Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008528.1 Hibiscus syriacus cultivar Beakdansim tig00111403_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: 1199389
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:310350 original size:13 final size:14
Alignment explanation
Indices: 310322--310353 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
310312 AATGGGAAGT
310322 AATCCCTGCAAAAA
1 AATCCCTGCAAAAA
310336 AATCCCTGCAAAAA
1 AATCCCTGCAAAAA
310350 AATC
1 AATC
310354 TATGCAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.28, G:0.06, T:0.16
Consensus pattern (14 bp):
AATCCCTGCAAAAA
Found at i:310359 original size:14 final size:14
Alignment explanation
Indices: 310322--310361 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
310312 AATGGGAAGT
*
310322 AATCCCTGCAAAAA
1 AATCCATGCAAAAA
*
310336 AATCCCTGCAAAAA
1 AATCCATGCAAAAA
*
310350 AATCTATGCAAA
1 AATCCATGCAAA
310362 TAGACAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.07, T:0.17
Consensus pattern (14 bp):
AATCCATGCAAAAA
Found at i:311042 original size:26 final size:27
Alignment explanation
Indices: 310983--311042 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 27
310973 CATAAGACCT
*
310983 TATAATACCATTAATGCTTATTATGAAA
1 TATAATACCATTAATCCTTATTAT-AAA
*
311011 TCATAATACTATTAATCCTTATTAT-AA
1 T-ATAATACCATTAATCCTTATTATAAA
311038 TATAA
1 TATAA
311043 AATTTATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 4 0.14
27 3 0.10
28 1 0.03
29 21 0.72
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.42
Consensus pattern (27 bp):
TATAATACCATTAATCCTTATTATAAA
Found at i:318903 original size:19 final size:20
Alignment explanation
Indices: 318859--318905 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
318849 TAATTTTTTG
318859 AGATAAAATCATAAGTAACA
1 AGATAAAATCATAAGTAACA
*
318879 TG-TAAAAGTCA-AAGTAA-A
1 AGATAAAA-TCATAAGTAACA
318897 AGATAAAAT
1 AGATAAAAT
318906 AGAGGTGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
18 3 0.13
19 16 0.70
20 4 0.17
ACGTcount: A:0.60, C:0.06, G:0.13, T:0.21
Consensus pattern (20 bp):
AGATAAAATCATAAGTAACA
Found at i:319795 original size:24 final size:24
Alignment explanation
Indices: 319763--319809 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
319753 AATAATAAGG
319763 ATTAATGGTCCACTGATGAAATGC
1 ATTAATGGTCCACTGATGAAATGC
319787 ATTAATGGTCCACTGATGAAATG
1 ATTAATGGTCCACTGATGAAATG
319810 TTTCGTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (24 bp):
ATTAATGGTCCACTGATGAAATGC
Found at i:319847 original size:22 final size:21
Alignment explanation
Indices: 319822--319865 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
319812 TCGTCTTCAA
319822 CTAT-TTAATTGTCATATCTTTT
1 CTATATTAATTGT-AT-TCTTTT
319844 CTATCATTAATTGTATTCTTTT
1 CTAT-ATTAATTGTATTCTTTT
319866 TACTTTCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.50
23 2 0.10
24 8 0.40
ACGTcount: A:0.23, C:0.14, G:0.05, T:0.59
Consensus pattern (21 bp):
CTATATTAATTGTATTCTTTT
Found at i:330407 original size:22 final size:22
Alignment explanation
Indices: 330381--330449 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
330371 GTCAATCCTA
330381 AAATAATTTTTGGGTTTGGACT
1 AAATAATTTTTGGGTTTGGACT
* *
330403 AAATAA--TTT--GTAT-G-CA
1 AAATAATTTTTGGGTTTGGACT
330419 AAATAATTTTTGGGTTTGGACT
1 AAATAATTTTTGGGTTTGGACT
330441 AAATAATTT
1 AAATAATTT
330450 GTATGCTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
16 7 0.19
17 1 0.03
18 6 0.16
20 6 0.16
21 1 0.03
22 16 0.43
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.43
Consensus pattern (22 bp):
AAATAATTTTTGGGTTTGGACT
Found at i:330431 original size:38 final size:38
Alignment explanation
Indices: 330380--330455 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
330370 TGTCAATCCT
330380 AAAATAATTTTTGGGTTTGGACTAAATAATTTGTATGC
1 AAAATAATTTTTGGGTTTGGACTAAATAATTTGTATGC
330418 AAAATAATTTTTGGGTTTGGACTAAATAATTTGTATGC
1 AAAATAATTTTTGGGTTTGGACTAAATAATTTGTATGC
330456 TTAGATTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.42
Consensus pattern (38 bp):
AAAATAATTTTTGGGTTTGGACTAAATAATTTGTATGC
Found at i:344773 original size:18 final size:18
Alignment explanation
Indices: 344750--344785 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
344740 AATAACCACC
*
344750 GGCGGAGGAGGGGGAGAA
1 GGCGGAGAAGGGGGAGAA
*
344768 GGCGGAGAATGGGGAGAA
1 GGCGGAGAAGGGGGAGAA
344786 AGAGGTTGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.61, T:0.03
Consensus pattern (18 bp):
GGCGGAGAAGGGGGAGAA
Found at i:348100 original size:29 final size:29
Alignment explanation
Indices: 347966--348204 Score: 218
Period size: 29 Copynumber: 8.3 Consensus size: 29
347956 AAAAATTACA
* * * *
347966 AAAATATCACCTTTATTAAAAATAATTACT
1 AAAATATCATCTTT-TTCAAAATAATTCCC
* *
347996 AAAATATCACCGTTTT-ACAAAT-ATTCCC
1 AAAATATCATCTTTTTCA-AAATAATTCCC
* * * * *
348024 AATATGTCATCGTTTTAAAAATAATTACC
1 AAAATATCATCTTTTTCAAAATAATTCCC
* * * * * *
348053 AGAATGTTA-CTGTTT-AAAAAAAATCCC
1 AAAATATCATCTTTTTCAAAATAATTCCC
* *
348080 AAAATGTCACCTTTTTCAAAATAATTCCC
1 AAAATATCATCTTTTTCAAAATAATTCCC
*
348109 AAAATGTCA-CTTTTTCAAAATAATTCCC
1 AAAATATCATCTTTTTCAAAATAATTCCC
* * *
348137 AAAATATCATATTTTTTAAAATAATTCTC
1 AAAATATCATCTTTTTCAAAATAATTCCC
348166 AAAATATCATCTTTTTCAAAATAATTCCC
1 AAAATATCATCTTTTTCAAAATAATTCCC
348195 AAAATATCAT
1 AAAATATCAT
348205 TGGGTCGGGT
Statistics
Matches: 176, Mismatches: 27, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
27 16 0.09
28 58 0.33
29 89 0.51
30 13 0.07
ACGTcount: A:0.43, C:0.18, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATATCATCTTTTTCAAAATAATTCCC
Found at i:348188 original size:58 final size:57
Alignment explanation
Indices: 347966--348204 Score: 205
Period size: 57 Copynumber: 4.2 Consensus size: 57
347956 AAAAATTACA
** * * * *
347966 AAAATATCACCTTTATTAAAAATAATTACTAAAATATCACCGTTTT-ACAAAT-ATTCCC
1 AAAATATCATATTT-TTCAAAATAATTCCCAAAATATCA-CTTTTTCA-AAATAATTCCC
* * ** * * * * * * * *
348024 AATATGTCATCGTTTTAAAAATAATTACCAGAATGTTACTGTTT-AAAAAAAATCCC
1 AAAATATCATATTTTTCAAAATAATTCCCAAAATATCACTTTTTCAAAATAATTCCC
* ** *
348080 AAAATGTCACCTTTTTCAAAATAATTCCCAAAATGTCACTTTTTCAAAATAATTCCC
1 AAAATATCATATTTTTCAAAATAATTCCCAAAATATCACTTTTTCAAAATAATTCCC
* *
348137 AAAATATCATATTTTTTAAAATAATTCTCAAAATATCATCTTTTTCAAAATAATTCCC
1 AAAATATCATATTTTTCAAAATAATTCCCAAAATATCA-CTTTTTCAAAATAATTCCC
348195 AAAATATCAT
1 AAAATATCAT
348205 TGGGTCGGGT
Statistics
Matches: 150, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
55 3 0.02
56 46 0.31
57 62 0.41
58 39 0.26
ACGTcount: A:0.43, C:0.18, G:0.03, T:0.36
Consensus pattern (57 bp):
AAAATATCATATTTTTCAAAATAATTCCCAAAATATCACTTTTTCAAAATAATTCCC
Found at i:348273 original size:19 final size:19
Alignment explanation
Indices: 348230--348273 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
348220 AACGGGTTGG
*
348230 GTCGGGTCAGACCGGTCAA
1 GTCGGTTCAGACCGGTCAA
**
348249 CCCGGTTCAGACCGGTCAA
1 GTCGGTTCAGACCGGTCAA
348268 GTCGGT
1 GTCGGT
348274 CACAACATCA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.18, C:0.30, G:0.34, T:0.18
Consensus pattern (19 bp):
GTCGGTTCAGACCGGTCAA
Found at i:353125 original size:12 final size:12
Alignment explanation
Indices: 353105--353135 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
353095 AAAATCATTT
353105 AAATATATTTTA
1 AAATATATTTTA
*
353117 AAATTTATTTTA
1 AAATATATTTTA
353129 AAATATA
1 AAATATA
353136 GATTGATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATATATTTTA
Found at i:353168 original size:44 final size:42
Alignment explanation
Indices: 353116--353458 Score: 400
Period size: 44 Copynumber: 7.9 Consensus size: 42
353106 AATATATTTT
353116 AAAATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGA
1 AAAATTTATTTTAAAATAT-GATTGATTTATTTTAAAATATGA
** * *
353159 ATTGATTTATTTTAAAATATTGATTTATTTATTTTAAATTATGGA
1 A-AAATTTATTTTAAAATA-TGATTGATTTATTTTAAAATAT-GA
*
353204 AAAATTTATTTTAAAATATGAATTAATTTATTTTAAAATATGGA
1 AAAATTTATTTTAAAATATG-ATTGATTTATTTTAAAATAT-GA
*** ***
353248 TTGATTTATTTTAAAATATGAAAAATTTTATTTTAAAATATGGA
1 AAAATTTATTTTAAAATATGATTGA-TTTATTTTAAAATAT-GA
****
353292 TTGGTTTATTTTAAAATATGGATTGATTTATTTTAAAATATGA
1 AAAATTTATTTTAAAATAT-GATTGATTTATTTTAAAATATGA
*
353335 AAAA-ATATTTTAAAATATGAATTGATTTATTTTAAAATATGGA
1 AAAATTTATTTTAAAATATG-ATTGATTTATTTTAAAATAT-GA
353378 AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGA
1 AAAATTTATTTTAAAATAT-GATTGATTTATTTTAAAATAT-GA
*
353422 AAAAGTTATTTTAAAATATAGATTGATTTATTTTAAA
1 AAAATTTATTTTAAAATAT-GATTGATTTATTTTAAA
353459 GAGAAAATAA
Statistics
Matches: 265, Mismatches: 25, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
41 1 0.00
42 33 0.12
43 14 0.05
44 209 0.79
45 8 0.03
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (42 bp):
AAAATTTATTTTAAAATATGATTGATTTATTTTAAAATATGA
Found at i:353192 original size:66 final size:65
Alignment explanation
Indices: 353119--353458 Score: 441
Period size: 66 Copynumber: 5.2 Consensus size: 65
353109 ATATTTTAAA
*** *
353119 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATATTGATT
1 ATTTATTTTAAAATAT-GAAAAATTTATTTTAAAATATGAATTGATTTATTTTAAAATATGGATT
*
353184 T
65 G
* *
353185 ATTTATTTTAAATTATGGAAAAATTTATTTTAAAATATGAATTAATTTATTTTAAAATATGGATT
1 ATTTATTTTAAAATAT-GAAAAATTTATTTTAAAATATGAATTGATTTATTTTAAAATATGGATT
353250 G
65 G
* *
353251 ATTTATTTTAAAATATGAAAAATTTTATTTTAAAATATGGATTGGTTTATTTTAAAATATGGATT
1 ATTTATTTTAAAATATGAAAAA-TTTATTTTAAAATATGAATTGATTTATTTTAAAATATGGATT
353316 G
65 G
* ***
353317 ATTTATTTTAAAATATGAAAAA-ATATTTTAAAATATGAATTGATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGAAAAATTTATTTTAAAATATGAATTGATTTATTTTAAAATATGGATTG
*** ** * *
353381 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGAA-AAAGTTATTTTAAAATATAGAT
1 ATTTATTTTAAAATAT-GAAAAATTTATTTTAAAATAT-GAATTGATTTATTTTAAAATATGGAT
353445 TG
64 TG
353447 ATTTATTTTAAA
1 ATTTATTTTAAA
353459 GAGAAAATAA
Statistics
Matches: 241, Mismatches: 29, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
64 52 0.22
65 9 0.04
66 177 0.73
67 3 0.01
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (65 bp):
ATTTATTTTAAAATATGAAAAATTTATTTTAAAATATGAATTGATTTATTTTAAAATATGGATTG
Found at i:353289 original size:22 final size:22
Alignment explanation
Indices: 353118--353458 Score: 352
Period size: 22 Copynumber: 15.6 Consensus size: 22
353108 TATATTTTAA
* *
353118 AATTTATTTTAAAATATAGATT
1 AATTTATTTTAAAATATGGAAT
