Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 136 of 322
Found at i:44433674 original size:3 final size:3
Alignment explanation
Indices: 44433666--44433690 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
44433656 TTCATCCCCT
44433666 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
44433691 TGTGTTATTT
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:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:44434766 original size:19 final size:20
Alignment explanation
Indices: 44434698--44434765 Score: 79
Period size: 22 Copynumber: 3.4 Consensus size: 20
44434688 TTTTTTAAAA
44434698 TTTTAAAAAATTAAAAATTAT
1 TTTTAAAAAATTAAAAA-TAT
44434719 TTTTAAAAAAATTAAAAA-A-
1 TTTT-AAAAAATTAAAAATAT
*
44434738 TATT-AAAAATATAAAAATAT
1 TTTTAAAAAAT-TAAAAATAT
44434758 TTTTAAAA
1 TTTTAAAA
44434766 TTTAAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
17 6 0.15
18 6 0.15
19 4 0.10
20 4 0.10
21 7 0.17
22 13 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTTAAAAAATTAAAAATAT
Found at i:44434771 original size:19 final size:19
Alignment explanation
Indices: 44434697--44434772 Score: 75
Period size: 22 Copynumber: 3.9 Consensus size: 19
44434687 CTTTTTTAAA
44434697 ATTTTAAAAAATTAAAAATT
1 ATTTTAAAAAATTAAAAA-T
44434717 ATTTTTAAAAAAATTAAAAA-
1 A-TTTT-AAAAAATTAAAAAT
*
44434737 ATATT-AAAAATATAAAAAT
1 ATTTTAAAAAAT-TAAAAAT
* *
44434756 ATTTTTAAAATTTAAAA
1 ATTTTAAAAAATTAAAA
44434773 TTTTAATTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
17 6 0.12
18 6 0.12
19 12 0.25
20 7 0.15
21 4 0.08
22 13 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTTTAAAAAATTAAAAAT
Found at i:44434782 original size:39 final size:39
Alignment explanation
Indices: 44434691--44434782 Score: 95
Period size: 39 Copynumber: 2.4 Consensus size: 39
44434681 ATAATTCTTT
44434691 TTTAAAATTTTA--AAAAATTAAAAATTATTTTTAAAAAA
1 TTTAAAATTTTATTAAAAATTAAAAATTATTTTT-AAAAA
* **
44434729 ATTAAAA-AATATTAAAAATATAAAAA-TATTTTT-AAAA
1 TTTAAAATTTTATTAAAAAT-TAAAAATTATTTTTAAAAA
44434766 TTTAAAATTTTAATTAA
1 TTTAAAATTTT-ATTAA
44434783 TTGTTGACAT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
37 12 0.28
38 7 0.16
39 18 0.42
40 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (39 bp):
TTTAAAATTTTATTAAAAATTAAAAATTATTTTTAAAAA
Found at i:44438039 original size:15 final size:15
Alignment explanation
Indices: 44438014--44438054 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
44438004 ACTGGACACC
44438014 AATTTTGACCAGGCTG
1 AATTTTGACCA-GCTG
*
44438030 -ATTTTAACCAGCTG
1 AATTTTGACCAGCTG
44438044 AATTTTGACCA
1 AATTTTGACCA
44438055 TAAGAGAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (15 bp):
AATTTTGACCAGCTG
Found at i:44447312 original size:18 final size:18
Alignment explanation
Indices: 44447282--44447354 Score: 92
Period size: 18 Copynumber: 4.1 Consensus size: 18
44447272 CATTTACGAC
*
44447282 ACTATTTACGTATACAAT
1 ACTATTAACGTATACAAT
*
44447300 ACCATTAACGTATACAAT
1 ACTATTAACGTATACAAT
* *
44447318 ACTATTTACATATACAAT
1 ACTATTAACGTATACAAT
* *
44447336 ACTGTTCACGTATACAAT
1 ACTATTAACGTATACAAT
44447354 A
1 A
44447355 GTTGGGATTG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.34
Consensus pattern (18 bp):
ACTATTAACGTATACAAT
Found at i:44447322 original size:36 final size:36
Alignment explanation
Indices: 44447282--44447354 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
44447272 CATTTACGAC
*
44447282 ACTATTTACGTATACAATACCATTAACGTATACAAT
1 ACTATTTACATATACAATACCATTAACGTATACAAT
** *
44447318 ACTATTTACATATACAATACTGTTCACGTATACAAT
1 ACTATTTACATATACAATACCATTAACGTATACAAT
44447354 A
1 A
44447355 GTTGGGATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.34
Consensus pattern (36 bp):
ACTATTTACATATACAATACCATTAACGTATACAAT
Found at i:44456506 original size:26 final size:26
Alignment explanation
Indices: 44456475--44456582 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
44456465 TGAAATTCCC
*
44456475 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
44456501 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
44456527 ATCATGGAATATTTATCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
44456553 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
44456579 ATCA
1 ATCA
44456583 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:44462171 original size:37 final size:37
Alignment explanation
Indices: 44462116--44462188 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
44462106 CCAAATTAGT
**
44462116 TGACTTCGACTCTGTAATGGATGAGGGACGTCCGATC
1 TGACTTCGACTCCATAATGGATGAGGGACGTCCGATC
44462153 TGACTTCGACTCCATAATGGATGAGGGACGTCCGAT
1 TGACTTCGACTCCATAATGGATGAGGGACGTCCGAT
44462189 TTCACCGGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (37 bp):
TGACTTCGACTCCATAATGGATGAGGGACGTCCGATC
Found at i:44468762 original size:43 final size:43
Alignment explanation
Indices: 44468701--44468786 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
44468691 TTGTAAGTTG
44468701 AACTTCATCAATTCTTAACTCCCCCATCAAGCATTCAGAATAT
1 AACTTCATCAATTCTTAACTCCCCCATCAAGCATTCAGAATAT
44468744 AACTTCATCAATTCTTAACTCCCCCATCAAGCATTCAGAATAT
1 AACTTCATCAATTCTTAACTCCCCCATCAAGCATTCAGAATAT
44468787 CTTACTTTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (43 bp):
AACTTCATCAATTCTTAACTCCCCCATCAAGCATTCAGAATAT
Found at i:44472238 original size:21 final size:21
Alignment explanation
Indices: 44472199--44472247 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
44472189 ATTTATTGGA
44472199 TTTTT-ATTTTGTGATTTTTGT
1 TTTTTAATTTTGTGATTTTT-T
*
44472220 TTTTTAATTTT-TGTTTTTTT
1 TTTTTAATTTTGTGATTTTTT
44472240 TATTTTAA
1 T-TTTTAA
44472248 CGGGCCCGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 18 0.72
22 5 0.20
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (21 bp):
TTTTTAATTTTGTGATTTTTT
Found at i:44472245 original size:15 final size:14
Alignment explanation
Indices: 44472198--44472238 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
44472188 CATTTATTGG
* * *
44472198 ATTTTTATTTTGTG
1 ATTTTTGTTTTTTA
44472212 ATTTTTGTTTTTTA
1 ATTTTTGTTTTTTA
44472226 ATTTTTGTTTTTT
1 ATTTTTGTTTTTT
44472239 TTATTTTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.78
Consensus pattern (14 bp):
ATTTTTGTTTTTTA
Found at i:44472693 original size:132 final size:132
Alignment explanation
Indices: 44472400--44472654 Score: 368
Period size: 133 Copynumber: 1.9 Consensus size: 132
44472390 TGGCTAAATT
* * * *
44472400 CTGCTCCATTACTGATACATGGAGATAAGATTCACCGTCATTGATCTGCTCCACAACTGTTTAGG
1 CTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCATTGATCTGCTCCACAACTGCTTAGG
* * *
44472465 GAGATAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTAGTGACTAA
66 GAGAAAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTAATCAC-AA
*
44472530 AAT
130 AAC
** * * *
44472533 CTGCTCCATTGCCGATACATGGAGATAAGATTTGCCATCTTTGATCTGCTCTACTACTGCTTAGG
1 CTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCATTGATCTGCTCCACAACTGCTTAGG
*
44472598 GA-AAAAGATCTTCAATCTTCAGTCTGCTTCCTTGTTACCTCAGGAAGATAAGACTAA
66 GAGAAAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTAA
44472655 AATCACCAAC
Statistics
Matches: 110, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
132 52 0.47
133 58 0.53
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (132 bp):
CTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCATTGATCTGCTCCACAACTGCTTAGG
GAGAAAAGATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTAATCACAAA
AC
Found at i:44472998 original size:177 final size:177
Alignment explanation
Indices: 44472496--44473049 Score: 805
Period size: 176 Copynumber: 3.1 Consensus size: 177
44472486 AGTCTGCTTC
* *
44472496 CTTGCTACCTCAG-GAAGATAAGACTAGTGACTAAAATCTGCTCCATTGCCGATACATGGAGATA
1 CTTGCTACCTCAGAG-AGATAAGGCTAGTGGCTAAAATCTGCTCCATTGCCGATACATGGAGATA
* * *
44472560 AGATTTGCCATCTTTGATCTGCTCTACTACTGCTTAGGGA-AAAAGATCTTCAATCTTCAGTCTG
65 AGATTCGCCATCTTCGATCTGCTCTACTACTGCTTAGGGAGATAAGATCTTCAATCTTCAGTCTG
* * *
44472624 CTTCCTTGTTACCTCAGGAAGATAAGACTAAAATCACCAACCTGCTCT
130 CTTCCTTGTTACCTCAAGAAGATAAGACTACAATCGCCAACCTGCTCT
* *
44472672 CTTGCTACCTCAGAGAGATAAGG-TCAATGGATAAAATCTGCTCCATTGCCTG-T-CATGGAGAT
1 CTTGCTACCTCAGAGAGATAAGGCT-AGTGGCTAAAATCTGCTCCATTGCC-GATACATGGAGAT
* *
44472734 AAGATTCGCCATCTTCGATCTGCTCTGCTACTGCTTAGGGAGATAAGATCTTCAATATTCAGTCT
64 AAGATTCGCCATCTTCGATCTGCTCTACTACTGCTTAGGGAGATAAGATCTTCAATCTTCAGTCT
* *
44472799 GTTTCCTTGTTACCTCAAGAAGATAAGACTACAATCGTCAACCTGCTCT
129 GCTTCCTTGTTACCTCAAGAAGATAAGACTACAATCGCCAACCTGCTCT
* * *
44472848 CTTGCTACCTTAGAGAGATAAGGCTGGTGGCTAAAACCTGCTCCATTGCCGATACATGGAGATAA
1 CTTGCTACCTCAGAGAGATAAGGCTAGTGGCTAAAATCTGCTCCATTGCCGATACATGGAGATAA
* * *
44472913 GATTCGCCATCTTCGATCTTCTCCACTACTGCTTAGGGAGATAAGA-CTTGCAATCCTCAGTCTG
66 GATTCGCCATCTTCGATCTGCTCTACTACTGCTTAGGGAGATAAGATCTT-CAATCTTCAGTCTG
** * *
44472977 CTTCCTTCCTACCTTAAGAAGATAAGACTACAAACGCCAACCTGCTCT
130 CTTCCTTGTTACCTCAAGAAGATAAGACTACAATCGCCAACCTGCTCT
*
44473025 CTTGCTACCTCACAGAGATAAGGCT
1 CTTGCTACCTCAGAGAGATAAGGCT
44473050 GGTAATCTTC
Statistics
Matches: 338, Mismatches: 32, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
175 49 0.14
176 155 0.46
177 134 0.40
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (177 bp):
CTTGCTACCTCAGAGAGATAAGGCTAGTGGCTAAAATCTGCTCCATTGCCGATACATGGAGATAA
GATTCGCCATCTTCGATCTGCTCTACTACTGCTTAGGGAGATAAGATCTTCAATCTTCAGTCTGC
TTCCTTGTTACCTCAAGAAGATAAGACTACAATCGCCAACCTGCTCT
Found at i:44473320 original size:64 final size:64
Alignment explanation
Indices: 44473160--44473409 Score: 350
Period size: 64 Copynumber: 4.0 Consensus size: 64
44473150 TTCTGTATTT
* *
44473160 ATGCTTATGCCAAATAATTAGGATGCTATGATCGAACTGAATCAAATGCTCCT-A-T-GA---G
1 ATGCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
* * * * *
44473218 ATGCTCATGTCAAACAATTAGGATGCTATGATCAAAATGAATAAAATGTTCCTAACTAGATGTG
1 ATGCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
44473282 ATGCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
1 ATGCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
* * * * *
44473346 ATGCTTATGTCAAATAATTAAGATTCTATAATCGAAATAAATCAAATGCTCCTAACTAAATGTG
1 ATGCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
