Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009611.1 Hibiscus syriacus cultivar Beakdansim tig00116997_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: 6671611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 27
Found at i:246328 original size:19 final size:19
Alignment explanation
Indices: 246287--246328 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
246277 TTCATTTATT
*
246287 TATTTTTTATCTATTTTCT
1 TATTTTTTATCTATTTTCA
*
246306 TATTTTTTTTCT-TTTTACA
1 TATTTTTTATCTATTTT-CA
246325 TATT
1 TATT
246329 ACTTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTTTATCTATTTTCA
Found at i:257255 original size:46 final size:47
Alignment explanation
Indices: 257188--257285 Score: 182
Period size: 46 Copynumber: 2.1 Consensus size: 47
257178 CCGAGAATAC
257188 AATACATCTTCCCAATTATTCATTTCTTAAACAGTGAGA-CCTCTCT
1 AATACATCTTCCCAATTATTCATTTCTTAAACAGTGAGACCCTCTCT
257234 AATACATCTTCCCAATTATTCATTTCTTAAACAGTGAGACCCTCTCT
1 AATACATCTTCCCAATTATTCATTTCTTAAACAGTGAGACCCTCTCT
257281 -ATACA
1 AATACA
257286 CCATAGCCCA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 44 0.86
47 7 0.14
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.36
Consensus pattern (47 bp):
AATACATCTTCCCAATTATTCATTTCTTAAACAGTGAGACCCTCTCT
Found at i:258486 original size:30 final size:30
Alignment explanation
Indices: 258431--258526 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
258421 CCCGAATGAG
*
258431 CTATCCAGAGGTCACACAG-ACCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGTAA
* *
258460 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGGTAA
* * * *
258490 CTGTCCATAGGTCCCAAAGAACCTAGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGTAA
*
258520 CTGTCCA
1 CTATCCA
258527 TATGTTCCTT
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
29 17 0.30
30 40 0.70
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.19
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGTAA
Found at i:258541 original size:30 final size:30
Alignment explanation
Indices: 258475--258580 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 30
258465 CAGAGGTCAT
* * *
258475 AAAGAACCTCGGCAACTGTCCATAGGTCCC
1 AAAGAACCTAGGTAACTGTCCATATGTCCC
*
258505 AAAGAACCTAGGTAACTGTCCATATGTTCC
1 AAAGAACCTAGGTAACTGTCCATATGTCCC
** * * *
258535 TTAGAACATAGGTATATTGTCCATATGTCTCG
1 AAAGAACCTAGGTA-ACTGTCCATATGTC-CC
*
258567 AAAG-ACATAGGTAA
1 AAAGAACCTAGGTAA
258581 AACCCTCGAC
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
30 38 0.61
31 21 0.34
32 3 0.05
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (30 bp):
AAAGAACCTAGGTAACTGTCCATATGTCCC
Found at i:259333 original size:64 final size:65
Alignment explanation
Indices: 259225--259384 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 65
259215 CAATGAATGT
* * *
259225 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTT-TATTTAATGGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAATGGGG
* * ***
259289 ATGCATTGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATTTAA-AAT
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAATCC-ATTCGATGTTTTCTATTTAATGGG
*
259352 C
65 G
* * *
259353 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTACTTATGCATCGATGCA
259385 CCTTAAACAA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
63 5 0.06
64 69 0.85
65 7 0.09
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (65 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAATGGGG
Found at i:268759 original size:220 final size:217
Alignment explanation
Indices: 268354--268797 Score: 782
Period size: 220 Copynumber: 2.0 Consensus size: 217
268344 TTTGTTAACC
268354 CAAATAAAAATTATAATGAATAATTTAAAGGATTTTGATCACTGACTTTGATGAAATTTACAAAC
1 CAAATAAAAATTATAATGAATAATTTAAAGGATTTTGATCACTGACTTTGATGAAATTTACAAAC
268419 CAATATTTACTAACTAGTCGTTGCCGTGCCCGATGTAAAAATTTTTTTTTAATTTATAAAAGAAA
66 CAATATTTACTAACTAGTCGTTGCCGTGCCCGATGTAAAAATTTTTTTTTAATTTATAAAAGAAA
268484 AATGGGAGGCTGCCACCAAAAGTTGTACAAGGTTATCATGGAATTGAAAGAAAGAAAATAAAGCA
131 AATGGGAGGCTGCCACCAAAAGTTGTACAAGGTTATCATGGAATT---AGAAAGAAAATAAAGCA
268549 TTGTTATTATATAGTTTTTCGTACT
193 TTGTTATTATATAGTTTTTCGTACT
268574 CAAATAAAAATTATAATGAATAATTTAAAGGATTTTGATCACTGACTTTGATGAAATTTACAAAC
1 CAAATAAAAATTATAATGAATAATTTAAAGGATTTTGATCACTGACTTTGATGAAATTTACAAAC
268639 CAATATTTACTAACTAGTCGTTGCCGTGCCCGATTGTAAAATGTATTTTTTTTTAATTTTATAAA
66 CAATATTTACTAACTAGTCGTTGCCGTGCCCGA-TGTAAAA---ATTTTTTTTTAA-TTTATAAA
268704 AGAAAAAT-GGAGGCTGCCACCAAAAGTTGTACAAGGTTATCATGGAATTGAAAGAAAGAAAATA
126 AGAAAAATGGGAGGCTGCCACCAAAAGTTGTACAAGGTTATCATGGAATT---AGAAAGAAAATA
268768 AAGCATTGTTATTATATAGTTTTTCGTACT
188 AAGCATTGTTATTATATAGTTTTTCGTACT
268798 TGCTCTTGAC
Statistics
Matches: 219, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
220 98 0.45
221 7 0.03
224 98 0.45
225 16 0.07
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (217 bp):
CAAATAAAAATTATAATGAATAATTTAAAGGATTTTGATCACTGACTTTGATGAAATTTACAAAC
CAATATTTACTAACTAGTCGTTGCCGTGCCCGATGTAAAAATTTTTTTTTAATTTATAAAAGAAA
AATGGGAGGCTGCCACCAAAAGTTGTACAAGGTTATCATGGAATTAGAAAGAAAATAAAGCATTG
TTATTATATAGTTTTTCGTACT
Found at i:273852 original size:61 final size:64
Alignment explanation
Indices: 273771--273895 Score: 193
Period size: 61 Copynumber: 2.0 Consensus size: 64
273761 TTCCCCCAGC
* *
273771 CCCAGGAGTCTATCTCTACCTTTTT-CTAATAATA-TTTTTT-TAATTGTGTTTATTTTGACTG
1 CCCAGGAGTCTATCTATACCTTTTTCCCAATAATATTTTTTTATAATTGTGTTTATTTTGACTG
* *
273832 CCCAGGAGTCTCTCTATACCTTTTTCCCAATAATATTTTTTTATAATTGTGTTTATTTTTACTG
1 CCCAGGAGTCTATCTATACCTTTTTCCCAATAATATTTTTTTATAATTGTGTTTATTTTGACTG
273896 TCCTTTTACA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
61 23 0.40
62 8 0.14
63 6 0.11
64 20 0.35
ACGTcount: A:0.22, C:0.18, G:0.10, T:0.50
Consensus pattern (64 bp):
CCCAGGAGTCTATCTATACCTTTTTCCCAATAATATTTTTTTATAATTGTGTTTATTTTGACTG
Found at i:273924 original size:98 final size:99
Alignment explanation
Indices: 273810--274003 Score: 363
Period size: 99 Copynumber: 2.0 Consensus size: 99
273800 TAATATTTTT
273810 TTAATTGTGTTTATTTTGACTGCCCAGGAGTCTCTCTATACC-TTTTTCCCAATAATATTTTTTT
1 TTAATTGTGTTTATTTTGACTGCCCAGGAGTCTCTCTATACCTTTTTTCCCAATAATATTTTTTT
273874 ATAATTGTGTTTATTTTTACTGTCCTTTTACATG
66 ATAATTGTGTTTATTTTTACTGTCCTTTTACATG
* *
273908 TTAATTGTGTTTATTTTGACTGCCCAGGATTCTCTCTATACCTTTTTTTCCAATAATATTTTTTT
1 TTAATTGTGTTTATTTTGACTGCCCAGGAGTCTCTCTATACCTTTTTTCCCAATAATATTTTTTT
273973 ATAATTGTGTTTATTTTTACTGTCCTTTTAC
66 ATAATTGTGTTTATTTTTACTGTCCTTTTAC
274004 TACTACCATG
Statistics
Matches: 93, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
98 41 0.44
99 52 0.56
ACGTcount: A:0.20, C:0.16, G:0.10, T:0.54
Consensus pattern (99 bp):
TTAATTGTGTTTATTTTGACTGCCCAGGAGTCTCTCTATACCTTTTTTCCCAATAATATTTTTTT
ATAATTGTGTTTATTTTTACTGTCCTTTTACATG
Found at i:274897 original size:22 final size:22
Alignment explanation
Indices: 274872--274931 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
274862 CGTTTCAACC
274872 AACAGTGACAGAAAATCAATCA
1 AACAGTGACAGAAAATCAATCA
274894 AACAGTGACAGAAAATCAATCA
1 AACAGTGACAGAAAATCAATCA
*
274916 AACAATG--AGAAAATCA
1 AACAGTGACAGAAAATCA
274932 GTAAAAAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
20 9 0.24
22 28 0.76
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (22 bp):
AACAGTGACAGAAAATCAATCA
Found at i:282628 original size:17 final size:17
Alignment explanation
Indices: 282606--282640 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
282596 ATAATTTCAA
282606 TATAGTTGAAGATATAT
1 TATAGTTGAAGATATAT
282623 TATAGTTGAAGATATAT
1 TATAGTTGAAGATATAT
282640 T
1 T
282641 TCTAACCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (17 bp):
TATAGTTGAAGATATAT
Found at i:287044 original size:12 final size:13
Alignment explanation
Indices: 287015--287069 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
287005 AAAATCAAAT
*
287015 TTTAATATTAATA
1 TTTAATTTTAATA
287028 TTTAATTTTAA-A
1 TTTAATTTTAATA
287040 TTTAATTTCATAATA
1 TTTAATTT--TAATA
*
287055 TTAAATCTTT-ATA
1 TTTAAT-TTTAATA
287068 TT
1 TT
287070 GTATTTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
12 9 0.25
13 15 0.42
14 4 0.11
15 6 0.17
16 2 0.06
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTAATTTTAATA
Found at i:290404 original size:20 final size:21
Alignment explanation
Indices: 290379--290471 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 21
290369 TTTTCCCAAT
*
290379 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* *
290399 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
290420 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
290440 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
290461 TCGCAATGCGA
1 TCGCAATGCGA
290472 TACTGACTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.47
21 32 0.53
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:290436 original size:41 final size:41
Alignment explanation
Indices: 290379--290471 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
290369 TTTTCCCAAT
290379 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGAAAA
*
