Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 66 of 150
Found at i:19782920 original size:21 final size:20
Alignment explanation
Indices: 19782874--19782922 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
19782864 TTTTGCCAAG
* **
19782874 TATCGATAAATTTAAATGAA
1 TATCGATAAATTCAAAAAAA
19782894 TATCGATAAATTCAAAAAAA
1 TATCGATAAATTCAAAAAAA
19782914 TTATCGATA
1 -TATCGATA
19782923 CATTTTCTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (20 bp):
TATCGATAAATTCAAAAAAA
Found at i:19784754 original size:29 final size:30
Alignment explanation
Indices: 19784709--19784768 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
19784699 TCTGATCCAA
*
19784709 TGTGCAATTTGATACA-TAAACTTTAATTT
1 TGTGCAATTTGACACATTAAACTTTAATTT
*
19784738 TGTGCAATTAT-ACACATTAAATTTTAATTT
1 TGTGCAATT-TGACACATTAAACTTTAATTT
19784768 T
1 T
19784769 AATTCATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (30 bp):
TGTGCAATTTGACACATTAAACTTTAATTT
Found at i:19793101 original size:3 final size:3
Alignment explanation
Indices: 19793093--19793135 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
19793083 ATATGTAGGT
* *
19793093 ATA ATA ATA ATA ATA TATA AT- ATA ATA ATA AAA ATA AAA ATA A
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
19793136 CAAAATTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:19793613 original size:24 final size:24
Alignment explanation
Indices: 19793566--19793655 Score: 74
Period size: 21 Copynumber: 4.2 Consensus size: 24
19793556 TACAAATTAA
* *
19793566 ATCTT-TAAGATTACA-AAATCAT
1 ATCTTCTAAGATTGCATATATCAT
*
19793588 ATCTTCTAAGATTGTATATATCAT
1 ATCTTCTAAGATTGCATATATCAT
19793612 A---TCTAAGATTGCATATAT--T
1 ATCTTCTAAGATTGCATATATCAT
*
19793631 AT-ATCTAAGATTGC--ATATCAT
1 ATCTTCTAAGATTGCATATATCAT
19793652 ATCT
1 ATCT
19793656 AAGATTGTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
19 6 0.11
21 30 0.54
22 5 0.09
23 8 0.14
24 7 0.12
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (24 bp):
ATCTTCTAAGATTGCATATATCAT
Found at i:19793618 original size:21 final size:21
Alignment explanation
Indices: 19793592--19793667 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
19793582 AATCATATCT
19793592 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
* *
19793613 TCTAAGATTGCATATATTATA
1 TCTAAGATTGTATATATCATA
*
19793634 TCTAAGATTG--CATATCATA
1 TCTAAGATTGTATATATCATA
19793653 TCTAAGATTGTATAT
1 TCTAAGATTGTATAT
19793668 CCTCGAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 17 0.35
21 31 0.65
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:19793627 original size:19 final size:19
Alignment explanation
Indices: 19793605--19793668 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
19793595 AAGATTGTAT
19793605 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
*
19793624 ATATATTATATCTAAGATTGC
1 --ATATCATATCTAAGATTGC
*
19793645 ATATCATATCTAAGATTGT
1 ATATCATATCTAAGATTGC
19793664 ATATC
1 ATATC
19793669 CTCGAAAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 22 0.55
21 18 0.45
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:19796337 original size:38 final size:38
Alignment explanation
Indices: 19796230--19796346 Score: 189
Period size: 39 Copynumber: 3.0 Consensus size: 38
19796220 ATCCAACCCA
19796230 ACCCAATTACCTAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACC-AACCCAATAAAACTAAAACTAAAGTCT
19796269 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTA-CCAACCCAATAAAACTAAAACTAAAGTCT
* * *
19796308 ACCCAATTACCGACCTAATAAAAATAAAACTAAAGTCT
1 ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTCT
19796346 A
1 A
19796347 ACTCTTAAGT
Statistics
Matches: 74, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
38 27 0.36
39 45 0.61
40 2 0.03
ACGTcount: A:0.50, C:0.27, G:0.03, T:0.20
Consensus pattern (38 bp):
ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTCT
Found at i:19796390 original size:27 final size:27
Alignment explanation
Indices: 19796349--19796403 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
19796339 AAAGTCTAAC
*
19796349 TCTTAAGTATCTACCCAATTACACATT
1 TCTTAAGTATATACCCAATTACACATT
19796376 TCTTAAGTATATACCCAATTACACATT
1 TCTTAAGTATATACCCAATTACACATT
19796403 T
1 T
19796404 TTTTTTTAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.38
Consensus pattern (27 bp):
TCTTAAGTATATACCCAATTACACATT
Found at i:19796606 original size:9 final size:9
Alignment explanation
Indices: 19796568--19796625 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 9
19796558 TTAGTGATTC
*
19796568 AATTCGGGT
1 AATTCGGTT
* *
19796577 AATTTGGGT
1 AATTCGGTT
* *
19796586 AATTTGGGT
1 AATTCGGTT
*
19796595 AATCCGGTT
1 AATTCGGTT
*
19796604 AATTCGATT
1 AATTCGGTT
19796613 AATTCGGTT
1 AATTCGGTT
19796622 AATT
1 AATT
19796626 TTTAACCAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:19806633 original size:30 final size:29
Alignment explanation
Indices: 19806599--19806660 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
19806589 TAAAAGACGT
19806599 TTTTTTTAAAAATTTATCGAAATGGGCCGA
1 TTTTTTTAAAAATTTATCGAAATGGGCC-A
* ** *
19806629 -TTTTTTGATTATTTATCGGAATGGGCCA
1 TTTTTTTAAAAATTTATCGAAATGGGCCA
19806657 TTTT
1 TTTT
19806661 CCGCAAACTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.47
Consensus pattern (29 bp):
TTTTTTTAAAAATTTATCGAAATGGGCCA
Found at i:19811349 original size:15 final size:15
Alignment explanation
Indices: 19811329--19811385 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
19811319 TTCACATATT
19811329 AATATTTTAATAATA
1 AATATTTTAATAATA
*
19811344 AATATTTATTATAATTATA
1 AATA--T-TT-TAATAATA
*
19811363 AATATATTAATAATA
1 AATATTTTAATAATA
*
19811378 AATGTTTT
1 AATATTTT
19811386 GCAGCATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 1 0.03
17 2 0.06
18 2 0.06
19 11 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:19811358 original size:19 final size:19
Alignment explanation
Indices: 19811331--19811367 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19811321 CACATATTAA
*
19811331 TATTTTAATAATAAATATT
1 TATTATAATAATAAATATT
*
19811350 TATTATAATTATAAATAT
1 TATTATAATAATAAATAT
19811368 ATTAATAATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTATAATAATAAATATT
Found at i:19814484 original size:18 final size:19
Alignment explanation
Indices: 19814449--19814485 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19814439 TTCTGTAGAA
19814449 GAGAAAGTAAATAATTTAG
1 GAGAAAGTAAATAATTTAG
*
19814468 GAGAAATTAAA-AATTTAG
1 GAGAAAGTAAATAATTTAG
19814486 ACTTAAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.19, T:0.27
Consensus pattern (19 bp):
GAGAAAGTAAATAATTTAG
Found at i:19822248 original size:19 final size:19
Alignment explanation
Indices: 19822224--19822267 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
19822214 TAAAAGCAAC
*
19822224 ACAACATCAGTCTAAATAA
1 ACAACATCAGTCCAAATAA
* *
19822243 ACAACATGAGTCCAAGTAA
1 ACAACATCAGTCCAAATAA
19822262 ACAACA
1 ACAACA
19822268 ACAAAACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.52, C:0.23, G:0.09, T:0.16
Consensus pattern (19 bp):
ACAACATCAGTCCAAATAA
Found at i:19822318 original size:74 final size:72
Alignment explanation
Indices: 19822240--19822384 Score: 202
Period size: 74 Copynumber: 2.0 Consensus size: 72
19822230 TCAGTCTAAA
* * *
19822240 TAAACAACATGAGTCCAAGTAAACAACAACAAAACAACAAGATTAT-AATAAAATAACATAATCA
1 TAAACAACATGAGTCCAAGTAAACAACAAC---ACAACAAGATTATAAAAAAAAAAACATAAGCA
19822304 AAAGTCCAAG
63 AAAGTCCAAG
** *
19822314 TAAACAACATGAGTTGAAGTAAACAACAACATAACAAGATTATAAAAAAAAAAACATAAGCAAAA
1 TAAACAACATGAGTCCAAGTAAACAACAACACAACAAGATTATAAAAAAAAAAACATAAGCAAAA
19822379 GTCCAA
66 GTCCAA
19822385 AATACGACAG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
71 12 0.19
72 24 0.38
74 28 0.44
ACGTcount: A:0.59, C:0.16, G:0.09, T:0.16
Consensus pattern (72 bp):
TAAACAACATGAGTCCAAGTAAACAACAACACAACAAGATTATAAAAAAAAAAACATAAGCAAAA
GTCCAAG
Found at i:19822480 original size:22 final size:22
Alignment explanation
Indices: 19822455--19822496 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19822445 AAAATCCAAT
19822455 AAACCAACAACAATAACACAAC
1 AAACCAACAACAATAACACAAC
* *
19822477 AAACTAATAACAATAACACA
1 AAACCAACAACAATAACACA
19822497 TCAGTTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.26, G:0.00, T:0.10
Consensus pattern (22 bp):
AAACCAACAACAATAACACAAC
Found at i:19828651 original size:26 final size:26
Alignment explanation
Indices: 19828622--19828675 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
19828612 GTCTGGACAC
19828622 ATGGCCGTCTAACCTCTGTATTGAAA
1 ATGGCCGTCTAACCTCTGTATTGAAA
*
19828648 ATGGCCGTCTGACCTCTGTATTGAAA
1 ATGGCCGTCTAACCTCTGTATTGAAA
19828674 AT
1 AT
19828676 TTTTAGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (26 bp):
ATGGCCGTCTAACCTCTGTATTGAAA
Found at i:19829602 original size:21 final size:22
Alignment explanation
Indices: 19829569--19829609 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
19829559 TAGTATATTA
19829569 AAATAATTAAAGAATTTGAATG
1 AAATAATTAAAGAATTTGAATG
19829591 AAATAA-TAAAGAATTTGAA
1 AAATAATTAAAGAATTTGAA
19829610 AGTGAAGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (22 bp):
AAATAATTAAAGAATTTGAATG
Found at i:19837986 original size:19 final size:18
Alignment explanation
Indices: 19837958--19837993 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19837948 GAATTCGCAC
19837958 ATTTGATTATCTAATTTA
1 ATTTGATTATCTAATTTA
*
19837976 ATTTCGATTATTTAATTT
1 ATTT-GATTATCTAATTT
19837994 TGCATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (18 bp):
ATTTGATTATCTAATTTA
Found at i:19842662 original size:21 final size:21
Alignment explanation
Indices: 19842599--19842667 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
19842589 TAAAAAAAAT
*
19842599 AATAGTGATAACAGTATTAAA
1 AATAATGATAACAGTATTAAA
* * * *
19842620 TATAATAATAATAGTAGTAAA