44473410 TTATGAATGA
Statistics
Matches: 169, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
58 46 0.27
59 1 0.01
60 1 0.01
61 2 0.01
64 119 0.70
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (64 bp):
ATGCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
Found at i:44474494 original size:9 final size:8
Alignment explanation
Indices: 44474479--44474548 Score: 59
Period size: 9 Copynumber: 8.1 Consensus size: 8
44474469 TGCCTTGGCC
44474479 TTTTCTTT
1 TTTTCTTT
44474487 TCTTTCTTCT
1 T-TTTCTT-T
*
44474497 TTTTTTTT
1 TTTTCTTT
*
44474505 TATTTTTTT
1 T-TTTCTTT
*
44474514 ATTTTATTT
1 -TTTTCTTT
*
44474523 TTTTAATTT
1 TTTT-CTTT
44474532 TTTTCTTT
1 TTTTCTTT
44474540 TTTTCTTT
1 TTTTCTTT
44474548 T
1 T
44474549 GATTTTTATT
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
8 19 0.35
9 32 0.59
10 3 0.06
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTCTTT
Found at i:44474512 original size:8 final size:8
Alignment explanation
Indices: 44474499--44474548 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
44474489 TTTCTTCTTT
44474499 TTTTTTTA
1 TTTTTTTA
44474507 TTTTTTTA
1 TTTTTTTA
44474515 ---TTTTA
1 TTTTTTTA
44474520 TTTTTTTAA
1 TTTTTTT-A
*
44474529 TTTTTTTC
1 TTTTTTTA
*
44474537 TTTTTTTC
1 TTTTTTTA
44474545 TTTT
1 TTTT
44474549 GATTTTTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
5 5 0.14
8 24 0.65
9 8 0.22
ACGTcount: A:0.10, C:0.04, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTTTA
Found at i:44474512 original size:13 final size:13
Alignment explanation
Indices: 44474496--44474555 Score: 57
Period size: 13 Copynumber: 4.2 Consensus size: 13
44474486 TTCTTTCTTC
44474496 TTTTTTTTTTATT
1 TTTTTTTTTTATT
*
44474509 TTTTTATTTTATT
1 TTTTTTTTTTATT
*
44474522 TTTTTAATTTTTTTCT
1 TTTTT--TTTTTAT-T
44474538 TTTTTTCTTTTGATT
1 TTTTTT-TTTT-ATT
44474553 TTT
1 TTT
44474556 ATTTCAATCT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 17 0.45
14 1 0.03
15 13 0.34
16 7 0.18
ACGTcount: A:0.10, C:0.03, G:0.02, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTTATT
Found at i:44474523 original size:22 final size:21
Alignment explanation
Indices: 44474496--44474555 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
44474486 TTCTTTCTTC
44474496 TTTTTTTTTT-ATTTTTTTAT
1 TTTTTTTTTTAATTTTTTTAT
*
44474516 TTTATTTTTTTAATTTTTTTCT
1 TTT-TTTTTTTAATTTTTTTAT
*
44474538 TTTTTTCTTTTGATTTTT
1 TTTTTT-TTTTAATTTTT
44474556 ATTTCAATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.09
21 10 0.29
22 22 0.63
ACGTcount: A:0.10, C:0.03, G:0.02, T:0.85
Consensus pattern (21 bp):
TTTTTTTTTTAATTTTTTTAT
Found at i:44479679 original size:17 final size:18
Alignment explanation
Indices: 44479657--44479690 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
44479647 TAAATCATCA
44479657 AATAAATAAAA-ATATAG
1 AATAAATAAAATATATAG
44479674 AATAAATAAAATATATA
1 AATAAATAAAATATATA
44479691 TATATAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AATAAATAAAATATATAG
Found at i:44481654 original size:14 final size:14
Alignment explanation
Indices: 44481635--44481683 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
44481625 CATTTATTAC
*
44481635 ATTTTTATTTTGTG
1 ATTTTTATTTTTTG
* *
44481649 ATTTTTGTTTTTTA
1 ATTTTTATTTTTTG
44481663 ATTTTTGGATTTTTTG
1 ATTTTT--ATTTTTTG
44481679 ATTTT
1 ATTTT
44481684 AACGGGCCCG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
14 17 0.61
16 11 0.39
ACGTcount: A:0.14, C:0.00, G:0.12, T:0.73
Consensus pattern (14 bp):
ATTTTTATTTTTTG
Found at i:44481666 original size:22 final size:21
Alignment explanation
Indices: 44481636--44481676 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
44481626 ATTTATTACA
44481636 TTTTTA-TTTTGTGATTTTTGT
1 TTTTTATTTTTG-GATTTTTGT
44481657 TTTTTAATTTTTGGATTTTT
1 TTTTT-ATTTTTGGATTTTT
44481677 TGATTTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 8 0.44
23 5 0.28
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (21 bp):
TTTTTATTTTTGGATTTTTGT
Found at i:44501852 original size:24 final size:24
Alignment explanation
Indices: 44501809--44501855 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
44501799 CCAATTAACT
*
44501809 TAGTTGTAGACATAATAGTAGATC
1 TAGTTGTAGACATAACAGTAGATC
* *
44501833 TAGTTGTAGACGTAGCAGTAGAT
1 TAGTTGTAGACATAACAGTAGAT
44501856 GTAGAAGTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.32
Consensus pattern (24 bp):
TAGTTGTAGACATAACAGTAGATC
Found at i:44505245 original size:44 final size:44
Alignment explanation
Indices: 44505182--44505799 Score: 266
Period size: 44 Copynumber: 14.1 Consensus size: 44
44505172 CAGGAACAAC
* * *
44505182 AATCTGTTATTTTCGATCTGCTCTCTGCCAATACAGAGACGCCA
1 AATCTGTCATCTTCGATCTGCTCTCTGACAATACAGAGACGCCA
*
44505226 AATCTGTCATCTTCGATCTGCTCTCTGACAATACAGATACGCCA
1 AATCTGTCATCTTCGATCTGCTCTCTGACAATACAGAGACGCCA
* * *
44505270 AATCTGTCATCTTTGATCTGCTCTCTGACAATACAAAGATGCCA
1 AATCTGTCATCTTCGATCTGCTCTCTGACAATACAGAGACGCCA
* * * * *
44505314 AA----TCATCTTAGATTTGCT-TC-AACGTAA-ACAGGTGAAAGCCA
1 AATCTGTCATCTTCGATCTGCTCTCTGAC--AATACA-GAG-ACGCCA
* * * * * *
44505355 AATCAG-CTATGTCTTCAATCTACTCCCTGTCGAATACAGAGATGCCA
1 AATCTGTC-A--TCTTCGATCTGCTCTCTGAC-AATACAGAGACGCCA
* *
44505402 AATCTG-CTATCTTCGATCTGCTCTCTGATAGTACAGAGACGCCA
1 AATCTGTC-ATCTTCGATCTGCTCTCTGACAATACAGAGACGCCA
** * *
44505446 AATCTGTTGTCTTCGATCTGCTCTCTGACAATGCAAAGACGCCA
1 AATCTGTCATCTTCGATCTGCTCTCTGACAATACAGAGACGCCA
* * * * *
44505490 AA----TCATCTTAGATTTGCT-TC-AACGTAA-ACACGTGAAAGCCA
1 AATCTGTCATCTTCGATCTGCTCTCTGAC--AATACA-GAG-ACGCCA
* * * * *
44505531 AATCAG-CTATGTCTTCGATCTGCTCCCTGTCGAATACAAAGATGCCA
1 AATCTGTC-A--TCTTCGATCTGCTCTCTGAC-AATACAGAGACGCCA
* * * * *
44505578 AATCTG-CTATCTTCAATCTGTTCTCTGACAAAATAGAGACGCTA
1 AATCTGTC-ATCTTCGATCTGCTCTCTGACAATACAGAGACGCCA
* * * * *
44505622 AA----TCATCTTAGATTTGCT-TC-AACGTAA-ACACGTGAAAGCCA
1 AATCTGTCATCTTCGATCTGCTCTCTGAC--AATACA-GAG-ACGCCA
* * * ** *
44505663 AATCAG-CTATGTCTTTGATCTGCTCCCTTTCGAATACAGAGATGCCA
1 AATCTGTC-A--TCTTCGATCTGCTCTCTGAC-AATACAGAGACGCCA
* * * * *
44505710 AATCTAT-TTCTTCGATTTGTTCTCTGACAATACAGAGATGCCA
1 AATCTGTCATCTTCGATCTGCTCTCTGACAATACAGAGACGCCA
* * * * *
44505753 AATCTGT-TTCTTCGATTTGTTCTCTGACAATACAGATATGCCA
1 AATCTGTCATCTTCGATCTGCTCTCTGACAATACAGAGACGCCA
44505796 AATC
1 AATC
44505800 ATCTTGGATT
Statistics
Matches: 435, Mismatches: 94, Indels: 91
0.70 0.15 0.15
Matches are distributed among these distances:
38 6 0.01
39 13 0.03
40 46 0.11
41 21 0.05
43 60 0.14
44 163 0.37
45 34 0.08
47 66 0.15
48 14 0.03
49 12 0.03
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (44 bp):
AATCTGTCATCTTCGATCTGCTCTCTGACAATACAGAGACGCCA
Found at i:44505505 original size:176 final size:176
Alignment explanation
Indices: 44505211--44505625 Score: 652
Period size: 176 Copynumber: 2.4 Consensus size: 176
44505201 GCTCTCTGCC
* *
44505211 AATACAGAGACGCCAAATCTG-TCATCTTCGATCTGCTCTCTGACAATACAGATACGCCAAATCT
1 AATACAGAGATGCCAAATCTGCT-ATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCT
* *
44505275 GTCATCTTTGATCTGCTCTCTGACAATACAAAGATGCCAAATCATCTTAGATTTGCTTCAACGTA
65 GTCATCTTCGATCTGCTCTCTGACAATACAAAGACGCCAAATCATCTTAGATTTGCTTCAACGTA
*
44505340 AACAGGTGAAAGCCAAATCAGCTATGTCTTCAATCTACTCCCTGTCG
130 AACACGTGAAAGCCAAATCAGCTATGTCTTCAATCTACTCCCTGTCG
* *
44505387 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGATAGTACAGAGACGCCAAATCTG
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTG
** *
44505452 TTGTCTTCGATCTGCTCTCTGACAATGCAAAGACGCCAAATCATCTTAGATTTGCTTCAACGTAA
66 TCATCTTCGATCTGCTCTCTGACAATACAAAGACGCCAAATCATCTTAGATTTGCTTCAACGTAA
* *
44505517 ACACGTGAAAGCCAAATCAGCTATGTCTTCGATCTGCTCCCTGTCG
131 ACACGTGAAAGCCAAATCAGCTATGTCTTCAATCTACTCCCTGTCG
* * * * * *
44505563 AATACAAAGATGCCAAATCTGCTATCTTCAATCTGTTCTCTGACAAAATAGAGACGCTAAATC
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATC
44505626 ATCTTAGATT
Statistics
Matches: 218, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
176 217 1.00
177 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (176 bp):
AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTG
TCATCTTCGATCTGCTCTCTGACAATACAAAGACGCCAAATCATCTTAGATTTGCTTCAACGTAA
ACACGTGAAAGCCAAATCAGCTATGTCTTCAATCTACTCCCTGTCG
Found at i:44505597 original size:132 final size:132
Alignment explanation
Indices: 44505398--44505756 Score: 494
Period size: 132 Copynumber: 2.8 Consensus size: 132
44505388 ATACAGAGAT
* * * * * *
44505398 GCCAAATCTGCTA--TCTTCGATCTGCTCTCTGAT--AGTACAGAGACGCCAAATCTGTTGTCTT
1 GCCAAATCAGCTATGTCTTCGATCTGCTCCCTG-TCGAATACAGAGATGCCAAATCTGATATCTT
* * *
44505459 CGATCTGCTCTCTGACAATGCAAAGACGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTG
65 CGATCTGTTCTCTGACAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTG
44505524 AAA
130 AAA
* *
44505527 GCCAAATCAGCTATGTCTTCGATCTGCTCCCTGTCGAATACAAAGATGCCAAATCTGCTATCTTC
1 GCCAAATCAGCTATGTCTTCGATCTGCTCCCTGTCGAATACAGAGATGCCAAATCTGATATCTTC
* * * *
44505592 AATCTGTTCTCTGACAAAATAGAGACGCTAAATCATCTTAGATTTGCTTCAACGTAAACACGTGA
66 GATCTGTTCTCTGACAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTGA
44505657 AA
131 AA
* * *
44505659 GCCAAATCAGCTATGTCTTTGATCTGCTCCCTTTCGAATACAGAGATGCCAAATCT-ATTTCTTC
1 GCCAAATCAGCTATGTCTTCGATCTGCTCCCTGTCGAATACAGAGATGCCAAATCTGATATCTTC
* *
44505723 GATTTGTTCTCTGACAATACAGAGATGCCAAATC
66 GATCTGTTCTCTGACAATACAGAGACGCCAAATC
44505757 TGTTTCTTCG
Statistics
Matches: 201, Mismatches: 25, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
129 12 0.06
130 1 0.00
131 51 0.25
132 137 0.68
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (132 bp):
GCCAAATCAGCTATGTCTTCGATCTGCTCCCTGTCGAATACAGAGATGCCAAATCTGATATCTTC
GATCTGTTCTCTGACAATACAGAGACGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTGA
AA
Found at i:44505745 original size:43 final size:43
Alignment explanation
Indices: 44505695--44505799 Score: 192
Period size: 43 Copynumber: 2.4 Consensus size: 43
44505685 CTCCCTTTCG
44505695 AATACAGAGATGCCAAATCTATTTCTTCGATTTGTTCTCTGAC
1 AATACAGAGATGCCAAATCTATTTCTTCGATTTGTTCTCTGAC
*
44505738 AATACAGAGATGCCAAATCTGTTTCTTCGATTTGTTCTCTGAC
1 AATACAGAGATGCCAAATCTATTTCTTCGATTTGTTCTCTGAC
*