290420 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGAAAA
290461 TCGCAATGCGA
1 TCGCAATGCGA
290472 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGAAAA
Found at i:290484 original size:41 final size:41
Alignment explanation
Indices: 290398--290532 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
290388 GAATAAGTAA
* *
290398 ATCGCAACGCGAATTGAGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCG-ATACTG-ACT
*
290439 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
* * * * * *
290480 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
*
290521 TTCGCAACGCGA
1 ATCGCAACGCGA
290533 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
Found at i:290485 original size:20 final size:20
Alignment explanation
Indices: 290460--290574 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
290450 AATTGGGAAA
*
290460 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
290480 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
290501 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
290521 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
290541 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
290561 TTCGCAACACGATA
1 ATCGCAACGCGATA
290575 ATACATAATC
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:290533 original size:41 final size:41
Alignment explanation
Indices: 290457--290594 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
290447 GCGAATTGGG
* * *
290457 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
290498 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** * *
290540 --TTTCGCAACGCGATTCTGACTTTCGCAACACGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
290579 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
290595 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 2 0.03
40 30 0.38
41 44 0.56
42 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:291094 original size:20 final size:20
Alignment explanation
Indices: 291069--291106 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
291059 CGATTCTCTC
291069 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
291089 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
291107 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:291298 original size:25 final size:24
Alignment explanation
Indices: 291244--291298 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
291234 GTAAAATTAT
* *
291244 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
291268 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
291294 TGTTT
1 TGTTT
291299 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:292256 original size:18 final size:18
Alignment explanation
Indices: 292235--292279 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
292225 TCCACTTCGG
292235 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
292253 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
292271 GAGCCATCA
1 GAGCCATCA
292280 TCTGATCGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.44, G:0.13, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:292815 original size:19 final size:20
Alignment explanation
Indices: 292761--292806 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
292751 TAGTTTACTT
*
292761 TCGCAACACGAAAATGACTA
1 TCGCAACACGGAAATGACTA
*
292781 TCGCAACACGGAAATGGCTA
1 TCGCAACACGGAAATGACTA
292801 TCGCAA
1 TCGCAA
292807 TGCGAAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACGGAAATGACTA
Found at i:292835 original size:14 final size:14
Alignment explanation
Indices: 292816--292873 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
292806 ATGCGAAATG
292816 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
292830 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
292846 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
292862 AAAATCGCAACG
1 AAAATCGCAACG
292874 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:292858 original size:32 final size:33
Alignment explanation
Indices: 292800--292890 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
292790 GGAAATGGCT
292800 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
292833 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
292865 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
292891 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:292967 original size:20 final size:19
Alignment explanation
Indices: 292933--292988 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
292923 TTGCGATTTT
*
292933 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
292952 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
292972 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
292989 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:294878 original size:14 final size:14
Alignment explanation
Indices: 294859--294894 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
294849 ATTGTTTAAT
294859 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
294873 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
294887 TGATTTGT
1 TGATTTGT
294895 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:295027 original size:33 final size:33
Alignment explanation
Indices: 294982--295097 Score: 142
Period size: 33 Copynumber: 3.4 Consensus size: 33
294972 AAAACAGACT
* * *
294982 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGACAATCGCAACGAGAAA
* *
295015 ATCGCAATGCGAAATGAAAATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGACAATCGCAA--CG--A-GAAA
295053 ATCGCAATGCGAAATGACAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGACAATCGCAACGAGAAA
295086 ATCGCAATGCGA
1 ATCGCAATGCGA
295098 TTTTCATTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
33 37 0.52
34 1 0.01
35 2 0.03
36 2 0.03
37 1 0.01
38 28 0.39
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGACAATCGCAACGAGAAA
Found at i:295033 original size:19 final size:19
Alignment explanation
Indices: 295011--295097 Score: 121
Period size: 19 Copynumber: 4.8 Consensus size: 19
295001 ATCGCAACGA
295011 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
295030 GAAAATCGTAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
295049 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
295068 GACAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
295082 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
295098 TTTTCATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
19 46 0.75
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:295141 original size:20 final size:20
Alignment explanation
Indices: 295116--295193 Score: 129
Period size: 20 Copynumber: 3.9 Consensus size: 20
295106 TCGCATTGCG
*
295116 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
295136 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
* *
295156 ATTTTCACGTTACGATAGCC
1 ATTTTCGCGTTGCGATAGCC
295176 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
295194 TCAAATGAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:296265 original size:24 final size:24
Alignment explanation
Indices: 296238--296291 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
296228 GTATTCGAAA
* *
296238 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
296262 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
296286 TTTGAT
1 TTTGAT
296292 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:296483 original size:12 final size:12
Alignment explanation
Indices: 296466--296490 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
296456 ATATAATCCT
296466 GAAGAAGAAAAA
1 GAAGAAGAAAAA
296478 GAAGAAGAAAAA
1 GAAGAAGAAAAA
296490 G
1 G
296491 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:298803 original size:19 final size:19
Alignment explanation
Indices: 298781--298839 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
298771 GGAAATTACT
298781 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
298800 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
298814 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
298833 ATCGCAA
1 ATCGCAA
298840 CGCTAATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 9 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.52
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:298985 original size:14 final size:14
Alignment explanation
Indices: 298966--299002 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
298956 CATCAATTAA
298966 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
298980 ACAAATCACCTTTT
1 ACAAATCAACTTTT
298994 ACAAATCAA
1 ACAAATCAA
299003 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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:300425 original size:21 final size:21
Alignment explanation
Indices: 300359--300425 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
300349 GTGAATCGGG
*
300359 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
300379 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
300401 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
300422 CTCT
1 CTCT
