Alignment explanation
Indices: 245916--246023 Score: 95
Period size: 21 Copynumber: 5.7 Consensus size: 20
245906 TACAGAAGAG
245916 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
245937 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
245957 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
245978 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
245992 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
*
246011 TCGCAACGCGAAA
1 TCGCAACGAGAAA
246024 CCAAAATCGC
Statistics
Matches: 71, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
14 11 0.15
16 2 0.03
17 2 0.03
19 12 0.17
20 18 0.25
21 26 0.37
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.11
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:245960 original size:20 final size:20
Alignment explanation
Indices: 245916--245992 Score: 100
Period size: 21 Copynumber: 3.8 Consensus size: 20
245906 TACAGAAGAG
*
245916 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
245937 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
245957 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
245978 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
245993 CGCAACGCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 20 0.42
21 28 0.58
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:245973 original size:41 final size:41
Alignment explanation
Indices: 245915--245992 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
245905 TTACAGAAGA
*
245915 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
245956 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
245993 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:246014 original size:19 final size:19
Alignment explanation
Indices: 245928--246034 Score: 80
Period size: 19 Copynumber: 5.7 Consensus size: 19
245918 GCAACGAGAT
*
245928 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
*** *
245947 AGAATGACTGTCGCAACGAGAG
1 A-AATGAAAATCGCAAC--GCG
245969 AAATGAAAATCGCAA--CG
1 AAATGAAAATCGCAACGCG
*
245986 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
246002 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
**
246021 AAACCAAAATCGCA
1 AAATGAAAATCGCA
246035 TTGCGATTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 1 0.01
18 1 0.01
19 27 0.39
20 12 0.17
21 11 0.16
22 4 0.06
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.10
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:246052 original size:19 final size:19
Alignment explanation
Indices: 246030--246155 Score: 101
Period size: 19 Copynumber: 7.1 Consensus size: 19
246020 GAAACCAAAA
*
246030 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
246049 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
246063 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
246082 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
246096 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
246115 TCTCGTTGCGACAGTCATT
1 TCGCGTTGCGATTTTCATT
*
246134 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
246154 TC
1 TC
246156 AACCAAAAGA
Statistics
Matches: 86, Mismatches: 10, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 38 0.44
20 16 0.19
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:246071 original size:14 final size:14
Alignment explanation
Indices: 246052--246108 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
246042 TTTCATTTCG
246052 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
246066 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
246085 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
246099 CGTTGCGATT
1 CGTTGCGATT
246109 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:246146 original size:39 final size:33
Alignment explanation
Indices: 246035--246155 Score: 179
Period size: 33 Copynumber: 3.5 Consensus size: 33
246025 CAAAATCGCA
246035 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
246068 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
246101 TTGCGATTTTCATTTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCG
246140 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
246156 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
33 53 0.65
35 1 0.01
36 1 0.01
37 1 0.01
39 25 0.31
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:248115 original size:92 final size:93
Alignment explanation
Indices: 247802--248263 Score: 825
Period size: 92 Copynumber: 5.1 Consensus size: 93
247792 TAGATTGCTT
* *
247802 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAATA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
247867 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
247895 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC-G-GTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
247958 -TTGTC-TTGTTTTGTCTTTTGGTT-AA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
247983 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
248048 TTTGTCTTTG-TTT-TCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
248074 AGTAAATTTGTTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTTG-TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
248139 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
248168 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTACACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
248233 -TTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
248259 AGTAA
1 AGTAA
248264 TGCAATCCAT
Statistics
Matches: 358, Mismatches: 3, Indels: 18
0.94 0.01 0.05
Matches are distributed among these distances:
88 38 0.11
89 19 0.05
90 41 0.11
91 51 0.14
92 94 0.26
93 92 0.26
94 23 0.06
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:248366 original size:19 final size:18
Alignment explanation
Indices: 248342--248439 Score: 77
Period size: 19 Copynumber: 5.7 Consensus size: 18
248332 GCAACGAGAG
248342 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
248361 AATCGCAA--C-AAA-AG
1 AATCGCAACGCGAAAGAA
*
248375 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
248394 AATCGCAA--CG--AGAG
1 AATCGCAACGCGAAAGAA
248408 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
248427 AATCGCAATGCGA
1 AATCGCAACGCGA
248440 TTTTGGTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 18 0.29
15 1 0.02
16 6 0.10
17 6 0.10
18 1 0.02
19 31 0.49
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.09
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:248368 original size:33 final size:33
Alignment explanation
Indices: 248310--248434 Score: 187
Period size: 33 Copynumber: 3.8 Consensus size: 33
248300 TAGTTTACTT
* *
248310 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAA-TGAAAATCGCAACGAGAGAA
* *
248344 TCGCAACGCGAAATGAAAATCGCAACAAAAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAGAGAA
**
248377 TCGCAACGCGAAACCAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAGAGAA
248410 TCGCAACGCGAAATGAAAATCGCAA
1 TCGCAACGCGAAATGAAAATCGCAA
248435 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 69 0.85
34 12 0.15
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
TCGCAACGCGAAATGAAAATCGCAACGAGAGAA
Found at i:248409 original size:66 final size:67
Alignment explanation
Indices: 248310--248434 Score: 225
Period size: 66 Copynumber: 1.9 Consensus size: 67
248300 TAGTTTACTT
*
248310 TCGCAACACGAAACTTAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACAAAAG
1 TCGCAACACGAAACTCAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACAAAAG
248375 AA
66 AA
*
248377 TCGCAACGCGAAAC-CAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAA
1 TCGCAACACGAAACTCAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAA
248435 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
66 43 0.77
67 13 0.23
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (67 bp):
TCGCAACACGAAACTCAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACAAAAG
AA
Found at i:248457 original size:19 final size:19
Alignment explanation
Indices: 248435--248585 Score: 124
Period size: 19 Copynumber: 8.5 Consensus size: 19
248425 AAAATCGCAA
*
248435 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCGTTTCGCGT
*
248454 TGCGA--TTC-TCTCG-GT
1 TGCGATTTTCGTTTCGCGT
* *
248469 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCGTTTCGCGT
* *
248488 TGTGA--TTC-TGT--CGT
1 TGCGATTTTCGTTTCGCGT
*
248502 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCGTTTCGCGT
*
248521 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCGTTTCGCGT
* *
248540 TGCGA-TTTGGTTTCTCGT
1 TGCGATTTTCGTTTCGCGT
* *
248558 TGCGATTCTCATTTCGCGT
1 TGCGATTTTCGTTTCGCGT
248577 TGCGATTTT
1 TGCGATTTT
248586 AAGTTTCGTG
Statistics
Matches: 105, Mismatches: 17, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
14 6 0.06
15 7 0.07
16 9 0.09
17 10 0.10
18 21 0.20
19 52 0.50
ACGTcount: A:0.09, C:0.19, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCGTTTCGCGT
Found at i:248509 original size:33 final size:34
Alignment explanation
Indices: 248435--248527 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 34
248425 AAAATCGCAA
**
248435 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGGT
* * *
248469 TGCGATTTTCATTTCGCATTGTGATTCTGTC-GT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGGT
248502 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTCATTTCGCGTTGCGATT
248528 TTGGTTTCGC
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
33 26 0.50
34 26 0.50
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (34 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGGT
Found at i:248571 original size:56 final size:56
Alignment explanation
Indices: 248429--248585 Score: 170
Period size: 56 Copynumber: 2.9 Consensus size: 56
248419 GAAATGAAAA
* *
248429 TCGCAATGCGATTTTGGTTTCGCGTTGCGATTCTC---TCG-GTTGCGATTTTCATT
1 TCGCATTGCGA-TTTGGTTTCTCGTTGCGATTCTCATTTCGCGTTGCGATTTTCATT
* * **
248482 TCGCATTGTGATTCT-G----TCGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCATTGCGATT-TGGTTTCTCGTTGCGATTCTCATTTCGCGTTGCGATTTTCATT
*
248534 TCGCGTTGCGATTTGGTTTCTCGTTGCGATTCTCATTTCGCGTTGCGATTTT
1 TCGCATTGCGATTTGGTTTCTCGTTGCGATTCTCATTTCGCGTTGCGATTTT
248586 AAGTTTCGTG
Statistics
Matches: 85, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
48 12 0.14
51 4 0.05
52 28 0.33
53 10 0.12
56 31 0.36
ACGTcount: A:0.10, C:0.20, G:0.25, T:0.46
Consensus pattern (56 bp):
TCGCATTGCGATTTGGTTTCTCGTTGCGATTCTCATTTCGCGTTGCGATTTTCATT
Found at i:248573 original size:37 final size:37
Alignment explanation
Indices: 248446--248584 Score: 116
Period size: 37 Copynumber: 3.9 Consensus size: 37
248436 GCGATTTTGG
248446 TTTCGCGTTGCGATTCTC---TCG-GTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCATTTCGCGTTGCGA-TTTCA
* * *
248480 TTTCGCATTGTGA-T-TC-TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCATTTCGCGTTGCGA-TTTCA
* ** **
248513 TTTCGCGTTGCGATTTTGGTTTCGCGTTGCGATTTGG
1 TTTCGCGTTGCGATTCTCATTTCGCGTTGCGATTTCA
*
248550 TTTCTCGTTGCGATTCTCATTTCGCGTTGCGATTT
1 TTTCGCGTTGCGATTCTCATTTCGCGTTGCGATTT
248585 TAAGTTTCGT
Statistics
Matches: 85, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
32 2 0.02
33 25 0.29
34 13 0.15
35 1 0.01
36 2 0.02
37 34 0.40
38 8 0.09
ACGTcount: A:0.09, C:0.20, G:0.24, T:0.47
Consensus pattern (37 bp):
TTTCGCGTTGCGATTCTCATTTCGCGTTGCGATTTCA
Found at i:250396 original size:13 final size:13
Alignment explanation
Indices: 250378--250416 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
250368 TTGATTGTTA
250378 ATGATTTGTAAAG
1 ATGATTTGTAAAG
250391 ATGATTTGTAAAAG
1 ATGATTTGT-AAAG
*
250405 TTGATTGTGTAA
1 ATGATT-TGTAA
250417 TTGATGCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 9 0.39
14 11 0.48
15 3 0.13
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (13 bp):
ATGATTTGTAAAG
Found at i:250409 original size:14 final size:14
Alignment explanation
Indices: 250378--250416 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
250368 TTGATTGTTA
250378 ATGATTTGT-AAAG
1 ATGATTTGTAAAAG
250391 ATGATTTGTAAAAG
1 ATGATTTGTAAAAG
*
250405 TTGATTGTGTAA
1 ATGATT-TGTAA
250417 TTGATGCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.39
14 9 0.39
15 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (14 bp):
ATGATTTGTAAAAG
Found at i:250534 original size:19 final size:18
Alignment explanation
Indices: 250518--250632 Score: 129
Period size: 19 Copynumber: 6.7 Consensus size: 18
250508 AAAAATGACT
250518 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
250537 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
250555 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
250569 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
250588 ATCGCAATGCGGAAATGAA
1 ATCGCAATGC-GAAATGAA
*
250607 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
250621 ATCGCAATGCGA
1 ATCGCAATGCGA
250633 TTTAATTTCG
Statistics
Matches: 85, Mismatches: 3, Indels: 19
0.79 0.03 0.18
Matches are distributed among these distances:
14 16 0.19
15 2 0.02
16 14 0.16
17 2 0.02
18 9 0.11
19 36 0.42
20 6 0.07
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:250594 original size:51 final size:52
Alignment explanation
Indices: 250518--250632 Score: 223
Period size: 52 Copynumber: 2.2 Consensus size: 52
250508 AAAAATGACT
250518 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
250569 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
250621 ATCGCAATGCGA
1 ATCGCAATGCGA
250633 TTTAATTTCG
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 29 0.46
52 34 0.54
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
Found at i:250664 original size:14 final size:17
Alignment explanation
Indices: 250628--250873 Score: 164
Period size: 18 Copynumber: 14.4 Consensus size: 17
250618 AGAATCGCAA
*
250628 TGCGATTTAATTTCGCAT
1 TGCGATTTCATTTCGC-T
*
250646 TGCGA-TTC-TCTCG-T
1 TGCGATTTCATTTCGCT
250660 TGCGATTTTCATTTCGCAT
1 TGCGA-TTTCATTTCGC-T
250679 TGCGATTTCATTTCGCAT
1 TGCGATTTCATTTCGC-T
*
250697 TGCGA-TTC-TCTCG-T
1 TGCGATTTCATTTCGCT
250711 TGCGATTTTCATTTCGCT
1 TGCGA-TTTCATTTCGCT
250729 TGCGATTTCATTTCCGCAT
1 TGCGATTTCATTT-CGC-T
*
250748 TGCGA-TTC-TCTCG-T
1 TGCGATTTCATTTCGCT
250762 TGCGATTTTCATTTCCGCAT
1 TGCGA-TTTCATTT-CGC-T
*
250782 TGCGA-TTC-TCTCG-T
1 TGCGATTTCATTTCGCT
*
250796 TGCGATTTTCATTTCACAT
1 TGCGA-TTTCATTTCGC-T
250815 TGCGATTTTCATTTCCGCAT
1 TGCGA-TTTCATTT-CGC-T
250835 TGCGATTTCA--T-G-T
1 TGCGATTTCATTTCGCT
*
250848 TGGGATTTTCATTTCGCAT
1 TGCGA-TTTCATTTCGC-T
250867 TGCGATT
1 TGCGATT
250874 CTCTCGTTGC
Statistics
Matches: 186, Mismatches: 13, Indels: 58
0.72 0.05 0.23
Matches are distributed among these distances:
13 5 0.03
14 29 0.16
15 1 0.01
16 25 0.13
17 32 0.17
18 42 0.23
19 37 0.20
20 15 0.08
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (17 bp):
TGCGATTTCATTTCGCT
Found at i:250683 original size:51 final size:51
Alignment explanation
Indices: 250622--250845 Score: 296
Period size: 51 Copynumber: 4.3 Consensus size: 51
250612 AACGAGAGAA
* *
250622 TCGCAATGCGATTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
250673 TCGCATTGCGATTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
250724 TCGC-TTGCGATTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATT
* * *
250775 TCCGCATTGCGA-TTC-TCTCG--TTGCGATTTTCATTTCACATTGCGATTTTCATT
1 T-CGCATTGCGATTTCATTTCGCATTGCGA--TTC---TCTCGTTGCGATTTTCATT