*
353140 GATTTATTTTAAAATAT-GAATT
1 AATTTATTTTAAAATATGGAA-T
* * *
353162 GATTTATTTTAAAATATTGATT
1 AATTTATTTTAAAATATGGAAT
* * *
353184 TATTTATTTTAAATTATGGAAA
1 AATTTATTTTAAAATATGGAAT
353206 AATTTATTTTAAAATAT-GAATT
1 AATTTATTTTAAAATATGGAA-T
*
353228 AATTTATTTTAAAATATGGATT
1 AATTTATTTTAAAATATGGAAT
* *
353250 GATTTATTTTAAAATAT-GAAA
1 AATTTATTTTAAAATATGGAAT
*
353271 AATTTTATTTTAAAATATGGATT
1 AA-TTTATTTTAAAATATGGAAT
** *
353294 GGTTTATTTTAAAATATGGATT
1 AATTTATTTTAAAATATGGAAT
*
353316 GATTTATTTTAAAATAT-GAA-
1 AATTTATTTTAAAATATGGAAT
**
353336 AAAATATTTTAAAATAT-GAATT
1 AATTTATTTTAAAATATGGAA-T
* *
353358 GATTTATTTTAAAATATGGAAA
1 AATTTATTTTAAAATATGGAAT
*
353380 AATTTATTTTAAAATATGGATT
1 AATTTATTTTAAAATATGGAAT
* *
353402 GATTTATTTTAAAATATGGAAA
1 AATTTATTTTAAAATATGGAAT
* * *
353424 AAGTTATTTTAAAATATAGATT
1 AATTTATTTTAAAATATGGAAT
*
353446 GATTTATTTTAAA
1 AATTTATTTTAAA
353459 GAGAAAATAA
Statistics
Matches: 268, Mismatches: 42, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
20 17 0.06
21 10 0.04
22 232 0.87
23 9 0.03
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (22 bp):
AATTTATTTTAAAATATGGAAT
Found at i:353620 original size:21 final size:21
Alignment explanation
Indices: 353604--353680 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
353594 GCGTTGCATT
353604 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
353625 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
* *
353645 TCGCGTTGCTATAGTTAAAAA
1 TCGCGTTGCGATAGTTGAAAA
353666 TCGCGTTGCGATAGT
1 TCGCGTTGCGATAGT
353681 CTACAATGTC
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:353645 original size:41 final size:41
Alignment explanation
Indices: 353600--353677 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
353590 ATTCGCGTTG
*
353600 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTAAAAATCGCGTTGCGATTTTC
*
353641 CATTTCGCGTTGCTATAGTTAAAAATCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTAAAAATCGCGTTGCGAT
353678 AGTCTACAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTAAAAATCGCGTTGCGATTTTC
Found at i:353735 original size:22 final size:22
Alignment explanation
Indices: 353708--353760 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
353698 TTTTCCAAAT
**
353708 TCGTTGCGGTAGTCTACAGTTG
1 TCGTTGCGAAAGTCTACAGTTG
* *
353730 TTGTTGCGAAAGTTTACAGTTG
1 TCGTTGCGAAAGTCTACAGTTG
353752 TCGTTGCGA
1 TCGTTGCGA
353761 TTTTCCAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.38
Consensus pattern (22 bp):
TCGTTGCGAAAGTCTACAGTTG
Found at i:353872 original size:6 final size:6
Alignment explanation
Indices: 353861--353893 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
353851 GACACGTATT
353861 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
353894 CGAAACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:354544 original size:41 final size:41
Alignment explanation
Indices: 354497--354592 Score: 131
Period size: 41 Copynumber: 2.3 Consensus size: 41
354487 GCAACGAATT
354497 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CAACTGTCA-ACTATCGCAACGCGAAA
* * * *
354539 TGAAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
354580 TGGAAAATCGCAA
1 TGGAAAATCGCAA
354593 TGCGATTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
41 33 0.69
42 15 0.31
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.17
Consensus pattern (41 bp):
TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
Found at i:354550 original size:20 final size:20
Alignment explanation
Indices: 354525--354597 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
354515 ACTGTAGACT
354525 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
** * **
354545 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
*
354566 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
*
354586 ATCGCAATGCGA
1 ATCGCAACGCGA
354598 TTTTTGGTCA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:354598 original size:41 final size:41
Alignment explanation
Indices: 354522--354601 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
354512 ACAACTGTAG
354522 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
* *
354563 ACTATCGCAACGCGAAATGGAAAATCGCAATGCGATTTT
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTT
354602 TGGTCACTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
Found at i:354734 original size:22 final size:22
Alignment explanation
Indices: 354727--354803 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
354717 ATGGAAAAAG
354727 TTATTTTAAAATATAGATTGAT
1 TTATTTTAAAATATAGATTGAT
354749 TTATTTTAAAATATAGATTGAT
1 TTATTTTAAAATATAGATTGAT
* *
354771 TTATTTTAAAATATGGTTTGAT
1 TTATTTTAAAATATAGATTGAT
354793 TTATTTTAAAA
1 TTATTTTAAAA
354804 AAAATTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
TTATTTTAAAATATAGATTGAT
Found at i:354886 original size:31 final size:31
Alignment explanation
Indices: 354829--354887 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
354819 AGTTGTATGG
*
354829 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
*
354860 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
354888 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:366050 original size:20 final size:20
Alignment explanation
Indices: 366025--366073 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
366015 GGAAGTTATT
*
366025 ATTTTTTGGCACAATTTGGA
1 ATTTTTGGGCACAATTTGGA
366045 ATTTTTGGGCACAATTTGGA
1 ATTTTTGGGCACAATTTGGA
*
366065 CTTTTTGGG
1 ATTTTTGGG
366074 TGAGTAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.10, G:0.24, T:0.45
Consensus pattern (20 bp):
ATTTTTGGGCACAATTTGGA
Found at i:366227 original size:12 final size:12
Alignment explanation
Indices: 366210--366234 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
366200 GTCAAATAAT
366210 TTAGGCACCAAA
1 TTAGGCACCAAA
366222 TTAGGCACCAAA
1 TTAGGCACCAAA
366234 T
1 T
366235 GGTGCTTTGT
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:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:371154 original size:198 final size:199
Alignment explanation
Indices: 370816--371212 Score: 771
Period size: 198 Copynumber: 2.0 Consensus size: 199
370806 GGTGCTTTGT
370816 CAAAGTCAAAAATTAGGCACCTAATTTTTGTTGAAATTGGCTAATGGGTTAATTAATTTTAGTCA
1 CAAAGTCAAAAATTAGGCACCTAATTTTTGTTGAAATTGGCTAATGGGTTAATTAATTTTAGTCA
370881 TTGTAATTTAGGGTATTTATAAGATTAGTCCTTAAGTTCAACTATAAATACCTTAGCTCATTTAG
66 TTGTAATTTAGGGTATTTATAAGATTAGTCCTTAAGTTCAACTATAAATACCTTAGCTCATTTAG
370946 CTTCAAAATCATCCCAAAGCATTATAGCTTTCTTCCAATACTAGAGAGATTTTAGAGAG-TTCTT
131 CTTCAAAATCATCCCAAAGCATTATAGCTTTCTTCCAATACTAGAGAGATTTTAGAGAGTTTCTT
371010 GAGA
196 GAGA
371014 CAAAGTCAAAAATTAGGCACCTAA-TTTTGTTGAAATTGGCTAATGGGTTAATTAATTTTAGTCA
1 CAAAGTCAAAAATTAGGCACCTAATTTTTGTTGAAATTGGCTAATGGGTTAATTAATTTTAGTCA
371078 TTGTAATTTAGGGTATTTATAAGATTAGTCCTTAAGTTTCAACTATAAATACCTTAGCTCATTTA
66 TTGTAATTTAGGGTATTTATAAGATTAGTCCTTAAG-TTCAACTATAAATACCTTAGCTCATTTA
371143 GCTTCAAAATCATCCCAAAGCATTATAGCTTTCTTCCAATACTAGAGAGATTTTAGAGAGTTTCT
130 GCTTCAAAATCATCCCAAAGCATTATAGCTTTCTTCCAATACTAGAGAGATTTTAGAGAGTTTCT
371208 TGAGA
195 TGAGA
371213 GTTGTTTTCT
Statistics
Matches: 197, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
197 76 0.39
198 112 0.57
199 9 0.05
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (199 bp):
CAAAGTCAAAAATTAGGCACCTAATTTTTGTTGAAATTGGCTAATGGGTTAATTAATTTTAGTCA
TTGTAATTTAGGGTATTTATAAGATTAGTCCTTAAGTTCAACTATAAATACCTTAGCTCATTTAG
CTTCAAAATCATCCCAAAGCATTATAGCTTTCTTCCAATACTAGAGAGATTTTAGAGAGTTTCTT
GAGA
Found at i:372172 original size:30 final size:33
Alignment explanation
Indices: 372138--372201 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
372128 TATTTTCCCT
372138 CTATTTAAG-TT-TAAATG-TTTTTTAATGAGG
1 CTATTTAAGTTTATAAATGTTTTTTTAATGAGG
372168 CTATTTAAGTTTATAAATGTTTTTTTAATGAGG
1 CTATTTAAGTTTATAAATGTTTTTTTAATGAGG
372201 C
1 C
372202 GCATGTCTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 9 0.29
31 2 0.06
32 6 0.19
33 14 0.45
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.50
Consensus pattern (33 bp):
CTATTTAAGTTTATAAATGTTTTTTTAATGAGG
Found at i:376366 original size:42 final size:42
Alignment explanation
Indices: 376307--376426 Score: 240
Period size: 42 Copynumber: 2.9 Consensus size: 42
376297 TTTTTCCGAA
376307 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
376349 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
376391 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
376427 TGTAATTCAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 78 1.00
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.45
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
Found at i:376651 original size:28 final size:29
Alignment explanation
Indices: 376619--376694 Score: 97
Period size: 28 Copynumber: 2.7 Consensus size: 29
376609 AATATTTAAA
376619 ATATATTATTAATATT-TATAATAATAAT-
1 ATATATTATTAATATTATATAA-AATAATC
*
376647 ATATATTTTTAATATTATATAAAATAATC
1 ATATATTATTAATATTATATAAAATAATC
*
376676 AT-TATTA-TAATAATATATA
1 ATATATTATTAATATTATATA
376695 TTATATTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 11 0.26
28 25 0.58
29 7 0.16
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
ATATATTATTAATATTATATAAAATAATC
Found at i:376672 original size:25 final size:25
Alignment explanation
Indices: 376619--376720 Score: 80
Period size: 27 Copynumber: 3.9 Consensus size: 25
376609 AATATTTAAA
* *
376619 ATATATTATTAATATTTATAATAATAAT
1 ATATATTTTTAATA-ATAT-ATAA-AAT
*
376647 ATATATTTTTAATATTATATAAAAT
1 ATATATTTTTAATAATATATAAAAT
**
376672 A-ATCATTATTATAATAATATATATTAT
1 ATAT-ATT-TT-TAATAATATATAAAAT
* *
376699 ATTTTTTTTTAATAATATATAA
1 ATATATTTTTAATAATATATAA
376721 TTTTTTTTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
24 2 0.03
25 19 0.30
26 8 0.13
27 20 0.32
28 14 0.22
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (25 bp):
ATATATTTTTAATAATATATAAAAT
Found at i:376696 original size:15 final size:15
Alignment explanation
Indices: 376619--376699 Score: 66
Period size: 15 Copynumber: 5.7 Consensus size: 15
376609 AATATTTAAA
376619 ATATATTAT--TAAT
1 ATATATTATAATAAT
* *
376632 ATTTATAATAATAAT
1 ATATATTATAATAAT
*
376647 ATATATT-T-TTAAT
1 ATATATTATAATAAT
*
376660 AT-TATATAAAATAAT
1 ATATAT-TATAATAAT
376675 CAT-TATTATAATAAT
1 -ATATATTATAATAAT
376690 ATATATTATA
1 ATATATTATA
376700 TTTTTTTTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