300426 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:300444 original size:42 final size:41
Alignment explanation
Indices: 300359--300481 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
300349 GTGAATCGGG
* * * *
300359 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
300401 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
300443 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
300482 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:302515 original size:20 final size:19
Alignment explanation
Indices: 302484--302544 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
302474 TCTTTTGGTT
302484 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
302503 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
302524 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
302543 GA
1 GA
302545 GAATCGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.11
20 29 0.83
21 2 0.06
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:302552 original size:14 final size:14
Alignment explanation
Indices: 302533--302597 Score: 121
Period size: 14 Copynumber: 4.6 Consensus size: 14
302523 GGAAATGACT
302533 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
302547 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
302561 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
302575 ATCGCAACAAGAGA
1 ATCGCAACGAGAGA
302589 ATCGCAACG
1 ATCGCAACG
302598 CGAAATGACT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 49 1.00
ACGTcount: A:0.43, C:0.23, G:0.26, T:0.08
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:302645 original size:33 final size:33
Alignment explanation
Indices: 302574--302686 Score: 109
Period size: 33 Copynumber: 3.2 Consensus size: 33
302564 GCAACGAGAG
* *
302574 AATCGCAACAAGAGAATCGCAACGCGAAATGAC
1 AATCGCAACAAGACAATCGCAACGCGAAATGAA
* * * *
302607 TATCGCGACCAGACAATCGCAACGCGAAATTAA
1 AATCGCAACAAGACAATCGCAACGCGAAATGAA
*
302640 AATCGCAACCGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAA---C--AA-GACAATCGCAACGCGAAATGAA
302679 AATCGCAA
1 AATCGCAA
302687 TGCGATTTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
33 33 0.52
36 1 0.02
38 1 0.02
39 28 0.44
ACGTcount: A:0.44, C:0.25, G:0.19, T:0.12
Consensus pattern (33 bp):
AATCGCAACAAGACAATCGCAACGCGAAATGAA
Found at i:302654 original size:20 final size:19
Alignment explanation
Indices: 302621--302691 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
302611 GCGACCAGAC
*
302621 AATCGCAACGCGAAATTAA
1 AATCGCAACGCGAAATGAA
302640 AATCGCAACCGCGAAATGAA
1 AATCGCAA-CGCGAAATGAA
302660 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
302679 AATCGCAATGCGA
1 AATCGCAACGCGA
302692 TTTTTGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 31 0.63
20 18 0.37
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:302723 original size:19 final size:19
Alignment explanation
Indices: 302687--302753 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
302677 AAAATCGCAA
*
302687 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
302706 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
302725 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
302745 TGCGATTTT
1 TGCGATTTT
302754 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 28 0.70
20 12 0.30
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.51
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:303296 original size:20 final size:20
Alignment explanation
Indices: 303271--303323 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
303261 GCGCTATGTA
303271 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
303291 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
303311 TATCTCGTTGCGA
1 AATCGCGTTGCGA
303324 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:303361 original size:20 final size:20
Alignment explanation
Indices: 303332--303385 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
303322 GATTTTGTAT
*
303332 TATCGCATTGCGATAGTAAG
1 TATCGTATTGCGATAGTAAG
*
303352 TATCGTATTGCGATAGTCAG
1 TATCGTATTGCGATAGTAAG
303372 TATC-TCATTGCGAT
1 TATCGT-ATTGCGAT
303386 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (20 bp):
TATCGTATTGCGATAGTAAG
Found at i:303404 original size:61 final size:61
Alignment explanation
Indices: 303272--303406 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
303262 CGCTATGTAA
* * * * ** *
303272 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCTCATTGCGATTTTCCAAT
* * * *
303333 ATCGCATTGCGATAGTAAGTATCGTATTGCGATAGTCAGTATCTCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCTCATTGCGATTTT-CCAAT
303395 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
303407 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCTCATTGCGATTTTCCAAT
Found at i:303496 original size:21 final size:21
Alignment explanation
Indices: 303456--303496 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
303446 ACTGTATACC
**
303456 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
303477 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
303497 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:303886 original size:23 final size:22
Alignment explanation
Indices: 303836--303886 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
303826 AAAATCACTA
* *
303836 AAATAAATTTAATAGTTTATTT
1 AAATTAATTTAATAGTTTAATT
*
303858 ATAATTAATTTAATATTTTAAATT
1 A-AATTAATTTAATAGTTT-AATT
303882 AAATT
1 AAATT
303887 TACTGTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 19 0.79
24 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
AAATTAATTTAATAGTTTAATT
Found at i:308870 original size:30 final size:31
Alignment explanation
Indices: 308834--308903 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 31
308824 AAGACATACT
* *
308834 ATATGGTCACTTTCGTTTTTATTTATTTAA-
1 ATATGGTCACTTTCATTTTTATTTAATTAAG
308864 ATATGGTCACTTTCATTTTTATTTAATTAAG
1 ATATGGTCACTTTCATTTTTATTTAATTAAG
*
308895 ATGTGGTCA
1 ATATGGTCA
308904 TCGTGGGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 28 0.78
31 8 0.22
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (31 bp):
ATATGGTCACTTTCATTTTTATTTAATTAAG
Found at i:327147 original size:66 final size:66
Alignment explanation
Indices: 327066--327191 Score: 225
Period size: 66 Copynumber: 1.9 Consensus size: 66
327056 TTTACCATTA
*
327066 ATGTTTGAAAAATTACAAATCGGTCACTAATATTATCATTTATTACAAAATGGTCACTAACGTCT
1 ATGTTTGAAAAATTACAAATCGGTCACTAACATTATCATTTATTACAAAATGGTCACTAACGTCT
327131 G
66 G
* *
327132 ATGTTTGAAAAATTACAAATCGTTCACTAACATTATCATTTGTTACAAAATGGTCACTAA
1 ATGTTTGAAAAATTACAAATCGGTCACTAACATTATCATTTATTACAAAATGGTCACTAA
327192 TGTTATTGTT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (66 bp):
ATGTTTGAAAAATTACAAATCGGTCACTAACATTATCATTTATTACAAAATGGTCACTAACGTCT
G
Found at i:327189 original size:30 final size:30
Alignment explanation
Indices: 327078--327191 Score: 81
Period size: 30 Copynumber: 3.6 Consensus size: 30
327068 GTTTGAAAAA
* *
327078 TTACAAATCGGTCACTAATATTATCATTTA
1 TTACAAATCGGTCACTAACATTATCATTTG
* *
327108 TTACAAAAT-GGTCACTAACGTCTGAT-GTTTG
1 TTAC-AAATCGGTCACTAACAT-T-ATCATTTG
*
327139 AAAAATTACAAATCGTTCACTAACATTATCATTTG
1 -----TTACAAATCGGTCACTAACATTATCATTTG
327174 TTACAAAAT-GGTCACTAA
1 TTAC-AAATCGGTCACTAA
327192 TGTTATTGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 22
0.68 0.08 0.23
Matches are distributed among these distances:
30 26 0.40
31 12 0.18
32 2 0.03
34 2 0.03
35 9 0.14
36 14 0.22
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (30 bp):
TTACAAATCGGTCACTAACATTATCATTTG
Found at i:327356 original size:25 final size:24
Alignment explanation
Indices: 327315--327361 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
327305 CCGACCCTTC
*
327315 TTTTTATTTTTCATCTTTTTTTCT
1 TTTTTATTTTTCATCTTCTTTTCT
* *
327339 TTTTTTTTTCTTCTTCTTCTTTT
1 TTTTTATTT-TTCATCTTCTTTT
327362 GTGAATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTTTATTTTTCATCTTCTTTTCT
Found at i:327722 original size:56 final size:56
Alignment explanation
Indices: 327656--327762 Score: 178
Period size: 56 Copynumber: 1.9 Consensus size: 56
327646 TATCGGTTCC
*
327656 TGGCGTTGCCTCTGTTTTGCGCCAACAACTCAATATCATCCTCGCAAGGTGTTACA
1 TGGCGTTGCCTCTGTTTTGCGCCAACAACTCAAGATCATCCTCGCAAGGTGTTACA
* * *
327712 TGGCGTTGCCTCTGTTTTGCGTCAACAACTCAAGATCATCCTTGTAAGGTG
1 TGGCGTTGCCTCTGTTTTGCGCCAACAACTCAAGATCATCCTCGCAAGGTG
327763 CAACTTCCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (56 bp):
TGGCGTTGCCTCTGTTTTGCGCCAACAACTCAAGATCATCCTCGCAAGGTGTTACA
Found at i:334285 original size:22 final size:22
Alignment explanation
Indices: 334258--334301 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
334248 AGTTAAAACT
*
334258 TTTTAAAT-TTTTATCATAATTA
1 TTTTAAATATTTTA-AATAATTA
334280 TTTTAAATATTTTAAATAATTA
1 TTTTAAATATTTTAAATAATTA
334302 AATTTCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAATATTTTAAATAATTA
Found at i:335961 original size:21 final size:21
Alignment explanation
Indices: 335936--336005 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
335926 TAATAGGGTA
335936 ATGATTTAGTGTTTAAAGATT