250828 TCCGCATTGCGATTTCAT
1 T-CGCATTGCGATTTCAT
250846 GTTGGGATTT
Statistics
Matches: 158, Mismatches: 5, Indels: 16
0.88 0.03 0.09
Matches are distributed among these distances:
48 6 0.04
50 19 0.12
51 88 0.56
52 6 0.04
53 35 0.22
54 3 0.02
55 1 0.01
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (51 bp):
TCGCATTGCGATTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:250776 original size:34 final size:32
Alignment explanation
Indices: 250628--250821 Score: 198
Period size: 34 Copynumber: 5.8 Consensus size: 32
250618 AGAATCGCAA
*
250628 TGCGATTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTCATTTCGCATTGCGATTCTCTCGT
*
250660 TGCGATTTTCATTTCGCATTGCGATTTCATTTCGCAT
1 TGCGA-TTTCATTTCGCATTGCGA-TTC-TCTCG--T
* *
250697 TGCGA-TTC-TCTCG--TTGCGATTTTCATTTCGCT
1 TGCGATTTCATTTCGCATTGCGA--TTC-TCTCG-T
250729 TGCGATTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTCATTT-CGCATTGCGATTCTCTCGT
250762 TGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGA-TTTCATTT-CGCATTGCGATTCTCTCGT
*
250796 TGCGATTTTCATTTCACATTGCGATT
1 TGCGA-TTTCATTTCGCATTGCGATT
250822 TTCATTTCCG
Statistics
Matches: 143, Mismatches: 7, Indels: 23
0.83 0.04 0.13
Matches are distributed among these distances:
32 17 0.12
33 47 0.33
34 55 0.38
35 12 0.08
37 12 0.08
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (32 bp):
TGCGATTTCATTTCGCATTGCGATTCTCTCGT
Found at i:250801 original size:85 final size:85
Alignment explanation
Indices: 250678--250887 Score: 347
Period size: 85 Copynumber: 2.5 Consensus size: 85
250668 TCATTTCGCA
*
250678 TTGCGA-TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGC-TTGCGA-TTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCACATTGCGATTTTCAT
250740 TTCCGCATTGCGATTCTC-TCG
66 TTCCGCATTGCGATT-TCAT-G
250761 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCACATTGCGATTTTCA
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCACATTGCGATTTTCA
250826 TTTCCGCATTGCGATTTCATG
65 TTTCCGCATTGCGATTTCATG
*
250847 TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
250888 GAATTTCCGT
Statistics
Matches: 120, Mismatches: 2, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
83 6 0.05
84 8 0.07
85 61 0.51
86 23 0.19
87 22 0.18
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.45
Consensus pattern (85 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCACATTGCGATTTTCAT
TTCCGCATTGCGATTTCATG
Found at i:250801 original size:136 final size:136
Alignment explanation
Indices: 250628--250873 Score: 401
Period size: 136 Copynumber: 1.8 Consensus size: 136
250618 AGAATCGCAA
*
250628 TGCGATTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA-TTTCATTT
1 TGCGATTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCACATTGCGATTTTCATTT
250692 -CGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGC-TTGCGATTTCATTTCCGCATTGCGAT
66 CCGCATTGCGATT-TCAT-GTTGCGATTTTCATTTCGCATTGCGATTTCATTTCCGCATTGCGAT
250754 TCTCTCGT
129 TCTCTCGT
*
250762 TGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCACATTGCGATTTTCAT
1 TGCGA-TTTAATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCACATTGCGATTTTCAT
*
250827 TTCCGCATTGCGATTTCATGTTGGGATTTTCATTTCGCATTGCGATT
64 TTCCGCATTGCGATTTCATGTTGCGATTTTCATTTCGCATTGCGATT
250874 CTCTCGTTGC
Statistics
Matches: 103, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
134 5 0.05
135 7 0.07
136 42 0.41
137 28 0.27
138 21 0.20
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (136 bp):
TGCGATTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCACATTGCGATTTTCATTT
CCGCATTGCGATTTCATGTTGCGATTTTCATTTCGCATTGCGATTTCATTTCCGCATTGCGATTC
TCTCGT
Found at i:250821 original size:53 final size:52
Alignment explanation
Indices: 250659--250873 Score: 214
Period size: 51 Copynumber: 4.2 Consensus size: 52
250649 GATTCTCTCG
* * *
250659 TTGCGATTTTCATTT-CGCATTGCGATTTCAT-TT-CGCA-TTGCGATTCTCTCG
1 TTGCGATTTTCATTTCCGCATTGCGATTTCATGTTGCG-ATTTTC-ATT-TCACA
* * * *
250710 TTGCGATTTTCATTT-CGC-TTGCGATTTCAT-TTCCGCA-TTGCGATTCTCTCG
1 TTGCGATTTTCATTTCCGCATTGCGATTTCATGTTGCG-ATTTTC-ATT-TCACA
250761 TTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCCGCATTGCGATT-TCAT-GTTGCGATTTTCATTTCACA
* *
250814 TTGCGATTTTCATTTCCGCATTGCGATTTCATGTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCCGCATTGCGATTTCATGTTGCGATTTTCATTTCACA
250866 TTGCGATT
1 TTGCGATT
250874 CTCTCGTTGC
Statistics
Matches: 150, Mismatches: 6, Indels: 15
0.88 0.04 0.09
Matches are distributed among these distances:
50 14 0.09
51 51 0.34
52 31 0.21
53 41 0.27
54 6 0.04
55 7 0.05
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (52 bp):
TTGCGATTTTCATTTCCGCATTGCGATTTCATGTTGCGATTTTCATTTCACA
Found at i:250843 original size:33 final size:32
Alignment explanation
Indices: 250806--250887 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 32
250796 TGCGATTTTC
*
250806 ATTTCACATTGCGATTTTCATTTCCGCATTGCG
1 ATTTCACGTTGCGATTTTCATTT-CGCATTGCG
* *
250839 ATTTCATGTTGGGATTTTCATTTCGCATTGCG
1 ATTTCACGTTGCGATTTTCATTTCGCATTGCG
*
250871 ATTCTCTCGTTGCGATT
1 ATT-TCACGTTGCGATT
250888 GAATTTCCGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 12 0.29
33 30 0.71
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (32 bp):
ATTTCACGTTGCGATTTTCATTTCGCATTGCG
Found at i:250901 original size:52 final size:52
Alignment explanation
Indices: 250761--250873 Score: 147
Period size: 53 Copynumber: 2.2 Consensus size: 52
250751 GATTCTCTCG
* *
250761 TTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCACA
1 TTGCGATTTTCAGTTCCGCATTGCAATT-TCAT-GTTGCGATTTTCATTTCACA
* * * *
250814 TTGCGATTTTCATTTCCGCATTGCGATTTCATGTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCAGTTCCGCATTGCAATTTCATGTTGCGATTTTCATTTCACA
250866 TTGCGATT
1 TTGCGATT
250874 CTCTCGTTGC
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
52 28 0.49
53 29 0.51
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (52 bp):
TTGCGATTTTCAGTTCCGCATTGCAATTTCATGTTGCGATTTTCATTTCACA
Found at i:253092 original size:12 final size:12
Alignment explanation
Indices: 253075--253099 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
253065 TCTTCGGGGA
253075 CTTTTTCTTCTT
1 CTTTTTCTTCTT
253087 CTTTTTCTTCTT
1 CTTTTTCTTCTT
253099 C
1 C
253100 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:253306 original size:24 final size:24
Alignment explanation
Indices: 253272--253318 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
253262 CTGAAACATC
253272 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
253296 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
253319 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:254039 original size:20 final size:20
Alignment explanation
Indices: 254011--254239 Score: 244
Period size: 20 Copynumber: 11.4 Consensus size: 20
254001 AAATTTCAGT
* * *
254011 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
254031 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
254051 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
254071 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
254091 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
254111 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
254131 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
254151 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
254171 GTTGCGATTTATGGATACGC
1 GTTGCGATTTACGGATTCGC
*
254191 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
254211 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
254231 GTTGCGATT
1 GTTGCGATT
254240 CTGTAAAATC
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 184 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:254257 original size:21 final size:20