1 AATAATGATAACAGTATTAAA
*
19842641 AATAATGATAACATTATTAAA
1 AATAATGATAACAGTATTAAA
*
19842662 ATTAAT
1 AATAAT
19842668 TAATAGCAAC
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (21 bp):
AATAATGATAACAGTATTAAA
Found at i:19845091 original size:18 final size:19
Alignment explanation
Indices: 19845070--19845118 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
19845060 ACACAACTAC
*
19845070 ATAATATTAA-ATTCTAAA
1 ATAATATTAATATTATAAA
19845088 ATAATATTAATTATTATAAA
1 ATAATATTAA-TATTATAAA
19845108 AT-ATATTAATA
1 ATAATATTAATA
19845119 ATACTTGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 12 0.43
19 7 0.25
20 9 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAATATTAATATTATAAA
Found at i:19846241 original size:16 final size:17
Alignment explanation
Indices: 19846220--19846252 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19846210 TTTTGTCATA
19846220 TAAAG-ATAAATATTTT
1 TAAAGAATAAATATTTT
19846236 TAAAGAATAAATATTTT
1 TAAAGAATAAATATTTT
19846253 ATATTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
TAAAGAATAAATATTTT
Found at i:19848515 original size:69 final size:69
Alignment explanation
Indices: 19848446--19848730 Score: 277
Period size: 69 Copynumber: 4.1 Consensus size: 69
19848436 CTGACCCTCC
* *
19848446 TTATCGCCTTTTCCACCATCTGCCTTTCC-CCTGGCTTCAAACTGCGAATCTTCCTTACCCTTTT
1 TTATCACCTTTTCCACCATCTGCCTTTCCTCC-GGCTTCAAACTGCGATTCTTCCTTACCCTTTT
*
19848510 GCTCC
65 GCTCA
** ** ** * * * *
19848515 TTATCACCTTTTGTACTGTCCACTTTTCCTCCGGCTTCAAACCGCGATTCGTCCTTACCCTTGTG
1 TTATCACCTTTTCCACCATCTGCCTTTCCTCCGGCTTCAAACTGCGATTCTTCCTTACCCTTTTG
19848580 CTCA
66 CTCA
* * * * * *
19848584 TTATCACCTTTTCCACCATCTGCCTTTCCTACGGCATCAAAATGTGATTCTTGCTTAGCCTTTTG
1 TTATCACCTTTTCCACCATCTGCCTTTCCTCCGGCTTCAAACTGCGATTCTTCCTTACCCTTTTG
*
19848649 CACA
66 CTCA
* * * * * ** *
19848653 TTATCACCTTCTCCACTATCGGTCTTTCCTCCGGCTTC-AACATGTGATTCTTCCCGACCCTTGT
1 TTATCACCTTTTCCACCATCTGCCTTTCCTCCGGCTTCAAAC-TGCGATTCTTCCTTACCCTTTT
19848717 GCTCA
65 GCTCA
*
19848722 ATATCACCT
1 TTATCACCT
19848731 CGTTGTTCAT
Statistics
Matches: 170, Mismatches: 44, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
68 2 0.01
69 166 0.98
70 2 0.01
ACGTcount: A:0.16, C:0.35, G:0.12, T:0.37
Consensus pattern (69 bp):
TTATCACCTTTTCCACCATCTGCCTTTCCTCCGGCTTCAAACTGCGATTCTTCCTTACCCTTTTG
CTCA
Found at i:19848702 original size:138 final size:138
Alignment explanation
Indices: 19848446--19848730 Score: 324
Period size: 138 Copynumber: 2.1 Consensus size: 138
19848436 CTGACCCTCC
* * * *
19848446 TTATCGCCTTTTCCACCATCTGCCTTTCCCCTGGCTTCAAACTGCGAATCTTCCTTACCCTTTTG
1 TTATCACCTTTTCCACCATCTGCCTTTCCACTGGCATCAAAATGCGAATCTTCCTTACCCTTTTG
* * * ** * **
19848511 CTCCTTATCACCTTTTGTACTGTCCACTTTTCCTCCGGCTTCAAACCGCGATTCGTCCTTACCCT
66 CACATTATCACCTTCTCCACTATCCACTTTTCCTCCGGCTTCAAACCGCGATTCGTCCCGACCCT
19848576 TGTGCTCA
131 TGTGCTCA
* * * *
19848584 TTATCACCTTTTCCACCATCTGCCTTTCCTAC-GGCATCAAAATGTGATTCTTGCTTAGCCTTTT
1 TTATCACCTTTTCCACCATCTGCCTTTCC-ACTGGCATCAAAATGCGAATCTTCCTTACCCTTTT
** * * *
19848648 GCACATTATCACCTTCTCCACTAT-CGGTCTTTCCTCCGGCTTC-AACATGTGATTCTTCCCGAC
65 GCACATTATCACCTTCTCCACTATCCACT-TTTCCTCCGGCTTCAAAC-CGCGATTCGTCCCGAC
19848711 CCTTGTGCTCA
128 CCTTGTGCTCA
*
19848722 ATATCACCT
1 TTATCACCT
19848731 CGTTGTTCAT
Statistics
Matches: 122, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
137 5 0.04
138 116 0.95
139 1 0.01
ACGTcount: A:0.16, C:0.35, G:0.12, T:0.37
Consensus pattern (138 bp):
TTATCACCTTTTCCACCATCTGCCTTTCCACTGGCATCAAAATGCGAATCTTCCTTACCCTTTTG
CACATTATCACCTTCTCCACTATCCACTTTTCCTCCGGCTTCAAACCGCGATTCGTCCCGACCCT
TGTGCTCA
Found at i:19850024 original size:15 final size:15
Alignment explanation
Indices: 19850001--19850030 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19849991 AATATAATAT
*
19850001 GAAATTAAAAAAAAA
1 GAAAATAAAAAAAAA
19850016 GAAAATAAAAAAAAA
1 GAAAATAAAAAAAAA
19850031 TAGGGTGAAG
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:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (15 bp):
GAAAATAAAAAAAAA
Found at i:19850708 original size:24 final size:24
Alignment explanation
Indices: 19850676--19850723 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
19850666 GATCTACAGG
19850676 AAGGAATCAAGTCGGAGGTACGTA
1 AAGGAATCAAGTCGGAGGTACGTA
19850700 AAGGAATCAAGTCGGAGGTACGTA
1 AAGGAATCAAGTCGGAGGTACGTA
19850724 CAAAACTTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.33, T:0.17
Consensus pattern (24 bp):
AAGGAATCAAGTCGGAGGTACGTA
Found at i:19854334 original size:31 final size:31
Alignment explanation
Indices: 19854298--19854357 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
19854288 AGGGTATAAA
*
19854298 AAAAGGATTAG-GGGATTTTGTTTAAGGTTGG
1 AAAAGGATTAGAGAG-TTTTGTTTAAGGTTGG
*
19854329 AAAAGGATTAGAGAGTTTTGTTTAGGGTT
1 AAAAGGATTAGAGAGTTTTGTTTAAGGTT
19854358 TAAAAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (31 bp):
AAAAGGATTAGAGAGTTTTGTTTAAGGTTGG
Found at i:19854902 original size:16 final size:17
Alignment explanation
Indices: 19854870--19854903 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
19854860 TGTAATGATA
*
19854870 TTGTTATACTATATTTG
1 TTGTAATACTATATTTG
19854887 TTGTAATACT-TATTTG
1 TTGTAATACTATATTTG
19854903 T
1 T
19854904 ATTACATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.59
Consensus pattern (17 bp):
TTGTAATACTATATTTG
Found at i:19858962 original size:24 final size:24
Alignment explanation
Indices: 19858915--19858960 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
19858905 TCGTTCTGTG
*
19858915 GCAAAGGATGAATTGACAGTAAAT
1 GCAAAGGATGAATTGACAGAAAAT
19858939 GCAAAGGATGAATTGAC-GAAAA
1 GCAAAGGATGAATTGACAGAAAA
19858961 ATTACCCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.48, C:0.09, G:0.26, T:0.17
Consensus pattern (24 bp):
GCAAAGGATGAATTGACAGAAAAT
Found at i:19864618 original size:96 final size:96
Alignment explanation
Indices: 19864470--19864678 Score: 251
Period size: 96 Copynumber: 2.2 Consensus size: 96
19864460 GTGTCCTAGG
** * * *
19864470 GTTTGGCTATGGCATTGGGCAGTCTGCCCAAGGGTGTGGTGACTTCCGGTTTGACCATGGCATTT
1 GTTTGGCTATGGCATTGAACAATCTGCCCAAGGGCGTGGAGACTTCCGGTTTGACCATGGCA-TT
* * * *
19864535 G-GCAGTCTGCCCATGAGTGTGGTGGGTTCCC
65 GAACAGTCTGCCCATGAGTGTGATGGCTTCCA
** * *
19864566 GTTTGGCTATGGCATTGAACAATCTGCCCATA-GGCGTGGAGGGTTCCTGTTTGGCCATGGCATT
1 GTTTGGCTATGGCATTGAACAATCTGCCCA-AGGGCGTGGAGACTTCCGGTTTGACCATGGCATT
*
19864630 GAACAGTCTGCCCATGGGTGTGATGGCTTCCA
65 GAACAGTCTGCCCATGAGTGTGATGGCTTCCA
*
19864662 GTTTGGCTGTGGCATTG
1 GTTTGGCTATGGCATTG
19864679 GGTAGTCTGG
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
95 3 0.03
96 92 0.96
97 1 0.01
ACGTcount: A:0.14, C:0.21, G:0.34, T:0.31
Consensus pattern (96 bp):
GTTTGGCTATGGCATTGAACAATCTGCCCAAGGGCGTGGAGACTTCCGGTTTGACCATGGCATTG
AACAGTCTGCCCATGAGTGTGATGGCTTCCA
Found at i:19864686 original size:48 final size:48
Alignment explanation
Indices: 19864470--19864693 Score: 218
Period size: 48 Copynumber: 4.7 Consensus size: 48
19864460 GTGTCCTAGG
* * * *
19864470 GTTTGGCTATGGCATTGGGCAGTCTGCCCAAGGGTGTGGTGACTTCCG
1 GTTTGGCTATGGCATTGGGCAGTCTGCCCATGGGTGTGATGGCTTCCA
* * * * * * *
19864518 GTTTGACCATGGCATTTGGCAGTCTGCCCATGAGTGTGGTGGGTTCCC
1 GTTTGGCTATGGCATTGGGCAGTCTGCCCATGGGTGTGATGGCTTCCA
** * * *
19864566 GTTTGGCTATGGCATTGAACAATCTGCCCATAGGCGTG-GA-GGGTTCCT
1 GTTTGGCTATGGCATTGGGCAGTCTGCCCAT-GG-GTGTGATGGCTTCCA
* **
19864614 GTTTGGCCATGGCATTGAACAGTCTGCCCATGGGTGTGATGGCTTCCA
1 GTTTGGCTATGGCATTGGGCAGTCTGCCCATGGGTGTGATGGCTTCCA
* * *
19864662 GTTTGGCTGTGGCATTGGGTAGTCTGGCCATG
1 GTTTGGCTATGGCATTGGGCAGTCTGCCCATG
19864694 ACCTTTAAAG
Statistics
Matches: 145, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
46 3 0.02
47 4 0.03
48 133 0.92
49 2 0.01
50 3 0.02
ACGTcount: A:0.14, C:0.21, G:0.34, T:0.30
Consensus pattern (48 bp):
GTTTGGCTATGGCATTGGGCAGTCTGCCCATGGGTGTGATGGCTTCCA
Found at i:19865557 original size:15 final size:15
Alignment explanation
Indices: 19865539--19865590 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
19865529 TACTAAAAAA
19865539 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
19865554 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
19865573 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
19865588 ATT
1 ATT
19865591 GATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:19865603 original size:28 final size:27
Alignment explanation
Indices: 19865570--19865640 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 27
19865560 AATTGTAATA
19865570 AATATTTATTATTAAAATATTGATATTG
1 AATATTTATTATTAAAATATT-ATATTG
* * *
19865598 AATATTT-TTA--AAATTATTATTTTT
1 AATATTTATTATTAAAATATTATATTG
*
19865622 AAAATTTATTATTAAAATA
1 AATATTTATTATTAAAATA
19865641 AAATTTAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
24 10 0.29
25 10 0.29
27 8 0.23
28 7 0.20
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (27 bp):
AATATTTATTATTAAAATATTATATTG
Found at i:19865620 original size:15 final size:16
Alignment explanation
Indices: 19865600--19865634 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
19865590 TGATATTGAA
19865600 TATTTTTAAAA-TTAT
1 TATTTTTAAAATTTAT
19865615 TATTTTTAAAATTTAT
1 TATTTTTAAAATTTAT
19865631 TATT
1 TATT
19865635 AAAATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTTTAAAATTTAT
Found at i:19865644 original size:18 final size:18
Alignment explanation
Indices: 19865621--19865704 Score: 59
Period size: 18 Copynumber: 4.7 Consensus size: 18
19865611 TTATTATTTT
19865621 TAAAATTTATTATTAAAA
1 TAAAATTTATTATTAAAA
*
19865639 TAAAATTTAAATATT-AAA
1 TAAAATTT-ATTATTAAAA
*
19865657 T--AATTTATTA-AAATAA
1 TAAAATTTATTATTAA-AA
* * *
19865673 TAAAATATATTTATTATAT
1 TAAAATTTA-TTATTAAAA
*
19865692 TAAATTTTATTAT
1 TAAAATTTATTAT
19865705 ATGACTAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
15 4 0.08
16 8 0.16
18 21 0.42