1 ATGATTTAGTGTTTAAAGATT
* * *
335957 ATGATTTAGGGTTTTAAG-CT
1 ATGATTTAGTGTTTAAAGATT
** *
335977 A-GAGATAGTGTTTAAGGATT
1 ATGATTTAGTGTTTAAAGATT
335997 ATGATTTAG
1 ATGATTTAG
336006 GGTTCTAAGC
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
19 11 0.31
20 4 0.11
21 21 0.58
ACGTcount: A:0.31, C:0.01, G:0.24, T:0.43
Consensus pattern (21 bp):
ATGATTTAGTGTTTAAAGATT
Found at i:335986 original size:40 final size:40
Alignment explanation
Indices: 335942--336018 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
335932 GGTAATGATT
*
335942 TAGTGTTTAAAGATTATGATTTAGGGTTTTAAGCTAGAGA
1 TAGTGTTTAAAGATTATGATTTAGGGTTCTAAGCTAGAGA
*
335982 TAGTGTTTAAGGATTATGATTTAGGGTTCTAAGCTAG
1 TAGTGTTTAAAGATTATGATTTAGGGTTCTAAGCTAG
336019 GGGTAGAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.30, C:0.04, G:0.26, T:0.40
Consensus pattern (40 bp):
TAGTGTTTAAAGATTATGATTTAGGGTTCTAAGCTAGAGA
Found at i:338926 original size:13 final size:13
Alignment explanation
Indices: 338908--338939 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
338898 TATATTCAGT
338908 ACAAAACATCTGA
1 ACAAAACATCTGA
338921 ACAAAACATCTGA
1 ACAAAACATCTGA
338934 ACAAAA
1 ACAAAA
338940 TTTGGCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.59, C:0.22, G:0.06, T:0.12
Consensus pattern (13 bp):
ACAAAACATCTGA
Found at i:349691 original size:21 final size:22
Alignment explanation
Indices: 349660--349700 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
349650 CACGTTTTCA
349660 TATGCCTTTTTGGCACGTTTAT
1 TATGCCTTTTTGGCACGTTTAT
*
349682 TATG-CTTTTTGGCATGTTT
1 TATGCCTTTTTGGCACGTTT
349701 TTCGGTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.15, G:0.20, T:0.54
Consensus pattern (22 bp):
TATGCCTTTTTGGCACGTTTAT
Found at i:353659 original size:2 final size:2
Alignment explanation
Indices: 353654--353680 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
353644 AGAGAGTAGG
353654 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
353681 TGGTTCTCAA
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:361330 original size:18 final size:18
Alignment explanation
Indices: 361307--361345 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
361297 CAATAAAAAG
*
361307 TTATATTCGTTTAATTAT
1 TTATATTCATTTAATTAT
*
361325 TTATATTCATTTATTTAT
1 TTATATTCATTTAATTAT
361343 TTA
1 TTA
361346 ACTAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (18 bp):
TTATATTCATTTAATTAT
Found at i:375341 original size:15 final size:15
Alignment explanation
Indices: 375292--375323 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
375282 AAATTCTAAA
375292 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
375307 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
375322 TA
1 TA
375324 AAAATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:375344 original size:21 final size:22
Alignment explanation
Indices: 375300--375341 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
375290 AATATTTAAA
375300 TAAAAATTATTTATATAAAAAT
1 TAAAAATTATTTATATAAAAAT
375322 TAAAAATTATTTATATAAAA
1 TAAAAATTATTTATATAAAA
375342 TTATATATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAAAATTATTTATATAAAAAT
Found at i:375682 original size:29 final size:29
Alignment explanation
Indices: 375637--375699 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
375627 TAAGATATAA
375637 TATTTATTATATCTTTTATATATAATAATT
1 TATTTATTATATCTTTTATAT-TAATAATT
* *
375667 TATTTATT-TATCTTTTATATTTATACTT
1 TATTTATTATATCTTTTATATTAATAATT
375695 TATTT
1 TATTT
375700 TGCATACTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 11 0.35
29 12 0.39
30 8 0.26
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (29 bp):
TATTTATTATATCTTTTATATTAATAATT
Found at i:377546 original size:20 final size:20
Alignment explanation
Indices: 377521--377558 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
377511 TAGACTACTA
377521 GGAAAAGAATCAAACACATG
1 GGAAAAGAATCAAACACATG
*
377541 GGAAAATAATCAAACACA
1 GGAAAAGAATCAAACACA
377559 AAATAGGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.11
Consensus pattern (20 bp):
GGAAAAGAATCAAACACATG
Found at i:381572 original size:6 final size:6
Alignment explanation
Indices: 381561--381594 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
381551 TACAAAAAGG
*
381561 CCCCCT CCCCCT CCCCCT CCACCT CCCCCCT CCC
1 CCCCCT CCCCCT CCCCCT CCCCCT -CCCCCT CCC
381595 TAGCATCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.03, C:0.82, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCCCT
Found at i:383399 original size:18 final size:18
Alignment explanation
Indices: 383376--383416 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
383366 ACTCTTTTAA
383376 TATGTCAATTTAAAATTG
1 TATGTCAATTTAAAATTG
383394 TATGTCAATTTAAAATTG
1 TATGTCAATTTAAAATTG
383412 TATGT
1 TATGT
383417 GTTATCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (18 bp):
TATGTCAATTTAAAATTG
Found at i:396623 original size:20 final size:20
Alignment explanation
Indices: 396609--396647 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
396599 CCATTATATT
*
396609 TTTACTGGTTACATTGTAAA
1 TTTACTGGTTACATTATAAA
* *
396629 TTTACTTGTTACATAATAA
1 TTTACTGGTTACATTATAA
396648 TTATCGATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (20 bp):
TTTACTGGTTACATTATAAA
Found at i:397698 original size:112 final size:112
Alignment explanation
Indices: 397326--397786 Score: 773
Period size: 112 Copynumber: 4.1 Consensus size: 112
397316 TTAAATTTCA
* * *
397326 AAAGTGTCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTT
*
397391 TGTCATTTTTTTTACTTGTTATATTGTTATGGATCGATACATTTTTAT
66 TGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTAT
* *
397439 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTATCTGTTTTGTCATTTATAGATCGG-TT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTT
397503 TGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTAT
66 TGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTAT
*
397550 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTT
*
397615 TGTCATTTTTTTATCTGTTATATTGTTATGGATCGATACATTTTTAT
66 TGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTAT
* * *
397662 AAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACTGATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTT
* *
397727 TGTCATTTTTTTACCTGTTATATTGTTATGGATCAAT-CTATTTTAAT
66 TGTCATTTTTTTACCTGTTATATTGTTATGGATCGATAC-ATTTTTAT
397774 AAAGTATCGACAC
1 AAAGTATCGACAC
397787 AAACCGACAA
Statistics
Matches: 329, Mismatches: 17, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
111 101 0.31
112 171 0.52
113 57 0.17
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.46
Consensus pattern (112 bp):
AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTT
TGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTAT
Found at i:401588 original size:2 final size:2
Alignment explanation
Indices: 401581--401636 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
401571 TGATATTATG
401581 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
401623 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
401637 TCAGTTCAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:403662 original size:22 final size:21
Alignment explanation
Indices: 403637--403677 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
403627 TATAAAAAAT
403637 TATTTTTATTTAATATTTTTGG
1 TATTTTTATTTAAT-TTTTTGG
403659 TATTTTTATTTAATTTTTT
1 TATTTTTATTTAATTTTTT
403678 AAATTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (21 bp):
TATTTTTATTTAATTTTTTGG
Found at i:405792 original size:41 final size:41
Alignment explanation
Indices: 405736--405855 Score: 143
Period size: 41 Copynumber: 2.9 Consensus size: 41
405726 TAATTAAACT
405736 CCTAATTTTTCAATCTTA-CTTTCTACTTTTATAATTGAGGTC
1 CCTAATTTTT-AATCTTACCTTT-TACTTTTATAATTGAGGTC
* * * *
405778 CCTAATTTTTAATCTAACCTTTTACTTTTATCATGGAGGCC
1 CCTAATTTTTAATCTTACCTTTTACTTTTATAATTGAGGTC
* *
405819 CCTACTTTTTTTAATCTTACCTTTTACTTATATAATT
1 CCTA--ATTTTTAATCTTACCTTTTACTTTTATAATT
405856 TAGACACTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
41 26 0.39
42 14 0.21
43 26 0.39
ACGTcount: A:0.24, C:0.20, G:0.06, T:0.50
Consensus pattern (41 bp):
CCTAATTTTTAATCTTACCTTTTACTTTTATAATTGAGGTC
Found at i:405871 original size:43 final size:43
Alignment explanation
Indices: 405783--405873 Score: 101
Period size: 43 Copynumber: 2.1 Consensus size: 43
405773 AGGTCCCTAA
* * * * *
405783 TTTTTAATCTAACCTTTTACTTTTATCATGGAGGCCCCTACTT
1 TTTTTAATCTAACCTTTTACTTATATAATGGAGACACCTAATT
* ** *
405826 TTTTTAATCTTACCTTTTACTTATATAATTTAGACACTTAATT
1 TTTTTAATCTAACCTTTTACTTATATAATGGAGACACCTAATT
405869 TTTTT
1 TTTTT
405874 TCAATCTCTC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.24, C:0.18, G:0.05, T:0.53
Consensus pattern (43 bp):
TTTTTAATCTAACCTTTTACTTATATAATGGAGACACCTAATT
Found at i:406951 original size:18 final size:19
Alignment explanation
Indices: 406930--406978 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
406920 AGCCAAATTT
*
406930 AGTATTGATACT-C-ATGG
1 AGTATCGATACTCCTATGG