Alignment explanation
Indices: 254233--254282 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
254223 ATATTCGCGT
254233 TGCGATTCTGTAAAATCGCAA
1 TGCGATT-TGTAAAATCGCAA
** *
254254 TGCGAATTTGTACTATCGCAT
1 TGCG-ATTTGTAAAATCGCAA
254275 TGCGATTT
1 TGCGATTT
254283 TCAAGAATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.16
21 18 0.72
22 3 0.12
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (20 bp):
TGCGATTTGTAAAATCGCAA
Found at i:258380 original size:2 final size:2
Alignment explanation
Indices: 258373--258401 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
258363 ATTAAAAATA
258373 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 A
258402 ATGTTGACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:267705 original size:2 final size:2
Alignment explanation
Indices: 267698--267727 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
267688 GCAGAATTGT
267698 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
267728 AAAGAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:271149 original size:25 final size:23
Alignment explanation
Indices: 271110--271156 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
271100 TTGGCTGTAT
* *
271110 TATTATTTTATATTATACAAAAATA
1 TATTATTTAAAATTA-A-AAAAATA
271135 TATTATTTAAAATTAAAAAAAT
1 TATTATTTAAAATTAAAAAAAT
271157 CTTTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 1 0.05
25 13 0.65
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTATTTAAAATTAAAAAAATA
Found at i:273588 original size:29 final size:28
Alignment explanation
Indices: 273545--273648 Score: 75
Period size: 29 Copynumber: 3.5 Consensus size: 28
273535 TCGACATATG
*
273545 AATAGTTGAGTGACTATTTTGTAACTTTT
1 AATAGTCGAG-GACTATTTTGTAACTTTT
**** * *
273574 AATAGTCGATGGACTCAACAAAGTAACACTCT
1 AATAGTCGA-GGACT--ATTTTGTAAC-TTTT
273606 -ATAGTCTGAGGACTATTTTGTAACTTTT
1 AATAGTC-GAGGACTATTTTGTAACTTTT
273634 AATAGTCGGAGGACT
1 AATAGTC-GAGGACT
273649 TAACAAAGCA
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
28 2 0.04
29 31 0.56
30 1 0.02
31 17 0.31
32 4 0.07
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (28 bp):
AATAGTCGAGGACTATTTTGTAACTTTT
Found at i:273623 original size:60 final size:61
Alignment explanation
Indices: 273546--273671 Score: 188
Period size: 60 Copynumber: 2.1 Consensus size: 61
273536 CGACATATGA
*
273546 ATAGT-TGAGTGACTATTTTGTAACTTTTAATAGTC-GATGGACTCAACAAAGTAACA-CTCT
1 ATAGTCTGAGTGACTATTTTGTAACTTTTAATAGTCGGA-GGACTCAACAAAGCAACACCT-T
*
273606 ATAGTCTGAG-GACTATTTTGTAACTTTTAATAGTCGGAGGACTTAACAAAGCAACACCTT
1 ATAGTCTGAGTGACTATTTTGTAACTTTTAATAGTCGGAGGACTCAACAAAGCAACACCTT
273666 ATAGTC
1 ATAGTC
273672 AGGAGATCAT
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
60 53 0.87
61 8 0.13
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (61 bp):
ATAGTCTGAGTGACTATTTTGTAACTTTTAATAGTCGGAGGACTCAACAAAGCAACACCTT
Found at i:277351 original size:22 final size:23
Alignment explanation
Indices: 277318--277379 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
277308 TAATGTTCAT
* *
277318 GTTCGAGCTT-AATCGAACTTGA
1 GTTCAAGCTTAAATCGAACTCGA
* *
277340 GTTTAAGCTTAAATCAAACTCGA
1 GTTCAAGCTTAAATCGAACTCGA
*
277363 GTTCAAGCTTCAATCGA
1 GTTCAAGCTTAAATCGA
277380 GTTAAATCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 8 0.25
23 24 0.75
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (23 bp):
GTTCAAGCTTAAATCGAACTCGA
Found at i:284291 original size:2 final size:2
Alignment explanation
Indices: 284284--284310 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
284274 TATTTTAGTT
284284 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 T
284311 TAAATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:284591 original size:26 final size:25
Alignment explanation
Indices: 284562--284614 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
284552 TAAAAAATAA
*
284562 AATATTAAAATTAATATTTTAATCCT
1 AATATTAAAACTAATATTTTAA-CCT
*
284588 AATATTAAAACTAATCTTTTAACCT
1 AATATTAAAACTAATATTTTAACCT
284613 AA
1 AA
284615 GGGTGCGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (25 bp):
AATATTAAAACTAATATTTTAACCT
Found at i:285886 original size:20 final size:20
Alignment explanation
Indices: 285861--285914 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
285851 TATTATCTAG
285861 TAATCTTACATTCCTACTAA
1 TAATCTTACATTCCTACTAA
* *
285881 TAATCTTACATTCCTATTGA
1 TAATCTTACATTCCTACTAA
*
285901 TAATCTTATATTCC
1 TAATCTTACATTCC
285915 GTGAATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.22, G:0.02, T:0.44
Consensus pattern (20 bp):
TAATCTTACATTCCTACTAA
Found at i:287026 original size:16 final size:16
Alignment explanation
Indices: 287007--287040 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
286997 CAATATACGA
287007 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
287023 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
287039 AT
1 AT
287041 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:287113 original size:16 final size:18
Alignment explanation
Indices: 287081--287114 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
287071 TATTAATGTA
287081 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
287099 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
287115 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:287785 original size:130 final size:130
Alignment explanation
Indices: 287581--287828 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
287571 AATTTTCTTC
* * *
287581 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGGT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
287646 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
287711 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
287776 CCTAATTAAATGATTAATTTATTAAATTCTATTTTATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
287829 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:288271 original size:35 final size:35
Alignment explanation
Indices: 288221--288296 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
288211 AATTGAATTT
* *
288221 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
288256 AATTGAATTACTTTGGAAATTAGGGTTTAGCATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
288291 AATTGA
1 AATTGA
288297 GGACTGCTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:289034 original size:26 final size:24
Alignment explanation
Indices: 288979--289038 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 24
288969 ACTTTTACAT
*
288979 TTTTACAT-TTAGGTTAAAAATTAG
1 TTTTA-ATATTAGGTTAAAAATTAA
289003 TTTTAATATTAGGATTAAAATATTAA
1 TTTTAATATTAGG-TTAAAA-ATTAA
289029 TTTTAATATT
1 TTTTAATATT
289039 TCATTTATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 2 0.06
24 10 0.31
25 6 0.19
26 14 0.44
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (24 bp):
TTTTAATATTAGGTTAAAAATTAA
Found at i:289679 original size:19 final size:19
Alignment explanation
Indices: 289651--289694 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
289641 TCAATTCGAG
* *
289651 CGTCGTGAGAAACTATTAA
1 CGTCGCGAGAAAATATTAA
289670 CGTCGCGAGAAAATATTAA
1 CGTCGCGAGAAAATATTAA
289689 CGTCGC
1 CGTCGC
289695 AAAATCGCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (19 bp):
CGTCGCGAGAAAATATTAA
Found at i:293274 original size:16 final size:15
Alignment explanation
Indices: 293187--293308 Score: 59
Period size: 16 Copynumber: 7.4 Consensus size: 15
293177 ATTAAAATTA
*
293187 ATAACAAATAAATAT
1 ATAATAAATAAATAT
293202 AATTAATAATATTAAATAT
1 -A-TAATAA-A-TAAATAT
293221 -TAAATATAATAAATA-
1 AT-AATA-AATAAATAT
*
293236 ATAAATAATTAAAATAT
1 AT-AATAAAT-AAATAT
293253 AATAATAAATAAATAT