44505781 AATACAGATATGCCAAATC
1 AATACAGAGATGCCAAATC
44505800 ATCTTGGATT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.34
Consensus pattern (43 bp):
AATACAGAGATGCCAAATCTATTTCTTCGATTTGTTCTCTGAC
Found at i:44513692 original size:16 final size:14
Alignment explanation
Indices: 44513651--44513703 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
44513641 TCTATAACTT
*
44513651 TGAATGCAAACG-A
1 TGAATGCAAATGCA
44513664 TGCAATG-AAATGCTA
1 TG-AATGCAAATGC-A
44513679 TGAGATGCAAATGCA
1 TGA-ATGCAAATGCA
44513694 TGAATGCAAA
1 TGAATGCAAA
44513704 AAGGACATCG
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
13 6 0.18
14 12 0.35
15 10 0.29
16 6 0.18
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (14 bp):
TGAATGCAAATGCA
Found at i:44517495 original size:23 final size:23
Alignment explanation
Indices: 44517436--44517507 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
44517426 AAATATGATG
*
44517436 TAATAATAATATAAAATAACAT-A
1 TAATAA-AATATAAAATAATATAA
* * *
44517459 TATTAAAGTGTAAAATAATATAA
1 TAATAAAATATAAAATAATATAA
*
44517482 TAATAAAATATAAAATAGTATAA
1 TAATAAAATATAAAATAATATAA
44517505 TAA
1 TAA
44517508 ATATTATGTA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 12 0.30
23 28 0.70
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (23 bp):
TAATAAAATATAAAATAATATAA
Found at i:44517527 original size:24 final size:25
Alignment explanation
Indices: 44517495--44517560 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 25
44517485 TAAAATATAA
* *
44517495 AATAGTATAATAAATATTATGT-AAT
1 AATAATATAATAAATA-TAGGTAAAT
44517520 AA-AATATAATATAGATATAGGTAAAT
1 AATAATATAATA-A-ATATAGGTAAAT
44517546 AATAATAT-ATAAATA
1 AATAATATAATAAATA
44517561 AAGTTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
24 11 0.31
25 8 0.23
26 11 0.31
27 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (25 bp):
AATAATATAATAAATATAGGTAAAT
Found at i:44519162 original size:19 final size:19
Alignment explanation
Indices: 44519135--44519171 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
44519125 AATTTATTTC
*
44519135 AACACAAGATCAAATCATT
1 AACAAAAGATCAAATCATT
*
44519154 AACAAAAGATCATATCAT
1 AACAAAAGATCAAATCAT
44519172 ATGCAACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.19, G:0.05, T:0.22
Consensus pattern (19 bp):
AACAAAAGATCAAATCATT
Found at i:44520977 original size:32 final size:32
Alignment explanation
Indices: 44520941--44521003 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
44520931 AGTATGAAAT
* *
44520941 TGTTTTGGAATATTAATTAGGAGGTCTTAAAA
1 TGTTTTGGAATATTAATGAGGACGTCTTAAAA
*
44520973 TGTTTTGGAATATTAATGAGGTCGTCTTAAA
1 TGTTTTGGAATATTAATGAGGACGTCTTAAA
44521004 TAGCAATTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (32 bp):
TGTTTTGGAATATTAATGAGGACGTCTTAAAA
Found at i:44529391 original size:43 final size:43
Alignment explanation
Indices: 44529340--44529445 Score: 167
Period size: 43 Copynumber: 2.5 Consensus size: 43
44529330 CTGACATTAC
44529340 GCCTGCTAGGCTCGAAGCCCGATATTAACTCACCAACATTATA
1 GCCTGCTAGGCTCGAAGCCCGATATTAACTCACCAACATTATA
* * ***
44529383 GCTTGCTAGGCTCAAAGCCCGATATTAACTCACCGGTATTATA
1 GCCTGCTAGGCTCGAAGCCCGATATTAACTCACCAACATTATA
44529426 GCCTGCTAGGCTCGAAGCCC
1 GCCTGCTAGGCTCGAAGCCC
44529446 TGAATAGTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (43 bp):
GCCTGCTAGGCTCGAAGCCCGATATTAACTCACCAACATTATA
Found at i:44531609 original size:13 final size:13
Alignment explanation
Indices: 44531591--44531616 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44531581 GCCATGAATG
44531591 TGAAATATTTGGT
1 TGAAATATTTGGT
44531604 TGAAATATTTGGT
1 TGAAATATTTGGT
44531617 GATATGATCT
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:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (13 bp):
TGAAATATTTGGT
Found at i:44533034 original size:44 final size:46
Alignment explanation
Indices: 44532955--44533061 Score: 121
Period size: 44 Copynumber: 2.4 Consensus size: 46
44532945 TAGTTATGTA
* * *
44532955 CACTTAGTGCGCGAAATCGAGATAGTGTCGACTATATAT-T-TTTG
1 CACTTAGTGTGCGAGATCGAGATAGTGTCGACTATATATATATTGG
* * *
44532999 TACTTAGTGTGCGAGATCGAGATAGCT-TTGGCTATATATATATTGG
1 CACTTAGTGTGCGAGATCGAGATAG-TGTCGACTATATATATATTGG
*
44533045 CACTTAGTGTGCAAGAT
1 CACTTAGTGTGCGAGAT
44533062 TCATACAGCT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
44 32 0.62
45 2 0.04
46 18 0.35
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (46 bp):
CACTTAGTGTGCGAGATCGAGATAGTGTCGACTATATATATATTGG
Found at i:44533072 original size:46 final size:43
Alignment explanation
Indices: 44533000--44533099 Score: 112
Period size: 46 Copynumber: 2.3 Consensus size: 43
44532990 ATATTTTTGT
* * *
44533000 ACTTAGTGTGCGAGATCGAGATAGCTTTGGCTATATATATATTGGC
1 ACTTAGTGTGCAAGATCGAGACAGCTTCGGCTAT-T-TAT-TTGGC
*
44533046 ACTTAGTGTGCAAGATTC-ATACAGCTTCGGCTATTTATTTGGC
1 ACTTAGTGTGCAAGA-TCGAGACAGCTTCGGCTATTTATTTGGC
*
44533089 ACTAAGTGTGC
1 ACTTAGTGTGC
44533100 GAGTTTCCCG
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
43 15 0.31
44 3 0.06
45 1 0.02
46 27 0.56
47 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (43 bp):
ACTTAGTGTGCAAGATCGAGACAGCTTCGGCTATTTATTTGGC
Found at i:44538432 original size:30 final size:29
Alignment explanation
Indices: 44538390--44538452 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 29
44538380 AAGTAGCCGG
44538390 AGCTAGTTAAATCGCACACCTAGTGCCAA
1 AGCTAGTTAAATCGCACACCTAGTGCCAA
*
44538419 AGCTAGTTTAAATCGCACACTTAGTGCCAA
1 AGCTAG-TTAAATCGCACACCTAGTGCCAA
44538449 AGCT
1 AGCT
44538453 TCCGATTCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (29 bp):
AGCTAGTTAAATCGCACACCTAGTGCCAA
Found at i:44541110 original size:21 final size:21
Alignment explanation
Indices: 44541086--44541130 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
44541076 AATCCCCACA
44541086 TGGTGTGTTGGTTGG-TATGGG
1 TGGTGTGTTGGTTGGAT-TGGG
44541107 TGGTGTGTTGGTTGGATTGGG
1 TGGTGTGTTGGTTGGATTGGG
44541128 TGG
1 TGG
44541131 GTTACATGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.04, C:0.00, G:0.53, T:0.42
Consensus pattern (21 bp):
TGGTGTGTTGGTTGGATTGGG
Found at i:44563249 original size:20 final size:21
Alignment explanation
Indices: 44563208--44563260 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
44563198 TTTTTTAAAA
*
44563208 TTTAA-AAATTTTAAAAATAT
1 TTTAATAATTTTTAAAAATAT
* * *
44563228 TTTTATACTTTTTAAATA-AT
1 TTTAATAATTTTTAAAAATAT
44563248 TTTAATAATTTTT
1 TTTAATAATTTTT
44563261 TATTTTTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAATAATTTTTAAAAATAT
Found at i:44563272 original size:28 final size:30
Alignment explanation
Indices: 44563214--44563272 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
44563204 AAAATTTAAA
*
44563214 AATTTTAAAAATATTTTTATACTTTTTAAAT
1 AATTTTAAAAATATTTTTATA-TTTTAAAAT
*
44563245 AATTTTAATAAT-TTTTTAT-TTTTAAAAT
1 AATTTTAAAAATATTTTTATATTTTAAAAT
44563273 TTAATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 8 0.31
30 7 0.27
31 11 0.42
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (30 bp):
AATTTTAAAAATATTTTTATATTTTAAAAT
Found at i:44563747 original size:19 final size:18
Alignment explanation
Indices: 44563719--44563766 Score: 78
Period size: 19 Copynumber: 2.6 Consensus size: 18
44563709 TAACCGAAAA
44563719 AATAATAAATAAAATTAT
1 AATAATAAATAAAATTAT
44563737 AATATATAAATAAAATTAT
1 AATA-ATAAATAAAATTAT
44563756 AATACATAAAT
1 AATA-ATAAAT
44563767 CCAAATACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAATAAATAAAATTAT
Found at i:44564008 original size:18 final size:18
Alignment explanation
Indices: 44563933--44564009 Score: 57
Period size: 18 Copynumber: 4.3 Consensus size: 18
44563923 TTTATTCAAA
* *
44563933 TAATTCGTTTAATTCAGT
1 TAATTCGGTTAATTCGGT
* *
44563951 TAATTTGGGTAATTCGAG-
1 TAATTCGGTTAATTCG-GT
** * **
44563969 TAATTTAGTCAATTCGAC
1 TAATTCGGTTAATTCGGT
44563987 TAATTCGGTTAATTCGGT
1 TAATTCGGTTAATTCGGT
44564005 TAATT
1 TAATT
44564010 TTATACTTTT
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
18 43 0.98
19 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (18 bp):
TAATTCGGTTAATTCGGT
Found at i:44564009 original size:27 final size:27
Alignment explanation
Indices: 44563933--44564009 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 27
44563923 TTTATTCAAA
* * **
44563933 TAATTCGTTTAATTCAGTTAATTTGGG
1 TAATTCGGTTAATTCAGTTAATTCGAC
* *
44563960 TAATTCGAG-TAATTTAGTCAATTCGAC
1 TAATTCG-GTTAATTCAGTTAATTCGAC
*
44563987 TAATTCGGTTAATTCGGTTAATT
1 TAATTCGGTTAATTCAGTTAATT
44564010 TTATACTTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 1 0.03
27 38 0.97
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (27 bp):
TAATTCGGTTAATTCAGTTAATTCGAC
Found at i:44573119 original size:48 final size:48
Alignment explanation
Indices: 44573064--44573283 Score: 233
Period size: 48 Copynumber: 4.6 Consensus size: 48
44573054 GTGAATTGTC
* * *
44573064 GATGCCATGTTCCAAACATGGCCTTACACTAGCTCACATGTCGAGGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCGAGGTT
* * * * * * *
44573112 GATGCCATGTCCCACACATGGTCTTACACTAGCTCTCGTCTCAATGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCGAGGTT
* * * * *
44573160 GATGCCATGGCCCAGACATGGTCTTACACTGGCTCTCATGTTGTGGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCGAGGTT
* * * * * **
44573208 GATGCCATGTCTCAGACATGGTCTTACACTAGCGCACATATCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCGAGGTT
*
44573256 GATGCCATGTCCCGGACATGGTCTTACA
1 GATGCCATGTCCCAGACATGGTCTTACA
44573284 TTGGCTCTTA
Statistics
Matches: 139, Mismatches: 33, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 139 1.00
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATGTCGAGGTT
Found at i:44573227 original size:96 final size:96
Alignment explanation
Indices: 44573060--44573291 Score: 311
Period size: 96 Copynumber: 2.4 Consensus size: 96
44573050 AAGGGTGAAT
* * * * *
44573060 TGTCGATGCCATGTTCCAAACATGGCCTTACACTAGCTCACATGTCGAGGTTGATGCCATGTCCC
1 TGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATGTCGAGGTTGATGCCATGTCCC
* * * *
44573125 ACACATGGTCTTACACTAGCTCTCGTCTCAA
66 ACACATGGTCTTACACTAGCGCACATATCAA
* * * *
44573156 TGTCGATGCCATGGCCCAGACATGGTCTTACACTGGCTCTCATGTTGTGGTTGATGCCATGTCTC