19 16 0.32
20 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAAATTTATTATTAAAA
Found at i:19867120 original size:21 final size:21
Alignment explanation
Indices: 19867095--19867172 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 21
19867085 ATATTCAAGG
19867095 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
19867116 ATATGCAATCTTGGATATG--
1 ATATGCAATCTTAGATATGAT
19867135 ATATGCAATCTTGGAAGATATGAT
1 ATATGCAATCTT---AGATATGAT
* *
19867159 -TTTGTAATCTTAGA
1 ATATGCAATCTTAGA
19867173 GATTTAATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
19 12 0.25
20 3 0.06
21 18 0.38
22 6 0.12
23 9 0.19
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:19867156 original size:17 final size:19
Alignment explanation
Indices: 19867094--19867149 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
19867084 AATATTCAAG
*
19867094 GATATGCAATCTTAGATAT
1 GATATGCAATCTTGGATAT
19867113 GATATATGCAATCTTGGATAT
1 G--ATATGCAATCTTGGATAT
19867134 GATATGCAATCTTGGA
1 GATATGCAATCTTGGA
19867150 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 16 0.47
21 18 0.53
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTGGATAT
Found at i:19874100 original size:44 final size:44
Alignment explanation
Indices: 19874052--19874370 Score: 200
Period size: 44 Copynumber: 7.2 Consensus size: 44
19874042 ATCACAAAGC
* *
19874052 CTTGCCTTCCTGGTTTGCAGCGGAGCAGGTTGAAAATAACAGAT
1 CTTGCCTTCCTGGTTTGCAGCGGAGCAGGTTGAAGATACCAGAT
* * * * * *
19874096 CTTGCCTTCCT-GTACTGACGGCGAAGCAGATCGAAGATACCAG-C
1 CTTGCCTTCCTGGT-TTG-CAGCGGAGCAGGTTGAAGATACCAGAT
* * * * *
19874140 CTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
1 CTTGCCTTCCTGGTTTGCAGCGGAGCAGGTTGAAGATACCAGAT
* * * * * *
19874184 CTTGCCTTTCT-GTATCGACAGCGAAGCAGATCGAAGATACCAG-C
1 CTTGCCTTCCTGGT-TTG-CAGCGGAGCAGGTTGAAGATACCAGAT
* * * * *
19874228 CTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
1 CTTGCCTTCCTGGTTTGCAGCGGAGCAGGTTGAAGATACCAGAT
** * * * * * *
19874272 CTTGCCTTCCTGCATCGACAGCGAAGTAGATCGAAGATACCAG-C
1 CTTGCCTTCCTGGTTTG-CAGCGGAGCAGGTTGAAGATACCAGAT
* * * **
19874316 CTTGCC-TCCTTGGGTTGTAGTGGAGCAGGTTGAAGATAGTAGAT
1 CTTGCCTTCC-TGGTTTGCAGCGGAGCAGGTTGAAGATACCAGAT
*
19874360 TTTGCCTTCCT
1 CTTGCCTTCCT
19874371 ATACCAACAG
Statistics
Matches: 197, Mismatches: 66, Indels: 24
0.69 0.23 0.08
Matches are distributed among these distances:
43 60 0.30
44 76 0.39
45 61 0.31
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (44 bp):
CTTGCCTTCCTGGTTTGCAGCGGAGCAGGTTGAAGATACCAGAT
Found at i:19874208 original size:88 final size:88
Alignment explanation
Indices: 19874049--19874462 Score: 578
Period size: 88 Copynumber: 4.7 Consensus size: 88
19874039 GAAATCACAA
* * * * * *
19874049 AGCCTTGCCTTCCTGGTTTGCAGCGGAGCAGGTTGAAAATAACAGATCTTGCCTTCCTGTA-CTG
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTATC-G
*
19874113 ACGGCGAAGCAGATCGAAGATACC
65 ACAGCGAAGCAGATCGAAGATACC
*
19874137 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTTCTGTATCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTATCGA
19874202 CAGCGAAGCAGATCGAAGATACC
66 CAGCGAAGCAGATCGAAGATACC
*
19874225 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTATCGA
*
19874290 CAGCGAAGTAGATCGAAGATACC
66 CAGCGAAGCAGATCGAAGATACC
* * * * * *
19874313 AGCCTTGCCTCCTTGGGTTGTAGTGGAGCAGGTTGAAGATAGTAGATTTTGCCTTCCTATACCAA
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTATCGA
* *
19874378 CAGTGAAGCAGATCAAAGATACC
66 CAGCGAAGCAGATCGAAGATACC
* * * * * * * *
19874401 AGCCTTGCCTCCCTGGGTTGTCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTAT
1 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTAT
19874463 TGGCATGAGT
Statistics
Matches: 291, Mismatches: 34, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
88 290 1.00
89 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (88 bp):
AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTATCGA
CAGCGAAGCAGATCGAAGATACC
Found at i:19874534 original size:44 final size:44
Alignment explanation
Indices: 19874422--19874875 Score: 479
Period size: 45 Copynumber: 10.3 Consensus size: 44
19874412 CCTGGGTTGT
19874422 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
1 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
* *
19874466 CATG-AGTAGATCAAAGATAA-CAGATCTTGTCTTCATGTATTGG
1 CGTGAAGTAGATCGAAGA-AAGCAGATCTTGTCTTCATGTATTGG
* * *
19874509 CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCTCATACTAGTGG
1 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTC-T-TCAT-GTATTGG
*
19874556 C--GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGA
1 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
* * *
19874598 CGTGAAGTAGATCAAAGATAGCAGATCTTATCTTCATGTATTGG
1 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
* *** *
19874642 CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACTGG
1 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
* * * *** *
19874686 TGGCGAAGTAGATCGAAGAAAGTAGATCTTGTCTTCCCATACTGG
1 -CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
* * * *** *
19874731 TGGCGAAGTAGATCGAAGAAAGTAGATCTTGTCTTCCCATACTGG
1 -CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
* * * *
19874776 TGGCGAAGTAGATCGAAAAAAGTAGATCTTGTCTTCATGTATTGG
1 -CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
* *
19874821 C--GAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATCGG
1 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
* *
19874863 CATGAAATAGATC
1 CGTGAAGTAGATC
19874876 AAAGGTAGTA
Statistics
Matches: 364, Mismatches: 35, Indels: 22
0.86 0.08 0.05
Matches are distributed among these distances:
42 43 0.12
43 43 0.12
44 114 0.31
45 154 0.42
46 4 0.01
47 6 0.02
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (44 bp):
CGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG
Found at i:19874644 original size:133 final size:133
Alignment explanation
Indices: 19874425--19874897 Score: 598
Period size: 133 Copynumber: 3.6 Consensus size: 133
19874415 GGGTTGTCGT
*
19874425 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATG-AGTAGATCAAAGATAACAG
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAG
19874489 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCTCATACTAGT
66 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCTCATACTAGT
19874554 GGC
131 GGC
* *
19874557 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCAAAGATAGCAG
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAG
* * *
19874622 ATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACTGGT
66 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCTCATACTAGT
19874687 GGC
131 GGC
* * ** * *
19874690 GAAGTAGATCGAAGAAAGTAGATCTTGTCTTCCCATACTGGTGGC--GAAGTAGATCGAAGAAAG
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTT--CAT-GTATTGGCATGAAGTAGATCAAAGATAG
* *** * * * * * * *
19874753 TAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAAAAAGTAGATCTTGTC-T-TCAT-G
63 CAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCTCATAC
*
19874815 TATTGGC
127 TAGTGGC
* * * * *
19874822 GAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATCGGCATGAAATAGATCAAAGGTAGTAG
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAG
*
19874887 ATATTGTCTTC
66 ATCTTGTCTTC
19874898 CCATATTGGT
Statistics
Matches: 295, Mismatches: 39, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
129 4 0.01
130 3 0.01
131 27 0.09
132 77 0.26
133 116 0.39
134 34 0.12
135 30 0.10
136 4 0.01
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (133 bp):
GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAG
ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCTCATACTAGT
GGC
Found at i:19874919 original size:45 final size:45
Alignment explanation
Indices: 19874516--19874923 Score: 348
Period size: 45 Copynumber: 9.2 Consensus size: 45
19874506 TGGCGTGAAG
* * * * *
19874516 TAGATCGAAGATAGCAGATCTTGTCTTCTCATACTAGTGGCGAAG
1 TAGATCGAAGAAAGTAGATCTTGTCTTCCCATACTGGTGGCGAAA
* *** * ** * *
19874561 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTA-TTGACGTGAAG
1 TAGATCGAAGAAAGTAGATCTTGTCTTCCCATACTGGTGGCGAAA
* * * * *** * * * *
19874605 TAGATCAAAGATAGCAGATCTTATCTTCATGTATTGG-CGTGAAG
1 TAGATCGAAGAAAGTAGATCTTGTCTTCCCATACTGGTGGCGAAA
* * *
19874649 TAGATCGAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAG
1 TAGATCGAAGAAAGTAGATCTTGTCTTCCCATACTGGTGGCGAAA
*
19874694 TAGATCGAAGAAAGTAGATCTTGTCTTCCCATACTGGTGGCGAAG
1 TAGATCGAAGAAAGTAGATCTTGTCTTCCCATACTGGTGGCGAAA
*
19874739 TAGATCGAAGAAAGTAGATCTTGTCTTCCCATACTGGTGGCGAAG
1 TAGATCGAAGAAAGTAGATCTTGTCTTCCCATACTGGTGGCGAAA
* * **
19874784 TAGATCGAAAAAAGTAGATCTTGTCTT--CAT-GTATTGGCGAAA
1 TAGATCGAAGAAAGTAGATCTTGTCTTCCCATACTGGTGGCGAAA
* * *
19874826 TAGATCGAAGAAAGCAGATCTTGTCTT--CAT-GT-ATCGGCATGAAA
1 TAGATCGAAGAAAGTAGATCTTGTCTTCCCATACTGGT-GGC--GAAA
* ** * *
19874870 TAGATCAAAGGTAGTAGATATTGTCTTCCCATATTGGTGGCGAAA
1 TAGATCGAAGAAAGTAGATCTTGTCTTCCCATACTGGTGGCGAAA
19874915 TAGATCGAA
1 TAGATCGAA
19874924 TATACAAGTC
Statistics
Matches: 316, Mismatches: 38, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.00
42 41 0.13
43 3 0.01
44 101 0.32
45 162 0.51
46 3 0.01
47 4 0.01
48 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (45 bp):
TAGATCGAAGAAAGTAGATCTTGTCTTCCCATACTGGTGGCGAAA
Found at i:19875316 original size:19 final size:19
Alignment explanation
Indices: 19875270--19875325 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
19875260 AATATTCAAG
*
19875270 GATATGCAATCTTAGATAT
1 GATATGCAATCTTGGATAT
19875289 GATATATGCAATCTTGGATAT
1 G--ATATGCAATCTTGGATAT
19875310 GATATGCAATCTTGGA
1 GATATGCAATCTTGGA
19875326 AGATAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 16 0.47
21 18 0.53
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTGGATAT
Found at i:19875542 original size:15 final size:15
Alignment explanation