1 -ATAATAAATAAATAT
*
293269 AGTAATTAAAATATATAT
1 A-TAA-T-AAATAAATAT
* * *
293287 TTTATAAATAATTATT
1 ATAATAAATAAATA-T
293303 ATAATA
1 ATAATA
293309 TATTTTATAA
Statistics
Matches: 83, Mismatches: 10, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
15 10 0.12
16 34 0.41
17 19 0.23
18 13 0.16
19 7 0.08
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.38
Consensus pattern (15 bp):
ATAATAAATAAATAT
Found at i:293277 original size:30 final size:31
Alignment explanation
Indices: 293176--293283 Score: 105
Period size: 32 Copynumber: 3.4 Consensus size: 31
293166 TAATTTTTTA
*
293176 AATTAAAAT-TAATAACAAATAAATATAATTAAT
1 AATTAAAATATAATAATAAATAAATAT-A--AAT
* *
293209 AATATTAAATATTA-AATATAATAAATAATAAAT
1 AAT-TAAAATATAATAATA-AATAAAT-ATAAAT
*
293242 AATTAAAATATAATAATAAATAAATAT-AGT
1 AATTAAAATATAATAATAAATAAATATAAAT
293272 AATTAAAATATA
1 AATTAAAATATA
293284 TATTTTATAA
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
30 14 0.22
31 2 0.03
32 15 0.23
33 13 0.20
34 8 0.12
35 10 0.16
36 2 0.03
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (31 bp):
AATTAAAATATAATAATAAATAAATATAAAT
Found at i:293282 original size:14 final size:14
Alignment explanation
Indices: 293200--293283 Score: 61
Period size: 14 Copynumber: 6.0 Consensus size: 14
293190 ACAAATAAAT
293200 ATAATTAATAATATTA
1 ATAATTAA-AATA-TA
293216 A-ATATT-AAATATA
1 ATA-ATTAAAATATA
*
293229 ATAA--ATAATA-A
1 ATAATTAAAATATA
293240 ATAATTAAAATATA
1 ATAATTAAAATATA
*
293254 ATAATAAATAAATATA
1 ATAAT-TA-AAATATA
*
293270 GTAATTAAAATATA
1 ATAATTAAAATATA
293284 TATTTTATAA
Statistics
Matches: 55, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
11 5 0.09
12 4 0.07
13 9 0.16
14 18 0.33
15 4 0.07
16 15 0.27
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (14 bp):
ATAATTAAAATATA
Found at i:293306 original size:13 final size:13
Alignment explanation
Indices: 293281--293320 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
293271 TAATTAAAAT
293281 ATATATTTTATAA
1 ATATATTTTATAA
293294 ATA-ATTATTAT-A
1 ATATATT-TTATAA
293306 ATATATTTTATAA
1 ATATATTTTATAA
293319 AT
1 AT
293321 TTTGAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATATATTTTATAA
Found at i:293316 original size:12 final size:12
Alignment explanation
Indices: 293281--293318 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
293271 TAATTAAAAT
293281 ATATATTTTATA
1 ATATATTTTATA
293293 A-ATAATTATTATA
1 ATAT-ATT-TTATA
293306 ATATATTTTATA
1 ATATATTTTATA
293318 A
1 A
293319 ATTTTGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 2 0.09
12 10 0.43
13 9 0.39
14 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATATTTTATA
Found at i:294911 original size:18 final size:17
Alignment explanation
Indices: 294888--294921 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
294878 GCCAACTTAC
*
294888 AAATAAACAAATCAAAAT
1 AAATAAAAAAAT-AAAAT
294906 AAATAAAAAAATAAAA
1 AAATAAAAAAATAAAA
294922 CATTATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (17 bp):
AAATAAAAAAATAAAAT
Found at i:296922 original size:19 final size:19
Alignment explanation
Indices: 296898--296939 Score: 77
Period size: 18 Copynumber: 2.3 Consensus size: 19
296888 AGGAGTGTGT
296898 AAAATTTATTTCAATTAAA
1 AAAATTTATTTCAATTAAA
296917 AAAA-TTATTTCAATTAAA
1 AAAATTTATTTCAATTAAA
296935 AAAAT
1 AAAAT
296940 AACTCGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATTTATTTCAATTAAA
Found at i:297147 original size:29 final size:26
Alignment explanation
Indices: 297089--297157 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 26
297079 ATTTATGTAA
297089 TTTTAATTTTTTTTTATAATTTAATC
1 TTTTAATTTTTTTTTATAATTTAATC
*
297115 -TTTAATTTTATATTTTATATATTTGATC
1 TTTTAATTTT-T-TTTTATA-ATTTAATC
* *
297143 TTTTACTATTTTTTT
1 TTTTAATTTTTTTTT
297158 GTAAATTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
25 9 0.25
26 1 0.03
27 11 0.31
28 8 0.22
29 7 0.19
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (26 bp):
TTTTAATTTTTTTTTATAATTTAATC
Found at i:297842 original size:20 final size:20
Alignment explanation
Indices: 297748--298116 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
297738 GATTTTCCAT
* ** *
297748 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
297768 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
297788 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
297808 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
297828 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
297848 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
297868 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
297888 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
297908 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
297928 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
297948 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
297968 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
297988 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
298008 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
298028 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
298048 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
298068 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
298088 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
298108 AATCACAAC
1 AATCGCAAC
298117 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:298838 original size:24 final size:24
Alignment explanation
Indices: 298799--298845 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
298789 AAATTTGGTC
298799 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
298823 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
298846 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:299037 original size:12 final size:12
Alignment explanation
Indices: 299020--299044 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
299010 ATATAATCCT
299020 GAAGAAGAAAAA
1 GAAGAAGAAAAA
299032 GAAGAAGAAAAA
1 GAAGAAGAAAAA
299044 G
1 G
299045 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:301349 original size:19 final size:19
Alignment explanation
Indices: 301327--301581 Score: 289
Period size: 19 Copynumber: 14.4 Consensus size: 19
301317 CGGAAAATAC
*
301327 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
301346 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
301360 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
301380 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
301394 AATCGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
* *
301413 AAACGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
*
301432 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
301446 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
301465 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
301484 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
301503 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
301522 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
301536 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
301555 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
301574 AATCGCAA
1 AATCGCAA
301582 CGAGATAATC
Statistics
Matches: 203, Mismatches: 12, Indels: 42
0.79 0.05 0.16
Matches are distributed among these distances:
14 38 0.19
15 1 0.00
16 13 0.06
17 11 0.05
18 2 0.01
19 125 0.62
20 13 0.06
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:301442 original size:52 final size:52
Alignment explanation
Indices: 301355--301581 Score: 257
Period size: 52 Copynumber: 4.2 Consensus size: 52
301345 AAATCCCAAC
*
301355 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * *
301408 ATGAAAAACGCAATGCAAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
301460 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
301517 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
301569 ATGAAAATCGCAA
1 ATGAAAATCGCAA
301582 CGAGATAATC
Statistics
Matches: 159, Mismatches: 10, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
52 108 0.68
53 15 0.09
54 3 0.02
55 5 0.03
56 1 0.01
57 27 0.17
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:301481 original size:71 final size:71
Alignment explanation
Indices: 301394--301619 Score: 284
Period size: 71 Copynumber: 3.2 Consensus size: 71
301384 GCAACGAGAG
* * * *
301394 AATCGCAATGCAAAATGAAAAACGCAATGCAAAATGAAAATCGCAACGACAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
301459 AATTAA
66 AATTAA
301465 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAA
*
301530 --CG-AA--AG
61 TGCGAAATTAA
* *
301536 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
301601 AATTATA
66 AATTA-A
*
301608 AA-CGCATTGCGA
1 AATCGCAATGCGA
301620 TTTTCATTTC
Statistics
Matches: 135, Mismatches: 9, Indels: 22
0.81 0.05 0.13
Matches are distributed among these distances:
66 8 0.06
68 2 0.01
69 6 0.04
71 100 0.74
72 2 0.01
73 6 0.04
74 3 0.02
76 8 0.06
ACGTcount: A:0.47, C:0.18, G:0.19, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATTAA
Found at i:301510 original size:90 final size:89
Alignment explanation
Indices: 301327--301581 Score: 360
Period size: 90 Copynumber: 2.9 Consensus size: 89
301317 CGGAAAATAC
* *
301327 AATCGCAACGCGAAATGAAAATCCCAACATGAA-AATCGCAATGCGGAAATGAAAATCGCAA--C
1 AATCGCAATGCGAAATGAAAATCGCAAC--GAAGAATCGCAATGC-GAAATGAAAATCGCAATGC
*
301389 G--A-GAGAATCGCAATGCAAAATGAA
63 GAAATGAAAATCGCAATGCAAAATGAA
* * *
301413 AAACGCAATGCAAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-AGAATCGCAATGCGAAATGAAAATCGCAATGCGA
*
301478 AATGAAAATCGCAATGCGAAATGAA
65 AATGAAAATCGCAATGCAAAATGAA
301503 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACG-AAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
301568 AATGAAAATCGCAA
65 AATGAAAATCGCAA
301582 CGAGATAATC
Statistics
Matches: 151, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
84 2 0.01
85 16 0.11
86 35 0.23
87 2 0.01
89 1 0.01
90 94 0.62
91 1 0.01
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (89 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAA
ATGAAAATCGCAATGCAAAATGAA
Found at i:301577 original size:142 final size:139
Alignment explanation
Indices: 301327--301619 Score: 439
Period size: 142 Copynumber: 2.1 Consensus size: 139
301317 CGGAAAATAC
* *
301327 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAG
1 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
301392 AGAATCGCAATGCAAAATGAAAAACGCAATGCAAAATGAAAATCGCAACGACAGAATCGCAATGC
66 AGAATCGCAATGCAAAATGAAAAACGCAATGCAAAATGAAAATCGCAACGACAGAATCGCAATGC
301457 GAAATTA-A
131 GAAATTATA
*
301465 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
* * * * *
301529 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGC
61 ACGAAAGAATCGCAATGCAAAATGAAAAACGCAATGCAAAATGAAAATCGCAACGACAGAATCGC
301594 AATGCGAAATTATA
126 AATGCGAAATTATA
*
301608 AA-CGCATTGCGA
1 AATCGCAATGCGA
301620 TTTTCATTTC
Statistics
Matches: 140, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
138 25 0.18
140 1 0.01
142 95 0.68
143 19 0.14
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (139 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
AGAATCGCAATGCAAAATGAAAAACGCAATGCAAAATGAAAATCGCAACGACAGAATCGCAATGC
GAAATTATA
Found at i:301619 original size:52 final size:52
Alignment explanation
Indices: 301446--301603 Score: 244
Period size: 52 Copynumber: 2.9 Consensus size: 52
301436 GCAACGACAG
*
301446 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
301503 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
* *
301555 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAAT
301604 TATAAACGCA
Statistics
Matches: 98, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
52 66 0.67
54 1 0.01
55 5 0.05
57 26 0.27
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.16
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
Found at i:301719 original size:19 final size:19
Alignment explanation
Indices: 301610--301711 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
301600 AAATTATAAA
301610 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
301629 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
301649 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
301665 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
301682 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
301701 CGCATTGCGAT
1 CGCATTGCGAT
301712 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:301837 original size:14 final size:14
Alignment explanation
Indices: 301818--301854 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
301808 CATCAATTAC
301818 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
301832 ACAAATCATCTTTT
1 ACAAATCAACTTTT
301846 ACAAATCAA
1 ACAAATCAA
301855 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:303853 original size:14 final size:14
Alignment explanation
Indices: 303834--303890 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
303824 GCGAAATGAA
*
303834 AATCGCAACGACAG
1 AATCGCAACGAAAG
303848 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
303865 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
303881 AATCGCAACG
1 AATCGCAACG
303891 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:303861 original size:33 final size:33
Alignment explanation
Indices: 303815--303907 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
303805 GCGAAACCAA
*
303815 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
303848 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
303881 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
303908 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:303872 original size:19 final size:19
Alignment explanation
Indices: 303778--303912 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
303768 TAGTTTACTT
* *
303778 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
303798 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
303817 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
303836 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
303850 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
303869 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
303883 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
303902 TCGCAATGCGA
1 TCGCAACGCGA
303913 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:303930 original size:19 final size:18
Alignment explanation
Indices: 303908--304017 Score: 83
Period size: 19 Copynumber: 6.3 Consensus size: 18
303898 AAAATCGCAA
303908 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
303927 TGCGATCTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
303941 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
303960 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
303974 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
303993 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
304013 TGCGA
1 TGCGA
304018 AAGTAAACTA
Statistics
Matches: 72, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
14 22 0.31
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 31 0.43
20 12 0.17
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.45
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:303950 original size:33 final size:33
Alignment explanation
Indices: 303908--303999 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