1 TGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATGTCGAGGTTGATGCCATGTCCC
*
44573221 AGACATGGTCTTACACTAGCGCACATATCAA
66 ACACATGGTCTTACACTAGCGCACATATCAA
* * *
44573252 TGCCGATGCCATGTCCCGGACATGGTCTTACATTGGCTCT
1 TGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT
44573292 TACAACATCG
Statistics
Matches: 118, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
96 118 1.00
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (96 bp):
TGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATGTCGAGGTTGATGCCATGTCCC
ACACATGGTCTTACACTAGCGCACATATCAA
Found at i:44573327 original size:144 final size:143
Alignment explanation
Indices: 44573063--44573377 Score: 332
Period size: 144 Copynumber: 2.2 Consensus size: 143
44573053 GGTGAATTGT
* * * * **
44573063 CGATGCCATGT-TCCAAACATGGCCTTACACTAGCTCACATGTCGAGGTTGATGCCATGTCCCAC
1 CGATGCCATGTCT-CAAACATGGTCTTACACTAGCGCACATATCAAGGCCGATGCCATGTCCCAC
* * * *
44573127 ACATGGTCTTACACTAGCTCTCGTCTCAATGTCGATGCCATGGCCCAGACATGGTCTTACACTGG
65 ACATGGTCTTACACTAGCTCTC-TCACAATGCCGATGCCATGGCCCAAACAAGGTCTTACACTGG
* * *
44573192 CTCTCATGTTGTGGT
129 CTCTCATATCGTGGC
* * * **
44573207 TGATGCCATGTCTCAGACATGGTCTTACACTAGCGCACATATCAATGCCGATGCCATGTCCCGGA
1 CGATGCCATGTCTCAAACATGGTCTTACACTAGCGCACATATCAAGGCCGATGCCATGTCCCACA
* * ** *
44573272 CATGGTCTTACATTGGCTCT-T-ACAACATCGCCGATGCCATGTTCCAAACAAGGTCTTACATTG
66 CATGGTCTTACACTAGCTCTCTCAC-A-AT-GCCGATGCCATGGCCCAAACAAGGTCTTACACTG
44573335 GCTCTCATATCGTGGC
128 GCTCTCATATCGTGGC
*
44573351 CGACGCCATGTC-CTAAACATGGTCTTA
1 CGATGCCATGTCTC-AAACATGGTCTTA
44573378 TGCTGGCACA
Statistics
Matches: 140, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
141 1 0.01
142 2 0.01
143 3 0.02
144 133 0.95
145 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (143 bp):
CGATGCCATGTCTCAAACATGGTCTTACACTAGCGCACATATCAAGGCCGATGCCATGTCCCACA
CATGGTCTTACACTAGCTCTCTCACAATGCCGATGCCATGGCCCAAACAAGGTCTTACACTGGCT
CTCATATCGTGGC
Found at i:44573344 original size:96 final size:96
Alignment explanation
Indices: 44573112--44573377 Score: 257
Period size: 96 Copynumber: 2.8 Consensus size: 96
44573102 TGTCGAGGTT
* * * * * *
44573112 GATGCCATGTCCCACACATGGTCTTACACTAGCTCTCGTCTCAATGTCGATGCCATGGCCCAGAC
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTCCCAGAC
***** * **
44573177 ATGGTCTTACACTGGCTCTCATGTTGTGGTT
66 ATGGTCTTACACTGGCTCTCACAACATCGCC
* * * *
44573208 GATGCCATG-TCTCAGACATGGTCTTACACTAGCGCACATATCAATGCCGATGCCATGTCCCGGA
1 GATGCCATGTTC-CAAACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTCCCAGA
* *
44573272 CATGGTCTTACATTGGCTCTTACAACATCGCC
65 CATGGTCTTACACTGGCTCTCACAACATCGCC
* * * * * * *
44573304 GATGCCATGTTCCAAACAAGGTCTTACATTGGCTCTCATATC-GTGGCCGACGCCATGTCCTAAA
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCAAT-GCCGATGCCATGTCCCAGA
44573368 CATGGTCTTA
65 CATGGTCTTA
44573378 TGCTGGCACA
Statistics
Matches: 137, Mismatches: 30, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
95 2 0.01
96 133 0.97
97 2 0.01
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (96 bp):
GATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTCCCAGAC
ATGGTCTTACACTGGCTCTCACAACATCGCC
Found at i:44573353 original size:48 final size:48
Alignment explanation
Indices: 44573063--44573377 Score: 226
Period size: 48 Copynumber: 6.6 Consensus size: 48
44573053 GGTGAATTGT
* * * *
44573063 CGATGCCATGTTCCAAACATGGCCTTACACTAGCTCACATGTCGA-GGT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATC-ATGGC
* * * * * *
44573111 TGATGCCATGTCCCACACATGGTCTTACACTAGCTCTCGTCTCAAT-GT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATC-ATGGC
** * * * ** *
44573159 CGATGCCATGGCCCAGACATGGTCTTACACTGGCTCTCATGTTGTGGT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCATGGC
* * * *
44573207 TGATGCCATG-TCTCAGACATGGTCTTACACTAGCGCACATATCAAT-GC
1 CGATGCCATGTTC-CAAACATGGTCTTACACTAGCTCTCATATC-ATGGC
* ** * * * * * *
44573255 CGATGCCATGTCCCGGACATGGTCTTACATTGGCTCTTACAACATCGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCATGGC
* * * *
44573303 CGATGCCATGTTCCAAACAAGGTCTTACATTGGCTCTCATATCGTGGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCATGGC
*
44573351 CGACGCCATG-TCCTAAACATGGTCTTA
1 CGATGCCATGTTCC-AAACATGGTCTTA
44573378 TGCTGGCACA
Statistics
Matches: 214, Mismatches: 46, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
47 7 0.03
48 205 0.96
49 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (48 bp):
CGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCATATCATGGC
Found at i:44575294 original size:22 final size:22
Alignment explanation
Indices: 44575268--44575314 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
44575258 AATATTAAAC
44575268 TAAGTATGGTAAATAGACCATT
1 TAAGTATGGTAAATAGACCATT
44575290 TAAGTATGGTAAATAGACCATT
1 TAAGTATGGTAAATAGACCATT
44575312 TAA
1 TAA
44575315 TGAGATAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.32
Consensus pattern (22 bp):
TAAGTATGGTAAATAGACCATT
Found at i:44577430 original size:18 final size:17
Alignment explanation
Indices: 44577407--44577442 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
44577397 TGAAAAAGGG
44577407 TTGAATCCCGATTGAATA
1 TTGAATCCCGA-TGAATA
*
44577425 TTGAATTCCGATGAATA
1 TTGAATCCCGATGAATA
44577442 T
1 T
44577443 ATAGGCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (17 bp):
TTGAATCCCGATGAATA
Found at i:44584285 original size:84 final size:84
Alignment explanation
Indices: 44584197--44584357 Score: 277
Period size: 84 Copynumber: 1.9 Consensus size: 84
44584187 AGTAGGGACT
* * * *
44584197 AAATTGAAATAATTAATTAGTTAAAAGATGATAAAAGGAAATATCATCTTATTTTTTCATCTTCA
1 AAATTGAAATAAATAATTAATTAAAAGATGATAAAAAGAAATATCATCTTATTTTGTCATCTTCA
44584262 ACCCCAAAATTAAAATTAG
66 ACCCCAAAATTAAAATTAG
*
44584281 AAATTGAAATAAATAATTAATTAAAAGATGATAAAAAGAAATATCCTCTTATTTTGTCATCTTCA
1 AAATTGAAATAAATAATTAATTAAAAGATGATAAAAAGAAATATCATCTTATTTTGTCATCTTCA
44584346 ACCCCAAAATTA
66 ACCCCAAAATTA
44584358 TATGGAAACC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 72 1.00
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (84 bp):
AAATTGAAATAAATAATTAATTAAAAGATGATAAAAAGAAATATCATCTTATTTTGTCATCTTCA
ACCCCAAAATTAAAATTAG
Found at i:44588169 original size:46 final size:48
Alignment explanation
Indices: 44588019--44588338 Score: 268
Period size: 46 Copynumber: 6.8 Consensus size: 48
44588009 TCACTGGTGT
* * *
44588019 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCA-C-ATTATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GGCATCGA-GATGA
* *
44588065 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATGA
* * * *
44588113 GTGCTAGTGTAAGA-CATGTCTGGGACAT-ACATCGGCCTCGAGATGTA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATG-A
* *
44588160 -AGCCAGTGTAAGA-CATGTCTGGGACAT-GCGTCGG-ATAG-GA-GA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATGA
* * * * * *
44588202 TGTGTCAGTGTAAGACCATGTCTAGGACATGGAATCGGCATGGATATGCGA
1 -GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGAT--GA
* * * *
44588253 GAGCTAGTGTAAGACCATGTCTGAGACATGGCATCAGCCTCGATGATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGA-GATGA
* * * *
44588302 TAGCCAATGTAAGACCATGTCAGGGACATGGCTTCGG
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG
44588339 AAACTTGCCA
Statistics
Matches: 218, Mismatches: 41, Indels: 27
0.76 0.14 0.09
Matches are distributed among these distances:
42 1 0.00
43 1 0.00
44 13 0.06
45 15 0.07
46 61 0.28
47 35 0.16
48 21 0.10
49 33 0.15
50 34 0.16
51 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.23
Consensus pattern (48 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATGA
Found at i:44591769 original size:11 final size:11
Alignment explanation
Indices: 44591753--44591777 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
44591743 TTCAATTCAA
44591753 ATAATCAATAT
1 ATAATCAATAT
44591764 ATAATCAATAT
1 ATAATCAATAT
44591775 ATA
1 ATA
44591778 TACCAATTCA
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATCAATAT
Found at i:44591802 original size:15 final size:16
Alignment explanation
Indices: 44591755--44591804 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
44591745 CAATTCAAAT
*
44591755 AATCAATATATAA-TC
1 AATCAATATACAATTC
44591770 AAT-ATATATACCAATTC
1 AATCA-ATATA-CAATTC
44591787 AATCAATATA-AATTC
1 AATCAATATACAATTC
44591802 AAT
1 AAT
44591805 AAATTCATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
16 2 0.07
17 10 0.33
18 1 0.03
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (16 bp):
AATCAATATACAATTC
Found at i:44591827 original size:24 final size:24
Alignment explanation
Indices: 44591782--44591828 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
44591772 TATATATACC
44591782 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
44591806 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
44591829 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:44592500 original size:11 final size:11
Alignment explanation
Indices: 44592484--44592553 Score: 61
Period size: 11 Copynumber: 6.2 Consensus size: 11
44592474 ATCTTTCTCC
44592484 TTTTCTTTCTT
1 TTTTCTTTCTT
44592495 TTTTCTTTCTT
1 TTTTCTTTCTT
*
44592506 TTTT-TTCCTT
1 TTTTCTTTCTT
*
44592516 CTATTTCGTTTGTT
1 -T-TTTC-TTTCTT
*
44592530 CTTTCTTTCTT
1 TTTTCTTTCTT
* *
44592541 TTCTATTTCTT
1 TTTTCTTTCTT
44592552 TT
1 TT
44592554 ATTATTATAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
10 5 0.11
11 31 0.66
12 7 0.15
14 4 0.09
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.76
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:44592614 original size:13 final size:13
Alignment explanation
Indices: 44592598--44592649 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
44592588 TAAGATTTAA
44592598 TATTATATAATAT
1 TATTATATAATAT
44592611 TATTATAT-ATAT
1 TATTATATAATAT
*
44592623 TATTACTTTAA-AT
1 TATTA-TATAATAT
*
44592636 TTTTATAATAATAT
1 TATTAT-ATAATAT
44592650 ATACCTTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 10 0.31
13 19 0.59
14 3 0.09
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTATATAATAT
Found at i:44594619 original size:22 final size:22
Alignment explanation