12 3 0.06
13 14 0.26
14 3 0.06
15 28 0.53
16 5 0.09
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATTATAATAAT
Found at i:376719 original size:20 final size:22
Alignment explanation
Indices: 376686--376742 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
376676 ATTATTATAA
*
376686 TAATATATATTATATTTTTTTT
1 TAATATATATTATAATTTTTTT
376708 TAATA-ATA-TATAATTTTTTT
1 TAATATATATTATAATTTTTTT
376728 T-ATATAT-TTAATAAT
1 TAATATATATT-ATAAT
376743 GAATAATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.10
20 15 0.48
21 8 0.26
22 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TAATATATATTATAATTTTTTT
Found at i:376737 original size:28 final size:28
Alignment explanation
Indices: 376678--376773 Score: 94
Period size: 28 Copynumber: 3.5 Consensus size: 28
376668 AAATAATCAT
*
376678 TATTATAATAATATAT-ATTATATTTT-T-
1 TATT-TAATAATATATAATT-TTTTTTATA
376705 T-TTTAATAATATATAATTTTTTTTATA
1 TATTTAATAATATATAATTTTTTTTATA
* *
376732 TATTTAATAATGA-ATAATATTATTTATA
1 TATTTAATAAT-ATATAATTTTTTTTATA
376760 TATTTCAATAATAT
1 TATTT-AATAATAT
376774 TTTAGTAAAG
Statistics
Matches: 59, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
25 16 0.27
26 6 0.10
27 2 0.03
28 28 0.47
29 7 0.12
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (28 bp):
TATTTAATAATATATAATTTTTTTTATA
Found at i:377004 original size:14 final size:15
Alignment explanation
Indices: 376983--377051 Score: 74
Period size: 14 Copynumber: 4.9 Consensus size: 15
376973 TTACAGAAAT
376983 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
** *
376998 G-AATTCAAATTACA
1 GTAATTCATTTTCCA
377012 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
*
377027 GT-ATTCA-ATTCCA
1 GTAATTCATTTTCCA
377040 GTAATTC-TTTTC
1 GTAATTCATTTTC
377052 TGGAAACCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
13 7 0.16
14 23 0.53
15 13 0.30
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:377008 original size:20 final size:20
Alignment explanation
Indices: 376932--377000 Score: 129
Period size: 20 Copynumber: 3.5 Consensus size: 20
376922 TTTCCAGATG
376932 TTTCCAGAAATGTAATTCAT
1 TTTCCAGAAATGTAATTCAT
376952 TTTCCAGAAATGTAATTCAT
1 TTTCCAGAAATGTAATTCAT
*
376972 TTTACAGAAATGTAATTCAT
1 TTTCCAGAAATGTAATTCAT
376992 TTTCCAGAA
1 TTTCCAGAA
377001 TTCAAATTAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.39
Consensus pattern (20 bp):
TTTCCAGAAATGTAATTCAT
Found at i:377045 original size:28 final size:29
Alignment explanation
Indices: 376983--377051 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
376973 TTACAGAAAT
376983 GTAATTCATTTTCCAGAATTCAAATTACA
1 GTAATTCATTTTCCAGAATTCAAATTACA
* *
377012 GTAATTCATTTTCCAGTATTC-AATTCCA
1 GTAATTCATTTTCCAGAATTCAAATTACA
377040 GTAATTC-TTTTC
1 GTAATTCATTTTC
377052 TGGAAACCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 5 0.13
28 13 0.34
29 20 0.53
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.43
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAAATTACA
Found at i:386018 original size:20 final size:20
Alignment explanation
Indices: 385993--386031 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
385983 CAAGTGGGAG
385993 ATTATTAGTTGTCATGCAAA
1 ATTATTAGTTGTCATGCAAA
386013 ATTATTAGTTGTCATGCAA
1 ATTATTAGTTGTCATGCAA
386032 CTAATAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (20 bp):
ATTATTAGTTGTCATGCAAA
Found at i:386057 original size:21 final size:20
Alignment explanation
Indices: 386033--386074 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
386023 GTCATGCAAC
*
386033 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
386054 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
386074 T
1 T
386075 GTAAGTTGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:390117 original size:18 final size:18
Alignment explanation
Indices: 390094--390135 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
390084 AAGCAAAAGC
390094 ATATAAGATCAAACCATA
1 ATATAAGATCAAACCATA
*
390112 ATATAAGATCAAACCATT
1 ATATAAGATCAAACCATA
390130 ATATAA
1 ATATAA
390136 TATATAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.55, C:0.14, G:0.05, T:0.26
Consensus pattern (18 bp):
ATATAAGATCAAACCATA
Found at i:392397 original size:2 final size:2
Alignment explanation
Indices: 392384--392422 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
392374 TTGATTCTTC
* * *
392384 TA TA TA TC TA TA TA TA TA TA TG TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
392423 TCATTTCTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:395541 original size:30 final size:31
Alignment explanation
Indices: 395505--395576 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
395495 ACGACCGGAA
**
395505 AAAGTTTAGTGCAAAAAATT-AAACTTTTTT
1 AAAGTTTAGTGCAAAAAATTGAAACACTTTT
** *
395535 AAAGTTTAGTG-GTAAAATTGACACACTTTT
1 AAAGTTTAGTGCAAAAAATTGAAACACTTTT
395565 AAAGTTTAGTGC
1 AAAGTTTAGTGC
395577 CTAAAACGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 6 0.17
30 29 0.83
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (31 bp):
AAAGTTTAGTGCAAAAAATTGAAACACTTTT
Found at i:401416 original size:21 final size:20
Alignment explanation
Indices: 401353--401416 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
401343 TTTTATCCTT
*
401353 TAATATAA-ATTAATTTTTAG
1 TAATATAATATTAA-TTATAG
401373 TAATAT-ATATTTAATTATAAG
1 TAATATAATA-TTAATTAT-AG
401394 TAATATTAATATTAATTATAG
1 TAATA-TAATATTAATTATAG
401415 TA
1 TA
401417 TGCAAAAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 1 0.03
20 10 0.26
21 15 0.39
22 9 0.24
23 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (20 bp):
TAATATAATATTAATTATAG
Found at i:403810 original size:25 final size:26
Alignment explanation
Indices: 403770--403818 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
403760 AATTGTATCA
*
403770 AATTTTATATTTTA-TTATTGAAATAG
1 AATTTTATATTATATTTATT-AAATAG
403796 AATTTTAT-TTATATTTATTAAAT
1 AATTTTATATTATATTTATTAAAT
403819 GTATTTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (26 bp):
AATTTTATATTATATTTATTAAATAG
Found at i:406133 original size:67 final size:67
Alignment explanation
Indices: 406025--406159 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
406015 AGCTAATCCT
*
406025 GTGTTTCGTGACCTTGACAATTAAGAGAGTGGTTGAACTATGGTCCTGTCTATGGACCCGGTTCT
1 GTGTTTCGTGACCTTGACAATTAAGAGAGTGGTTGAACTATGATCCTGTCTATGGACCCGGTTCT
406090 TC
66 TC
*
406092 GTGTTTCGTGACCTTGACAATTAAGAGAGTGGTTGAACTATGATTCTGTCTATGGACCCGGTTCT
1 GTGTTTCGTGACCTTGACAATTAAGAGAGTGGTTGAACTATGATCCTGTCTATGGACCCGGTTCT
406157 TC
66 TC
406159 G
1 G
406160 GGTCACGGAG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.35
Consensus pattern (67 bp):
GTGTTTCGTGACCTTGACAATTAAGAGAGTGGTTGAACTATGATCCTGTCTATGGACCCGGTTCT
TC
Found at i:412162 original size:13 final size:13
Alignment explanation
Indices: 412146--412171 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
412136 TCTTTTATTT
412146 TTTATTTTTTTCA
1 TTTATTTTTTTCA
412159 TTTATTTTTTTCA
1 TTTATTTTTTTCA
412172 ATACTTAAGA
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:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTTTTTCA
Found at i:413664 original size:22 final size:20
Alignment explanation
Indices: 413623--413681 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 20
413613 TAAGAGGGAG
413623 GAAAAAATATAATAATAATA
1 GAAAAAATATAATAATAATA
*
413643 GAAAAAATA-AATAAT-GTA
1 GAAAAAATATAATAATAATA
*
413661 -AATAAATATAATAATAA-A
1 GAAAAAATATAATAATAATA
413679 GAA
1 GAA
413682 GTAAAGAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 7 0.21
18 9 0.27
19 8 0.24
20 9 0.27
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (20 bp):
GAAAAAATATAATAATAATA
Found at i:413699 original size:37 final size:37
Alignment explanation
Indices: 413627--413699 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
413617 AGGGAGGAAA
* *
413627 AAATATAATAATAATAGAAAAAATAAATAATGTAAAT
1 AAATATAATAATAATAGAAAAAAGAAATAAGGTAAAT
* *
413664 AAATATAATAATAA-AGAAGTAAAGAAATAGGGTAAA
1 AAATATAATAATAATAGAA-AAAAGAAATAAGGTAAA
413700 ATACAAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 4 0.13
37 27 0.87
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (37 bp):
AAATATAATAATAATAGAAAAAAGAAATAAGGTAAAT
Found at i:413722 original size:2 final size:2
Alignment explanation
Indices: 413715--413764 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
413705 AAATGTGTAC
413715 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
413757 AT A- AT AT A
1 AT AT AT AT A
413765 ACATATAAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:413770 original size:12 final size:13
Alignment explanation
Indices: 413715--413800 Score: 83
Period size: 12 Copynumber: 6.7 Consensus size: 13
413705 AAATGTGTAC
413715 ATATATAT-ATAT
1 ATATATATAATAT
413727 ATATATAT-ATAT
1 ATATATATAATAT
413739 ATATATAT-ATAT
1 ATATATATAATAT
413751 ATATATATAATAT
1 ATATATATAATAT
*
413764 A-ACATATAAGTA-
1 ATATATATAA-TAT
413776 ATACTATACTAATAAT
1 ATA-TATA-TAAT-AT
*
413792 ACATATATA
1 ATATATATA
413801 CGAGTGTAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
12 40 0.62
13 8 0.12
14 6 0.09
15 8 0.12
16 2 0.03
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (13 bp):
ATATATATAATAT
Found at i:415794 original size:211 final size:211
Alignment explanation
Indices: 415429--416344 Score: 1451
Period size: 211 Copynumber: 4.3 Consensus size: 211
415419 GTATATAGCT
**** * * *
415429 CCTTCGTCGTGAAGTTGAACTTATACTGTCTTGAGTCCAAAATCCTTCGTTGTGATGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * * * *
415494 GGCTCTGAAGTTGGGAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GGCTCTGAAATTGGGAAGATGTTTACTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTAC
* *
415559 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-TTGAGAAGTTATT
131 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-AAATTTGAGAA-ATGTT
415623 TGTTGACAACCAGCGGTC
194 TGTTGACAACCAGCGGTC
* *
415641 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* *
415706 GGCTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GGCTCTGAAATTGGGAAGATGTTTACTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTAC
* * *
415770 GTTGTCTGGAGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA-TTGGGAAATGTTT
131 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-AAATTTGAGAAATGTTT
*
415834 ATTGACAACCAGCGGTC
195 GTTGACAACCAGCGGTC
*
415851 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * * *
415916 GGCTCTGAATTTGAGAAGTTGTTTGCTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTAC
66 GGCTCTGAAATTGGGAAGATGTTTACTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTAC
415981 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTG
131 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTG
416046 TTGACAACCAGCGGTC
196 TTGACAACCAGCGGTC
*
416062 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCCCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* ** * * *
416127 GGCTCTGAATTTGAAAAGTTGTTTGCTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTAC
66 GGCTCTGAAATTGGGAAGATGTTTACTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTAC
416192 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTG
131 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTG
416257 TTGACAACCAGCGGTC
196 TTGACAACCAGCGGTC
* * *
416273 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCCCGAATCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
416338 GGCTCTG
66 GGCTCTG
416345 GGTAAAACCA
Statistics
Matches: 668, Mismatches: 34, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
210 102 0.15
211 493 0.74
212 73 0.11
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (211 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
GGCTCTGAAATTGGGAAGATGTTTACTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTAC
GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTG
TTGACAACCAGCGGTC
Found at i:415807 original size:105 final size:105
Alignment explanation
Indices: 415429--416344 Score: 1424
Period size: 105 Copynumber: 8.7 Consensus size: 105
415419 GTATATAGCT
**** * * * *
415429 CCTTCGTCGTGAAGTTGAACTTATACTGTCTTGAGTCCAAAATCCTTCGTTGTGATGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* * * * *
415494 GGCTCTGAAGTTGGGAAGTTATTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTC
415535 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* *
415600 GGCTCTGAAATTGAGAAGTTATTTGTTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTC
415641 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* *
415706 GGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTC
* *
415746 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATGTCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* *
415811 GGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTC
*
415851 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* * *
415916 GGCTCTGAATTTGAGAAGTTGTTTGCTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTC
*
415957 CCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
416022 GGCTCT-AAATTTGAGAAATGTTTGTTGACAACCAGCGGTC
66 GGCTCTGAAA-TTGAGAAATGTTTGTTGACAACCAGCGGTC
** *
416062 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCCCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* *
416127 GGCTCTGAATTTGA-AAAGTTGTTTGCTGACAACCAGCGGTC
66 GGCTCTGAAATTGAGAAA--TGTTTGTTGACAACCAGCGGTC
* *
416168 CCTTCATCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
416233 GGCTCT-AAATTTGAGAAATGTTTGTTGACAACCAGCGGTC
66 GGCTCTGAAA-TTGAGAAATGTTTGTTGACAACCAGCGGTC
** *
416273 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCCCGAATCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
416338 GGCTCTG
66 GGCTCTG
416345 GGTAAAACCA
Statistics
Matches: 756, Mismatches: 46, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
104 3 0.00
105 385 0.51
106 365 0.48
107 3 0.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (105 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
GGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTC
Found at i:416003 original size:316 final size:317
Alignment explanation
Indices: 415429--416344 Score: 1498
Period size: 316 Copynumber: 2.9 Consensus size: 317
415419 GTATATAGCT
**** * * *
415429 CCTTCGTCGTGAAGTTGAACTTATACTGTCTTGAGTCCAAAATCCTTCGTTGTGATGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * *
415494 GGCTCTGAAGTTGGGAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GGCTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
415559 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTT
130 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAGTTGTTT
415624 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
195 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
*
415689 GCTGTGAAGTTGAAATTGGCTCTGAAA-TTGGGAAATGTTTATTGACAACCAGCGGTC
260 GCTGTGAAGTTGAAATTGGCTCTGAAATTTGAGAAATGTTTATTGACAACCAGCGGTC
* *
415746 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATGTCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
415811 GGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
66 GGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
*
415876 TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAGTTGTTTG
131 TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAGTTGTTTG
* *
415941 CTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCG
196 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
416006 CTGTGAAGTTGAAATTGGCTCT-AAATTTGAGAAATGTTTGTTGACAACCAGCGGTC
261 CTGTGAAGTTGAAATTGGCTCTGAAATTTGAGAAATGTTTATTGACAACCAGCGGTC
*
416062 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCCCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * ** * *
416127 GGCTCTG-AATTTGAAAAGTTGTTTGCTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTA
66 GGCTCTGAAATTGGGAAA--TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
* *
416191 CGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAATTTGAGAA-ATGTT
129 CGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAGTTGTT
** *
416255 TGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCCCGAATCCAATATCCTT
194 TGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTT
416320 CGCTGTGAAGTTGAAATTGGCTCTG
259 CGCTGTGAAGTTGAAATTGGCTCTG
416345 GGTAAAACCA
Statistics
Matches: 560, Mismatches: 35, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
315 11 0.02
316 378 0.68
317 171 0.31
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (317 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
GGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
TTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAGTTGTTTG
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
CTGTGAAGTTGAAATTGGCTCTGAAATTTGAGAAATGTTTATTGACAACCAGCGGTC
Found at i:417182 original size:5 final size:5
Alignment explanation
Indices: 417174--417210 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
417164 GTTCTTCTCT
*
417174 TTTTG TTTTG -TTT- TTTTG TTTTG TTTTT TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
417211 TTTACCAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
4 6 0.21
5 22 0.79
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (5 bp):
TTTTG
Found at i:417191 original size:13 final size:13
Alignment explanation
Indices: 417173--417203 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
417163 CGTTCTTCTC
417173 TTTTTGTTTTGTT
1 TTTTTGTTTTGTT
417186 TTTTTGTTTTGTT
1 TTTTTGTTTTGTT
417199 TTTTT
1 TTTTT
417204 TTGTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (13 bp):
TTTTTGTTTTGTT
Found at i:417192 original size:8 final size:8
Alignment explanation
Indices: 417179--417213 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
417169 TCTCTTTTTG
417179 TTTTGTTT
1 TTTTGTTT
417187 TTTTGTTT
1 TTTTGTTT
*
417195 TGTT-TTT
1 TTTTGTTT
417202 TTTTGTTT
1 TTTTGTTT
417210 TTTT
1 TTTT
417214 ACCAACTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTTGTTT
Found at i:417213 original size:13 final size:13
Alignment explanation
Indices: 417173--417213 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
417163 CGTTCTTCTC
*
417173 TTTTTGTTTTGTT
1 TTTTTGTTTTTTT
417186 TTTTTGTTTTGTTTT
1 TTTTTG-TTT-TTTT
417201 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
417214 ACCAACTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 10 0.40
14 6 0.24
15 9 0.36
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTTGTTTTTTT
Found at i:427815 original size:21 final size:20
Alignment explanation
Indices: 427768--427821 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
427758 AAATATGTAC
427768 ATATAAAATAAAAAATAATGA
1 ATATAAAATAAAAAATAAT-A
*
427789 AAATAAAATAAGAAAAT-ATA
1 ATATAAAATAA-AAAATAATA
427809 TATATAACAATAA
1 -ATATAA-AATAA
427822 TAGAAAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 1 0.04
21 17 0.61
22 10 0.36
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (20 bp):
ATATAAAATAAAAAATAATA
Found at i:427983 original size:22 final size:20
Alignment explanation
Indices: 427942--428000 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 20
427932 TAAGAGGGAG
427942 GAAAAAATATAATAATAATA
1 GAAAAAATATAATAATAATA
*
427962 GAAAAAATA-AATAAT-GTA
1 GAAAAAATATAATAATAATA
*
427980 -AATAAATATAATAATAA-A
1 GAAAAAATATAATAATAATA
427998 GAA
1 GAA
428001 GTAAAGAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 7 0.21
18 9 0.27
19 8 0.24
20 9 0.27
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (20 bp):
GAAAAAATATAATAATAATA
Found at i:428018 original size:37 final size:37
Alignment explanation
Indices: 427946--428018 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
427936 AGGGAGGAAA
* *
427946 AAATATAATAATAATAGAAAAAATAAATAATGTAAAT
1 AAATATAATAATAATAGAAAAAAGAAATAAGGTAAAT
* *
427983 AAATATAATAATAA-AGAAGTAAAGAAATAGGGTAAA
1 AAATATAATAATAATAGAA-AAAAGAAATAAGGTAAA
428019 ATACAAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 4 0.13
37 27 0.87
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (37 bp):
AAATATAATAATAATAGAAAAAAGAAATAAGGTAAAT
Found at i:428044 original size:8 final size:8
Alignment explanation
Indices: 428031--428068 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
428021 ACAAAATGTG
428031 TACATATA
1 TACATATA
428039 TACATATA
1 TACATATA
*
428047 TATATATA
1 TACATATA
428055 TA-ATATA
1 TACATATA
428062 -ACATATA
1 TACATATA
428069 AGTGAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (8 bp):
TACATATA
Found at i:433456 original size:16 final size:16
Alignment explanation
Indices: 433429--433462 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
433419 ATCTACAATC
433429 AACCCAAAAAAAAACGA
1 AACCCAAAAAAAAA-GA
433446 AACCC-AAAAAAAAGA
1 AACCCAAAAAAAAAGA
433461 AA
1 AA
433463 GAAAACAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 8 0.47
17 5 0.29
ACGTcount: A:0.74, C:0.21, G:0.06, T:0.00
Consensus pattern (16 bp):