406947 AAGTATCGATACTCCTATGG
1 -AGTATCGATACTCCTATGG
406967 AGTATCGATACT
1 AGTATCGATACT
406979 GAGGAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 11 0.39
19 13 0.46
20 4 0.14
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (19 bp):
AGTATCGATACTCCTATGG
Found at i:407571 original size:184 final size:186
Alignment explanation
Indices: 407262--407632 Score: 728
Period size: 184 Copynumber: 2.0 Consensus size: 186
407252 CATTGCTTTC
407262 AAATAAGATTACAAGTGAAAACAATAATAATGTTAAATTACACTTAGAAATGAGATAGATTAGGG
1 AAATAAGATTACAAGTGAAAACAATAATAATGTTAAATTACACTTAGAAATGAGATAGATTAGGG
407327 TGACATAAAGACAATTCTTATAAACAAAGAAAAAATAAAGATGTGAGATAAAATGAAAATATTAG
66 TGACATAAAGACAATTCTTATAAACAAAGAAAAAATAAAGATGTGAGATAAAATGAAAATATTAG
407392 TGACAACAACTAGCACCAAGACT-GTGTCGTCGT-TGCTCATGAAAGACAAAAAGG
131 TGACAACAACTAGCACCAAGACTGGTGTCGTCGTCTGCTCATGAAAGACAAAAAGG
407446 AAATAAGATTACAAGTGAAAACAATAATAATGTTAAATTACACTTAGAAATGAGATAGATTAGGG
1 AAATAAGATTACAAGTGAAAACAATAATAATGTTAAATTACACTTAGAAATGAGATAGATTAGGG
407511 TGACATAAAGACAATTCTTATAAACAAAGAAAAAATAAAGATGTGAGATAAAATGAAAATATTAG
66 TGACATAAAGACAATTCTTATAAACAAAGAAAAAATAAAGATGTGAGATAAAATGAAAATATTAG
407576 TGACAACAACTAGCACCAAGACTGGTGTCGTCGTCTGCTCATGAAAGACAAAAAGG
131 TGACAACAACTAGCACCAAGACTGGTGTCGTCGTCTGCTCATGAAAGACAAAAAGG
407632 A
1 A
407633 TTGAGGTAGA
Statistics
Matches: 185, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
184 153 0.83
185 10 0.05
186 22 0.12
ACGTcount: A:0.49, C:0.11, G:0.18, T:0.23
Consensus pattern (186 bp):
AAATAAGATTACAAGTGAAAACAATAATAATGTTAAATTACACTTAGAAATGAGATAGATTAGGG
TGACATAAAGACAATTCTTATAAACAAAGAAAAAATAAAGATGTGAGATAAAATGAAAATATTAG
TGACAACAACTAGCACCAAGACTGGTGTCGTCGTCTGCTCATGAAAGACAAAAAGG
Found at i:407677 original size:2 final size:2
Alignment explanation
Indices: 407670--407736 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
407660 TTATCTTTTA
407670 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
407711 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
407737 TGGTGTGTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:413739 original size:3 final size:3
Alignment explanation
Indices: 413726--413792 Score: 98
Period size: 3 Copynumber: 22.0 Consensus size: 3
413716 ATTATATTTT
* * *
413726 TAA TAAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TGA TAA TGA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
413772 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
413793 AAAAAAATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 54 0.95
4 3 0.05
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:414333 original size:113 final size:113
Alignment explanation
Indices: 414106--414780 Score: 964
Period size: 113 Copynumber: 5.9 Consensus size: 113
414096 ATAGAATTAT
* * * * *
414106 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTATTCTTTCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
* * * * * *
414171 CTCATTATGAACTCTAC-CTGGCAATGTTGATCAATTAAATGATGAATTCAA
63 CTCATTATGAAC-CTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAA
414222 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
414287 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAA
66 ATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAA
* *
414335 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
414400 ATTATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTC-A
66 ATTATGAACCTTCTCTGGAAAAGCTGATCCATCAA-ATGATGAATTCAA
*
414448 GAAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 G-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* *
414513 CATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGTGATAGAATT-AG
65 CATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAATGAT-GAATTCAA
* *
414562 GCAGAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
414627 ATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGTGATAGAATT-AG
66 ATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAATGAT-GAATTCAA
* *
414675 GCAGAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
414740 ATTATGAACCTTCTCTTGGAAAAG-TCAATCCATCAAATGAT
66 ATTATGAACCTTCTC-TGGAAAAGCT-GATCCATCAAATGAT
414781 AGATTTGAAT
Statistics
Matches: 521, Mismatches: 31, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
112 2 0.00
113 340 0.65
114 130 0.25
116 49 0.09
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAA
Found at i:414510 original size:227 final size:225
Alignment explanation
Indices: 414101--414785 Score: 973
Period size: 227 Copynumber: 3.0 Consensus size: 225
414091 CTGCGATAGA
* * * * *
414101 ATTATGCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTATTCTTTCTTCTTCAGATGACGAG
1 ATTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGAT---GAG
* * * * * *
414166 TTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCAATTAAATGATGAATTCA-AGCAAAAG
63 TTCTTCTCATTATGAACT-TTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGA-CAAAAG
414229 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
126 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
*
414294 ACTTTCTCTGGAAAAGCTGATCCATCAAATGATGG
191 ACCTTCTCTGGAAAAGCTGATCCATCAAATGATGG
*
414329 ATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTT
1 ATT-AAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTT
* * *
414394 CTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGAAAAAAGGTT
65 CTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAA-ATGATGAATTCAGACAAAAGGTT
414459 GAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACC
129 GAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACC
* *
414524 TTCTCTGGAAAAGCTGATCCATCAAGTGATAGA
194 TTCTCTGGAAAAGCTGATCCATCAAATGAT-GG
* * * *
414557 ATTAGGCAGAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTC
1 ATTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTC
* * * * *
414622 TTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCAAGTGATAGAATT-AGGCAGAAGGTTG
66 TTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGAT-GAATTCAGACAAAAGGTTG
*
414686 AACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCT
130 AACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCT
* *
414751 TCTCTTGGAAAAG-TCAATCCATCAAATGATAG
195 TCTC-TGGAAAAGCT-GATCCATCAAATGATGG
414783 ATT
1 ATT
414786 TGAATCTTTG
Statistics
Matches: 414, Mismatches: 35, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
225 2 0.00
226 122 0.29
227 232 0.56
228 8 0.02
229 50 0.12
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (225 bp):
ATTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTC
TTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGACAAAAGGTTGA
ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTT
CTCTGGAAAAGCTGATCCATCAAATGATGG
Found at i:414585 original size:340 final size:341
Alignment explanation
Indices: 414108--414775 Score: 1024
Period size: 340 Copynumber: 2.0 Consensus size: 341
414098 AGAATTATGC
* * *
414108 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTATTCTTTCTTCTTCAGATGACGAGTTCTTCT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGAT-A-GAGTTCTTCT
* * * *
414173 CATTATGAACTCTACCTGGCAATGTTGATCAATTAAATGATGAATTCAAGCAAAAGGTTGAACAA
64 CATTATGAACTCTACCTGGAAAAGCTGATCAATCAAATGATGAATTCAAGCAAAAGGTTGAACAA
*
414238 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
129 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCT
* *
414303 GGAAAAGCTGATCCATCAAATGAT-GGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGA
194 GGAAAAGCTGATCCATCAAATGATAGAATT-AAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
* *
414367 ACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC-TGGAAAAGAT-AATCC
258 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTTGGAAAAG-TCAATCC
414430 ATCAATTTGATGAATTCAGA
322 ATCAATTTGATGAATTCAGA
*
414450 AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTC
1 AAAAA-GTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATAGAGTTCTTCTC
* * * * *
414514 ATTATGAAC-CTTCTCTGGAAAAGCTGATCCATCAAGTGATAGAATT-AGGCAGAAGGTTGAACA
65 ATTATGAACTCTAC-CTGGAAAAGCTGATCAATCAAATGAT-GAATTCAAGCAAAAGGTTGAACA
*
414577 AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
128 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
* * *
414642 TGGAAAAGCTGATCCATCAAGTGATAGAATTAGGCAGAAGGTTGAACAAATTCTTCTCATTATGA
193 TGGAAAAGCTGATCCATCAAATGATAGAATTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
*
414707 ATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTTGGAAAAGTCAATCCA
258 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTTGGAAAAGTCAATCCA
414772 TCAA
323 TCAA
414776 ATGATAGATT
Statistics
Matches: 297, Mismatches: 23, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
339 3 0.01
340 219 0.74
341 27 0.09
342 5 0.02
343 43 0.14
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (341 bp):
AAAAAGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATAGAGTTCTTCTCA
TTATGAACTCTACCTGGAAAAGCTGATCAATCAAATGATGAATTCAAGCAAAAGGTTGAACAAAT
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGG
AAAAGCTGATCCATCAAATGATAGAATTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACT
TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTTGGAAAAGTCAATCCATCA
ATTTGATGAATTCAGA
Found at i:415570 original size:83 final size:83
Alignment explanation
Indices: 415430--415738 Score: 521
Period size: 83 Copynumber: 3.7 Consensus size: 83
415420 TAGTTCTTAC
* * **
415430 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCCAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTCTAAA
415495 TTCAATGATTGGTTCTG-
66 TTCAATGATTGGTTCTGT
* *
415512 CTAAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
1 C-AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTCTAA
415577 ATTCAATGATTGGTTCTGT
65 ATTCAATGATTGGTTCTGT
* *
415596 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTCTAAA
415661 TTCAATGATTGGTTCTGT
66 TTCAATGATTGGTTCTGT
*
415679 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTT
415739 TCAGTTAATG
Statistics
Matches: 216, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
82 1 0.00
83 214 0.99
84 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.27
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTCTAAA
TTCAATGATTGGTTCTGT
Found at i:416894 original size:5 final size:5
Alignment explanation
Indices: 416878--416936 Score: 54
Period size: 5 Copynumber: 12.2 Consensus size: 5
416868 TGACCCCCCT
*
416878 TTTTC -TTT- TTTTC TTTTC TTTTC TCTCTT- TTTT- TTTTC TTTTT TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC T-T-TTC TTTTC TTTTC TTTTC TTTTC
*
416926 TTTTC TCTTC T
1 TTTTC TTTTC T
416937 CTTCAAGCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
4 12 0.26
5 30 0.65
6 2 0.04
7 2 0.04
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:416896 original size:13 final size:12
Alignment explanation
Indices: 416878--416924 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
416868 TGACCCCCCT
416878 TTTTCTTTTTTTC
1 TTTT-TTTTTTTC
* *
416891 TTTTCTTTTCTC
1 TTTTTTTTTTTC
416903 TCTTTTTTTTTTC
1 T-TTTTTTTTTTC
416916 TTTTTTTTT
1 TTTTTTTTT
416925 CTTTTCTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 15 0.52
13 14 0.48
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:416914 original size:20 final size:19
Alignment explanation
Indices: 416876--416936 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
416866 CTTGACCCCC
416876 CTTTTTCTTTTTTTCTTTT
1 CTTTTTCTTTTTTTCTTTT
416895 CTTTTCTCTCTTTTTT-TTTT
1 CTTTT-TCT-TTTTTTCTTTT
* *
416915 CTTTTTTTTTCTTTTCTCTT
1 CTTTTTCTTT-TTTTCTTTT
416935 CT
1 CT
416937 CTTCAAGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
18 2 0.06
19 11 0.31
20 17 0.47
21 6 0.17
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
CTTTTTCTTTTTTTCTTTT
Found at i:416925 original size:30 final size:29
Alignment explanation
Indices: 416877--416933 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
416867 TTGACCCCCC
416877 TTTTTCTTTTTTTCTTTTCTTTTCTCTCT
1 TTTTTCTTTTTTTCTTTTCTTTTCTCTCT
* *
416906 TTTTTTTTTCTTTTTTTTTCTTTTCTCT
1 TTTTTCTTT-TTTTCTTTTCTTTTCTCT
416934 TCTCTTCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (29 bp):
TTTTTCTTTTTTTCTTTTCTTTTCTCTCT
Found at i:427539 original size:13 final size:15
Alignment explanation
Indices: 427517--427553 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
427507 TTTGACAGAA
427517 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
427529 AAATAAAATACTTGC
1 AAATAAAATACTTGC
427544 AAATAAAATA
1 AAATAAAATA
427554 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:427592 original size:18 final size:17
Alignment explanation
Indices: 427544--427594 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
427534 AAATACTTGC
*
427544 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
427562 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
427580 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
427595 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:428304 original size:20 final size:21
Alignment explanation
Indices: 428281--428321 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
428271 TATTATATGT
**
428281 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
428301 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
428322 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:428956 original size:13 final size:13
Alignment explanation
Indices: 428938--428963 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
428928 GCGAGTTCTA
428938 CCGCCGGCCACCG
1 CCGCCGGCCACCG
428951 CCGCCGGCCACCG
1 CCGCCGGCCACCG
428964 TCTTTGGTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGGCCACCG
Found at i:429728 original size:3 final size:3
Alignment explanation
Indices: 429720--429818 Score: 171
Period size: 3 Copynumber: 33.0 Consensus size: 3
429710 TTAATATATT
*
429720 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
429768 TAA TAA TAA TGA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
429816 TAA
1 TAA
429819 AAAAATATTA
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:430907 original size:17 final size:17
Alignment explanation
Indices: 430885--430921 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
430875 GAGAAACGTC
430885 ATGGCAATCAAGTTTAG
1 ATGGCAATCAAGTTTAG
430902 ATGGCAATCAAGTTTAG
1 ATGGCAATCAAGTTTAG
430919 ATG
1 ATG
430922 ACATTCATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (17 bp):
ATGGCAATCAAGTTTAG
Found at i:438673 original size:42 final size:41
Alignment explanation
Indices: 438596--438674 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 41
438586 TAGTATTATT
* * *
438596 TATTATAAAAATTTAATATTATTATTTTTGAAATATTTAAA
1 TATTATAAAAATTTAATATTATCATTATTAAAATATTTAAA
*
438637 TATT-TAAATAATTTATTCATTATCATTATTAAAATATT
1 TATTATAAA-AATTTAAT-ATTATCATTATTAAAATATT
438675 ATTTCTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 4 0.12
41 11 0.34
42 17 0.53
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (41 bp):
TATTATAAAAATTTAATATTATCATTATTAAAATATTTAAA
Found at i:439111 original size:23 final size:23
Alignment explanation
Indices: 439085--439137 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
439075 AAATTAATAA
*
439085 ATAATATAATATCA-TATATTATT
1 ATAATAT-ATATCAGTATATAATT
*
439108 ATAATATATATGAGTATATAATT
1 ATAATATATATCAGTATATAATT
439131 ATAATAT
1 ATAATAT
439138 TAAAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 5 0.19
23 22 0.81
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (23 bp):
ATAATATATATCAGTATATAATT
Found at i:439116 original size:13 final size:13
Alignment explanation
Indices: 439085--439154 Score: 56
Period size: 13 Copynumber: 5.2 Consensus size: 13
439075 AAATTAATAA
*
439085 ATAATATAATATC
1 ATAATATAATATT
439098 AT-ATAT--TATT
1 ATAATATAATATT
439108 ATAATATATATGAGTAT
1 ATAATATA-AT-A-T-T
439125 ATAATTATAATATT
1 ATAA-TATAATATT
*
439139 AAAATATAATATT
1 ATAATATAATATT
439152 ATA
1 ATA
439155 TTTTTTAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 16
0.71 0.05 0.25
Matches are distributed among these distances:
10 5 0.11
11 4 0.09
12 4 0.09
13 13 0.28
14 5 0.11
15 2 0.04
16 2 0.04
17 7 0.15
18 4 0.09
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (13 bp):
ATAATATAATATT
Found at i:439224 original size:11 final size:10
Alignment explanation
Indices: 439208--439261 Score: 51
Period size: 11 Copynumber: 5.5 Consensus size: 10
439198 TTTATATTTT
439208 TATTAAATCAA
1 TATTAAAT-AA
439219 TATT-AA-AA
1 TATTAAATAA
*
439227 TATTATATTAA
1 TATTA-AATAA
439238 TATTAAAT-A
1 TATTAAATAA
*
439247 TATAAAATAA
1 TATTAAATAA
439257 TATTA
1 TATTA
439262 TTTTGAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
8 6 0.17
9 8 0.23
10 10 0.29
11 11 0.31
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (10 bp):
TATTAAATAA
Found at i:439230 original size:19 final size:19
Alignment explanation
Indices: 439208--439261 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
439198 TTTATATTTT
439208 TATTAAATCAATATTAAA-A
1 TATTAAAT-AATATTAAATA
*
439227 TATTATATTAATATTAAATA
1 TATTA-AATAATATTAAATA
*
439247 TATAAAATAATATTA
1 TATTAAATAATATTA
439262 TTTTGAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 23 0.77
20 7 0.23
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TATTAAATAATATTAAATA
Found at i:439235 original size:30 final size:27
Alignment explanation
Indices: 439199--439265 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 27
439189 TTTTAATATT
439199 TTATATTTTTATTAAATCAATATTAAAATA
1 TTATATTTTTATTAAAT--ATA-TAAAATA
**
439229 TTATATTAATATTAAATATATAAAATA
1 TTATATTTTTATTAAATATATAAAATA
*
439256 ATATTATTTT
1 TTA-TATTTT
439266 GAATATTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
27 9 0.29
28 7 0.23
30 15 0.48
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (27 bp):
TTATATTTTTATTAAATATATAAAATA
Found at i:440025 original size:17 final size:18
Alignment explanation
Indices: 439989--440029 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
439979 ATATTATGTA
*
439989 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
440007 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
440024 TTTACT
1 TTTACT