Indices: 19875522--19875551 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19875512 CTTACTGTCT
*
19875522 TTTTTTATTTTTTTA
1 TTTTTTATTTATTTA
19875537 TTTTTTATTTATTTA
1 TTTTTTATTTATTTA
19875552 CGATTTTAAA
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:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTATTTATTTA
Found at i:19877035 original size:29 final size:29
Alignment explanation
Indices: 19876979--19877036 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
19876969 GGCGACTCCC
* *
19876979 AATTTTTGTTTTTTTTTAAAGTCGAAAACT
1 AATTTTTGTTTTTTTTCAAAATC-AAAACT
*
19877009 AATTTTTGTTTTTTTTCCAAAATAAAAA
1 AATTTTTGTTTTTTTT-CAAAATCAAAA
19877037 ATGGTTTCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (29 bp):
AATTTTTGTTTTTTTTCAAAATCAAAACT
Found at i:19885478 original size:50 final size:50
Alignment explanation
Indices: 19885383--19885976 Score: 338
Period size: 50 Copynumber: 11.9 Consensus size: 50
19885373 GTGATGTATA
* * * * * *
19885383 GCTTCAATATTTTTAAACTCCAATGT-TGGGAAAGTAAGATTCGCCGTTGCG
1 GCTTCAAT-CTTTTCAACTGCAATGTCAGGG-AAGCAAGATTCGCCGTTGTG
* * * *
19885434 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTA
1 GCTTCAATCTTTTCAACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTG
* ** * ** * * * ** *
19885484 GCTTTAATCTGCTCCACTGCACCGCCAGGAAAGTAAGATTCATCGTTGCG
1 GCTTCAATCTTTTCAACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTG
* * * * *
19885534 GCTTCAATCTTTTTAATTACAATGTCAGGGAA-CAAGATTCTCCGTTGTA
1 GCTTCAATCTTTTCAACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTG
** * * * * * **
19885583 GCTTCAATCTAATCCACTGCATTGCCAGGAAAGTAAGATTCGCCGTTACG
1 GCTTCAATCTTTTCAACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTG
* * * * * * * *
19885633 ACTTCAATATTTTAAATTGCAATATCAGGGAAGCAAGATTTGCCGTCGTA
1 GCTTCAATCTTTTCAACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTG
* ** * * * * ** *
19885683 GCTTTAATCTGCTCCACTGTACTGCCAGGGAAGTGAGATTCGCCATTGTG
1 GCTTCAATCTTTTCAACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTG
* * * *
19885733 GCTTCAATCATTTT-AATTGCAATGTCGGGGAA-CAAGATTCGCTGTTGTA
1 GCTTCAATC-TTTTCAACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTG
** * ** * * *
19885782 GCTTCAATCTGATCCACTGCACCG-CTAGGAAAGTAAGATTCGCCGTTGCG
1 GCTTCAATCTTTTCAACTGCAATGTC-AGGGAAGCAAGATTCGCCGTTGTG
* * * * *
19885832 GCTTCAATCTTTTAAATTGCAATGCCAGGGAAGCAAGATT-GACCGTCGTA
1 GCTTCAATCTTTTCAACTGCAATGTCAGGGAAGCAAGATTCG-CCGTTGTG
* ** * * * * *
19885882 GCTTTAATCTGCTCCACTGCACTGCCAGGGAAGTAAGATTCGCCGTTGCG
1 GCTTCAATCTTTTCAACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTG
* * * * *
19885932 GCTTTAATCTTTTAAATTGCAATGTCGGGGAA-CAAGATTCCCCGT
1 GCTTCAATCTTTTCAACTGCAATGTCAGGGAAGCAAGATTCGCCGT
19885977 CTTCGATCTG
Statistics
Matches: 386, Mismatches: 148, Indels: 20
0.70 0.27 0.04
Matches are distributed among these distances:
48 3 0.01
49 78 0.20
50 290 0.75
51 15 0.04
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (50 bp):
GCTTCAATCTTTTCAACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTG
Found at i:19885531 original size:100 final size:99
Alignment explanation
Indices: 19885411--19885976 Score: 758
Period size: 100 Copynumber: 5.7 Consensus size: 99
19885401 TCCAATGTTG
* *
19885411 GGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCG
1 GGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCAGGGAA-CAAGATTCG
*
19885476 CCGTTGTAGCTTTAATCTGCTCCACTGCACCGCCA
65 CCGTTGTAGCTTTAATCTGCTCCACTGCACTGCCA
** * * *
19885511 GGAAAGTAAGATTCATCGTTGCGGCTTCAATCTTTTTAATTACAATGTCAGGGAACAAGATTCTC
1 GGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCAGGGAACAAGATTCGC
* ** *
19885576 CGTTGTAGCTTCAATCTAATCCACTGCATTGCCA
66 CGTTGTAGCTTTAATCTGCTCCACTGCACTGCCA
* * * * *
19885610 GGAAAGTAAGATTCGCCGTTACGACTTCAATATTTTAAATTGCAATATCAGGGAAGCAAGATTTG
1 GGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCAGGGAA-CAAGATTCG
* *
19885675 CCGTCGTAGCTTTAATCTGCTCCACTGTACTGCCA
65 CCGTTGTAGCTTTAATCTGCTCCACTGCACTGCCA
* * * * *
19885710 GGGAAGTGAGATTCGCCATTGTGGCTTCAATCATTTT-AATTGCAATGTCGGGGAACAAGATTCG
1 GGAAAGTAAGATTCGCCGTTGCGGCTTCAATC-TTTTAAATTGCAATGTCAGGGAACAAGATTCG
* * * * *
19885774 CTGTTGTAGCTTCAATCTGATCCACTGCACCGCTA
65 CCGTTGTAGCTTTAATCTGCTCCACTGCACTGCCA
*
19885809 GGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGCCAGGGAAGCAAGATT-G
1 GGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCAGGGAA-CAAGATTCG
*
19885873 ACCGTCGTAGCTTTAATCTGCTCCACTGCACTGCCA
65 -CCGTTGTAGCTTTAATCTGCTCCACTGCACTGCCA
* * * *
19885909 GGGAAGTAAGATTCGCCGTTGCGGCTTTAATCTTTTAAATTGCAATGTCGGGGAACAAGATTCCC
1 GGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCAGGGAACAAGATTCGC
19885974 CGT
66 CGT
19885977 CTTCGATCTG
Statistics
Matches: 400, Mismatches: 60, Indels: 13
0.85 0.13 0.03
Matches are distributed among these distances:
98 4 0.01
99 177 0.44
100 215 0.54
101 4 0.01
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (99 bp):
GGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCAGGGAACAAGATTCGC
CGTTGTAGCTTTAATCTGCTCCACTGCACTGCCA
Found at i:19885758 original size:199 final size:198
Alignment explanation
Indices: 19885411--19885976 Score: 846
Period size: 199 Copynumber: 2.8 Consensus size: 198
19885401 TCCAATGTTG
* * *
19885411 GGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCG
1 GGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGCAAGATTTG
* * * **
19885476 CCGTTGTAGCTTTAATCTGCTCCACTGCACCGCCAGGAAAGTAAGATTCATCGTTGCGGCTTCAA
66 CCGTCGTAGCTTTAATCTGCTCCACTGCACTGCCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAA
* * * **
19885541 TCTTTTTAATTACAATGTCAGGGAACAAGATTCTCCGTTGTAGCTTCAATCTAATCCACTGCATT
131 TC-TTTTAATTGCAATGTCGGGGAACAAGATTCCCCGTTGTAGCTTCAATCTAATCCACTGCACC
19885606 GCCA
195 GCCA
* * * *
19885610 GGAAAGTAAGATTCGCCGTTACGACTTCAATATTTTAAATTGCAATATCAGGGAAGCAAGATTTG
1 GGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGCAAGATTTG
* * * *
19885675 CCGTCGTAGCTTTAATCTGCTCCACTGTACTGCCAGGGAAGTGAGATTCGCCATTGTGGCTTCAA
66 CCGTCGTAGCTTTAATCTGCTCCACTGCACTGCCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAA
* * *
19885740 TCATTTTAATTGCAATGTCGGGGAACAAGATTCGCTGTTGTAGCTTCAATCTGATCCACTGCACC
131 TC-TTTTAATTGCAATGTCGGGGAACAAGATTCCCCGTTGTAGCTTCAATCTAATCCACTGCACC
*
19885805 GCTA
195 GCCA
*
19885809 GGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGCCAGGGAAGCAAGA-TTG
1 GGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGCAAGATTTG
*
19885873 ACCGTCGTAGCTTTAATCTGCTCCACTGCACTGCCAGGGAAGTAAGATTCGCCGTTGCGGCTTTA
66 -CCGTCGTAGCTTTAATCTGCTCCACTGCACTGCCAGGGAAGTAAGATTCGCCGTTGCGGCTTCA
19885938 ATCTTTTAAATTGCAATGTCGGGGAACAAGATTCCCCGT
130 ATCTTTT-AATTGCAATGTCGGGGAACAAGATTCCCCGT
19885977 CTTCGATCTG
Statistics
Matches: 328, Mismatches: 37, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
198 7 0.02
199 321 0.98
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (198 bp):
GGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGCAAGATTTG
CCGTCGTAGCTTTAATCTGCTCCACTGCACTGCCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAA
TCTTTTAATTGCAATGTCGGGGAACAAGATTCCCCGTTGTAGCTTCAATCTAATCCACTGCACCG
CCA
Found at i:19887443 original size:21 final size:21
Alignment explanation
Indices: 19887417--19887459 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
19887407 CTTTACTTTT
19887417 ATTTTTCGTTTGTTTTTTTCA
1 ATTTTTCGTTTGTTTTTTTCA
19887438 ATTTTTCGTTTGTTTTTTTCA
1 ATTTTTCGTTTGTTTTTTTCA
19887459 A
1 A
19887460 GTGAAGTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.70
Consensus pattern (21 bp):
ATTTTTCGTTTGTTTTTTTCA
Found at i:19887924 original size:8 final size:8
Alignment explanation
Indices: 19887889--19887938 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
19887879 CCCGGTAGAG
19887889 GTTTTTTT
1 GTTTTTTT
19887897 GTTTCTTTT
1 GTTT-TTTT
*
19887906 GTCTCTTTT
1 GT-TTTTTT
19887915 GTTTTTTT
1 GTTTTTTT
**
19887923 GTTTTTGG
1 GTTTTTTT
19887931 GTTTTTTT
1 GTTTTTTT
19887939 TGCCTACGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
8 21 0.62
9 12 0.35
10 1 0.03
ACGTcount: A:0.00, C:0.06, G:0.16, T:0.78
Consensus pattern (8 bp):
GTTTTTTT
Found at i:19888519 original size:17 final size:16
Alignment explanation
Indices: 19888497--19888532 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
19888487 TTCAGAAAAG
19888497 AAATATATATATTTTAA
1 AAATAT-TATATTTTAA
*
19888514 AAATATTGTATTTTAA
1 AAATATTATATTTTAA
19888530 AAA
1 AAA
19888533 ATTTTCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AAATATTATATTTTAA
Found at i:19888915 original size:14 final size:15
Alignment explanation
Indices: 19888898--19888927 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
19888888 AACATGGAAT
19888898 TTATTTTT-AAATTA
1 TTATTTTTGAAATTA
19888912 TTATTTTTGAAATTA
1 TTATTTTTGAAATTA
19888927 T
1 T
19888928 ACAAAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
TTATTTTTGAAATTA
Found at i:19889083 original size:15 final size:15
Alignment explanation
Indices: 19889063--19889097 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
19889053 AATTCAAGAA
* *
19889063 AAAATATAAAAATAT
1 AAAATAGAAAAATAG
19889078 AAAATAGAAAAATAG
1 AAAATAGAAAAATAG
19889093 AAAAT
1 AAAAT
19889098 TTCATAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (15 bp):
AAAATAGAAAAATAG
Found at i:19896674 original size:16 final size:16
Alignment explanation
Indices: 19896653--19896704 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
19896643 TTTGGTTCGC
19896653 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
19896669 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
19896685 TGTATTTGATTAGAGG
1 TGTATTGGATTAGAGG
19896701 TGTA
1 TGTA
19896705 ATAGCAAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.25, C:0.00, G:0.35, T:0.40
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:19896957 original size:16 final size:16
Alignment explanation