Indices: 44594585--44594628 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
44594575 CAAATTCAAA
* *
44594585 TTAAATATTAAAACATTTAAAT
1 TTAAATATAAAAACATATAAAT
* *
44594607 TTAATTATAAAAATATATAAAT
1 TTAAATATAAAAACATATAAAT
44594629 GTTATTAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAAATATAAAAACATATAAAT
Found at i:44598622 original size:46 final size:45
Alignment explanation
Indices: 44598569--44598739 Score: 182
Period size: 46 Copynumber: 3.7 Consensus size: 45
44598559 TCTTGTAGTT
* * *
44598569 GATGCATGTCCCAGACATTTCTTACACTGGCT-TACATCTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATAT-GAGGCC
* * * * * *
44598615 GATGCATGTTCTAGACATGTCTTACACTAGCTCTCATTTAAATGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAT-GAGGCC
*
44598661 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCAT-ATGAGGCC
*
44598709 AATGCATGTCCCAGACATGTCTTACACTAGC
1 GATGCATGTCCCAGACATGTCTTACACTAGC
44598740 ACACAATTAA
Statistics
Matches: 104, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
46 52 0.50
47 27 0.26
48 24 0.23
49 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATATGAGGCC
Found at i:44598688 original size:94 final size:92
Alignment explanation
Indices: 44598568--44598739 Score: 231
Period size: 94 Copynumber: 1.8 Consensus size: 92
44598558 ATCTTGTAGT
* * * * * *
44598568 TGATGCATGTCCCAGACATTTCTTACACTGGCT-TACAT-CTCGAGGCCGATGCATGTTCTAGAC
1 TGATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATAAT-GAGGCCAATGCATGTCCCAGAC
44598631 ATGTCTTACACTAGCTCTCATTTAAATGC
64 ATGTCTTACACTAGCTCTCATTTAAATGC
*
44598660 TGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGGCCAATGCATGTCCCAGAC
1 TGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATAATGAGGCCAATGCATGTCCCAGAC
44598725 ATGTCTTACACTAGC
64 ATGTCTTACACTAGC
44598740 ACACAATTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
92 5 0.07
93 14 0.20
94 48 0.70
95 2 0.03
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.30
Consensus pattern (92 bp):
TGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAATGAGGCCAATGCATGTCCCAGACAT
GTCTTACACTAGCTCTCATTTAAATGC
Found at i:44600640 original size:34 final size:34
Alignment explanation
Indices: 44600558--44600645 Score: 94
Period size: 34 Copynumber: 2.6 Consensus size: 34
44600548 AGGAATGAAC
*
44600558 TATATACAT-AATAGATTTAAAAATATATATACA
1 TATATAAATAAATAGATTTAAAAATATATATACA
*
44600591 TATATATATAAATAGATTTAAAAGA-A-AT-TACA
1 TATATAAATAAATAGATTTAAAA-ATATATATACA
*
44600623 TATATAAAATAACATAGAATTAA
1 TATAT-AAATAA-ATAGATTTAA
44600646 TAATGTACAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
32 9 0.19
33 15 0.31
34 23 0.48
35 1 0.02
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.34
Consensus pattern (34 bp):
TATATAAATAAATAGATTTAAAAATATATATACA
Found at i:44600967 original size:15 final size:16
Alignment explanation
Indices: 44600937--44600972 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
44600927 AATTAAAGGG
44600937 ATAATTGATAAATGAA
1 ATAATTGATAAATGAA
*
44600953 ATAATTGA-AATTGAA
1 ATAATTGATAAATGAA
44600968 ATAAT
1 ATAAT
44600973 GACCAAAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (16 bp):
ATAATTGATAAATGAA
Found at i:44601911 original size:25 final size:23
Alignment explanation
Indices: 44601877--44601922 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
44601867 TAAAGAAATG
44601877 GAAAAAAAAAGAGAAAGAAAATGAT
1 GAAAAAAAAAGA-AAA-AAAATGAT
*
44601902 GAAAACAAAAGAAAAAAAATG
1 GAAAAAAAAAGAAAAAAAATG
44601923 TGTCCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.07
Consensus pattern (23 bp):
GAAAAAAAAAGAAAAAAAATGAT
Found at i:44603354 original size:40 final size:40
Alignment explanation
Indices: 44603163--44603347 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
44603153 TCGAATGATG
* * * *
44603163 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
44603203 TCCGGACTAAGAT-CCGAAGGCATTTTTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
44603243 TTCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
44603282 TTCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
44603323 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
44603348 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
39 34 0.28
40 78 0.64
41 9 0.07
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:44603369 original size:79 final size:78
Alignment explanation
Indices: 44603200--44603380 Score: 179
Period size: 79 Copynumber: 2.3 Consensus size: 78
44603190 CTAAGTGACC
* * **
44603200 ATATCCGGACTAAGATCC-GAAGGCATTTTTGCGAGTTACTAATTTCGGGCTAAGCCCGAAGGCA
1 ATATCCGG-TTAAG-TCCTGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCA
**
44603264 TTGGTGCGAGTTACT
64 TTGGAACGAGTTACT
* * *
44603279 AAATTCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGC
1 ATA-TCCGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGC
*
44603343 ATTTGAACGAG-TAGCT
63 ATTGGAACGAGTTA-CT
* *
44603359 ATATCCGGTTAAATTCTGAAGG
1 ATATCCGGTTAAGTCCTGAAGG
44603381 TACGTGATTC
Statistics
Matches: 83, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
78 5 0.06
79 53 0.64
80 25 0.30
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (78 bp):
ATATCCGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATT
GGAACGAGTTACT
Found at i:44609950 original size:25 final size:24
Alignment explanation
Indices: 44609914--44609962 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
44609904 TAATAAAGAA
*
44609914 ATGAAAAAAAAAGAGAAAGAAAATG
1 ATGAAAAAAAAAGA-AAAAAAAATG
*
44609939 ATGAAAACAAAAGAAAAAAAAATG
1 ATGAAAAAAAAAGAAAAAAAAATG
44609963 TGTCCATCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.73, C:0.02, G:0.16, T:0.08
Consensus pattern (24 bp):
ATGAAAAAAAAAGAAAAAAAAATG
Found at i:44611312 original size:39 final size:40
Alignment explanation
Indices: 44611204--44611388 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
44611194 TCGAATGATG
* * *
44611204 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
44611243 ATCCGGACTAAGAT-CTGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
44611284 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
44611323 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
44611362 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
44611389 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:44611410 original size:79 final size:79
Alignment explanation
Indices: 44611259--44611411 Score: 204
Period size: 79 Copynumber: 1.9 Consensus size: 79
44611249 ACTAAGATCT
* **
44611259 GAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAAT
1 GAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAAT
44611324 CCGGGTTAAGTCCC
66 CCGGGTTAAGTCCC
* *
44611338 GAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTA
1 GAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTA
*
44611401 TATCC-GGTTAA
63 AATCCGGGTTAA
44611412 ATTCTGAAGG
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
78 2 0.03
79 39 0.60
80 24 0.37
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (79 bp):
GAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAAT
CCGGGTTAAGTCCC
Found at i:44613758 original size:44 final size:45
Alignment explanation
Indices: 44613710--44613809 Score: 114
Period size: 44 Copynumber: 2.2 Consensus size: 45
44613700 TACTACCTCG
* * * * **
44613710 GGGAGATAAGAT-TCACCATCTTCAATTTGCTCTGCTACTGCTT-A
1 GGGAGATAAGATCT-ACAACCTTCAATCTGCTCCGCTACAACTTCA
*
44613754 GGGAGATAAGATCTACAACCTTCAGTCTGCTCCGCTACAACTTCA
1 GGGAGATAAGATCTACAACCTTCAATCTGCTCCGCTACAACTTCA
44613799 GGGAGATAAGA
1 GGGAGATAAGA
44613810 CTTGCTTTGA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
44 34 0.72
45 13 0.28
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (45 bp):
GGGAGATAAGATCTACAACCTTCAATCTGCTCCGCTACAACTTCA
Found at i:44614065 original size:176 final size:176
Alignment explanation
Indices: 44613814--44614337 Score: 629
Period size: 176 Copynumber: 3.0 Consensus size: 176
44613804 ATAAGACTTG
* * * * *
44613814 CTTTGATCTGCTCCACTGCAACTTCAGGGAGATAAGGTATTCAATCCTT-AGTCTCCTTCCCTGC
1 CTTTGATCTGCTCCACTGC-TC-TCAGGGAGATAAGATCTTCAAT-CTTCAGTCTGCTTCCATGC
* * *
44613878 TACCTCAAGAAGATAAGACTACAATCTTCAACCTGCTCTCTTGCTAGCACAGAGAGATAAGGTTG
63 TACCTCAAGAAGATAAGACTACAATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTG
*
44613943 GTGGCTAAAATCTGCTCCCCTGCTACCTCGGGAAGATAAGATTCGCCAT
128 GTGGCTAAAATCTGCTCCCCTGCTACCTCGGGAAGATAAGATTCACCAT
* * *
44613992 CTTTGATCTGCTCCACTGCTCTCAGGGAGATAAGTTCTTCGATCTTCAGTCTGCTTCCTTGCTAC
1 CTTTGATCTGCTCCACTGCTCTCAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCATGCTAC
* * * * * * * *
44614057 CACAAGAAGATAAGACTAGAATCTTTAACATGCTCTCTTGTTACCTCAAAAAGATAAGGCTGGTA
66 CTCAAGAAGATAAGACTACAATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTG
* * * * * *
44614122 GCTAAAATCTGCTTCCCTACCACATCGGGAAGATAACATTCACTAT
131 GCTAAAATCTGCTCCCCTGCTACCTCGGGAAGATAAGATTCACCAT
* * * * * * * *
44614168 CTTCGATCCGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCCTCAGTTTGCTTCCATACTA
1 CTTTGATCTGCTCCACTGCT-CTCAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCATGCTA
* * * *
44614233 CCTC-AGAAAGATAAGACTATAATTTTCAACCTACTCTCTTGCTTCCTCAGAGAGATAAGGCTGG
65 CCTCAAG-AAGATAAGACTACAATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGG
* *
44614297 TGGCTAAAACCTGCTCCCCTGCTACCTCGGGAAAATAAGAT
129 TGGCTAAAATCTGCTCCCCTGCTACCTCGGGAAGATAAGAT
44614338 CTAAATTCAC
Statistics
Matches: 290, Mismatches: 53, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
175 3 0.01
176 147 0.51
177 121 0.42
178 19 0.07
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (176 bp):
CTTTGATCTGCTCCACTGCTCTCAGGGAGATAAGATCTTCAATCTTCAGTCTGCTTCCATGCTAC
CTCAAGAAGATAAGACTACAATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTG
GCTAAAATCTGCTCCCCTGCTACCTCGGGAAGATAAGATTCACCAT
Found at i:44615583 original size:16 final size:16
Alignment explanation
Indices: 44615541--44615583 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
44615531 TTGGCCTCTC
*
44615541 TTTTTTATCTTTTTAT
1 TTTTTTATATTTTTAT
*
44615557 TTTCATT-TATTTTTAT
1 TTT-TTTATATTTTTAT
44615573 TTTTTTATATT
1 TTTTTTATATT
44615584 GGGTCTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