440030 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:441154 original size:19 final size:20
Alignment explanation
Indices: 441121--441159 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
441111 AAAATCAATT
441121 TTAGATTATAGTTAT-ATAA
1 TTAGATTATAGTTATGATAA
441140 TTAGATTATTA-TTATGATAA
1 TTAGATTA-TAGTTATGATAA
441160 AAAATTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (20 bp):
TTAGATTATAGTTATGATAA
Found at i:443955 original size:9 final size:9
Alignment explanation
Indices: 443938--443971 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
443928 TAAAAGTTTA
443938 TTTTAATAT
1 TTTTAATAT
*
443947 TTTTTATAT
1 TTTTAATAT
443956 TTTTAAATAT
1 TTTT-AATAT
443966 TTTTAA
1 TTTTAA
443972 ACAATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTAATAT
Found at i:444037 original size:26 final size:27
Alignment explanation
Indices: 443995--444045 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
443985 AAAGTCAATA
443995 AATTTTTTAAAAATATATAAA-ATTTAT
1 AATTTTTTAAAAATATA-AAATATTTAT
*
444022 AATTTTTT-AAATTATAAAATATTT
1 AATTTTTTAAAAATATAAAATATTT
444046 CTTATCATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 3 0.14
26 11 0.50
27 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AATTTTTTAAAAATATAAAATATTTAT
Found at i:449529 original size:99 final size:99
Alignment explanation
Indices: 449358--449552 Score: 309
Period size: 99 Copynumber: 2.0 Consensus size: 99
449348 CAGTTGATGT
* * * ** *
449358 AGATGGAACTAAGAAAGAAAGTGACCCTGCAAGTGATTCAGGGGCAAAATTGCTGAAGAAGTCAT
1 AGATGAAACTAAGAAAGAAAGTGACACTGCAAGTGATTCAGAGGCAAAATCACTGAAAAAGTCAT
*
449423 CAAAGAAGGTAGACTCTAGTGGTAACAATGCGGC
66 CAAAGAAGGTAGACTCTAGTCGTAACAATGCGGC
*
449457 AGATGAAACTAAGAAAGAGAGTGACACTGCAAGTGATTCAGAGGCAAAATCACTGAAAAAGTCAT
1 AGATGAAACTAAGAAAGAAAGTGACACTGCAAGTGATTCAGAGGCAAAATCACTGAAAAAGTCAT
*
449522 CAAAGAAGGTAGATTCTAGTCGTAACAATGC
66 CAAAGAAGGTAGACTCTAGTCGTAACAATGC
449553 AGATGAATCC
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
99 87 1.00
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18
Consensus pattern (99 bp):
AGATGAAACTAAGAAAGAAAGTGACACTGCAAGTGATTCAGAGGCAAAATCACTGAAAAAGTCAT
CAAAGAAGGTAGACTCTAGTCGTAACAATGCGGC
Found at i:457737 original size:3 final size:3
Alignment explanation
Indices: 457729--457757 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
457719 CTCCGTCAAC
457729 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
457758 TAGAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:459440 original size:3 final size:3
Alignment explanation
Indices: 459434--459492 Score: 79
Period size: 3 Copynumber: 20.0 Consensus size: 3
459424 ACCCATTTTT
459434 TTA TTA TTGA -TA TTA TTA TTA TTA TT- TTA TTTA TTA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
459479 TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA
459493 CAAACAGGCC
Statistics
Matches: 51, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 5 0.10
3 42 0.82
4 4 0.08
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:461077 original size:17 final size:17
Alignment explanation
Indices: 461055--461088 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
461045 CTATTTTATA
461055 AATTATATATTAATTTT
1 AATTATATATTAATTTT
* *
461072 AATTATTTATTTATTTT
1 AATTATATATTAATTTT
461089 TTAATATCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTATATATTAATTTT
Found at i:461185 original size:30 final size:29
Alignment explanation
Indices: 461146--461205 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
461136 TTCTGATATT
* *
461146 TTTAAATAAATAAATAATTTTATTTATAAA
1 TTTAAATAAATAAATAAATTTACTTA-AAA
* *
461176 TTTATATAAATTAATAAATTTACTTAAAA
1 TTTAAATAAATAAATAAATTTACTTAAAA
461205 T
1 T
461206 CATAATTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTAAATAAATAAATAAATTTACTTAAAA
Found at i:464881 original size:3 final size:3
Alignment explanation
Indices: 464875--464908 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
464865 GATGATGATG
464875 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
464909 ACAAGGGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:477149 original size:29 final size:29
Alignment explanation
Indices: 477073--477131 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
477063 ATTTTCACCT
*
477073 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAACAATGACATCAA
477102 AACTAAATTGATGTAAACAATGACATCAA
1 AACTAAATTGATGTAAACAATGACATCAA
477131 A
1 A
477132 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAACAATGACATCAA
Found at i:481796 original size:29 final size:29
Alignment explanation
Indices: 481754--481812 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
481744 ATTTTCACCT
481754 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
481783 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
481812 A
1 A
481813 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:484196 original size:24 final size:24
Alignment explanation
Indices: 484169--484217 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
484159 TATTGTTCCC
484169 GAGCTTAGTCAACTAAATGTCCTT
1 GAGCTTAGTCAACTAAATGTCCTT
484193 GAGCTTAGTCAACTAAATGTCCTT
1 GAGCTTAGTCAACTAAATGTCCTT
484217 G
1 G
484218 TCCAAAGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (24 bp):
GAGCTTAGTCAACTAAATGTCCTT
Found at i:489029 original size:22 final size:22
Alignment explanation
Indices: 488986--489029 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
488976 ATATAAAAGT
** *
488986 AATTAAATATAATTTTTTAATA
1 AATTAAATATAAAGTTTAAATA
489008 AATTAAATATAAAGTTTAAATA
1 AATTAAATATAAAGTTTAAATA
489030 GCTTTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTAAATATAAAGTTTAAATA
Found at i:494756 original size:28 final size:31
Alignment explanation
Indices: 494724--494790 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 31
494714 TCCGAAAAAT
494724 CACATTTTTCAT-TTA-ATATTTTTGA-TTAA
1 CACATTTTTCATATTATAT-TTTTTGATTTAA
**
494753 -ACATAGTTCATATTATATTTTTTGATTTAA
1 CACATTTTTCATATTATATTTTTTGATTTAA
494783 CACATTTT
1 CACATTTT
494791 ACAGAAAGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
28 9 0.30
29 10 0.33
30 6 0.20
31 5 0.17
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.54
Consensus pattern (31 bp):
CACATTTTTCATATTATATTTTTTGATTTAA
Found at i:497850 original size:29 final size:32
Alignment explanation
Indices: 497778--497850 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 32
497768 ATGAATATTG
*
497778 TATTATCTTATTTGGATTTAACAAAAATATAA
1 TATTATTTTATTTGGATTTAACAAAAATATAA
* * *
497810 AATT-TTAGTATTT-GATTT-A-AGAAATATAA
1 TATTATT-TTATTTGGATTTAACAAAAATATAA
497839 TATTATTTTATT
1 TATTATTTTATT
497851 ATATATTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
29 16 0.48
30 3 0.09
31 6 0.18
32 8 0.24
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (32 bp):
TATTATTTTATTTGGATTTAACAAAAATATAA
Found at i:504840 original size:198 final size:199
Alignment explanation
Indices: 504503--504899 Score: 771
Period size: 198 Copynumber: 2.0 Consensus size: 199
504493 CTTAGGATTG
504503 AGAATTGCAAAGTTAGTTTTCCCCAATGTGCTAAAGATGGAGTTGGATCATTTTTTCTTGAAAGT
1 AGAATTGCAAAGTTAGTTTTCCCCAATGTGCTAAAGATGGAGTTGGATCATTTTTTCTTGAAAGT
504568 TTTGACATCTGCCATCTATGAGGTGCTAATATTCTTGTATCTTCTTGCGCTGTTCTTTCAGGAGA
66 TTTGACATCTGCCATCTATGAGGTGCTAATATTCTTGTATCTTCTTGCGCTGTTCTTTCAGGAGA
504633 GTGGTGTGAAGT-GGCATCTAGAT-GGATGCATATCTTTTAATGAATGATGACCAAATACACTGG
131 GTGGTGTGAAGTGGGCATCTAGATGGGATGCATATCTTTTAATGAATGATGACCAAATACACTGG
504696 TTCT
196 TTCT
504700 AGAATTGCAAAGTTAGTTTTCCCCAATGTGCTAAAGATGGAGTTGGATCATTTTTTCTTGAAATG
1 AGAATTGCAAAGTTAGTTTTCCCCAATGTGCTAAAGATGGAGTTGGATCATTTTTTCTTGAAA-G
504765 TTTTGACATCTGCCATCTATGAGGTGCTAATATTCTTGTATCTTCTTGCGCTGTTCTTTCAGGAG
65 TTTTGACATCTGCCATCTATGAGGTGCTAATATTCTTGTATCTTCTTGCGCTGTTCTTTCAGGAG
504830 AGTGGTGTGAAGTGGGCATCTAGATGGGATGCATATCTTTTAATGAATGATGACCAAATACACTG
130 AGTGGTGTGAAGTGGGCATCTAGATGGGATGCATATCTTTTAATGAATGATGACCAAATACACTG
504895 GTTCT
195 GTTCT
504900 CAATTGTCAA
Statistics
Matches: 197, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
197 63 0.32
198 79 0.40
199 11 0.06
200 44 0.22
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (199 bp):
AGAATTGCAAAGTTAGTTTTCCCCAATGTGCTAAAGATGGAGTTGGATCATTTTTTCTTGAAAGT
TTTGACATCTGCCATCTATGAGGTGCTAATATTCTTGTATCTTCTTGCGCTGTTCTTTCAGGAGA
GTGGTGTGAAGTGGGCATCTAGATGGGATGCATATCTTTTAATGAATGATGACCAAATACACTGG
TTCT
Found at i:506373 original size:108 final size:108
Alignment explanation
Indices: 506184--506381 Score: 315
Period size: 108 Copynumber: 1.8 Consensus size: 108
506174 AAGTTTGCAT
* * * * *
506184 CAATTCAAGTTGAACGGAGGGAAGCATCGTCACTTTCGATTCAAGTCGAACGGAGGGAAGCATCG
1 CAATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCG
*
506249 ACTCTTCTGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTC
66 ACACTTCTGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTC
*
506292 CAATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGTATCG
1 CAATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCG
* *
506357 GCACTTCTGATTCAAGTTGAACGGA
66 ACACTTCTGATTCAAGTCGAACGGA