Indices: 19896920--19896961 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
19896910 TTAATCATAT
*
19896920 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
19896936 TT-AAATATATTATAA
1 TTAAAATATATTATAA
19896951 TTAAAATATAT
1 TTAAAATATAT
19896962 AATTTAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:19897088 original size:14 final size:15
Alignment explanation
Indices: 19897039--19897090 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
19897029 ATAAAATATA
19897039 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
19897054 TATTAAATATATTAT
1 AATTAAATATATTAT
19897069 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
19897082 AATTTAATA
1 AATTAAATA
19897091 AAATTATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:19906094 original size:28 final size:28
Alignment explanation
Indices: 19906044--19906097 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
19906034 AAAATTGAAC
*
19906044 GTCAATTTCTGTTTCTCTTTTTTTTTCT
1 GTCAAATTCTGTTTCTCTTTTTTTTTCT
*
19906072 GTCAAATTCT-TTTTTCTTGTTTTTTT
1 GTCAAATTCTGTTTCTCTT-TTTTTTT
19906098 TTTATTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.09, C:0.15, G:0.07, T:0.69
Consensus pattern (28 bp):
GTCAAATTCTGTTTCTCTTTTTTTTTCT
Found at i:19911033 original size:18 final size:18
Alignment explanation
Indices: 19911010--19911066 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
19911000 TAGAAATAAG
*
19911010 TATATAAAAAATTAAAAA
1 TATATATAAAATTAAAAA
* * *
19911028 TATATATAATACTGAAAA
1 TATATATAAAATTAAAAA
*
19911046 TATATATAAATTATAAAAA
1 TATATATAAAAT-TAAAAA
19911065 TA
1 TA
19911067 AAATTTACAA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
18 23 0.77
19 7 0.23
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
TATATATAAAATTAAAAA
Found at i:19911584 original size:13 final size:13
Alignment explanation
Indices: 19911568--19911618 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
19911558 AAATATTTAA
*
19911568 TATTATAATTTTT
1 TATTTTAATTTTT
*
19911581 TATTTTAAATTTT
1 TATTTTAATTTTT
* **
19911594 AATTTTAATTTAA
1 TATTTTAATTTTT
19911607 TATTTTAATTTT
1 TATTTTAATTTT
19911619 AAATAAATTT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTTAATTTTT
Found at i:19911597 original size:6 final size:6
Alignment explanation
Indices: 19911563--19911620 Score: 53
Period size: 6 Copynumber: 8.8 Consensus size: 6
19911553 TATTTAAATA
* *
19911563 TTTAAT ATTATAATT TTTTAT TTTAAAT TTTAAT TTTAAT TTAATAT TTTAAT
1 TTTAAT -TT-TAA-T TTTAAT TTT-AAT TTTAAT TTTAAT TTTA-AT TTTAAT
19911616 TTTAA
1 TTTAA
19911621 ATAAATTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
6 23 0.53
7 14 0.33
8 5 0.12
9 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
TTTAAT
Found at i:19912058 original size:2 final size:2
Alignment explanation
Indices: 19912045--19912104 Score: 111
Period size: 2 Copynumber: 29.5 Consensus size: 2
19912035 CAAGGCCTTA
19912045 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19912088 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
19912105 ATAATAATAA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 55 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19914843 original size:18 final size:18
Alignment explanation
Indices: 19914820--19914854 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19914810 AATTACATAC
*
19914820 ATTTTTTAATTTAAAAAT
1 ATTTTTAAATTTAAAAAT
19914838 ATTTTTAAATTTAAAAA
1 ATTTTTAAATTTAAAAA
19914855 AAATTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTTAAATTTAAAAAT
Found at i:19914887 original size:36 final size:38
Alignment explanation
Indices: 19914835--19914929 Score: 101
Period size: 38 Copynumber: 2.6 Consensus size: 38
19914825 TTAATTTAAA
* *
19914835 AATA-TTTTTAAATTTAAAAAAA-ATTA-AATA-TTTTT
1 AATATTTTTTAATTTTAAAAAAATATTATAA-ACATTTT
*
19914870 AATATTTTTTAATTTTAAAATAAATTTTATAAACATTTT
1 AATATTTTTTAATTTTAAAA-AAATATTATAAACATTTT
*
19914909 GA-ATTTTTTAATTTTAAAAAA
1 AATATTTTTTAATTTTAAAAAA
19914930 TTAATTGTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
35 4 0.08
36 14 0.27
37 5 0.10
38 21 0.41
39 7 0.14
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (38 bp):
AATATTTTTTAATTTTAAAAAAATATTATAAACATTTT
Found at i:19930125 original size:22 final size:23
Alignment explanation
Indices: 19930097--19930155 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
19930087 AATTAGTTGC
**
19930097 TTTGTTGTTATTTCGT-TATTGT
1 TTTGTTGTTATTTCGTCTATTAA
*
19930119 TTTGTTGTCATTTC-TCTATTAA
1 TTTGTTGTTATTTCGTCTATTAA
*
19930141 TTTATTGTTATTTCG
1 TTTGTTGTTATTTCG
19930156 CTGTTATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.14, C:0.08, G:0.14, T:0.64
Consensus pattern (23 bp):
TTTGTTGTTATTTCGTCTATTAA
Found at i:19935908 original size:6 final size:6
Alignment explanation
Indices: 19935897--19935953 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
19935887 ATAATGTTGC
19935897 TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT
1 TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT
19935945 TCTGAT TCT
1 TCTGAT TCT
19935954 TCACCTTTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.51
Consensus pattern (6 bp):
TCTGAT
Found at i:19936839 original size:11 final size:11
Alignment explanation
Indices: 19936820--19936852 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
19936810 TTAATATAAA
19936820 TAATAAATAATT
1 TAAT-AATAATT
19936832 TAATAATAATT
1 TAATAATAATT
19936843 TAA-AATAATT
1 TAATAATAATT
19936853 ATTATTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 10 0.48
12 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAATAATAATT
Found at i:19936873 original size:24 final size:21
Alignment explanation
Indices: 19936784--19936908 Score: 80
Period size: 22 Copynumber: 5.7 Consensus size: 21
19936774 ATTTATTGTT
*
19936784 ATTATTATTA-AATTTTAATAA
1 ATTATTAATATAA-TTTAATAA
*
19936805 GATTATTAATATAA-ATAATAA
1 -ATTATTAATATAATTTAATAA
*
19936826 ATAATTTAATAATAATTTAAAATAA
1 ATTA-TTAAT-ATAATTT--AATAA
19936851 TTATTATTAAATATAATTTAATAA
1 --ATTATT-AATATAATTTAATAA
*
19936875 A--AAT-ATATAATTTAATAAA
1 ATTATTAATATAATTTAAT-AA
*
19936894 ATTCTTAATATAATT
1 ATTATTAATATAATT
19936909 ATTCTTATAT
Statistics
Matches: 82, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
18 12 0.15
19 3 0.04
20 5 0.06
21 12 0.15
22 22 0.27
23 3 0.04
24 5 0.06
25 5 0.06
26 9 0.11
27 6 0.07
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.45
Consensus pattern (21 bp):
ATTATTAATATAATTTAATAA
Found at i:19936886 original size:55 final size:55
Alignment explanation
Indices: 19936815--19936931 Score: 148
Period size: 55 Copynumber: 2.1 Consensus size: 55
19936805 GATTATTAAT
19936815 ATAAATAATAAATAATTTAATAATAA-T-TTAAAATAATTATTATTAAATATAATTTA
1 ATAAA-AATAAATAATTTAATAA-AATTCTTAAAATAATTATTATTAAAT-TAATTTA
* * * *
19936871 ATAAAAATATATAATTTAATAAAATTCTTAATATAATTATTCTTATATTAATTTA
1 ATAAAAATAAATAATTTAATAAAATTCTTAAAATAATTATTATTAAATTAATTTA
*
19936926 CTAAAA
1 ATAAAA
19936932 TCATAATATG
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 2 0.04
55 29 0.54
56 23 0.43
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (55 bp):
ATAAAAATAAATAATTTAATAAAATTCTTAAAATAATTATTATTAAATTAATTTA
Found at i:19936946 original size:55 final size:56
Alignment explanation
Indices: 19936815--19936947 Score: 132
Period size: 55 Copynumber: 2.4 Consensus size: 56
19936805 GATTATTAAT
* *
19936815 ATAAATAATAAATAATTTAATAATAA-T-TTAAAATAATTATTATTAAATATAATTTA
1 ATAAA-AATATATAATGTAATAA-AATTCTTAAAATAATTATTATTAAATATAATTTA
* * * *
19936871 ATAAAAATATATAATTTAATAAAATTCTTAATATAATTATTCTTATAT-TAATTTA
1 ATAAAAATATATAATGTAATAAAATTCTTAAAATAATTATTATTAAATATAATTTA
*
19936926 CT-AAAATCATA-ATATGTAATAA
1 ATAAAAAT-ATATA-ATGTAATAA
19936948 TGTAAAAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
54 8 0.12
55 36 0.54
56 23 0.34
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (56 bp):
ATAAAAATATATAATGTAATAAAATTCTTAAAATAATTATTATTAAATATAATTTA
Found at i:19937360 original size:77 final size:77
Alignment explanation
Indices: 19937233--19937391 Score: 309
Period size: 77 Copynumber: 2.1 Consensus size: 77
19937223 ATTTTTTGTC
19937233 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
1 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
*
19937298 TTATTGGCATAA
66 TTATTGACATAA
19937310 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
1 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
19937375 TTATTGACATAA
66 TTATTGACATAA
19937387 CACTT
1 CACTT
19937392 CAAGATTGTC
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 81 1.00
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (77 bp):
CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
TTATTGACATAA
Found at i:19943192 original size:42 final size:42
Alignment explanation
Indices: 19943147--19943301 Score: 177
Period size: 42 Copynumber: 3.7 Consensus size: 42
19943137 CCGAAGGCTG
* * *
19943147 AACAGAAGCTCATGAGAGCTAAACGGAAACCCGTAAGGGTTG
1 AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
* * * *
19943189 AACAAAAGCTCGTAAGAGCTGAACGAAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
* *
19943231 AACAGAAGCTCAAAAGAGCTGAACGGAAACCCAT-AGGGTTA
1 AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
* * * * *
19943272 AACGGAAACTCATATGAGTTAAACAGAAAC
1 AACAGAAGCTCATAAGAGCTAAACGGAAAC
19943302 TTGTGAAAGC
Statistics
Matches: 95, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 30 0.32
42 65 0.68
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACGGAAACCCATAAGGGTTA
Found at i:19943204 original size:21 final size:21
Alignment explanation
Indices: 19943178--19943241 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
19943168 AACGGAAACC
19943178 CGTAAGGGTTGAACAAAAGCT
1 CGTAAGGGTTGAACAAAAGCT
* * *
19943199 CGTAAGAGCTGAACGAAAA-CC
1 CGTAAGGGTTGAAC-AAAAGCT
* * *
19943220 CATAAGGGTTAAACAGAAGCT
1 CGTAAGGGTTGAACAAAAGCT