15 2 0.09
16 18 0.82
17 2 0.09
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTATATTTTTAT
Found at i:44627636 original size:15 final size:16
Alignment explanation
Indices: 44627606--44627641 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
44627596 AATTAAAGGG
44627606 ATAATTGATAAATGAA
1 ATAATTGATAAATGAA
*
44627622 ATAATTGA-AATTGAA
1 ATAATTGATAAATGAA
44627637 ATAAT
1 ATAAT
44627642 GACCAAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (16 bp):
ATAATTGATAAATGAA
Found at i:44629843 original size:24 final size:24
Alignment explanation
Indices: 44629815--44629935 Score: 100
Period size: 25 Copynumber: 4.9 Consensus size: 24
44629805 CAACTCGTAT
*
44629815 GAGCTTACCAATTACAGCTCATGA
1 GAGCTTACCGATTACAGCTCATGA
** * *
44629839 GAGCTTACCGATTGTAACTCGTGA
1 GAGCTTACCGATTACAGCTCATGA
*
44629863 GAGCTTACCGATTCTCAGCTCAT-A
1 GAGCTTACCGATT-ACAGCTCATGA
* * *
44629887 TGAGTTTACCAATTTACAGCTCGTGA
1 -GAGCTTACCGA-TTACAGCTCATGA
* *
44629913 GAGCATACCGATTCATAGCTCAT
1 GAGCTTACCGATT-ACAGCTCAT
44629936 ACGAGCATAC
Statistics
Matches: 74, Mismatches: 18, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
24 35 0.47
25 36 0.49
26 3 0.04
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (24 bp):
GAGCTTACCGATTACAGCTCATGA
Found at i:44631390 original size:16 final size:16
Alignment explanation
Indices: 44631369--44631399 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
44631359 TTTCAATATT
44631369 TTACAGTATGTTTATA
1 TTACAGTATGTTTATA
44631385 TTACAGTATGTTTAT
1 TTACAGTATGTTTAT
44631400 GCTAGGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (16 bp):
TTACAGTATGTTTATA
Found at i:44634834 original size:46 final size:46
Alignment explanation
Indices: 44634780--44635138 Score: 385
Period size: 46 Copynumber: 7.7 Consensus size: 46
44634770 TGGTTGAGCA
*
44634780 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
* * * *
44634826 TCCAAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--AGG
*
44634871 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
* * * *
44634919 TCCAAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--AGG
*
44634964 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
* * * *
44635012 TCCAAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--AGG
*
44635057 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
* *
44635105 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
44635139 GGGGCGGGTT
Statistics
Matches: 260, Mismatches: 32, Indels: 42
0.78 0.10 0.13
Matches are distributed among these distances:
43 18 0.07
45 12 0.05
46 116 0.45
47 84 0.32
48 12 0.05
50 18 0.07
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAGG
Found at i:44634936 original size:93 final size:93
Alignment explanation
Indices: 44634777--44635133 Score: 678
Period size: 93 Copynumber: 3.8 Consensus size: 93
44634767 GGATGGTTGA
44634777 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAACTCGTTGAGT
44634842 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
44634870 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAACTCGTTGAGT
44634935 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
44634963 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAACTCGTTGAGT
44635028 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
44635056 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAACTCGTTGAGT
44635121 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
44635134 ACTTAGGGGC
Statistics
Matches: 260, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 260 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:44637318 original size:27 final size:28
Alignment explanation
Indices: 44637209--44637331 Score: 185
Period size: 28 Copynumber: 4.4 Consensus size: 28
44637199 GAGATTGGCG
* * * *
44637209 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
44637238 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
44637266 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
44637294 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
44637321 CTGAGTGTGCG
1 CTAAGTGTGCG
44637332 GACTTAATAT
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
27 24 0.27
28 50 0.56
29 15 0.17
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:44650885 original size:30 final size:30
Alignment explanation
Indices: 44650849--44650910 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
44650839 AATTGGAAGT
44650849 TTTGGCACTAAGTGTGCGATTTAAACTAGC
1 TTTGGCACTAAGTGTGCGATTTAAACTAGC
44650879 TTTGGCACTAAGTGTGCGATTTAAACTAGC
1 TTTGGCACTAAGTGTGCGATTTAAACTAGC
44650909 TT
1 TT
44650911 CGGCTACTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (30 bp):
TTTGGCACTAAGTGTGCGATTTAAACTAGC
Found at i:44653140 original size:55 final size:54
Alignment explanation
Indices: 44653045--44653194 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
44653035 CTACTTTGTT
* ** * *
44653045 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
44653099 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
44653154 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
44653195 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:44653157 original size:27 final size:27
Alignment explanation
Indices: 44653017--44653194 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
44653007 TAAATTGTAC
44653017 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
44653044 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
44653070 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
44653098 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
44653126 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
44653153 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
44653180 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
44653195 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:44653158 original size:82 final size:81
Alignment explanation
Indices: 44653018--44653173 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
44653008 AAATTGTACA
* * * *
44653018 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
44653083 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
44653099 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
44653162 TGTGCGAGTTGA
63 TGTGCGAATTGA
44653174 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:44661771 original size:40 final size:40
Alignment explanation
Indices: 44661693--44661916 Score: 285
Period size: 40 Copynumber: 5.5 Consensus size: 40
44661683 ACCCAAGTAT
* *
44661693 CTTCGGGATTTAG-CCGGATATA-TCAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
**
44661732 CTTC-GGATCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCACTAGCACAAATGC
*
44661772 CTTCGGGACTTAACCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
44661812 CTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* * *
44661855 CTTTGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
44661895 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
44661917 CATCCGAATA
Statistics
Matches: 162, Mismatches: 14, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
38 3 0.02
39 9 0.06
40 110 0.68
41 5 0.03
43 35 0.22
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:44661889 original size:83 final size:80
Alignment explanation
Indices: 44661693--44661916 Score: 285
Period size: 83 Copynumber: 2.8 Consensus size: 80
44661683 ACCCAAGTAT
* *
44661693 CTTCGGGATTTAG-CCGGATATA-TCAACTCGCACAAATGCCTTC-GGATCTTAGCCCGGATATA
1 CTTCGGGACTTAGCCCGGATATAGT-AACTAGCACAAATGCCTTCGGGA-CTTAGCCCGGATATA
**
44661755 GTCACTAGCATGAATGC
64 GTCACTAGCACAAATGC
* * *
44661772 CTTCGGGACTTAACCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
44661836 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
* *
44661855 CTTTGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
44661917 CATCCGAATA
Statistics
Matches: 126, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
79 12 0.10
80 45 0.36
81 4 0.03
83 65 0.52
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:44670423 original size:21 final size:21
Alignment explanation
Indices: 44670397--44670437 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
44670387 ATCTTATGGC
44670397 AAAA-GGTTAAAAGATATTTGG
1 AAAAGGGTT-AAAGATATTTGG
44670418 AAAAGGGTTAAAGATATTTG
1 AAAAGGGTTAAAGATATTTG
44670438 ACAGAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (21 bp):
AAAAGGGTTAAAGATATTTGG
Found at i:44678538 original size:28 final size:28
Alignment explanation
Indices: 44678501--44678567 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
44678491 AATATATAAC
44678501 ATAAATTATTTTTTAATATTTTAGTAAA
1 ATAAATTATTTTTTAATATTTTAGTAAA
*
44678529 ATAGATTATTTTTTAATATTTTAGTAAA
1 ATAAATTATTTTTTAATATTTTAGTAAA
44678557 ATAAATT-TTTT
1 ATAAATTATTTT
44678568 GAGGGAACCA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
27 4 0.11
28 33 0.89
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (28 bp):
ATAAATTATTTTTTAATATTTTAGTAAA
Found at i:44679034 original size:19 final size:19
Alignment explanation
Indices: 44679010--44679070 Score: 86
Period size: 20 Copynumber: 3.1 Consensus size: 19
44679000 ATTTGATCCT
44679010 AATTTTAAAAATACATAAA
1 AATTTTAAAAATACATAAA
*
44679029 AATTTTAAAAATAAAATAAA
1 AATTTTAAAAAT-ACATAAA
*
44679049 AATATTAAAAATACATTAAA
1 AATTTTAAAAATACA-TAAA
44679069 AA
1 AA
44679071 ACTTCAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 14 0.38
20 23 0.62
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTTTAAAAATACATAAA
Found at i:44685640 original size:7 final size:7
Alignment explanation
Indices: 44685634--44685688 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
44685624 TTTTTGATTT
*
44685634 TCAATTT
1 TCAATTC
* *
44685641 TCATTTT
1 TCAATTC
*
44685648 TCAATTT
1 TCAATTC
*
44685655 TCAATCC
1 TCAATTC
*
44685662 TCAATCC
1 TCAATTC
44685669 TCAATTC
1 TCAATTC
44685676 TCAATTC
1 TCAATTC
44685683 TCAATT
1 TCAATT
44685689 ATTTTTTTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.27, C:0.25, G:0.00, T:0.47
Consensus pattern (7 bp):
TCAATTC
Found at i:44685656 original size:14 final size:14
Alignment explanation