AACCCAAAAAAAAAGA
Found at i:435325 original size:2 final size:2
Alignment explanation
Indices: 435320--435347 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
435310 AAAAAAAAAA
435320 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
435348 TATTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:440859 original size:43 final size:43
Alignment explanation
Indices: 440798--440881 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
440788 CGACCCGACT
* *
440798 CGAAAATTTTATATCCTTCACCCGATTAGACCTGAAAAGTACC
1 CGAAAATTTTATATCCTTCACCCGATCAGACCGGAAAAGTACC
*
440841 CGAAAATTTTATATCCTTCACCCGATCCGACCGGAAAAGTA
1 CGAAAATTTTATATCCTTCACCCGATCAGACCGGAAAAGTA
440882 TATATCTTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (43 bp):
CGAAAATTTTATATCCTTCACCCGATCAGACCGGAAAAGTACC
Found at i:442127 original size:46 final size:46
Alignment explanation
Indices: 442050--442142 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 46
442040 GTGAAATGGG
*
442050 TAGTCGATATGTTTAACGGTGAAGCGAATGAGGAACATCTCGAGAA
1 TAGTCGATATGTTTAACGGTGAAGCGAATGAGGAACACCTCGAGAA
* * *
442096 TAGTCGATATGTTTAACGGTGAA-CTGGATGAGGGACACCTCGGGAA
1 TAGTCGATATGTTTAACGGTGAAGC-GAATGAGGAACACCTCGAGAA
442142 T
1 T
442143 GTACTACTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 1 0.02
46 41 0.98
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (46 bp):
TAGTCGATATGTTTAACGGTGAAGCGAATGAGGAACACCTCGAGAA
Found at i:444543 original size:30 final size:30
Alignment explanation
Indices: 444509--444573 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
444499 TTAACTTTGA
* *
444509 AGTTTATAATACCATTTTTTAATATTTCGG
1 AGTTTATAATACCAATTTTCAATATTTCGG
** *
444539 AGTTTATAATATTAATTTTCAATATTTTGG
1 AGTTTATAATACCAATTTTCAATATTTCGG
444569 AGTTT
1 AGTTT
444574 GAATTAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.52
Consensus pattern (30 bp):
AGTTTATAATACCAATTTTCAATATTTCGG
Found at i:444748 original size:11 final size:11
Alignment explanation
Indices: 444732--444756 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
444722 TGGATTGAAG
444732 TTTTTTGTTTT
1 TTTTTTGTTTT
444743 TTTTTTGTTTT
1 TTTTTTGTTTT
444754 TTT
1 TTT
444757 GACCAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:455364 original size:128 final size:128
Alignment explanation
Indices: 455136--455890 Score: 1336
Period size: 128 Copynumber: 5.9 Consensus size: 128
455126 TAATCGGAGT
* * *
455136 ACTATTCACATGAAGGCACGTTCCTGGGGGCGTGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
455201 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
**
455264 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGTACCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
455329 CATTGCCCTATTATGTCCCTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
455392 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTTCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
455457 CATTGCCCTATTATGTCACTCATGTCTCTCGGGGACACTAG--ATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
455518 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
455583 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
455646 ACTATTCACATGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
455711 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** * *
455774 TC-AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
*
455838 TCATTGCCCTATTATGTCACTCATGTCCCTCAGGGACACTAGATATATCAGTA
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
455891 AATCAGGTAA
Statistics
Matches: 604, Mismatches: 20, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
126 124 0.21
127 1 0.00
128 479 0.79
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:455593 original size:254 final size:255
Alignment explanation
Indices: 455136--455890 Score: 1325
Period size: 254 Copynumber: 3.0 Consensus size: 255
455126 TAATCGGAGT
* * *
455136 ACTATTCACATGAAGGCACGTTCCTGGGGGCGTGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
455201 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGA-ATATCAGTACCTATTATTTCAC
**
455266 TATTCACATGAAGGCGCGTTCCCGGGGGCGTACCTTCCATTATTTCGTCAGAGAATATGTTATCA
130 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
455331 TTGCCCTATTATGTCCCTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
195 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
455392 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTTCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
455457 CATTGCCCTATTATGTCACTCATGTCTCTCGGGGACACTAG-ATATCAGTACCTATTATTTCACT
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGAATATCAGTACCTATTATTTCACT
455521 ATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCAT
131 ATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCAT
455586 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
196 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
455646 ACTATTCACATGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
455711 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGA-ATATCAGTACCTATTATTTCAC
*** * *
455776 -AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATC
130 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
*
455840 ATTGCCCTATTATGTCACTCATGTCCCTCAGGGACACTAGATATATCAGTA
194 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
455891 AATCAGGTAA
Statistics
Matches: 478, Mismatches: 18, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
254 248 0.52
255 1 0.00
256 229 0.48
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (255 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGAATATCAGTACCTATTATTTCACT
ATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCAT
TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:455842 original size:382 final size:382
Alignment explanation
Indices: 455136--455883 Score: 1336
Period size: 382 Copynumber: 2.0 Consensus size: 382
455126 TAATCGGAGT
* *
455136 ACTATTCACATGAAGGCACGTTCCTGGGGGCGTGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCACGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
455201 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *
455266 TATTCACATGAAGGCGCGTTCCCGGGGGCGTACCTTCCATTATTTCGTCAGAGAATATGTTATCA
131 TATTCACATGAAGGCGCATTCCCGGGGGCGCACCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
455331 TTGCCCTATTATGTCCCTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA
196 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA
** *
455396 TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTTCATTATTTCGTCAGAGAATATGTTATCATT
261 GGCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATT
* *
455461 GCCCTATTATGTCACTCATGTCTCTCGGGGACACTAGATATCAGTACCTATTATTTC
326 GCCCTATTATGTCACTCATGTCCCTCAGGGACACTAGATATCAGTACCTATTATTTC
*
455518 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCACGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
455583 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
455648 TATTCACATGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
131 TATTCACATGAAGGCGCATTCCCGGGGGCGCACCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
455713 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC-A
196 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA
* * *
455777 GGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCAT
261 -GGCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCAT
455842 TGCCCTATTATGTCACTCATGTCCCTCAGGGACACTAGATAT
325 TGCCCTATTATGTCACTCATGTCCCTCAGGGACACTAGATAT
455884 ATCAGTAAAT
Statistics
Matches: 349, Mismatches: 16, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
381 1 0.00
382 348 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (382 bp):
ACTATTCACATGAAGGCACGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
TATTCACATGAAGGCGCATTCCCGGGGGCGCACCTTCCATTATTTCGTCAGAGAATATGTTATCA
TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA
GGCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATT
GCCCTATTATGTCACTCATGTCCCTCAGGGACACTAGATATCAGTACCTATTATTTC
Found at i:456350 original size:33 final size:34
Alignment explanation
Indices: 456289--456388 Score: 148
Period size: 34 Copynumber: 3.0 Consensus size: 34
456279 AAATTTAATG
* *
456289 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTTTATTTTAAAT
* * *
456323 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTTTATTTTAAAT
456356 TTAAATTTCGAATAATATAATTTTTATTTTAAA
1 TTAAATTTCGAATAATATAATTTTTATTTTAAA
456389 AACATTTATC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 28 0.49
34 29 0.51
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTTTATTTTAAAT
Found at i:456937 original size:21 final size:21
Alignment explanation
Indices: 456907--457000 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
456897 TATGGTATAA
*
456907 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
456928 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
456949 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
456970 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
456991 AACCCTGCGG
1 AACCCTGCGG
457001 AGATGACATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.28, G:0.34, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:458821 original size:34 final size:31
Alignment explanation
Indices: 458777--458856 Score: 90
Period size: 34 Copynumber: 2.5 Consensus size: 31
458767 TTAATAATTC
*
458777 TAAATAAATAATAATT-CTATAAATATTATTTTAA
1 TAAAAAAATAATAATTAC-ATAAATA-TA--TTAA
*
458811 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTACATAAATATATTAA
458842 TATAAAAAATAATAA
1 TA-AAAAAATAATAA
458857 CTATTTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 6 0.15
32 11 0.27
33 2 0.05
34 21 0.51
35 1 0.02
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTACATAAATATATTAA
Found at i:469553 original size:17 final size:17
Alignment explanation
Indices: 469531--469590 Score: 75
Period size: 17 Copynumber: 3.2 Consensus size: 17
469521 CAACCGGTTC
469531 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
469548 TGACCCAACCCGACCCGACCGT
1 TG-----ACCCGACCCGACCGT
469570 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
469587 TGAC
1 TGAC
469591 TGTTGACTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
17 21 0.55
22 17 0.45
ACGTcount: A:0.20, C:0.47, G:0.22, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:469558 original size:22 final size:22
Alignment explanation
Indices: 469533--469584 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