19943241 C
1 C
19943242 AAAAGAGCTG
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
20 3 0.09
21 25 0.78
22 4 0.12
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.16
Consensus pattern (21 bp):
CGTAAGGGTTGAACAAAAGCT
Found at i:19943277 original size:20 final size:21
Alignment explanation
Indices: 19943252--19943301 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
19943242 AAAAGAGCTG
*
19943252 AACGGAAACCCATA-GGGTTA
1 AACGGAAACCCATATGAGTTA
*
19943272 AACGGAAACTCATATGAGTTA
1 AACGGAAACCCATATGAGTTA
*
19943293 AACAGAAAC
1 AACGGAAAC
19943302 TTGTGAAAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (21 bp):
AACGGAAACCCATATGAGTTA
Found at i:19943294 original size:21 final size:20
Alignment explanation
Indices: 19943252--19943302 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
19943242 AAAAGAGCTG
* *
19943252 AACGGAAACCCATAGGGTTA
1 AACGGAAACTCATAGAGTTA
19943272 AACGGAAACTCATATGAGTTA
1 AACGGAAACTCATA-GAGTTA
*
19943293 AACAGAAACT
1 AACGGAAACT
19943303 TGTGAAAGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.18
Consensus pattern (20 bp):
AACGGAAACTCATAGAGTTA
Found at i:19945768 original size:23 final size:23
Alignment explanation
Indices: 19945738--19945788 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
19945728 TAACAGACAG
*
19945738 TGGTTGGTTAATTTCTATGAGGT
1 TGGTTGGTTAATTTCCATGAGGT
*
19945761 TGGTTGGTTGATTTCCATGAGGT
1 TGGTTGGTTAATTTCCATGAGGT
19945784 TGGTT
1 TGGTT
19945789 AACCTTCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.14, C:0.06, G:0.33, T:0.47
Consensus pattern (23 bp):
TGGTTGGTTAATTTCCATGAGGT
Found at i:19948313 original size:13 final size:13
Alignment explanation
Indices: 19948297--19948344 Score: 69
Period size: 13 Copynumber: 3.5 Consensus size: 13
19948287 ACGGTGTTGC
19948297 AGAACGAATGAAT
1 AGAACGAATGAAT
19948310 AGAACGATCATGAAT
1 AGAACGA--ATGAAT
*
19948325 AGAATGAATGAAT
1 AGAACGAATGAAT
19948338 AGAACGA
1 AGAACGA
19948345 TCATGAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 19 0.61
15 12 0.39
ACGTcount: A:0.52, C:0.08, G:0.23, T:0.17
Consensus pattern (13 bp):
AGAACGAATGAAT
Found at i:19948324 original size:15 final size:15
Alignment explanation
Indices: 19948304--19948351 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
19948294 TGCAGAACGA
19948304 ATGAATAGAACGATC
1 ATGAATAGAACGATC
*
19948319 ATGAATAGAATGA--
1 ATGAATAGAACGATC
19948332 ATGAATAGAACGATC
1 ATGAATAGAACGATC
19948347 ATGAA
1 ATGAA
19948352 GAAGGTTCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 12 0.41
15 17 0.59
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.21
Consensus pattern (15 bp):
ATGAATAGAACGATC
Found at i:19948333 original size:28 final size:28
Alignment explanation
Indices: 19948297--19948351 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
19948287 ACGGTGTTGC
19948297 AGAACGAATGAATAGAACGATCATGAAT
1 AGAACGAATGAATAGAACGATCATGAAT
*
19948325 AGAATGAATGAATAGAACGATCATGAA
1 AGAACGAATGAATAGAACGATCATGAA
19948352 GAAGGTTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.51, C:0.09, G:0.22, T:0.18
Consensus pattern (28 bp):
AGAACGAATGAATAGAACGATCATGAAT
Found at i:19963121 original size:20 final size:21
Alignment explanation
Indices: 19963086--19963136 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
19963076 ATATACATTT
*
19963086 AAAAAATACA-AAAAA-TAGA
1 AAAAAATATATAAAAATTAGA
*
19963105 AATAAATATATAAAAATTTAGA
1 AAAAAATATATAAAAA-TTAGA
19963127 AAAAAATATA
1 AAAAAATATA
19963137 AATTATAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 8 0.31
20 5 0.19
22 13 0.50
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.22
Consensus pattern (21 bp):
AAAAAATATATAAAAATTAGA
Found at i:19965966 original size:28 final size:29
Alignment explanation
Indices: 19965892--19965974 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 29
19965882 AAATACAATT
*
19965892 AAATATAAAAAGATATATATAGACATAAACTA
1 AAATATATAAAG-TATATATA-A-ATAAACTA
* * *
19965924 AAATATGTATA-TATATATAAATTAAC-A
1 AAATATATAAAGTATATATAAATAAACTA
*
19965951 AAATATATAAAGTATATTTAAATA
1 AAATATATAAAGTATATATAAATA
19965975 TATATAAAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
27 10 0.24
28 15 0.36
29 1 0.02
30 8 0.19
32 8 0.19
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.33
Consensus pattern (29 bp):
AAATATATAAAGTATATATAAATAAACTA
Found at i:19966184 original size:3 final size:3
Alignment explanation
Indices: 19966176--19966204 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19966166 AATAAGTAGG
19966176 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
19966205 GGACTGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:19966816 original size:19 final size:19
Alignment explanation
Indices: 19966765--19966816 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
19966755 CAAATAACTC
19966765 GAAAAAGAAAA-AAAAATA
1 GAAAAAGAAAATAAAAATA
* *
19966783 GAGAAAA-AAATTAAAATTA
1 GA-AAAAGAAAATAAAAATA
19966802 GAAAAAGAAAATAAA
1 GAAAAAGAAAATAAA
19966817 TATACCTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (19 bp):
GAAAAAGAAAATAAAAATA
Found at i:19978067 original size:3 final size:3
Alignment explanation
Indices: 19978059--19978110 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
19978049 TTTAGACAGT
19978059 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
19978107 AGA A
1 AGA A
19978111 ATAGAGATTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:19979200 original size:21 final size:21
Alignment explanation
Indices: 19979151--19979221 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
19979141 ATCTTATTGG
*
19979151 TGAGTTGGGGTAGTTTGTTGA
1 TGAGTTGGGGTAGTCTGTTGA
* * * *
19979172 AGATTTGGGGTAGTCTCTTGT
1 TGAGTTGGGGTAGTCTGTTGA
* * *
19979193 TGAGTTGGGTTAGCCTGTTGC
1 TGAGTTGGGGTAGTCTGTTGA
19979214 TGAGTTGG
1 TGAGTTGG
19979222 AACAACCACT
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.13, C:0.07, G:0.39, T:0.41
Consensus pattern (21 bp):
TGAGTTGGGGTAGTCTGTTGA
Found at i:19981410 original size:20 final size:19
Alignment explanation
Indices: 19981350--19981410 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 19
19981340 CTTTGAAACA
19981350 ATTTTAAAATCAAGTGCAAATG
1 ATTTT-AAA-CAAGT-CAAATG
* *
19981372 ATTTTAACCAAGTTAAAATG
1 ATTTTAAACAAG-TCAAATG
19981392 ATTTTCAAACAAGTCAAAT
1 ATTTT-AAACAAGTCAAAT
19981411 TTGCTCCAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 19 0.58
21 9 0.27
22 5 0.15
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (19 bp):
ATTTTAAACAAGTCAAATG
Found at i:19984304 original size:2 final size:2
Alignment explanation
Indices: 19984297--19984328 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
19984287 ATAGGATAGA
*
19984297 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19984329 GGTGCATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19985594 original size:3 final size:3
Alignment explanation
Indices: 19985582--19985631 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
19985572 AATGAAAACT
* *
19985582 ATA A-A ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19985629 ATA
1 ATA
19985632 TTAACGAAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:19986961 original size:22 final size:23
Alignment explanation
Indices: 19986933--19986978 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
19986923 GGGCTTTATT
19986933 TATTTGGTTT-TTATATTT-TTTG
1 TATTTGGTTTATTAT-TTTCTTTG
19986955 TATTTGGTTTATTATTTTCTTTG
1 TATTTGGTTTATTATTTTCTTTG
19986978 T
1 T
19986979 GTATGCGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.13, C:0.02, G:0.13, T:0.72
Consensus pattern (23 bp):
TATTTGGTTTATTATTTTCTTTG
Found at i:19987429 original size:45 final size:44
Alignment explanation
Indices: 19987210--19987845 Score: 335
Period size: 44 Copynumber: 14.4 Consensus size: 44
19987200 CTTTCTTCTG
*
19987210 TCTGCTCCACTGCAACTTCAGGG-GTATAAGATCTGCTTGC-TTAG
1 TCTGCTCCACTGCAACTTCAGGGAG-ATAAGAT-TGCTTGCTTTAA
* ** * * * * *
19987254 TTTGCTCTGCTACAACTTTAGGGAGATAAGACTAG-ATGC---GA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGCTTGCTTTAA
* * * **
19987295 TTTGCT-CTCTGCAACTTCAGAGAGATAAGATCTG-TCACTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGCTTGCTTTAA
* * * * *
19987338 TCTGCTCCGCTACAACTTCAGGGAAATATGATT-ATTGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGCTT-GCTTTAA
* * *
19987382 TCTGATCCACTGCAACTTCAGGAAGCTAAGATTCGCTTGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GCTTGCTTTAA
* * ** * *
19987427 TCTGCCCCACTGTAACTTCAGCGG-GATAAGATT-CGTTTATTCAG
1 TCTGCTCCACTGCAACTTCAG-GGAGATAAGATTGC-TTGCTTTAA
* * * * *
19987471 TTTGCTCCGCTACAACTTCAGGGAGATAGGATT-ATTGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGCTT-GCTTTAA
* * * *
19987515 TCTACTCCACTGCAACTTCAGGGAGATAAGATTTGCTTAC-TCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGCTTGCTTTAA
* ** *
19987559 TCTACTCTGCTGCAACATCAGGGAGATAAGACTTGCTAT-CTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGCT-TGCTTTAA
* * *
19987604 TCTGCTCCACTGCAACTTCAGGGAGATAGGATTTGCTAT-CTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGCT-TGCTTTAA
* * * * *
19987649 TCTGCTCCGCTGCAACTTCAGAGAGATAAGACTTACTAT-ATTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGCT-TGCTTTAA
* * * *
19987694 TCTGCTCCACTGAAACTTCAGGGAGATAGGATTTG-TAT-CTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGCT-TGCTTTAA
* * * * * * *
19987738 CCAGCCCCACTACAACTTCAGGTG-GATAAGGTTTGCTAT-CTTCAG
1 TCTGCTCCACTGCAACTTCAGG-GAGATAA-GATTGCT-TGCTTTAA
* *
19987783 TCTGCTCCACTGCAACCTT-AGGGAGATAAGACTTGCTAT-CCTCAA
1 TCTGCTCCACTGCAA-CTTCAGGGAGATAAGA-TTGCT-TGCTTTAA
*
19987828 TCCGCTCCACTGCAACTT
1 TCTGCTCCACTGCAACTT
19987846 TAAAGAGATA
Statistics
Matches: 459, Mismatches: 108, Indels: 50
0.74 0.18 0.08
Matches are distributed among these distances:
39 1 0.00
40 21 0.05
41 6 0.01
43 16 0.03
44 207 0.45
45 200 0.44