Indices: 44685631--44685657 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44685621 TGGTTTTTGA
44685631 TTTTCAATTTTCAT
1 TTTTCAATTTTCAT
44685645 TTTTCAATTTTCA
1 TTTTCAATTTTCA
44685658 ATCCTCAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTTCAT
Found at i:44685672 original size:21 final size:21
Alignment explanation
Indices: 44685648--44685687 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44685638 TTTTCATTTT
*
44685648 TCAATTTTCAATCCTCAATCC
1 TCAATTCTCAATCCTCAATCC
*
44685669 TCAATTCTCAATTCTCAAT
1 TCAATTCTCAATCCTCAAT
44685688 TATTTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (21 bp):
TCAATTCTCAATCCTCAATCC
Found at i:44685735 original size:20 final size:20
Alignment explanation
Indices: 44685712--44685760 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
44685702 CTTTTTCTGA
44685712 ATTTTATTCTCTTCTATTTT
1 ATTTTATTCTCTTCTATTTT
44685732 ATTTTATTCTCTTCTATTTT
1 ATTTTATTCTCTTCTATTTT
44685752 ATTTTATTC
1 ATTTTATTC
44685761 CTTACAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTTATTCTCTTCTATTTT
Found at i:44690516 original size:67 final size:68
Alignment explanation
Indices: 44690396--44690635 Score: 263
Period size: 67 Copynumber: 3.6 Consensus size: 68
44690386 GCTGAACAAA
** * *
44690396 GGTTACAAGGTGTAAGAGTATAGCTCGACTATGGCAACTAATAGTG-TCTACCAGGACATTAAAC
1 GGTTACAAGGTGTAAGACCATAGCTCGACTATGGCAACCAATAGAGTTC-ACCAGGACATTAAAC
44690460 ATGG
65 ATGG
* * * **
44690464 GGTTAC-ATGTGTAAGACCATAGCTCAACTATGGCAACGAATAGAGTTCACCAGGATGTTAAACA
1 GGTTACAAGGTGTAAGACCATAGCTCGACTATGGCAACCAATAGAGTTCACCAGGACATTAAACA
44690528 TGG
66 TGG
* * * ** * * * *
44690531 AGATACAAGGTGTAAGCCCATAGCTCGACTATGAAAACCTATAGAGTCCACAAGGACATTAAGCA
1 GGTTACAAGGTGTAAGACCATAGCTCGACTATGGCAACCAATAGAGTTCACCAGGACATTAAACA
44690596 TGG
66 TGG
*
44690599 GGTTATATA--TGTAAGACCATAGCTCGACTATGGCAAC
1 GGTTACA-AGGTGTAAGACCATAGCTCGACTATGGCAAC
44690636 ATGTTGATTT
Statistics
Matches: 141, Mismatches: 28, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
67 79 0.56
68 61 0.43
69 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (68 bp):
GGTTACAAGGTGTAAGACCATAGCTCGACTATGGCAACCAATAGAGTTCACCAGGACATTAAACA
TGG
Found at i:44694430 original size:67 final size:64
Alignment explanation
Indices: 44694306--44694478 Score: 179
Period size: 64 Copynumber: 2.7 Consensus size: 64
44694296 TCTCTTGTAC
* * * * * * *
44694306 ACATGGTGAACAC-TCAGTACCACCCATGTGACCTAACCA-ATTTATCTCGTAGCTCTCTTATCT
1 ACATGGTGTACACAT-AGAACCACCCATGCGACCTAGCTACATATATCCCGTAGCTCTCTTATCT
* * * *
44694369 ACATGGTGTCCTTCACCTAGAACCACGCATGCGACCTAGCTACATATATCCCGTAGCTCTCTTGT
1 ACATGGTG---TACACATAGAACCACCCATGCGACCTAGCTACATATATCCCGTAGCTCTCTTAT
44694434 CT
63 CT
* *
44694436 ACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACATA
1 ACATGGTGTACACATAGAACCACCCATGCGACCTAGCTACATA
44694479 ATAATGTCTT
Statistics
Matches: 90, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
63 8 0.09
64 30 0.33
66 22 0.24
67 30 0.33
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.28
Consensus pattern (64 bp):
ACATGGTGTACACATAGAACCACCCATGCGACCTAGCTACATATATCCCGTAGCTCTCTTATCT
Found at i:44694727 original size:29 final size:29
Alignment explanation
Indices: 44694694--44694755 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
44694684 GTATTACTTA
*
44694694 CATATAAGCTTACAATATCCCATAATATC
1 CATATAAACTTACAATATCCCATAATATC
44694723 CATATAAACTTACAATATCCCATAATATC
1 CATATAAACTTACAATATCCCATAATATC
44694752 CATA
1 CATA
44694756 ATCATAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.44, C:0.24, G:0.02, T:0.31
Consensus pattern (29 bp):
CATATAAACTTACAATATCCCATAATATC
Found at i:44698860 original size:23 final size:22
Alignment explanation
Indices: 44698815--44698858 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
44698805 AATGAGAAAG
* *
44698815 ATGATAATTTTTTTTCATCTTT
1 ATGACAATTTTTTTTAATCTTT
44698837 ATGACAATTTTTTTTAATCTTT
1 ATGACAATTTTTTTTAATCTTT
44698859 TAATTAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.09, G:0.05, T:0.61
Consensus pattern (22 bp):
ATGACAATTTTTTTTAATCTTT
Found at i:44700582 original size:57 final size:58
Alignment explanation
Indices: 44700487--44700627 Score: 142
Period size: 57 Copynumber: 2.4 Consensus size: 58
44700477 ATCATATAAC
** * * * **
44700487 AGGATTACTTGTCCAAGCTAAATCCTATGTCCAACATATGCTTATA-AGAGCTTA-ATT
1 AGGATTACCAGTCCAGGCTAAATCCTATCTACAACATATGCCCA-AGAGAGCTTATATT
* ** * *
44700544 AGGATTACCCGTCTGGGCTAAATCCTATCTATATCATATGCCCAAGAGAGCTTATATT
1 AGGATTACCAGTCCAGGCTAAATCCTATCTACAACATATGCCCAAGAGAGCTTATATT
*
44700602 AGGATTACTAGTCCAGGCTAAATCCT
1 AGGATTACCAGTCCAGGCTAAATCCT
44700628 TACTGTAATG
Statistics
Matches: 67, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
56 1 0.01
57 41 0.61
58 25 0.37
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (58 bp):
AGGATTACCAGTCCAGGCTAAATCCTATCTACAACATATGCCCAAGAGAGCTTATATT
Found at i:44705001 original size:22 final size:22
Alignment explanation
Indices: 44704983--44705031 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
44704973 TTGGGCCATG
44704983 TGGGTCCACACGGCAGGCCACA
1 TGGGTCCACACGGCAGGCCACA
44705005 TGGGTCCACACGGCAGGCCACA
1 TGGGTCCACACGGCAGGCCACA
44705027 TGGGT
1 TGGGT
44705032 GTGTGAGCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.33, G:0.35, T:0.12
Consensus pattern (22 bp):
TGGGTCCACACGGCAGGCCACA
Found at i:44711696 original size:57 final size:58
Alignment explanation
Indices: 44711616--44711724 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 58
44711606 TACTTGTCCA
* * * *
44711616 AGCTAAATCCTATGTCCAACATATGCTCATAAGAGCTTA-ATCAGGATTACCCATCTG
1 AGCTAAATCCTATCTACAACATATGCTCAAAAGAGCTTATATCAAGATTACCCATCTG
* *
44711673 AGCTAAATCCTATCTATATCATATGCTCAAAAGAGCTTATATCAAGATTACC
1 AGCTAAATCCTATCTACAACATATGCTCAAAAGAGCTTATATCAAGATTACC
44711725 AGTCCAGACT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
57 34 0.76
58 11 0.24
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (58 bp):
AGCTAAATCCTATCTACAACATATGCTCAAAAGAGCTTATATCAAGATTACCCATCTG
Found at i:44715186 original size:12 final size:12
Alignment explanation
Indices: 44715171--44715200 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
44715161 GGCTATGTAA
44715171 CAGGCCATGTCC
1 CAGGCCATGTCC
44715183 CAGGCCATGTCC
1 CAGGCCATGTCC
44715195 CAGGCC
1 CAGGCC
44715201 GTGTGCTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.17, C:0.43, G:0.27, T:0.13
Consensus pattern (12 bp):
CAGGCCATGTCC
Found at i:44721237 original size:23 final size:22
Alignment explanation
Indices: 44721206--44721257 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
44721196 TATCTAATCT
* *
44721206 TTCTTTTTTTATATCTTTTCTC
1 TTCTTTTTTCATATCATTTCTC
*
44721228 TTCTTCTTTTCATTTCATTTCTC
1 TTCTT-TTTTCATATCATTTCTC
44721251 TTCTTTT
1 TTCTTTT
44721258 GATCTAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (22 bp):
TTCTTTTTTCATATCATTTCTC
Found at i:44723648 original size:26 final size:27
Alignment explanation
Indices: 44723591--44723655 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 27
44723581 ACCATCATTG
* *
44723591 ATTAATATTATTATCACTATTATAGATGT
1 ATTATTATTATGATCACTATTAT--ATGT
*
44723620 ATTATTATTATGATCACTATTAT-TTT
1 ATTATTATTATGATCACTATTATATGT
*
44723646 ATTCTTATTA
1 ATTATTATTA
44723656 ATTTTTGCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 11 0.34
29 21 0.66
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.54
Consensus pattern (27 bp):
ATTATTATTATGATCACTATTATATGT
Found at i:44726701 original size:22 final size:23
Alignment explanation
Indices: 44726657--44726704 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
44726647 TTTAATGAAA
44726657 TTTTTTGCTTTCCAAGATAATTT
1 TTTTTTGCTTTCCAAGATAATTT
*
44726680 TTTTTTGCTTTCCAAGA-CATTT
1 TTTTTTGCTTTCCAAGATAATTT
44726702 TTT
1 TTT
44726705 GAAATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.19, C:0.15, G:0.08, T:0.58
Consensus pattern (23 bp):
TTTTTTGCTTTCCAAGATAATTT
Found at i:44729787 original size:17 final size:18
Alignment explanation
Indices: 44729755--44729789 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
44729745 AGAATAAGAC
44729755 AATTTTATTATCTTTTTA
1 AATTTTATTATCTTTTTA
*
44729773 AATTTT-TTTTCTTTTTA
1 AATTTTATTATCTTTTTA
44729790 TTTCACTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (18 bp):
AATTTTATTATCTTTTTA
Found at i:44731697 original size:92 final size:92
Alignment explanation
Indices: 44731439--44731716 Score: 246
Period size: 92 Copynumber: 3.0 Consensus size: 92
44731429 ACTAATCCAC
* * * * * *
44731439 TCAGATAATAATATGCAG--TAGGGCTAGCGTATGTGTTGTACGGTGCAATGCGGTAGAT-TGCT
1 TCAGATAATGATACGCAGCATA-GGCTAACGTATGTGCTGTACAGTGCAATGCAGTA-ATCTGCT
* * *
44731501 ATATAGAAAAGTTGCAGTTAAACTGCCAGA
64 ATACAGAAAA-TTGCAGTTTAACTACCAGA
* * * * * * * *
44731531 TCAGATAATGGTACGTAGCATA-GCTAACGTACGTACGGTACAGTGCGATGCATTAAACTGCTAT
1 TCAGATAATGATACGCAGCATAGGCTAACGTATGTGCTGTACAGTGCAATGCAGTAATCTGCTAT
* *
44731595 ACTAGTAAATTGCAGTTTAACTATCAGA
66 AC-AGAAAATTGCAGTTTAACTACCAGA
44731623 TCAGATAAAT-ATACGCAGCA-AGGCTAACGTATGTGCTGTACAGTGCAATGCAGTAATCTGC-A
1 TCAGAT-AATGATACGCAGCATAGGCTAACGTATGTGCTGTACAGTGCAATGCAGTAATCTGCTA
* *
44731685 GTACAGACAAATTGTAGTTTGAACTGCCAGA
65 -TACAGA-AAATTGCAGTTT-AACTACCAGA
44731716 T
1 T
44731717 TAGACCAGAA
Statistics
Matches: 146, Mismatches: 31, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
91 5 0.03
92 122 0.84
93 17 0.12
94 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.27
Consensus pattern (92 bp):
TCAGATAATGATACGCAGCATAGGCTAACGTATGTGCTGTACAGTGCAATGCAGTAATCTGCTAT
ACAGAAAATTGCAGTTTAACTACCAGA
Found at i:44736176 original size:27 final size:26
Alignment explanation
Indices: 44736146--44736208 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
44736136 AGATAATTAA
44736146 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
44736173 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
44736200 AATATAAAT
1 AATA-AAAT
44736209 AAAATGGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Found at i:44736195 original size:15 final size:15
Alignment explanation
Indices: 44736175--44736204 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44736165 ATAATCCTAA