506382 AGGATGTATG
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 81 1.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (108 bp):
CAATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCG
ACACTTCTGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTC
Found at i:506382 original size:36 final size:36
Alignment explanation
Indices: 506186--506385 Score: 276
Period size: 36 Copynumber: 5.6 Consensus size: 36
506176 GTTTGCATCA
* * *
506186 ATTCAAGTTGAACGGAGGGAAGCATCGTCACTT-TCG
1 ATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCT-G
* * *
506222 ATTCAAGTCGAACGGAGGGAAGCATCGACTCTTCTG
1 ATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCTG
* **
506258 ATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCCA
1 ATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCTG
*
506294 ATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCCG
1 ATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCTG
*
506330 ATTCAAGTCGAACGGAAGGAAGTATCGGCACTTCTG
1 ATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCTG
*
506366 ATTCAAGTTGAACGGAAGGA
1 ATTCAAGTCGAACGGAAGGA
506386 TGTATGTCTT
Statistics
Matches: 151, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
36 150 0.99
37 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.20
Consensus pattern (36 bp):
ATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCTG
Found at i:510743 original size:22 final size:22
Alignment explanation
Indices: 510702--510744 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
510692 CTTTTGGTTT
* *
510702 GGGTTAATTCCGCTTTCAGTTC
1 GGGTTAATTCCGATTCCAGTTC
*
510724 GGGTTAATTTCGATTCCAGTT
1 GGGTTAATTCCGATTCCAGTT
510745 GATTTCAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (22 bp):
GGGTTAATTCCGATTCCAGTTC
Found at i:540244 original size:18 final size:20
Alignment explanation
Indices: 540222--540281 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
540212 TTTTTGTTTT
540222 TTTTTTATTA-AAAACAATA
1 TTTTTTATTATAAAACAATA
540241 TTTTTT-TTATTAAAACAATA
1 TTTTTTATTA-TAAAACAATA
*
540261 TTTTTTATTATTAAAAAAATA
1 TTTTTTATTA-TAAAACAATA
540282 GAAAATATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 3 0.08
19 6 0.16
20 15 0.41
21 13 0.35
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTTTTATTATAAAACAATA
Found at i:540246 original size:21 final size:21
Alignment explanation
Indices: 540220--540281 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
540210 GTTTTTTGTT
540220 TTTTTTTTATTAAAAACAATA
1 TTTTTTTTATTAAAAACAATA
540241 TTTTTTTTATT-AAAACAATA
1 TTTTTTTTATTAAAAACAATA
540261 TTTTTTATTATTAAAAA-AATA
1 TTTTTT-TTATTAAAAACAATA
540282 GAAAATATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
20 15 0.38
21 20 0.51
22 4 0.10
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTTTTTATTAAAAACAATA
Found at i:540383 original size:32 final size:32
Alignment explanation
Indices: 540340--540407 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
540330 TTCGACCAAG
* * * *
540340 CCGACCCGACCCGAAAATTGTACATCTTTCAC
1 CCGACCCGACCCAAAAAATATACATCTTCCAC
* *
540372 CCGACCTGACCCAAAAAATATATATCTTCCAC
1 CCGACCCGACCCAAAAAATATACATCTTCCAC
540404 CCGA
1 CCGA
540408 TCCAATCCGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.32, C:0.37, G:0.10, T:0.21
Consensus pattern (32 bp):
CCGACCCGACCCAAAAAATATACATCTTCCAC
Found at i:542895 original size:26 final size:24
Alignment explanation
Indices: 542818--542890 Score: 71
Period size: 27 Copynumber: 3.0 Consensus size: 24
542808 ACCCTTACTT
542818 ATGTAATTGCATTTTCT-ATTTCA
1 ATGTAATTGCATTTTCTAATTTCA
*
542841 ATGT-A-TGTCTTTGTTTCTAATATTTCA
1 ATGTAATTG-C-AT-TTTCT-A-ATTTCA
542868 ATGTAATTGCATTTTCTAATTTC
1 ATGTAATTGCATTTTCTAATTTC
542891 CCAATATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 15
0.70 0.04 0.26
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 5 0.12
24 10 0.25
25 1 0.03
26 5 0.12
27 11 0.28
28 2 0.05
29 2 0.05
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (24 bp):
ATGTAATTGCATTTTCTAATTTCA
Found at i:543033 original size:25 final size:25
Alignment explanation
Indices: 543005--543097 Score: 82
Period size: 25 Copynumber: 3.7 Consensus size: 25
542995 ACAACCCTTG
*
543005 ACCACTCTCACCTTAAAAATCCTAA
1 ACCACTTTCACCTTAAAAATCCTAA
* * **
543030 ACCACTTTAACC-TACAAAATCTTTC
1 ACCACTTTCACCTTA-AAAATCCTAA
* *
543055 ACCACTTTCACCTTAACGAATCCTAT
1 ACCACTTTCACCTTAA-AAATCCTAA
*
543081 ACCACTTTAACC-TAAAA
1 ACCACTTTCACCTTAAAA
543098 TCACTCCAAC
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
24 3 0.06
25 32 0.60
26 18 0.34
ACGTcount: A:0.38, C:0.33, G:0.01, T:0.28
Consensus pattern (25 bp):
ACCACTTTCACCTTAAAAATCCTAA
Found at i:543039 original size:50 final size:51
Alignment explanation
Indices: 542975--543094 Score: 161
Period size: 50 Copynumber: 2.4 Consensus size: 51
542965 CGAACCTTAC
* * *
542975 CCTAAACCACTTTAATCTACACAACCCTTGACCACTCTCACCTTAA-AAAT
1 CCTAAACCACTTTAACCTACAAAACCCTTCACCACTCTCACCTTAACAAAT
* * * *
543025 CCTAAACCACTTTAACCTACAAAATCTTTCACCACTTTCACCTTAACGAAT
1 CCTAAACCACTTTAACCTACAAAACCCTTCACCACTCTCACCTTAACAAAT
*
543076 CCTATACCACTTTAACCTA
1 CCTAAACCACTTTAACCTA
543095 AAATCACTCC
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
50 40 0.66
51 21 0.34
ACGTcount: A:0.35, C:0.35, G:0.02, T:0.28
Consensus pattern (51 bp):
CCTAAACCACTTTAACCTACAAAACCCTTCACCACTCTCACCTTAACAAAT
Found at i:545250 original size:16 final size:17
Alignment explanation
Indices: 545229--545260 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
545219 GATAGAAACT
545229 ATTAAT-AAAATAAATA
1 ATTAATCAAAATAAATA
545245 ATTAATCAAAATAAAT
1 ATTAATCAAAATAAAT
545261 TCAGATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
ATTAATCAAAATAAATA
Found at i:546040 original size:2 final size:2
Alignment explanation
Indices: 546029--546061 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
546019 CATCATTTAA
546029 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
546062 TGAATAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:563718 original size:457 final size:459
Alignment explanation
Indices: 562831--563747 Score: 1788
Period size: 457 Copynumber: 2.0 Consensus size: 459
562821 ACCTAGGCTC
562831 TAGCCTCTAAGTAGTTTTACCTATTTAGTGGTTACTATTTCGTGCATAATTGATTCTTATAGCCT
1 TAGCCTCTAAGTAGTTTTACCTATTTAGTGGTTACTATTTCGTGCATAATTGATTCTTATAGCCT
562896 CTAAGTAGTCATTACCTGGTTAGTGCTTGCATCACATATCATAAGCCTCCTTTTGCATAATTGAT
66 CTAAGTAGTCATTACCTGGTTAGTGCTTGCATCACATATCATAAGCCTCCTTTTGCATAATTGAT
562961 TTTAGAGCTTGTTTTATTATTTTGTAATCCACGTTTTTCATTTTTTCATGTTTGTTATTTTATAT
131 TTTAGAGCTTGTTTTATTATTTTGTAATCCACGTTTTTCATTTTTTCATGTTTGTTATTTTATAT
563026 ATGAAGAATGTTGATGTTGAGTTTTGCTAGTTATTTCCATGAGGTTGTGTTCGTGTTGATAAGTT
196 ATGAAGAATGTTGATGTTGAGTTTTGCTAGTTATTTCCATGAGGTTGTGTTCGTGTTGATAAGTT
563091 CTTGCTTCTCTCAGCTTGTGCACTTTGTTAACCGTGACTCTCTGGGATTGGCAAATGACTTTCAT
261 CTTGCTTCTCTCAGCTTGTGCACTTTGTTAACCGTGACTCTCTGGGATTGGCAAATGACTTTCAT
563156 TCTTTGGGATTTATTCCTGAAGGAGTTGACATACAATCTGTGGCAGATACATTACAGACGTCGTT
326 TCTTTGGGATTTATTCCTGAAGGAGTTGACATACAATCTGTGGCAGATACATTACAGACGTCGTT
563221 TCGACAAGGGTACTCGACAATCTCAAGACTTCCAGTTTTTGCTGTAGTCGCCTTACCTTATTATT
391 TCGACAAGGGTACTCGACAATCTCAAGACTTCCAGTTTTTGCTGTAGTCGCCTTACCTTATTATT
563286 GAGA
456 GAGA
563290 TAGCCTCTAAGTAGTTGTTACCTATTTAGTGGTTACTATTTCGTGCATAATTGATTCTTATAGCC
1 TAGCCTCTAAGTAGTT-TTACCTATTTAGTGGTTACTATTTCGTGCATAATTGATTCTTATAGCC
563355 TCTAAGTA-TCATTACCTGGTTAGTGCTTGCATCACATATCATAAGCCTCCTTTTGCATAATTGA
65 TCTAAGTAGTCATTACCTGGTTAGTGCTTGCATCACATATCATAAGCCTCCTTTTGCATAATTGA
563419 -TTTAGAGCTTGTTTTATTA-TTTGTAATCCACGTTTTTCATTTTTTCATGTTTGTTATTTTATA
130 TTTTAGAGCTTGTTTTATTATTTTGTAATCCACGTTTTTCATTTTTTCATGTTTGTTATTTTATA
563482 TATGAAGAATGTTGATGTTGAGTTTTGCTAGTTATTTCCATGAGGTTGTGTTCGTGTTGATAAGT
195 TATGAAGAATGTTGATGTTGAGTTTTGCTAGTTATTTCCATGAGGTTGTGTTCGTGTTGATAAGT
563547 TCTTGCTTCTCTCAGCTTGTGCACTTTGTTAACCGTGACTCTCTGGGATTGGCAAATGACTTTCA
260 TCTTGCTTCTCTCAGCTTGTGCACTTTGTTAACCGTGACTCTCTGGGATTGGCAAATGACTTTCA
563612 TTCTTTGGGATTTATTCCTGAAGGAGTTGACATACAATCTGTGGCAGATACATTACAGACGTCG-
325 TTCTTTGGGATTTATTCCTGAAGGAGTTGACATACAATCTGTGGCAGATACATTACAGACGTCGT
563676 TTCGACAAGGGTACTCGACAATCTCAAGACTTCCAGGTTTTTGCTGTAGTCGCCTTACCTTATTA
390 TTCGACAAGGGTACTCGACAATCTCAAGACTTCCA-GTTTTTGCTGTAGTCGCCTTACCTTATTA
563741 TTGAGA
454 TTGAGA
563747 T
1 T
563748 CCATCTCTTG
Statistics
Matches: 456, Mismatches: 0, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
456 35 0.08
457 274 0.60
458 19 0.04
459 72 0.16
460 56 0.12
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (459 bp):
TAGCCTCTAAGTAGTTTTACCTATTTAGTGGTTACTATTTCGTGCATAATTGATTCTTATAGCCT
CTAAGTAGTCATTACCTGGTTAGTGCTTGCATCACATATCATAAGCCTCCTTTTGCATAATTGAT
TTTAGAGCTTGTTTTATTATTTTGTAATCCACGTTTTTCATTTTTTCATGTTTGTTATTTTATAT
ATGAAGAATGTTGATGTTGAGTTTTGCTAGTTATTTCCATGAGGTTGTGTTCGTGTTGATAAGTT
CTTGCTTCTCTCAGCTTGTGCACTTTGTTAACCGTGACTCTCTGGGATTGGCAAATGACTTTCAT
TCTTTGGGATTTATTCCTGAAGGAGTTGACATACAATCTGTGGCAGATACATTACAGACGTCGTT
TCGACAAGGGTACTCGACAATCTCAAGACTTCCAGTTTTTGCTGTAGTCGCCTTACCTTATTATT
GAGA
Done.