46 8 0.02
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGCTTGCTTTAA
Found at i:19987487 original size:89 final size:88
Alignment explanation
Indices: 19987190--19987813 Score: 409
Period size: 89 Copynumber: 7.1 Consensus size: 88
19987180 CCACTGTGAC
* * * * *
19987190 GATAGGATTTCTTTCTTCTGTCTGCTCCACTGCAACTTCAGGG-GTATAAGATCTGCTTGC-TTA
1 GATAAGATTTGTTTATTCAGTCTGCTCCGCTGCAACTTCAGGGAG-ATAAGAT-TGCTTGCTTTA
* * ** * *
19987253 GTTTGCTCTGCTACAACTTTAGGGA
64 ATCTGCTCCACTGCAACTTCAGGGA
* * * * * * **
19987278 GATAAGACTAG---ATGC-GATTTGCT-CTCTGCAACTTCAGAGAGATAAGATCTG-TCACTTTA
1 GATAAGATTTGTTTATTCAG-TCTGCTCCGCTGCAACTTCAGGGAGATAAGAT-TGCTTGCTTTA
* *
19987337 ATCTGCTCCGCTACAACTTCAGGGA
64 ATCTGCTCCACTGCAACTTCAGGGA
* * ** * * * * *
19987362 AATATGATTATTGGCT-TT-AATCTGATCCACTGCAACTTCAGGAAGCTAAGATTCGCTTGCTTT
1 GATAAGA-T-TTGTTTATTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGATT-GCTTGCTTT
* *
19987425 AATCTGCCCCACTGTAACTTCAGCGG-
63 AATCTGCTCCACTGCAACTTCAG-GGA
* * * * *
19987451 GATAAGATTCGTTTATTCAGTTTGCTCCGCTACAACTTCAGGGAGATAGGATT-ATTGGCTTTAA
1 GATAAGATTTGTTTATTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGCTT-GCTTTAA
*
19987515 TCTACTCCACTGCAACTTCAGGGA
65 TCTGCTCCACTGCAACTTCAGGGA
* * * * *
19987539 GATAAGATTTGCTTACTCAGTCTACTCTGCTGCAACATCAGGGAGATAAGACTTGCTAT-CTTTA
1 GATAAGATTTGTTTATTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGA-TTGCT-TGCTTTA
19987603 ATCTGCTCCACTGCAACTTCAGGGA
64 ATCTGCTCCACTGCAACTTCAGGGA
* * * * * * *
19987628 GATAGGATTTGCTATCTTCAGTCTGCTCCGCTGCAACTTCAGAGAGATAAGACTTACTAT-ATTC
1 GATAAGATTTG-TTTATTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGA-TTGCT-TGCTTT
*
19987692 AATCTGCTCCACTGAAACTTCAGGGA
63 AATCTGCTCCACTGCAACTTCAGGGA
* * * * * * * * * *
19987718 GATAGGATTTGTATCTTCAGCCAGCCCCACTACAACTTCAGGTG-GATAAGGTTTGCTAT-CTTC
1 GATAAGATTTGTTTATTCAGTCTGCTCCGCTGCAACTTCAGG-GAGATAA-GATTGCT-TGCTTT
*
19987781 AGTCTGCTCCACTGCAACCTT-AGGGA
63 AATCTGCTCCACTGCAA-CTTCAGGGA
19987807 GATAAGA
1 GATAAGA
19987814 CTTGCTATCC
Statistics
Matches: 426, Mismatches: 86, Indels: 47
0.76 0.15 0.08
Matches are distributed among these distances:
83 2 0.00
84 54 0.13
85 8 0.02
86 2 0.00
87 12 0.03
88 100 0.23
89 162 0.38
90 85 0.20
91 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (88 bp):
GATAAGATTTGTTTATTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGATTGCTTGCTTTAAT
CTGCTCCACTGCAACTTCAGGGA
Found at i:19987610 original size:133 final size:132
Alignment explanation
Indices: 19987299--19987636 Score: 373
Period size: 133 Copynumber: 2.5 Consensus size: 132
19987289 ATGCGATTTG
*
19987299 CTCTCTGCAACTTCAGAGAGATAAGATCTG-TCA-CTTTAATCTGCTCCGCTACAACTTCAGGGA
1 CTCTCTGCAACTTCAGGGAGATAAGAT-TGCT-ATCTTTAATCTGCTCCGCTACAACTTCAGGGA
* * * * *
19987362 AATATGATTATTGGCTTTAATCTGATCCACTGCAACTTCAGGAAGCTAAGATTCGCTTGCTTTAA
64 GATAGGATTATTGGCTTTAATCTGATCCACTGCAACTTCAGGAAGATAAGATTCGCTTACTTCAA
*
19987427 TCTGC
129 TCT-A
* * * * * * * *
19987432 CCCACTGTAACTTCAGCGG-GATAAGATT-CGTTTATTCAGTTTGCTCCGCTACAACTTCAGGGA
1 CTCTCTGCAACTTCAG-GGAGATAAGATTGC-TATCTTTAATCTGCTCCGCTACAACTTCAGGGA
* *
19987495 GATAGGATTATTGGCTTTAATCT-ACTCCACTGCAACTTCAGGGAGATAAGATTTGCTTAC-TCA
64 GATAGGATTATTGGCTTTAATCTGA-TCCACTGCAACTTCAGGAAGATAAGATTCGCTTACTTCA
*
19987558 GTCTA
128 ATCTA
* * *
19987563 CTCTGCTGCAACATCAGGGAGATAAGACTTGCTATCTTTAATCTGCTCCACTGCAACTTCAGGGA
1 CTCT-CTGCAACTTCAGGGAGATAAGA-TTGCTATCTTTAATCTGCTCCGCTACAACTTCAGGGA
19987628 GATAGGATT
64 GATAGGATT
19987637 TGCTATCTTC
Statistics
Matches: 167, Mismatches: 29, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
131 4 0.02
132 24 0.14
133 137 0.82
134 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (132 bp):
CTCTCTGCAACTTCAGGGAGATAAGATTGCTATCTTTAATCTGCTCCGCTACAACTTCAGGGAGA
TAGGATTATTGGCTTTAATCTGATCCACTGCAACTTCAGGAAGATAAGATTCGCTTACTTCAATC
TA
Found at i:19987734 original size:134 final size:134
Alignment explanation
Indices: 19987303--19987863 Score: 444
Period size: 134 Copynumber: 4.2 Consensus size: 134
19987293 GATTTGCTCT
* * * * * * * *
19987303 CTGCAACTTCAGAGAGATAAGATCTGTCA-CTTTAATCTGCTCCGCTACAACTTCAGGGAAATAT
1 CTGCAACTTCAGGGAGATAGGATTTGT-ATCTTCAACCTGCTCCACTACAACTTCAGGGAGATAG
** * * * * * * *
19987367 GATTAT--TGGCTTTAATCTGATCCACTGCAACTTCAGGAAGCTAAGA-TTCGCT-TGCTTTAAT
65 GATT-TGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATAC-TCAAT
*
19987428 CTGCCCCA
127 CTGCTCCA
* * * * * *** *
19987436 CTGTAACTTCAGCGG-GATAAGATTCGTTTATTCAGTTTGCTCCGCTACAACTTCAGGGAGATAG
1 CTGCAACTTCAG-GGAGATAGGATTTGTATCTTCAACCTGCTCCACTACAACTTCAGGGAGATAG
** * * * * *
19987500 GATTAT--TGGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGCT-TACTCAGTCT
65 GATT-TGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATACTCAATCT
* **
19987562 ACTCTG
129 GCTCCA
* * * * * *
19987568 CTGCAACATCAGGGAGATAAGACTTGCTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAG
1 CTGCAACTTCAGGGAGATAGGATTTG-TATCTTCAACCTGCTCCACTACAACTTCAGGGAGATAG
* * * *
19987633 GATTTGCTATCTTCAGTCTGCTCCGCTGCAACTTCAGAGAGATAAGACTTACTATATTCAATCTG
65 GATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATACTCAATCTG
19987698 CTCCA
130 CTCCA
* * * *
19987703 CTGAAACTTCAGGGAGATAGGATTTGTATCTTCAGCCAGCCCCACTACAACTTCAGGTG-GATAA
1 CTGCAACTTCAGGGAGATAGGATTTGTATCTTCAACCTGCTCCACTACAACTTCAGG-GAGAT-A
*
19987767 GG-TTTGCTATCTTCAGTCTGCTCCACTGCAACCTT-AGGGAGATAAGACTTGCTATCCTCAATC
64 GGATTTGCTATCTTCAGTCTGCTCCACTGCAA-CTTCAGGGAGATAAGACTTGCTATACTCAATC
*
19987830 CGCTCCA
128 TGCTCCA
* **
19987837 CTGCAACTTTAAAGAGATAGGATTTGT
1 CTGCAACTTCAGGGAGATAGGATTTGT
19987864 GGTTTCACCG
Statistics
Matches: 350, Mismatches: 67, Indels: 21
0.80 0.15 0.05
Matches are distributed among these distances:
131 2 0.01
132 27 0.08
133 132 0.38
134 149 0.43
135 40 0.11
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (134 bp):
CTGCAACTTCAGGGAGATAGGATTTGTATCTTCAACCTGCTCCACTACAACTTCAGGGAGATAGG
ATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATACTCAATCTGC
TCCA
Found at i:19987776 original size:179 final size:178
Alignment explanation
Indices: 19987421--19987860 Score: 444
Period size: 179 Copynumber: 2.5 Consensus size: 178
19987411 GATTCGCTTG
* * * * * * *
19987421 CTTTAATCTGCCCCACTGTAACTTCAGCGG-GATAAGATTCG-TTTATTCAGTTTGCTCCGCTAC
1 CTTTAATCTGCTCCACTGCAACTTCAG-GGAGATAAGATTTGCTATCTTCAGTCTGCTCCGCTGC
* * * * * * *
19987484 AACTTCAGGGAGATAGGATTATTGGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTT
65 AACTTCAGAGAGATAAGATTACTAGATTCAATCTACTCCACTGAAACTTCAGGGAGATAAGATTT
* * ** *
19987549 GCTTACTCAGTCTACTCTGCTGCAACATCAGGGAGATAAGACTTGCTAT
130 GCTTACTCAGTCCACCCCACTACAACATCAGGGAGATAAGACTTGCTAT
*
19987598 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTTGCTATCTTCAGTCTGCTCCGCTGCA
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCGCTGCA
* * *
19987663 ACTTCAGAGAGATAAGACTTACTATATTCAATCTGCTCCACTGAAACTTCAGGGAGATAGGATTT
66 ACTTCAGAGAGATAAGA-TTACTAGATTCAATCTACTCCACTGAAACTTCAGGGAGATAAGATTT
* **
19987728 G--TATCTTCAG-CCAGCCCCACTACAACTTCAGGTG-GATAAGGTTTGCTAT
130 GCTTA-C-TCAGTCCA-CCCCACTACAACATCAGG-GAGATAAGACTTGCTAT
* * * * * * *
19987777 CTTCAGTCTGCTCCACTGCAACCTT-AGGGAGATAAGACTTGCTATCCTCAATCCGCTCCACTGC
1 CTTTAATCTGCTCCACTGCAA-CTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCGCTGC
* * *
19987841 AACTTTAAAGAGATAGGATT
65 AACTTCAGAGAGATAAGATT
19987861 TGTGGTTTCA
Statistics
Matches: 218, Mismatches: 37, Indels: 15
0.81 0.14 0.06
Matches are distributed among these distances:
176 2 0.01
177 36 0.17
178 39 0.18
179 137 0.63
180 4 0.02
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.30
Consensus pattern (178 bp):
CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCGCTGCA
ACTTCAGAGAGATAAGATTACTAGATTCAATCTACTCCACTGAAACTTCAGGGAGATAAGATTTG
CTTACTCAGTCCACCCCACTACAACATCAGGGAGATAAGACTTGCTAT
Found at i:19987855 original size:45 final size:45
Alignment explanation
Indices: 19987303--19987845 Score: 387
Period size: 45 Copynumber: 12.2 Consensus size: 45
19987293 GATTTGCTCT
* * *
19987303 CTGCAACTTCAGAGAGATAAGA-TCTG-TCA-CTTTAATCTGCTCCG
1 CTGCAACTTCAGGGAGATAAGACT-TGCT-ATCTTCAATCTGCTCCA
* * * ** ** * *
19987347 CTACAACTTCAGGGAAATATGA-TTATTGGCTTTAATCTGATCCA
1 CTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTGCTCCA
* * * *
19987391 CTGCAACTTCAGGAAGCTAAGA-TTCGCT-TGCTTTAATCTGCCCCA
1 CTGCAACTTCAGGGAGATAAGACTT-GCTAT-CTTCAATCTGCTCCA
* * * * * *
19987436 CTGTAACTTCAGCGG-GATAAGA-TT-CGTTTATTCAGTTTGCTCCG
1 CTGCAACTTCAG-GGAGATAAGACTTGC-TATCTTCAATCTGCTCCA
* * ** ** * *
19987480 CTACAACTTCAGGGAGATAGGA-TTATTGGCTTTAATCTACTCCA
1 CTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTGCTCCA
* * * **
19987524 CTGCAACTTCAGGGAGATAAGATTTGCT-TAC-TCAGTCTACTCTG
1 CTGCAACTTCAGGGAGATAAGACTTGCTAT-CTTCAATCTGCTCCA
* *
19987568 CTGCAACATCAGGGAGATAAGACTTGCTATCTTTAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTGCTCCA
* * * *
19987613 CTGCAACTTCAGGGAGATAGGATTTGCTATCTTCAGTCTGCTCCG
1 CTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTGCTCCA
* * *
19987658 CTGCAACTTCAGAGAGATAAGACTTACTATATTCAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTGCTCCA
* * * ** * *
19987703 CTGAAACTTCAGGGAGATAGGATTTG-TATCTTCAGCCAGCCCCA
1 CTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTGCTCCA
* ** *
19987747 CTACAACTTCAGGTG-GATAAGGTTTGCTATCTTCAGTCTGCTCCA
1 CTGCAACTTCAGG-GAGATAAGACTTGCTATCTTCAATCTGCTCCA
* *
19987792 CTGCAACCTT-AGGGAGATAAGACTTGCTATCCTCAATCCGCTCCA
1 CTGCAA-CTTCAGGGAGATAAGACTTGCTATCTTCAATCTGCTCCA
19987837 CTGCAACTT
1 CTGCAACTT
19987846 TAAAGAGATA
Statistics
Matches: 391, Mismatches: 91, Indels: 34
0.76 0.18 0.07
Matches are distributed among these distances:
43 4 0.01
44 183 0.47
45 200 0.51
46 4 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.30
Consensus pattern (45 bp):
CTGCAACTTCAGGGAGATAAGACTTGCTATCTTCAATCTGCTCCA
Found at i:19996719 original size:10 final size:10