303898 AAAATCGCAA
303908 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
303941 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
303974 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
304000 TTAAGTTTCG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:304220 original size:93 final size:93
Alignment explanation
Indices: 304061--304718 Score: 1293
Period size: 93 Copynumber: 7.1 Consensus size: 93
304051 TTGAATGGAT
304061 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
304126 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
304154 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
304219 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
304247 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
304311 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
304339 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
304404 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
304432 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
304497 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
304525 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
304589 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
304617 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
304682 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
304710 AAATTTACT
1 AAATTTACT
304719 AAGCAATCTA
Statistics
Matches: 562, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.33
93 378 0.67
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:304374 original size:185 final size:186
Alignment explanation
Indices: 304061--304718 Score: 1293
Period size: 185 Copynumber: 3.5 Consensus size: 186
304051 TTGAATGGAT
304061 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
304126 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
304191 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
304247 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
304311 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
304376 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
304432 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
304497 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
304562 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
304617 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
304682 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
304719 AAGCAATCTA
Statistics
Matches: 470, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
185 339 0.72
186 131 0.28
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:304558 original size:278 final size:278
Alignment explanation
Indices: 304061--304718 Score: 1307
Period size: 278 Copynumber: 2.4 Consensus size: 278
304051 TTGAATGGAT
304061 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
304126 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
304191 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
304256 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
196 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
304321 AATTGGCAGCAACCGAAC
261 AATTGGCAGCAACCGAAC
304339 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
304404 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
304469 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
304534 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
196 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
304599 AATTGGCAGCAACCGAAC
261 AATTGGCAGCAACCGAAC
304617 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
304682 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
304719 AAGCAATCTA
Statistics
Matches: 379, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
278 379 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (278 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
AATTGGCAGCAACCGAAC
Found at i:306443 original size:14 final size:14
Alignment explanation
Indices: 306424--306513 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
306414 TTGAAATGAA
306424 AATCGCAACGAGAG
1 AATCGCAACGAGAG
306438 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
306455 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
306471 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
306490 AATCGCAACGAGAG
1 AATCGCAACGAGAG
306504 AATCGCAACG
1 AATCGCAACG
306514 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:306461 original size:33 final size:33
Alignment explanation
Indices: 306416--306530 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
306406 TCTTTTGGTT
306416 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
306449 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
306482 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
306515 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
306531 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:306462 original size:19 final size:18
Alignment explanation
Indices: 306423--306535 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
306413 GTTGAAATGA
306423 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
306438 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
306455 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
306471 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
306488 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
306504 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
306521 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
306536 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:306566 original size:14 final size:14
Alignment explanation
Indices: 306547--306601 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
306537 TTTGGTTTCG
306547 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
306561 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
306580 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
306594 CGTTGCGA
1 CGTTGCGA
306602 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:306579 original size:33 final size:33
Alignment explanation
Indices: 306531--306601 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
306521 AAAATCGCAA
**
306531 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
306564 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
306597 TGCGA
1 TGCGA
306602 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:306609 original size:33 final size:33
Alignment explanation
Indices: 306542--306623 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
306532 GCGATTTTGG
***
306542 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
306575 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
306608 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
306624 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:306628 original size:20 final size:20
Alignment explanation
Indices: 306554--306642 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
306544 TCGCGTTGCG
306554 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
306574 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
306587 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
306607 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
306627 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
306643 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:306764 original size:33 final size:33
Alignment explanation
Indices: 306722--306792 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
306712 AATACTAACT
*
306722 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
306755 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
306788 TGAAA
1 TGAAA