469523 ACCGGTTCTG
469533 ACCCGACCCGACCGTTGACCCA
1 ACCCGACCCGACCGTTGACCCA
*
469555 ACCCGACCCGACCGTTGACCCG
1 ACCCGACCCGACCGTTGACCCA
469577 ACCCGACC
1 ACCCGACC
469585 GTTGACTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.52, G:0.19, T:0.08
Consensus pattern (22 bp):
ACCCGACCCGACCGTTGACCCA
Found at i:476794 original size:10 final size:9
Alignment explanation
Indices: 476759--476838 Score: 70
Period size: 10 Copynumber: 8.3 Consensus size: 9
476749 GCTGCTGGAA
*
476759 ACCGGTTTA
1 ACCGGTTTG
*
476768 ACCGGTTTTCA
1 ACCGG-TTT-G
476779 ACCGGTTCTG
1 ACCGGTT-TG
476789 ACCGGTTTG
1 ACCGGTTTG
*
476798 ACCGGTTTCA
1 ACCGGTTT-G
*
476808 ACCGGTTCG
1 ACCGGTTTG
476817 AACCGGTTTG
1 -ACCGGTTTG
*
476827 ACCGGTCTG
1 ACCGGTTTG
476836 ACC
1 ACC
476839 CAACCCGACC
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
9 26 0.43
10 27 0.45
11 7 0.12
ACGTcount: A:0.16, C:0.29, G:0.26, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:476821 original size:29 final size:30
Alignment explanation
Indices: 476758--476832 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
476748 GGCTGCTGGA
*
476758 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
476789 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
476817 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
476833 CTGACCCAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:476856 original size:17 final size:17
Alignment explanation
Indices: 476834--476893 Score: 66
Period size: 17 Copynumber: 3.3 Consensus size: 17
476824 TTGACCGGTC
476834 TGACCCAACCCGACCGT
1 TGACCCAACCCGACCGT
*
476851 TGACCCGACCCGACCGACCGT
1 TGACCC-A-AC--CCGACCGT
*
476872 TGACCCGACCCGACCGT
1 TGACCCAACCCGACCGT
476889 TGACC
1 TGACC
476894 GTTGACCGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 19 0.53
18 1 0.03
19 2 0.06
21 14 0.39
ACGTcount: A:0.20, C:0.47, G:0.22, T:0.12
Consensus pattern (17 bp):
TGACCCAACCCGACCGT
Found at i:476868 original size:21 final size:21
Alignment explanation
Indices: 476843--476887 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
476833 CTGACCCAAC
476843 CCGACCGTTGACCCGACCCGA
1 CCGACCGTTGACCCGACCCGA
476864 CCGACCGTTGACCCGACCCGA
1 CCGACCGTTGACCCGACCCGA
476885 CCG
1 CCG
476888 TTGACCGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.49, G:0.24, T:0.09
Consensus pattern (21 bp):
CCGACCGTTGACCCGACCCGA
Found at i:476893 original size:12 final size:12
Alignment explanation
Indices: 476841--476881 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
476831 GTCTGACCCA
476841 ACCCGACCGTTG
1 ACCCGACCGTTG
*
476853 ACCCGACC--CG
1 ACCCGACCGTTG
476863 A-CCGACCGTTG
1 ACCCGACCGTTG
476874 ACCCGACC
1 ACCCGACC
476882 CGACCGTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
9 6 0.25
10 2 0.08
11 2 0.08
12 14 0.58
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.10
Consensus pattern (12 bp):
ACCCGACCGTTG
Found at i:481219 original size:15 final size:15
Alignment explanation
Indices: 481182--481225 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
481172 AAAATAATAT
*
481182 TAAAATTAAAACTAAA
1 TAAAAATAAAAC-AAA
481198 -AAAAATAAAACAAA
1 TAAAAATAAAACAAA
481212 TAAAAAT-AAACAAA
1 TAAAAATAAAACAAA
481226 CAAACACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (15 bp):
TAAAAATAAAACAAA
Found at i:484466 original size:23 final size:22
Alignment explanation
Indices: 484440--484487 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
484430 ATAAAGAACC
484440 AAAATAAACTTAAACATACCATTA
1 AAAAT-AACTTAAACAT-CCATTA
**
484464 AAAATAGTTTAAACATCCATTA
1 AAAATAACTTAAACATCCATTA
484486 AA
1 AA
484488 CCAACCACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 9 0.41
24 5 0.23
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAATAACTTAAACATCCATTA
Found at i:488247 original size:31 final size:31
Alignment explanation
Indices: 488212--488287 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
488202 TATGTGTTAT
* *
488212 ATATTTAAAGTGATAATATGACATATATTAC
1 ATATTTAAAGTGATAACATGACATATACTAC
* * *
488243 ATATTTAAAGTGTTAACGTGACATTTACTAC
1 ATATTTAAAGTGATAACATGACATATACTAC
*
488274 ATATTTAAAATGAT
1 ATATTTAAAGTGAT
488288 GATAAGAAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (31 bp):
ATATTTAAAGTGATAACATGACATATACTAC
Found at i:489681 original size:2 final size:2
Alignment explanation
Indices: 489634--489668 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
489624 GATGTGTAAG
489634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
489669 CAAAAGTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:499390 original size:18 final size:18
Alignment explanation
Indices: 499364--499398 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
499354 TCGAAAGGAC
*
499364 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
499382 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
499399 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:504850 original size:2 final size:2
Alignment explanation
Indices: 504843--504881 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
504833 CATTTAAATC
504843 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
504882 GCATCATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:513935 original size:22 final size:21
Alignment explanation
Indices: 513896--513936 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
513886 AATATTTAGA
513896 GTTTAGAGTTTAAATTTTATC
1 GTTTAGAGTTTAAATTTTATC
* *
513917 GTTTAAGATTTTAAGTTTTA
1 GTTT-AGAGTTTAAATTTTA
513937 AAATTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.54
Consensus pattern (21 bp):
GTTTAGAGTTTAAATTTTATC
Found at i:514587 original size:20 final size:22
Alignment explanation
Indices: 514562--514602 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
514552 ATGTCCATCG
514562 TTTTTTA-ACCTTAGC-TTAAT
1 TTTTTTAGACCTTAGCGTTAAT
*
514582 TTTTTTAGACTTTAGCGTTAA
1 TTTTTTAGACCTTAGCGTTAA
514603 ATACAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.54
Consensus pattern (22 bp):
TTTTTTAGACCTTAGCGTTAAT
Found at i:525837 original size:57 final size:57
Alignment explanation
Indices: 525744--525855 Score: 172
Period size: 57 Copynumber: 2.0 Consensus size: 57
525734 TTGTAGATGA
*
525744 AGCCTGATCTTCCGGATCTTGCAAGCATAAACGTTTAGGCAATCTGCTAGACTCAAC
1 AGCCTGATCTTCCGGATCTTGCAAGCATAAACGTTTAGGCAATCGGCTAGACTCAAC
* * *
525801 AGCCTGATCTTCCGGATCTTGCAAGCGT-AGCTGTTTAGGTAATCGGCTAGACTCA
1 AGCCTGATCTTCCGGATCTTGCAAGCATAAAC-GTTTAGGCAATCGGCTAGACTCA
525856 CCATGCTCCA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 2 0.04
57 48 0.96
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (57 bp):
AGCCTGATCTTCCGGATCTTGCAAGCATAAACGTTTAGGCAATCGGCTAGACTCAAC
Found at i:527935 original size:31 final size:32
Alignment explanation
Indices: 527860--528012 Score: 184
Period size: 31 Copynumber: 4.7 Consensus size: 32
527850 AGAAATTTCA
*
527860 TCTTGGTTGGTGGTCAATTTATTGAAAAACTCATC
1 TCTTGGTTGGTGGCCAATTTATTGAAAAA-T--TC
*
527895 TCTTGGTTGGTGGCCAATTTATTGGAAAATTC
1 TCTTGGTTGGTGGCCAATTTATTGAAAAATTC
*
527927 T-TTGGTTGGTGGCCAACTTATTGAAAAATTC
1 TCTTGGTTGGTGGCCAATTTATTGAAAAATTC
* **
527958 ATCTTGGTTGGTGGCTAATTTATTGGGAAATTC
1 -TCTTGGTTGGTGGCCAATTTATTGAAAAATTC
* *
527991 T-TTGGTAGGTGGCCAACTTATT
1 TCTTGGTTGGTGGCCAATTTATT
528013 TTTTATCTTT
Statistics
Matches: 105, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
31 46 0.44
32 5 0.05
33 26 0.25
34 1 0.01
35 27 0.26
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.41
Consensus pattern (32 bp):
TCTTGGTTGGTGGCCAATTTATTGAAAAATTC
Found at i:527989 original size:64 final size:65
Alignment explanation
Indices: 527862--528012 Score: 232
Period size: 64 Copynumber: 2.3 Consensus size: 65
527852 AAATTTCATC
* *
527862 TTGGTTGGTGGTCAATTTATTGAAAAACTCATCTCTTGGTTGGTGGCCAATTTATTGGAAAATTC
1 TTGGTTGGTGGCCAACTTATTGAAAAACTCA-CTCTTGGTTGGTGGCCAATTTATTGGAAAATTC
527927 T
65 T
* * *
527928 TTGGTTGGTGGCCAACTTATTGAAAAATTCA-TCTTGGTTGGTGGCTAATTTATTGGGAAATTCT
1 TTGGTTGGTGGCCAACTTATTGAAAAACTCACTCTTGGTTGGTGGCCAATTTATTGGAAAATTCT
*
527992 TTGGTAGGTGGCCAACTTATT
1 TTGGTTGGTGGCCAACTTATT
528013 TTTTATCTTT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
64 51 0.65
66 28 0.35
ACGTcount: A:0.23, C:0.12, G:0.25, T:0.40
Consensus pattern (65 bp):
TTGGTTGGTGGCCAACTTATTGAAAAACTCACTCTTGGTTGGTGGCCAATTTATTGGAAAATTCT
Found at i:528165 original size:3 final size:3
Alignment explanation
Indices: 528157--528181 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
528147 TCGCCTTGGG
528157 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
528182 AACCCAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:534360 original size:21 final size:19
Alignment explanation
Indices: 534312--534370 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
534302 GTCCGAGTTA
*
534312 CCCGCGACGGTCTCAATAG
1 CCCGCGACGGCCTCAATAG
534331 CCTCTGCGACGGCCTCAATAATG
1 CC-C-GCGACGGCCTCAAT-A-G
*
534354 CCCGCGACGGCCGCAAT
1 CCCGCGACGGCCTCAAT
534371 CACGGTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 2 0.06
20 1 0.03
21 26 0.76
22 2 0.06
23 3 0.09
ACGTcount: A:0.20, C:0.39, G:0.25, T:0.15
Consensus pattern (19 bp):
CCCGCGACGGCCTCAATAG
Found at i:550815 original size:44 final size:44
Alignment explanation
Indices: 550752--550841 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
550742 ATAAACATTG
550752 GGGATTTACTTTGGTATTATGCCAAGAAAAAAGTGCATTCGAAA
1 GGGATTTACTTTGGTATTATGCCAAGAAAAAAGTGCATTCGAAA
550796 GGGATTTACTTTGGTATTATGCCAAGAAAAAAGTGCATTCGAAA
1 GGGATTTACTTTGGTATTATGCCAAGAAAAAAGTGCATTCGAAA
550840 GG
1 GG
550842 TAGGTACAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (44 bp):
GGGATTTACTTTGGTATTATGCCAAGAAAAAAGTGCATTCGAAA
Found at i:551542 original size:82 final size:81
Alignment explanation
Indices: 551393--551837 Score: 411
Period size: 82 Copynumber: 5.4 Consensus size: 81
551383 TTTTTATACA
* * * * *
551393 AAACGCCGCGACAGAGTAGTACTTTCGCGGTGTTTGTATAAAAATGCCGCAATAAGGTTCATCTA
1 AAACGCCGCAACAGAGTAGTACTTTAGCGGTGTTT-TATACAAATGCAGCAATAGGGTTCATCTA
* *
551458 TAGTAGCTTTTTTTCAGC
65 TAGT-GCATTTTTTCAAC
* * **
551476 AAACGCTGCAACATAGTAGTACTTTAGCGGTGTTTTATACAAATGCAGCAATAAAGTTCATCTAT
1 AAACGCCGCAACAGAGTAGTACTTTAGCGGTGTTTTATACAAATGCAGCAATAGGGTTCATCTAT
551541 AGTGGCATTTTTTCAAC
66 AGT-GCATTTTTTCAAC
* * *
551558 AAA-GCCGCAATAGAGTAGTACATTAGCGGCAT-TTTTATACAAATGTC-GTAATAGGGTTCATC
1 AAACGCCGCAACAGAGTAGTACTTTAGCGG--TGTTTTATACAAATG-CAGCAATAGGGTTCATC