*
44736175 TAATTATCTTAATAT
1 TAATTATCCTAATAT
44736190 TAATTATCCTAATAT
1 TAATTATCCTAATAT
44736205 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:44737659 original size:34 final size:34
Alignment explanation
Indices: 44737581--44737661 Score: 83
Period size: 34 Copynumber: 2.4 Consensus size: 34
44737571 TGGATACTGT
* **
44737581 ACTGAGATGGGCTAAGACCCACACTAATACTATT
1 ACTGATATGGGCTAAGACCCACACTAATACTACC
* * * *
44737615 ACTG-TCATGGGCTAAGGCCCACACTGATATTGCC
1 ACTGAT-ATGGGCTAAGACCCACACTAATACTACC
44737649 ACTGATATGGGCT
1 ACTGATATGGGCT
44737662 CGGGCCCAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
34 37 0.97
35 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (34 bp):
ACTGATATGGGCTAAGACCCACACTAATACTACC
Found at i:44746085 original size:15 final size:14
Alignment explanation
Indices: 44746063--44746094 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
44746053 CGGATAAAAT
44746063 TTTAATTTTTATAA
1 TTTAATTTTTATAA
44746077 TTTATATTTTTATAA
1 TTTA-ATTTTTATAA
44746092 TTT
1 TTT
44746095 GTAAAAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTAATTTTTATAA
Found at i:44746873 original size:20 final size:20
Alignment explanation
Indices: 44746848--44746899 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
44746838 TTAGTTTCTA
*
44746848 CTCTGTTTCGTTCTGCTTTG
1 CTCTGTTTCGTTCTGCTCTG
*
44746868 CTCTGTTTAGTTCTGCTCTG
1 CTCTGTTTCGTTCTGCTCTG
*
44746888 CTCTGTTCCGTT
1 CTCTGTTTCGTT
44746900 ATGTTCTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.02, C:0.27, G:0.19, T:0.52
Consensus pattern (20 bp):
CTCTGTTTCGTTCTGCTCTG
Found at i:44746886 original size:15 final size:15
Alignment explanation
Indices: 44746801--44746887 Score: 50
Period size: 15 Copynumber: 5.4 Consensus size: 15
44746791 CCTTTGCGTA
*
44746801 GCTCTGTTCAGTTCT
1 GCTCTGTTTAGTTCT
* *
44746816 GCTCTGCTCTA-TTTT
1 GCTCTG-TTTAGTTCT
*
44746831 GTTCTGTTTAGTTTCT
1 GCTCTGTTTAG-TTCT
* *
44746847 ACTCTGTTTCGTTCTGCTTT
1 GCTCTGTTTAG-T-T-C--T
44746867 GCTCTGTTTAGTTCT
1 GCTCTGTTTAGTTCT
44746882 GCTCTG
1 GCTCTG
44746888 CTCTGTTCCG
Statistics
Matches: 54, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
14 3 0.06
15 21 0.39
16 15 0.28
17 2 0.04
18 2 0.04
19 1 0.02
20 10 0.19
ACGTcount: A:0.06, C:0.23, G:0.18, T:0.53
Consensus pattern (15 bp):
GCTCTGTTTAGTTCT
Found at i:44748492 original size:26 final size:26
Alignment explanation
Indices: 44748463--44748727 Score: 216
Period size: 26 Copynumber: 10.2 Consensus size: 26
44748453 CGGCACAGAT
** *
44748463 CCTGACAACAAATCACCTACACGAAG
1 CCTGACAGTAAATCACCGACACGAAG
44748489 CCTGACAGTAAATCACCGACAC-AGAG
1 CCTGACAGTAAATCACCGACACGA-AG
* *
44748515 -CTAGACAGTAAATCATCAACACGAAG
1 CCT-GACAGTAAATCACCGACACGAAG
* *
44748541 CCTGACAATAAATCACCGATACGAAG
1 CCTGACAGTAAATCACCGACACGAAG
* *
44748567 CCTGATAGTAAATCATC-AGCACGAAG
1 CCTGACAGTAAATCACCGA-CACGAAG
* ** *
44748593 CCTGACAGTAAATAATTGGCAC-AGAG
1 CCTGACAGTAAATCACCGACACGA-AG
* * * * *
44748619 CCTGATAGTAAATCATCGGCACAAAT
1 CCTGACAGTAAATCACCGACACGAAG
*
44748645 CCTGACAGTAAATCACC-AGCACAAAG
1 CCTGACAGTAAATCACCGA-CACGAAG
* * *
44748671 CCTGACAATAAATCATCGACACAAAG
1 CCTGACAGTAAATCACCGACACGAAG
* * * *
44748697 CCTAACAGTAAATCACTGGCACAAAG
1 CCTGACAGTAAATCACCGACACGAAG
44748723 CCTGA
1 CCTGA
44748728 TAGAATATTT
Statistics
Matches: 196, Mismatches: 33, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
25 5 0.03
26 186 0.95
27 5 0.03
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (26 bp):
CCTGACAGTAAATCACCGACACGAAG
Found at i:44748528 original size:52 final size:52
Alignment explanation
Indices: 44748448--44748727 Score: 271
Period size: 52 Copynumber: 5.4 Consensus size: 52
44748438 TGCGGTCCAT
* * ** * *
44748448 ATCACCGGCACAGATCCTGACAACAAATCACCTACACGAAGCCTGACAGTAA
1 ATCACCGACACAGAGCCTGACAGTAAATCATCGACACGAAGCCTGACAGTAA
* *
44748500 ATCACCGACACAGAG-CTAGACAGTAAATCATCAACACGAAGCCTGACAATAA
1 ATCACCGACACAGAGCCT-GACAGTAAATCATCGACACGAAGCCTGACAGTAA
* *
44748552 ATCACCGATAC-GAAGCCTGATAGTAAATCATC-AGCACGAAGCCTGACAGTAA
1 ATCACCGACACAG-AGCCTGACAGTAAATCATCGA-CACGAAGCCTGACAGTAA
* ** * * * * *
44748604 ATAATTGGCACAGAGCCTGATAGTAAATCATCGGCACAAATCCTGACAGTAA
1 ATCACCGACACAGAGCCTGACAGTAAATCATCGACACGAAGCCTGACAGTAA
* * * *
44748656 ATCACC-AGCACAAAGCCTGACAATAAATCATCGACACAAAGCCTAACAGTAA
1 ATCACCGA-CACAGAGCCTGACAGTAAATCATCGACACGAAGCCTGACAGTAA
* * *
44748708 ATCACTGGCACAAAGCCTGA
1 ATCACCGACACAGAGCCTGA
44748728 TAGAATATTT
Statistics
Matches: 190, Mismatches: 30, Indels: 16
0.81 0.13 0.07
Matches are distributed among these distances:
51 4 0.02
52 183 0.96
53 3 0.02
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (52 bp):
ATCACCGACACAGAGCCTGACAGTAAATCATCGACACGAAGCCTGACAGTAA
Found at i:44748600 original size:78 final size:75
Alignment explanation
Indices: 44748463--44748727 Score: 244
Period size: 78 Copynumber: 3.4 Consensus size: 75
44748453 CGGCACAGAT
* * * *
44748463 CCTGACAACAAATCACCTACACGAAGCCTGACAGTAAATCACCGACACAGAG-CTAGACAGTAAA
1 CCTGACAATAAATCACCGACACAAAGCCTGACAGTAAATCACAG-CACA-AGCCT-GACAGTAAA
*
44748527 TCATCAACACGAAG
63 TCATCGACAC-AAG
* * *
44748541 CCTGACAATAAATCACCGATACGAAGCCTGATAGTAAATCATCAGCACGAAGCCTGACAGTAAAT
1 CCTGACAATAAATCACCGACACAAAGCCTGACAGTAAATCA-CAGCAC-AAGCCTGACAGTAAAT
* * *
44748606 AATTGGCACAGAG
64 CATCGACACA-AG
* * * * * *
44748619 CCTGATAGTAAATCATCGGCACAAATCCTGACAGTAAATCACCAGCACAAAGCCTGACAATAAAT
1 CCTGACAATAAATCACCGACACAAAGCCTGACAGTAAATCA-CAGCAC-AAGCCTGACAGTAAAT
44748684 CATCGACACAAAG
64 CATCGACAC-AAG
* * * *
44748697 CCTAACAGTAAATCACTGGCACAAAGCCTGA
1 CCTGACAATAAATCACCGACACAAAGCCTGA
44748728 TAGAATATTT
Statistics
Matches: 154, Mismatches: 28, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
77 1 0.01
78 147 0.95
79 6 0.04
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (75 bp):
CCTGACAATAAATCACCGACACAAAGCCTGACAGTAAATCACAGCACAAGCCTGACAGTAAATCA
TCGACACAAG
Found at i:44749355 original size:17 final size:17
Alignment explanation
Indices: 44749333--44749370 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
44749323 ACAAGTCCTT
44749333 ACATTTTTA-TCACTTTA
1 ACATTTTTAGTCA-TTTA
44749350 ACA-TTTTAGTCATTTA
1 ACATTTTTAGTCATTTA
44749366 ACATT
1 ACATT
44749371 AAAATTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.50
Consensus pattern (17 bp):
ACATTTTTAGTCATTTA
Found at i:44751210 original size:19 final size:18
Alignment explanation
Indices: 44751186--44751231 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
44751176 ATTATTTTTT
* *
44751186 AAATTAATTTTTTTAAAAA
1 AAATTAAATTATTT-AAAA
44751205 AAATTATAATTATTTAAAA
1 AAATTA-AATTATTTAAAA
44751224 AAATTAAA
1 AAATTAAA
44751232 AAATTGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 16 0.67
20 6 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTAAATTATTTAAAA
Found at i:44753595 original size:36 final size:36
Alignment explanation
Indices: 44753548--44753619 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
44753538 GAGACACTTT
44753548 GGTGTTCGAACATCAAGGTGAAATGTGAAATAGGTC
1 GGTGTTCGAACATCAAGGTGAAATGTGAAATAGGTC
44753584 GGTGTTCGAACATCAAGGTGAAATGTGAAATAGGTC
1 GGTGTTCGAACATCAAGGTGAAATGTGAAATAGGTC
44753620 CTTTGGGATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.11, G:0.31, T:0.25
Consensus pattern (36 bp):
GGTGTTCGAACATCAAGGTGAAATGTGAAATAGGTC
Found at i:44755602 original size:21 final size:20
Alignment explanation
Indices: 44755578--44755626 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
44755568 ATTCTATTTG
44755578 GCCTTTGTGGAC-TTCTGATTA
1 GCCTTTGTGG-CTTTCTG-TTA
*
44755599 GCCTTGGTGGCTTTCTGTTA
1 GCCTTTGTGGCTTTCTGTTA
*
44755619 TCCTTTGT
1 GCCTTTGT
44755627 AGTGTACTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.08, C:0.20, G:0.24, T:0.47
Consensus pattern (20 bp):
GCCTTTGTGGCTTTCTGTTA
Found at i:44759359 original size:67 final size:67
Alignment explanation
Indices: 44759251--44759383 Score: 239
Period size: 67 Copynumber: 2.0 Consensus size: 67
44759241 TGAGCATATG
*
44759251 TTACAGGGGATTTAACCTAGACTGGTAATCCTGCTATAAGAAATGAGGTTTGCGGGAGTGTGCTC
1 TTACAGGGGATTTAACCTAGACTGGTAATCCTGCTATAAGAAATGAGGTTCGCGGGAGTGTGCTC
44759316 TC
66 TC
* *
44759318 TTACAGGGGATTTAGCCTAGACTGGTAATCCTGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTC
1 TTACAGGGGATTTAACCTAGACTGGTAATCCTGCTATAAGAAATGAGGTTCGCGGGAGTGTGCTC
44759383 T
66 T
44759384 TTGAAAAGGA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (67 bp):
TTACAGGGGATTTAACCTAGACTGGTAATCCTGCTATAAGAAATGAGGTTCGCGGGAGTGTGCTC
TC
Found at i:44760233 original size:32 final size:32
Alignment explanation
Indices: 44760195--44760257 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
44760185 CTAGCCATTG
44760195 GTATGGCTTATATTTAGTAAGTTTTGAGTTAT
1 GTATGGCTTATATTTAGTAAGTTTTGAGTTAT
44760227 GTATGGCTTATATTTAGTAAGTTTTGAGTTA
1 GTATGGCTTATATTTAGTAAGTTTTGAGTTA
44760258 CATATAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.22, T:0.49
Consensus pattern (32 bp):
GTATGGCTTATATTTAGTAAGTTTTGAGTTAT
Found at i:44763348 original size:34 final size:34
Alignment explanation
Indices: 44763310--44763380 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
44763300 AATTTTGAGA
44763310 TAGTAAATTTTTATTTAATTTAAGGTTTATGTTG
1 TAGTAAATTTTTATTTAATTTAAGGTTTATGTTG
*
44763344 TAGTAAATTTTTATTTAATTTAAGGTTTCTGTTG
1 TAGTAAATTTTTATTTAATTTAAGGTTTATGTTG
44763378 TAG
1 TAG
44763381 GAAGATTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.28, C:0.01, G:0.15, T:0.55
Consensus pattern (34 bp):
TAGTAAATTTTTATTTAATTTAAGGTTTATGTTG
Found at i:44763395 original size:34 final size:33
Alignment explanation
Indices: 44763319--44763395 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 33
44763309 ATAGTAAATT
*
44763319 TTTA-TTTAATTTAAGGTTTATGTTGTAGTAAA
1 TTTATTTTAATTTAAGGTTTATGTTGTAGGAAA
* *
44763351 TTTTTATTTAATTTAAGGTTTCTGTTGTAGGAAGA
1 TTTAT-TTTAATTTAAGGTTTATGTTGTAGGAA-A
44763386 TTTATTTTAA
1 TTTATTTTAA
44763396 GAAATAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 3 0.08
34 30 0.79
35 5 0.13
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.55
Consensus pattern (33 bp):
TTTATTTTAATTTAAGGTTTATGTTGTAGGAAA
Done.