306793 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:307199 original size:20 final size:20
Alignment explanation
Indices: 307174--307366 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
307164 CTTTAAATAT
307174 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
307194 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
307216 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
307235 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
307255 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
307275 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
307295 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
307315 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
307335 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
307355 CGCGTTGCGATT
1 CGCGTTGCGATT
307367 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:307361 original size:60 final size:60
Alignment explanation
Indices: 307174--307366 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
307164 CTTTAAATAT
**
307174 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
307235 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
307295 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
307355 CGCGTTGCGATT
1 CGCGTTGCGATT
307367 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:307447 original size:20 final size:20
Alignment explanation
Indices: 307422--307473 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
307412 AAGAATCGCG
*
307422 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
307442 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
307462 TTGCGATTCTGG
1 TTGCGATTCTGG
307474 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:320872 original size:11 final size:11
Alignment explanation
Indices: 320856--320881 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
320846 AAAAAATCTT
320856 GTCATGCGTCC
1 GTCATGCGTCC
320867 GTCATGCGTCC
1 GTCATGCGTCC
320878 GTCA
1 GTCA
320882 AGCTTCGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.12, C:0.35, G:0.27, T:0.27
Consensus pattern (11 bp):
GTCATGCGTCC
Found at i:321813 original size:33 final size:35
Alignment explanation
Indices: 321758--321827 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 35
321748 ATCAAATATG
321758 TTAGCTATTATTGTGTGTGTATTCTCGTTTTTTCT
1 TTAGCTATTATTGTGTGTGTATTCTCGTTTTTTCT
*
321793 TTAGCTATTA-T-TGTGTGTATTCTGGTTTTTTCT
1 TTAGCTATTATTGTGTGTGTATTCTCGTTTTTTCT
321826 TT
1 TT
321828 GGACCACACT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 23 0.68
34 1 0.03
35 10 0.29
ACGTcount: A:0.11, C:0.10, G:0.17, T:0.61
Consensus pattern (35 bp):
TTAGCTATTATTGTGTGTGTATTCTCGTTTTTTCT
Found at i:323835 original size:22 final size:23
Alignment explanation
Indices: 323807--323866 Score: 86
Period size: 22 Copynumber: 2.6 Consensus size: 23
323797 ATATTTTATA
323807 TATATTAACTTAAAAATAT-TTT
1 TATATTAACTTAAAAATATATTT
*
323829 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA-AAAATATATTT
323853 TATTATTAACTTAA
1 TA-TATTAACTTAA
323867 TTTAAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 12 0.36
23 6 0.18
24 5 0.15
25 10 0.30
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
TATATTAACTTAAAAATATATTT
Found at i:323871 original size:27 final size:25
Alignment explanation
Indices: 323796--323883 Score: 94
Period size: 25 Copynumber: 3.5 Consensus size: 25
323786 TTAAATTCAT
323796 AATATTTTATATATATTAACTTAA--A
1 AATATTTT-TAT-TATTAACTTAATTA
323821 AATATTTTTA-TATTAACTT-ATTA
1 AATATTTTTATTATTAACTTAATTA
323844 AATATATTTTATTATTAACTTAATTTA
1 AATAT-TTTTATTATTAACTTAA-TTA
*
323871 AAAATGTTTTATT
1 AATAT-TTTTATT
323884 TTCATTTTCA
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
21 1 0.02
22 9 0.16
23 6 0.11
24 7 0.13
25 17 0.31
26 1 0.02
27 14 0.25
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.53
Consensus pattern (25 bp):
AATATTTTTATTATTAACTTAATTA
Found at i:324092 original size:31 final size:31
Alignment explanation
Indices: 324054--324112 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
324044 CAGCTTAATT
*
324054 AAATAAAAACGAAAGTGATCATATCTTAGTC
1 AAATAAAAACGAAAGTGATAATATCTTAGTC
324085 AAATAAAAACGAAAGTGATAATATCTTA
1 AAATAAAAACGAAAGTGATAATATCTTA
324113 TGCTTTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (31 bp):
AAATAAAAACGAAAGTGATAATATCTTAGTC
Found at i:328903 original size:3 final size:3
Alignment explanation
Indices: 328897--328935 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
328887 TTTCTACTAC
328897 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
328936 GAGGGCTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:337312 original size:154 final size:155
Alignment explanation
Indices: 337103--337410 Score: 602
Period size: 153 Copynumber: 2.0 Consensus size: 155
337093 ATCACGCTTG
337103 ATCCCACATTTTGGACTAAAACAAATAGGTGGGAAAAGGCGGGAGGACTTGAAAAAAGCATTAAA
1 ATCCCACATTTTGGACTAAAACAAATAGGTGGGAAAAGGCGGGAGGACTTGAAAAAAGCATTAAA
337168 GGAGTTTAATGGTAAACAGTAAAGGGTATTTGGAGATCCGAGCATTGTCATGATTGGGCCTACTA
66 GGAGTTTAATGGTAAACAGTAAAGGGTATTTGGAGATCCGAGCATTGTCATGATTGGGCCTACTA
337233 ATCACACGCTTGCCAATTGTACGGC
131 ATCACACGCTTGCCAATTGTACGGC
337258 ATCCCACATTTTGGACT-AAACAAATAGGTGGG-AAAGGCGGGAGGACTTGAAAAAAGCATTAAA
1 ATCCCACATTTTGGACTAAAACAAATAGGTGGGAAAAGGCGGGAGGACTTGAAAAAAGCATTAAA
337321 GGAGTTTAATGGTAAACAGTAAAGGGTATTTGGAGATCCGAGCATTGTCATGATTGGGCCTACTA
66 GGAGTTTAATGGTAAACAGTAAAGGGTATTTGGAGATCCGAGCATTGTCATGATTGGGCCTACTA
337386 ATCACACGCTTGCCAATTGTACGGC
131 ATCACACGCTTGCCAATTGTACGGC
337411 CTTCACTCCC
Statistics
Matches: 153, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
153 121 0.79
154 15 0.10
155 17 0.11
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (155 bp):
ATCCCACATTTTGGACTAAAACAAATAGGTGGGAAAAGGCGGGAGGACTTGAAAAAAGCATTAAA
GGAGTTTAATGGTAAACAGTAAAGGGTATTTGGAGATCCGAGCATTGTCATGATTGGGCCTACTA
ATCACACGCTTGCCAATTGTACGGC
Found at i:337801 original size:5 final size:5
Alignment explanation
Indices: 337791--337819 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
337781 CCACGACCAC
337791 GACGA GACGA GACGA GACGA GACG- GACGA
1 GACGA GACGA GACGA GACGA GACGA GACGA
337820 CGGCGGCGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.38, C:0.21, G:0.41, T:0.00
Consensus pattern (5 bp):
GACGA
Found at i:338576 original size:21 final size:21
Alignment explanation
Indices: 338547--338607 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
338537 ACCAGTCGTT
* *
338547 GCGATTTTGGACT-ATCGCAA
1 GCGAATTTGGAATAATCGCAA
338567 CGCGAATTTGGAATAAATCGCAA
1 -GCGAATTTGGAAT-AATCGCAA
338590 -CGAATTTGGAA-AATCGCA
1 GCGAATTTGGAATAATCGCA
338608 TTGCGATAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
19 7 0.19
21 22 0.61
23 7 0.19
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (21 bp):
GCGAATTTGGAATAATCGCAA
Found at i:339832 original size:19 final size:19
Alignment explanation
Indices: 339808--339844 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
339798 ATATTTAGTA
339808 AAAAATAATGTCATTTGCT
1 AAAAATAATGTCATTTGCT
339827 AAAAATAATGTCATTTGC
1 AAAAATAATGTCATTTGC
339845 CCTCATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (19 bp):
AAAAATAATGTCATTTGCT
Found at i:340707 original size:17 final size:17
Alignment explanation
Indices: 340685--340728 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
340675 AAGTTGTATA
*
340685 AAATTTAAACTAA-AATT
1 AAATTTAAAATAAGAA-T
340702 AAATTTAAAATAAGAAT
1 AAATTTAAAATAAGAAT
340719 AAA-TTAAAAT
1 AAATTTAAAAT
340729 TAAATTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 7 0.28
17 16 0.64
18 2 0.08
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
AAATTTAAAATAAGAAT
Done.