*
551620 TATAGTG--GTTTTTCAAC
63 TATAGTGCATTTTTTCAAC
* * * * * * *
551637 AAACACCGTAATAGAGTAGTAATTTAACGGTGTTTTTATACAAACT-CTGCAATAGGGTTAATCT
1 AAACGCCGCAACAGAGTAGTACTTTAGCGGTG-TTTTATACAAA-TGCAGCAATAGGGTTCATCT
* * *
551701 ATAATGATATTTTTTCAAT
64 ATAGTG-CATTTTTTCAAC
* * * *
551720 AAACGCCGCAAAAGAGTAGTACTTTAGC-ATCGTTTTATACAAATGCCA-TAATAGGGTTAATCT
1 AAACGCCGCAACAGAGTAGTACTTTAGCGGT-GTTTTATACAAATG-CAGCAATAGGGTTCATCT
* *
551783 ATAGTGGCACTTTTTCAAT
64 ATAGT-GCATTTTTTCAAC
* * * *
551802 AAAAGCTGCAACAGAGTATTACTTTAGCGGCGTTTT
1 AAACGCCGCAACAGAGTAGTACTTTAGCGGTGTTTT
551838 TTTTACAAAC
Statistics
Matches: 301, Mismatches: 45, Indels: 33
0.79 0.12 0.09
Matches are distributed among these distances:
78 1 0.00
79 13 0.04
80 51 0.17
81 25 0.08
82 144 0.48
83 67 0.22
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (81 bp):
AAACGCCGCAACAGAGTAGTACTTTAGCGGTGTTTTATACAAATGCAGCAATAGGGTTCATCTAT
AGTGCATTTTTTCAAC
Found at i:551715 original size:162 final size:161
Alignment explanation
Indices: 551490--551789 Score: 397
Period size: 162 Copynumber: 1.9 Consensus size: 161
551480 GCTGCAACAT
* * * * *
551490 AGTAGTACTTTAGCGGTGTTTTATACAAATGCAGCAATAAAGTTCATCTATAGTGGCATTTTTTC
1 AGTAGTAATTTAACGGTGTTTTATACAAATGCAGCAATAAAGTTAATCTATAATGACATTTTTTC
* * * * * *
551555 AACAAA-GCCGCAATAGAGTAGTACATTAGCGGCATTTTTATACAAATGTCGTAATAGGGTTCAT
66 AACAAACGCCGCAAAAGAGTAGTACATTAGCAGC-GTTTTATACAAATGCCATAATAGGGTTAAT
551619 CTATAGTGGTTTTTCAACAAACACCGTAATAG
130 CTATAGTGGTTTTTCAACAAACACCGTAATAG
* ** *
551651 AGTAGTAATTTAACGGTGTTTTTATACAAACT-CTGCAATAGGGTTAATCTATAATGATATTTTT
1 AGTAGTAATTTAACGGTG-TTTTATACAAA-TGCAGCAATAAAGTTAATCTATAATGACATTTTT
* * *
551715 TCAATAAACGCCGCAAAAGAGTAGTACTTTAGCATCGTTTTATACAAATGCCATAATAGGGTTAA
64 TCAACAAACGCCGCAAAAGAGTAGTACATTAGCAGCGTTTTATACAAATGCCATAATAGGGTTAA
551780 TCTATAGTGG
129 TCTATAGTGG
551790 CACTTTTTCA
Statistics
Matches: 118, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
161 16 0.14
162 78 0.66
163 24 0.20
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (161 bp):
AGTAGTAATTTAACGGTGTTTTATACAAATGCAGCAATAAAGTTAATCTATAATGACATTTTTTC
AACAAACGCCGCAAAAGAGTAGTACATTAGCAGCGTTTTATACAAATGCCATAATAGGGTTAATC
TATAGTGGTTTTTCAACAAACACCGTAATAG
Found at i:560358 original size:31 final size:31
Alignment explanation
Indices: 560309--560382 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
560299 GGTCATCAAA
*
560309 AACCTTGG-AAACTATCCATAGGTCCCGAAG
1 AACCTAGGTAAACTATCCATAGGTCCCGAAG
* * * **
560339 AACCTAGGTAAACTGTCCATATGTTCCTTAG
1 AACCTAGGTAAACTATCCATAGGTCCCGAAG
*
560370 AACATAGGTAAAC
1 AACCTAGGTAAAC
560383 CCTCGACTCT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 7 0.19
31 29 0.81
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (31 bp):
AACCTAGGTAAACTATCCATAGGTCCCGAAG
Found at i:560673 original size:2 final size:2
Alignment explanation
Indices: 560668--560700 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
560658 CACAACTCAT
560668 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
560701 GTACATGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:582317 original size:350 final size:349
Alignment explanation
Indices: 581662--582363 Score: 1200
Period size: 350 Copynumber: 2.0 Consensus size: 349
581652 AACATTCACA
581662 TTCAAAACAAGAGACAAATTAGATTTCCATTGCAGTTAAAAAATTTCATATCTACTGCAGTTTCA
1 TTCAAAACAAGAGA-AAATTAGATTTCCATTGCAGTTAAAAAATTTCATATCTACTGCAGTTTCA
581727 TTCTAATCAACAGAAAGCATAAAATGAGAAGAAAGGTTATCTTCTCTTTAATACAAAAAAATGAG
65 TTCTAATCAACA-AAAGCATAAAATGAGAAGAAAGGTTATCTTCTCTTTAATACAAAAAAATGAG
*
581792 CTTATCATGAAAGGTTTTTCCATACCTTGAAAATCTGCAGCTGGTACCTGGAAATAATTTAGTTA
129 CTTATCATGAAAGGTTTTTCCATACCTCGAAAATCTGCAGCTGGTACCTGGAAATAATTTAGTTA
* *
581857 GTAGAACTCTGAAAATTGGGGAAGAATGAGAGGAAAACGGGGATAATTTAGCTGTTTGAGTTTGA
194 GTAGAACTCTGAAAATTGGGGAAAAATGAGAAGAAAACGGGGATAATTTAGCTGTTTGAGTTTGA
*
581922 TTGTAATTGCGTAGTACTACTTAAGGAAAAACTCTCGAGAAATGGGGGGAAAGTAGACGTTATGC
259 TTGTAATTGCGTACTACTACTTAAGGAAAAACTCTCGAGAAATGGGGGGAAAGTAGACGTTATGC
581987 CAACGGCTATATCTTGGCCCGTTATT
324 CAACGGCTATATCTTGGCCCGTTATT
582013 TTCAAAACAAGAG-AAATTAGATTTCCATTGCAGTTAAAAAATTTCATATCTACTGCAGTTTCAT
1 TTCAAAACAAGAGAAAATTAGATTTCCATTGCAGTTAAAAAATTTCATATCTACTGCAGTTTCAT
* *
582077 TCTAATTCAAC-AAAGCATAAATTGAGAAGAAAGGTTTATCTTCTCTTTTAATACAGAAAAATGA
66 TCTAA-TCAACAAAAGCATAAAATGAGAAGAAAGG-TTATCTTCTC-TTTAATACAAAAAAATGA
*
582141 GCTTATCATGAAAGGTTTTTCCATCCCTCGAAAATCTGCAGCTGGTTACCTGGAAATAA-TTAGT
128 GCTTATCATGAAAGGTTTTTCCATACCTCGAAAATCTGCAGCTGG-TACCTGGAAATAATTTAGT
*
582205 TAGTAG-A-TCTGAAGATTGGGGAGAAAATGAGAAG-AAACGGGGATAATTTAGCTGTTTGAGTT
192 TAGTAGAACTCTGAAAATTGGGGA-AAAATGAGAAGAAAACGGGGATAATTTAGCTGTTTGAGTT
582267 TGATTGTAATTGCGAGTACTACTACTTAAGGAAAAACTCTCGAGAAATGGGGGGAAAGTAGACGT
256 TGATTGTAATTGC--GTACTACTACTTAAGGAAAAACTCTCGAGAAATGGGGGGAAAGTAGACGT
*
582332 TATTCCAACGGCTATATCTTGGCCCGTTATT
319 TATGCCAACGGCTATATCTTGGCCCGTTATT
582363 T
1 T
582364 AATTTTTCTT
Statistics
Matches: 335, Mismatches: 9, Indels: 15
0.93 0.03 0.04
Matches are distributed among these distances:
348 77 0.23
349 76 0.23
350 156 0.47
351 26 0.08
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.30
Consensus pattern (349 bp):
TTCAAAACAAGAGAAAATTAGATTTCCATTGCAGTTAAAAAATTTCATATCTACTGCAGTTTCAT
TCTAATCAACAAAAGCATAAAATGAGAAGAAAGGTTATCTTCTCTTTAATACAAAAAAATGAGCT
TATCATGAAAGGTTTTTCCATACCTCGAAAATCTGCAGCTGGTACCTGGAAATAATTTAGTTAGT
AGAACTCTGAAAATTGGGGAAAAATGAGAAGAAAACGGGGATAATTTAGCTGTTTGAGTTTGATT
GTAATTGCGTACTACTACTTAAGGAAAAACTCTCGAGAAATGGGGGGAAAGTAGACGTTATGCCA
ACGGCTATATCTTGGCCCGTTATT
Found at i:584281 original size:21 final size:20
Alignment explanation
Indices: 584243--584281 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
584233 AAATAGTAAA
* *
584243 TTTTAAAAGTATTTTTATAG
1 TTTTAAAAATATTATTATAG
584263 TTTTAAAAATAATTATTAT
1 TTTTAAAAAT-ATTATTAT
584282 TTTCATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTTAAAAATATTATTATAG
Found at i:585318 original size:26 final size:27
Alignment explanation
Indices: 585280--585330 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
585270 GAGAAAATTT
585280 TATAATTTAAAAAA-TTATAAATTTCA
1 TATAATTTAAAAAATTTATAAATTTCA
* * *
585306 TATATTTTGAAAAATTTATTAATTT
1 TATAATTTAAAAAATTTATAAATTT
585331 TTAAAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
TATAATTTAAAAAATTTATAAATTTCA
Found at i:585329 original size:27 final size:26
Alignment explanation
Indices: 585280--585330 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
585270 GAGAAAATTT
585280 TATAATTTAAAAAATTATAAATTTCA
1 TATAATTTAAAAAATTATAAATTTCA
* * *
585306 TATATTTTGAAAAATTTATTAATTT
1 TATAATTT-AAAAAATTATAAATTT
585331 TTAAAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
TATAATTTAAAAAATTATAAATTTCA
Found at i:587311 original size:166 final size:163
Alignment explanation
Indices: 587032--587448 Score: 449
Period size: 166 Copynumber: 2.5 Consensus size: 163
587022 ACTTTTTTAC
*
587032 TACCGGTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACATGTTATTGTTATGGATCGATAC
1 TACCGGTTTGTCATTTCGAGACCGA-TTTGTCATATTTTTACATGTTATTGTTATGGATCGATA-
* *
587097 ATTTTTATAAAGTATCGACTTTATTGGCGCTATACTTCTTTCTTTAAATTCTAAAAGTATCGATA
64 ATTTTTATAAAGTATCGACTTTATTAGCGCTATACTTCTTTCTTTAAATTCCAAAAGTATCG--A
587162 CTTATAATAAAGTATCG-CACTATCACCTTCGCTCTT
127 CTTATAATAAAGTATCGACACTATCACCTTCGCTCTT
* *
587198 TACCGGTTTGTCATTTCGAGACCG-TTT-TCATTTTTTTACCTGTTATATTGTTATGGATCGAT-
1 TACCGGTTTGTCATTTCGAGACCGATTTGTCATATTTTTACATG-T-TATTGTTATGGATCGATA
*
587260 A-TTTTAT-AAGTATTAAC-ACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTG
64 ATTTTTATAAAGTA-T--CGACTTTATTAGCGCTAT-ACTTCTT-TC-TTTAAATTCCAAAAGTA
* *
587322 TCGACTTATAATAAAGTATCGACACTATCAACATATTTAGTCTCTT
123 TCGACTTATAATAAAGTATCGACACTATC-AC---CTTCG-CTCTT
* ** * * * *
587368 TACCTGTTTTGTCATTTATAAACCGGTTTATCATTTTTTTACATG-T-TTG-TATGGATCGATAC
1 TACC-GGTTTGTCATTTCGAGACCGATTTGTCATATTTTTACATGTTATTGTTATGGATCGATA-
*
587430 ATTTTTATAAAATATCGAC
64 ATTTTTATAAAGTATCGAC
587449 ACTATCAATA
Statistics
Matches: 215, Mismatches: 14, Indels: 40
0.80 0.05 0.15
Matches are distributed among these distances:
161 5 0.02
162 7 0.03
163 29 0.13
164 30 0.14
165 26 0.12
166 43 0.20
168 11 0.05
169 7 0.03
170 13 0.06
171 23 0.11
172 7 0.03
173 14 0.07
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.44
Consensus pattern (163 bp):
TACCGGTTTGTCATTTCGAGACCGATTTGTCATATTTTTACATGTTATTGTTATGGATCGATAAT
TTTTATAAAGTATCGACTTTATTAGCGCTATACTTCTTTCTTTAAATTCCAAAAGTATCGACTTA
TAATAAAGTATCGACACTATCACCTTCGCTCTT
Found at i:587735 original size:110 final size:111
Alignment explanation
Indices: 587332--587926 Score: 743
Period size: 109 Copynumber: 5.5 Consensus size: 111
587322 TCGACTTATA
* * * * *
587332 ATAAAGTATCGACACTATCAACATAT---TTAGTCTCTTTACCTGTTTTGTCATTTATAAACCGG
1 ATAAAGTATCGACACTTTCAATATATCCGGTAG-CGCTTTACCTGTTTTGTCATTTATAGACCGG
* * *
587394 -TTTATCATTTTTTTACATG---T-TTG-TATGGATCGATACATTTTT
65 TTTTGTCA-TTTTTTACCTGTTATATTGTTATAGATCGATACATTTTT
* * *
587436 ATAAAATATCGACACTATC-A-ATAT-CGGTAGCGCTTTACTTG-TTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
587497 TTTGT-ATTTTTTACCTGTTATA-TGTTATAGATCGATACATTTTT
66 TTTGTCATTTTTTACCTGTTATATTGTTATAGATCGATACATTTTT
587541 ATAAAGTATCGACAC-TTCAATATATATCCGGTAGCGCTTTA-CTGTTTTGTCATTTATAGACCG
1 ATAAAGTATCGACACTTTC-A-ATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
587604 GTTTTGTCA-TTTTTACCTGTTATATTGTTATAGATCGATACA-TTTT
64 GTTTTGTCATTTTTTACCTGTTATATTGTTATAGATCGATACATTTTT
*
587650 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACAGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
587715 TTTGTCATTTTTTACCTGTTATATTATTATGGATCGATACATTTTT
66 TTTGTCATTTTTTACCTGTTATATTGTTATAGATCGATACATTTTT
* * * *
587761 ATAAAGTATCGACATTTTCAATATATCTGGTAGCACTTTACCTG-TTTATCATTTAT--ACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
587823 TTTGTCATTTTTTTTACTTATTATATTGTTAT-GAATAGATACATTTTT
66 TTTGTCA--TTTTTTACCTGTTATATTGTTATAG-ATCGATACATTTTT
* * *
587871 ATAAAGTATCGACACTTT-TATATATTCGGTAGCGCTTTACCTGTTTTGTTATTTAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTAT
587927 GATTTTACCA
Statistics
Matches: 437, Mismatches: 30, Indels: 42
0.86 0.06 0.08
Matches are distributed among these distances:
101 10 0.02
102 23 0.05
103 14 0.03
104 26 0.06
105 32 0.07
107 1 0.00
108 38 0.09
109 125 0.29
110 123 0.28
111 45 0.10
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (111 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTACCTGTTATATTGTTATAGATCGATACATTTTT
Found at i:587771 original size:220 final size:216
Alignment explanation
Indices: 587365--587926 Score: 738
Period size: 220 Copynumber: 2.6 Consensus size: 216
587355 TATTTAGTCT
*
587365 CTTTACCTGTTTTGTCATTTATAAACCGG-TTTATCATTTTTTTACATG---T-TTG-TATGGAT
1 CTTTACCTGTTTTGTCATTTAT-AACCGGTTTTGTCA-TTTTTTACATGTTATATTGTTAT-GAT
* * *
587424 CGATACATTTTTATAAAATATCGACACTATCA-ATATCGGTAGCGCTTTACTTG-TTTGTCATTT
63 CGATACATTTTTATAAAGTATCGACACTTTCATATATCGGTAGCGCTTTACCTGTTTTGTCATTT
* *
587487 ATAGACCGGTTTTGTATTTTTTACCTGTTATATGTTATAGATCGATACATTTTTATAAAGTATCG
128 ATAGACAGGTTTTGTATTTTTTACCTGTTATATATTATAGATCGATACATTTTTATAAAGTATCG
*
587552 ACA-CTTCAATATATATCCGGTAGCG
193 ACATCTTC-A-ATATATCCGGTAGCA
*
587577 CTTTA-CTGTTTTGTCATTTATAGACCGGTTTTGTCA-TTTTTACCTGTTATATTGTTATAGATC
1 CTTTACCTGTTTTGTCATTTATA-ACCGGTTTTGTCATTTTTTACATGTTATATTGTTAT-GATC
587640 GATACA-TTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATT
64 GATACATTTTTATAAAGTATCGACACTTTC-ATATAT-CGGTAGCGCTTTACCTGTTTTGTCATT
*
587704 TATAGACAGGTTTTGTCATTTTTTACCTGTTATATTATTATGGATCGATACATTTTTATAAAGTA
127 TATAGACAGGTTTTGT-ATTTTTTACCTGTTATA-TATTATAGATCGATACATTTTTATAAAGTA
* *
587769 TCGACATTTTCAATATATCTGGTAGCA
190 TCGACATCTTCAATATATCCGGTAGCA
* * *
587796 CTTTACCTG-TTTATCATTTAT-ACCGGTTTTGTCATTTTTTTTACTTATTATATTGTTATGAAT
1 CTTTACCTGTTTTGTCATTTATAACCGGTTTTGTCA--TTTTTTACATGTTATATTGTTATG-AT
* * *
587859 AGATACATTTTTATAAAGTATCGACACTTTTATATATTCGGTAGCGCTTTACCTGTTTTGTTATT
63 CGATACATTTTTATAAAGTATCGACACTTTCATATA-TCGGTAGCGCTTTACCTGTTTTGTCATT
587924 TAT
127 TAT
587927 GATTTTACCA
Statistics
Matches: 311, Mismatches: 18, Indels: 34
0.86 0.05 0.09
Matches are distributed among these distances:
210 10 0.03
211 21 0.07
212 11 0.04
213 1 0.00
214 24 0.08
215 14 0.05
216 4 0.01
217 29 0.09
218 24 0.08
219 47 0.15
220 100 0.32
221 26 0.08
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (216 bp):
CTTTACCTGTTTTGTCATTTATAACCGGTTTTGTCATTTTTTACATGTTATATTGTTATGATCGA
TACATTTTTATAAAGTATCGACACTTTCATATATCGGTAGCGCTTTACCTGTTTTGTCATTTATA
GACAGGTTTTGTATTTTTTACCTGTTATATATTATAGATCGATACATTTTTATAAAGTATCGACA
TCTTCAATATATCCGGTAGCA
Found at i:590922 original size:27 final size:27
Alignment explanation
Indices: 590884--590941 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
590874 CTCCTAAATT
590884 GTCTCATATTCATAAGTCAAACCCCTC
1 GTCTCATATTCATAAGTCAAACCCCTC
590911 GTCTCATATTCATAAGTCAAACCCCTC
1 GTCTCATATTCATAAGTCAAACCCCTC
590938 GTCT
1 GTCT
590942 GCTCCTATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.28, C:0.33, G:0.09, T:0.31
Consensus pattern (27 bp):
GTCTCATATTCATAAGTCAAACCCCTC
Found at i:605439 original size:35 final size:34
Alignment explanation
Indices: 605400--605494 Score: 92
Period size: 35 Copynumber: 2.8 Consensus size: 34
605390 TTTTAAACAG
605400 TTATTATATTTTATATTAATATAATTATATAAATA
1 TTATT-TATTTTATATTAATATAATTATATAAATA
* *
605435 TTATTT-TTTT-TATTAAAATAATATTTATATAATTA
1 TTATTTATTTTATATT--AAT-ATAATTATATAAATA
605470 TTATTTA-TTTATAATT-AT-TAATTAT
1 TTATTTATTTTAT-ATTAATATAATTAT
605495 TTTTTGTGTG
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
32 10 0.20
33 4 0.08
34 6 0.12
35 27 0.53
36 1 0.02
37 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (34 bp):
TTATTTATTTTATATTAATATAATTATATAAATA
Found at i:605470 original size:32 final size:32
Alignment explanation
Indices: 605401--605475 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 32
605391 TTTAAACAGT
* * *
605401 TATTATATTTTATATTAATATAATTATATAAA
1 TATTATTTTTTTTATTAAAATAATTATATAAA
*
605433 TATTATTTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTTATTAAAAT-A-A-TTATATAAA
605468 TATTATTT
1 TATTATTT
605476 ATTTATAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 18 0.50
33 1 0.03
34 1 0.03
35 16 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (32 bp):
TATTATTTTTTTTATTAAAATAATTATATAAA
Found at i:605484 original size:17 final size:17
Alignment explanation
Indices: 605462--605496 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
605452 ATAATATTTA
*
605462 TATAATTATTATTTATT
1 TATAATTATTAATTATT
605479 TATAATTATTAATTATT
1 TATAATTATTAATTATT
605496 T
1 T
605497 TTTGTGTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATAATTATTAATTATT
Found at i:605648 original size:17 final size:16
Alignment explanation
Indices: 605626--605679 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
605616 TAATGTTAAT
605626 ATTTAAATTTATTTTTA
1 ATTTAAA-TTATTTTTA
* *
605643 ATTTAAAGTTATTATGA
1 ATTTAAA-TTATTTTTA
* *
605660 ATTTATATTAATTTTA
1 ATTTAAATTATTTTTA
605676 ATTT
1 ATTT
605680 TTTATAATGC
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 10 0.33
17 20 0.67
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (16 bp):
ATTTAAATTATTTTTA
Found at i:607234 original size:21 final size:21
Alignment explanation
Indices: 607204--607251 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
607194 GCAGGGGTAC
* *
607204 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
*
607225 ATGCCAAGCCCACCAGTTCAT
1 ATGCCAAGCCCACCACTTCAT
607246 ATGCCA
1 ATGCCA
607252 TCTCCGCAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.42, G:0.12, T:0.21
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:607281 original size:21 final size:21
Alignment explanation
Indices: 607255--607369 Score: 135
Period size: 21 Copynumber: 5.5 Consensus size: 21
607245 TATGCCATCT
*
607255 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
*
607276 CCGCAGGGTTATATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
* *
607297 CCGCCA-GGTTACATTCCAATC
1 CCG-CAGGGTTACATTCCTAGC
607318 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
* *
607339 CCGCTA-TGTTACATGCCTAGC
1 CCGC-AGGGTTACATTCCTAGC
*
607360 CCGCATGGTT
1 CCGCAGGGTT
607370 TTATACCGTA
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
20 3 0.04
21 74 0.93
22 3 0.04
ACGTcount: A:0.19, C:0.33, G:0.23, T:0.25
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:607940 original size:35 final size:35
Alignment explanation
Indices: 607886--607984 Score: 137
Period size: 35 Copynumber: 2.9 Consensus size: 35
607876 GATAAATGTT
* *
607886 TTTAAAATACAAATTATATTATTCAAAATTCAAAA
1 TTTAAAATAAAAATTATATTATTCGAAATTCAAAA
* *
607921 TTTAAAATAAAAATAATATTATTCGAAATTTAAAA
1 TTTAAAATAAAAATTATATTATTCGAAATTCAAAA
* *
607956 -TTAAAATATAAATTATAGTATTCGAAATT
1 TTTAAAATAAAAATTATATTATTCGAAATT
607985 TAACATTAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
34 26 0.46
35 31 0.54
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (35 bp):
TTTAAAATAAAAATTATATTATTCGAAATTCAAAA
Found at i:607944 original size:28 final size:29
Alignment explanation
Indices: 607913--607971 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
607903 ATTATTCAAA
607913 ATTCAAAATTTAAAA-TAAAA-ATAATATT
1 ATTCAAAATTTAAAATTAAAATATAA-ATT
*
607941 ATTCGAAATTTAAAATTAAAATATAAATT
1 ATTCAAAATTTAAAATTAAAATATAAATT
607970 AT
1 AT
607972 AGTATTCGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 14 0.50
29 10 0.36
30 4 0.14
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (29 bp):
ATTCAAAATTTAAAATTAAAATATAAATT
Found at i:607978 original size:34 final size:34
Alignment explanation
Indices: 607887--607994 Score: 144
Period size: 34 Copynumber: 3.1 Consensus size: 34
607877 ATAAATGTTT
* * *
607887 TTAAAATACAAATTATATTATTCAAAATTCAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
*
607921 TTTAAAATAAAAATAATATTATTCGAAATTTAAAA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* * *
607956 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
607990 TTAAA
1 TTAAA
607995 TTTCAACTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
34 35 0.54
35 30 0.46
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.37
Consensus pattern (34 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAAA
Found at i:608246 original size:23 final size:23
Alignment explanation
Indices: 608227--608279 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
608217 ACATTTATTC
*
608227 AATTTATCCATACCATTTTATCT
1 AATTTATCCATAACATTTTATCT
*
608250 AATTTATCTATAACATTTTATCT
1 AATTTATCCATAACATTTTATCT
608273 AATTTAT
1 AATTTAT
608280 TCAAACTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.34, C:0.15, G:0.00, T:0.51
Consensus pattern (23 bp):
AATTTATCCATAACATTTTATCT
Found at i:611512 original size:6 final size:6
Alignment explanation
Indices: 611492--611532 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
611482 GGCAAATCTG
611492 CCAAAT CCAACAT CCAAAT CCACAAT -C-AAT CCAAAT CCAAA
1 CCAAAT CCAA-AT CCAAAT CCA-AAT CCAAAT CCAAAT CCAAA
611533 CAACACAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
4 3 0.10
5 1 0.03
6 18 0.58
7 9 0.29
ACGTcount: A:0.49, C:0.37, G:0.00, T:0.15
Consensus pattern (6 bp):
CCAAAT
Found at i:613536 original size:127 final size:126
Alignment explanation
Indices: 613375--613631 Score: 408
Period size: 127 Copynumber: 2.0 Consensus size: 126
613365 TTCAGTCTTT
*
613375 ATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGG
1 ATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGG
* * *
613440 ATCTGGCATGTGTTAGCACATGATCATGACACGTGTCATTGGTGACACATGTTACCACCTA
66 ATCTGACATGTGTTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTA
*
613501 ATTATTTATATGCTATCAA-TTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCA
1 ATTATTTATAT--AATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCA
* * * *
613565 GGATCTGACATGTGTTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTA
64 GGATCTGACATGTGTTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTA
613628 ATTA
1 ATTA
613632 GAAGAAAATT
Statistics
Matches: 120, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
126 11 0.09
127 104 0.87
128 5 0.04
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (126 bp):
ATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGG
ATCTGACATGTGTTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTA
Found at i:613988 original size:28 final size:27
Alignment explanation
Indices: 613957--614019 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
613947 AGTTGATACA
*
613957 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
613985 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
614013 ATATTTT
1 ATATTTT
614020 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Done.