Alignment explanation
Indices: 19996704--19996730 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
19996694 TCTCTTCAAT
19996704 CTTGCTTAAA
1 CTTGCTTAAA
19996714 CTTGCTTAAA
1 CTTGCTTAAA
19996724 CTTGCTT
1 CTTGCTT
19996731 TCAACTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (10 bp):
CTTGCTTAAA
Found at i:19997910 original size:13 final size:13
Alignment explanation
Indices: 19997892--19997931 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
19997882 TGGGCTTATT
19997892 TATTTGGTTTTTA
1 TATTTGGTTTTTA
*
19997905 TATTT-GTTTTTG
1 TATTTGGTTTTTA
19997917 TATTTGGTTTATTA
1 TATTTGGTTT-TTA
19997931 T
1 T
19997932 TTTCTTTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 11 0.48
13 9 0.39
14 3 0.13
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (13 bp):
TATTTGGTTTTTA
Found at i:19997921 original size:25 final size:25
Alignment explanation
Indices: 19997892--19997944 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
19997882 TGGGCTTATT
* *
19997892 TATTTGGTTT-TTATATTTGTTTTTG
1 TATTTGGTTTATTAT-TTTCTTTGTG
19997917 TATTTGGTTTATTATTTTCTTTGTG
1 TATTTGGTTTATTATTTTCTTTGTG
19997942 TAT
1 TAT
19997945 GCAGGCCTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.13, C:0.02, G:0.15, T:0.70
Consensus pattern (25 bp):
TATTTGGTTTATTATTTTCTTTGTG
Found at i:20002188 original size:9 final size:9
Alignment explanation
Indices: 20002174--20002208 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
20002164 AAAATCAATC
20002174 AAAAAATTA
1 AAAAAATTA
20002183 AAAAAATTA
1 AAAAAATTA
20002192 AAAAAATTCA
1 AAAAAATT-A
20002202 AAAAAAT
1 AAAAAAT
20002209 CAAGAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAAATTA
Found at i:20002211 original size:9 final size:9
Alignment explanation
Indices: 20002170--20002217 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
20002160 AAAAAAAATC
20002170 AATC-AAAA
1 AATCAAAAA
*
20002178 AATTAAAAA
1 AATCAAAAA
*
20002187 AATTAAAAA
1 AATCAAAAA
20002196 AATTCAAAAA
1 AA-TCAAAAA
20002206 AATCAAGAAA
1 AATCAA-AAA
20002216 AA
1 AA
20002218 AAGGAAGGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 3 0.09
9 19 0.54
10 13 0.37
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.17
Consensus pattern (9 bp):
AATCAAAAA
Found at i:20002238 original size:6 final size:6
Alignment explanation
Indices: 20002227--20002261 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
20002217 AAAGGAAGGG
*
20002227 AAATCA AAATCA AAATCA AAATAAA AAATCA AAAT
1 AAATCA AAATCA AAATCA AAAT-CA AAATCA AAAT
20002262 AACAAATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:20002256 original size:13 final size:13
Alignment explanation
Indices: 20002227--20002268 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
20002217 AAAGGAAGGG
*
20002227 AAATCAAAAT-CA
1 AAATCAAAATAAA
20002239 AAATCAAAATAAA
1 AAATCAAAATAAA
*
20002252 AAATCAAAATAAC
1 AAATCAAAATAAA
20002265 AAAT
1 AAAT
20002269 GAAATGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.17
Consensus pattern (13 bp):
AAATCAAAATAAA
Found at i:20003163 original size:15 final size:15
Alignment explanation
Indices: 20003136--20003173 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
20003126 TTGAGTCAGA
20003136 AAAAATATGAAAAA-T
1 AAAAA-ATGAAAAAGT
*
20003151 GAAAAATGAAAAAGT
1 AAAAAATGAAAAAGT
20003166 AAAAAATG
1 AAAAAATG
20003174 GAGAGGCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (15 bp):
AAAAAATGAAAAAGT
Found at i:20004243 original size:19 final size:19
Alignment explanation
Indices: 20004221--20004261 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
20004211 ATTCTGTATT
20004221 CATGCAAACATCATTTATA
1 CATGCAAACATCATTTATA
20004240 CATGCAAACATCATTTATA
1 CATGCAAACATCATTTATA
20004259 CAT
1 CAT
20004262 ACCTAGTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32
Consensus pattern (19 bp):
CATGCAAACATCATTTATA
Found at i:20004439 original size:44 final size:44
Alignment explanation
Indices: 20004376--20004606 Score: 261
Period size: 44 Copynumber: 5.2 Consensus size: 44
20004366 CCGGTGAAAC
* *
20004376 TATAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAATAT
1 TATAAATCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGAT
* *
20004420 TATAAATCCTAGCTCCCTG-ACTAGTAGTGGAATAGGTGGAAGACT
1 TATAAATCCTAGCTCCCTGAAC-AGCAGTGGAATAGGCGGAAGA-T
* * *
20004465 GA-AAGTCCTAGCTCCCTAAACAGCAGTGGAATAGGCGGAAGAT
1 TATAAATCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGAT
* * * * *
20004508 TGTAAATCCTAGCTCCTTGACCAACAGTGGAATAGGTGGAAGACT
1 TATAAATCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGA-T
* * * *
20004553 GA-AAGTCCTAGCTCCCTGAACAGTAGTGGAATAGGCAGAAGAT
1 TATAAATCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGAT
*
20004596 TGTAAATCCTA
1 TATAAATCCTA
20004607 TGTAACAACC
Statistics
Matches: 152, Mismatches: 29, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
43 4 0.03
44 143 0.94
45 5 0.03
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (44 bp):
TATAAATCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGAT
Found at i:20004537 original size:88 final size:88
Alignment explanation
Indices: 20004379--20004606 Score: 375
Period size: 88 Copynumber: 2.6 Consensus size: 88
20004369 GTGAAACTAT
* * * *
20004379 AAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAATATTATAAATCCTAGCTCCCTGACTAG
1 AAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGATTGTAAATCCTAGCTCCCTGACCAA
*
20004444 TAGTGGAATAGGTGGAAGACTGA
66 CAGTGGAATAGGTGGAAGACTGA
* *
20004467 AAGTCCTAGCTCCCTAAACAGCAGTGGAATAGGCGGAAGATTGTAAATCCTAGCTCCTTGACCAA
1 AAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGATTGTAAATCCTAGCTCCCTGACCAA
20004532 CAGTGGAATAGGTGGAAGACTGA
66 CAGTGGAATAGGTGGAAGACTGA
* *
20004555 AAGTCCTAGCTCCCTGAACAGTAGTGGAATAGGCAGAAGATTGTAAATCCTA
1 AAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGATTGTAAATCCTA
20004607 TGTAACAACC
Statistics
Matches: 130, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 130 1.00
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (88 bp):
AAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGATTGTAAATCCTAGCTCCCTGACCAA
CAGTGGAATAGGTGGAAGACTGA
Found at i:20006435 original size:41 final size:41
Alignment explanation
Indices: 20006378--20006479 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
20006368 GCATAGCGCT
*
20006378 TAGCAGGCTTATTGCCGGTGAAACACTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
* *
20006419 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
20006460 TAGCAGGC-TAAGTGCCGGTG
1 TAGCAGGCTTAA-TGCCGGTG
20006480 TACTGAGTCA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 3 0.05
41 54 0.95
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
Found at i:20014110 original size:41 final size:41
Alignment explanation
Indices: 20014049--20014150 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 41
20014039 GCATAGCGCT
* *
20014049 TAGCAGGCTTATTGCAGGTGAAACACTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
* *
20014090 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
20014131 TAGCAGGC-TAAGTGCCGGTG
1 TAGCAGGCTTAA-TGCCGGTG
20014151 TACTGAATCA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
40 3 0.05
41 53 0.95
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
Found at i:20015407 original size:88 final size:88
Alignment explanation
Indices: 20015106--20015384 Score: 468
Period size: 88 Copynumber: 3.2 Consensus size: 88
20015096 GGGGTGTTAC
* *
20015106 ATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGAAAGTCCTAGCTCCCTGAACAGCA
1 ATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAGTCCTAGCTCCCTGAACAGCA
* *
20015171 GTGGAATAGGCGGATGATTGTAA
66 GTGGAATAGGCAGAAGATTGTAA
* * *
20015194 ATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAAACTATAAGTCCTAGCTCCCTGAATAGCA
1 ATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAGTCCTAGCTCCCTGAACAGCA
20015259 GTGGAATAGGCAGAAGATTGTAA
66 GTGGAATAGGCAGAAGATTGTAA
*
20015282 ATCCTAGCTCCCTGACCAGCAGTGGAATAGGTAGAAGACTGTAAGTCCTAGCTCCCTGAACAGCA
1 ATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAGTCCTAGCTCCCTGAACAGCA
*
20015347 GTGGAATAAGCAGAAGATTGTAA
66 GTGGAATAGGCAGAAGATTGTAA
*
20015370 GTCCTAGCTCCCTGA
1 ATCCTAGCTCCCTGA
20015385 GCAACAATGG
Statistics
Matches: 178, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 178 1.00
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.22
Consensus pattern (88 bp):
ATCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAGTCCTAGCTCCCTGAACAGCA
GTGGAATAGGCAGAAGATTGTAA
Found at i:20015408 original size:44 final size:44
Alignment explanation
Indices: 20015107--20015384 Score: 385
Period size: 44 Copynumber: 6.3 Consensus size: 44
20015097 GGGTGTTACA
* * *
20015107 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGAAAG
1 TCCTAGCTCCCTGAACAGCAGTGGAATAGGTAGAAGATTGTAAG
** * *
20015151 TCCTAGCTCCCTGAACAGCAGTGGAATAGGCGGATGATTGTAAA
1 TCCTAGCTCCCTGAACAGCAGTGGAATAGGTAGAAGATTGTAAG
* * * * *
20015195 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAAACTATAAG
1 TCCTAGCTCCCTGAACAGCAGTGGAATAGGTAGAAGATTGTAAG
* * *
20015239 TCCTAGCTCCCTGAATAGCAGTGGAATAGGCAGAAGATTGTAAA
1 TCCTAGCTCCCTGAACAGCAGTGGAATAGGTAGAAGATTGTAAG
* *
20015283 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTAGAAGACTGTAAG
1 TCCTAGCTCCCTGAACAGCAGTGGAATAGGTAGAAGATTGTAAG
* *
20015327 TCCTAGCTCCCTGAACAGCAGTGGAATAAGCAGAAGATTGTAAG
1 TCCTAGCTCCCTGAACAGCAGTGGAATAGGTAGAAGATTGTAAG
20015371 TCCTAGCTCCCTGA
1 TCCTAGCTCCCTGA
20015385 GCAACAATGG
Statistics
Matches: 205, Mismatches: 29, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 205 1.00
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.22
Consensus pattern (44 bp):
TCCTAGCTCCCTGAACAGCAGTGGAATAGGTAGAAGATTGTAAG
Found at i:20015469 original size:88 final size:88
Alignment explanation
Indices: 20015377--20015539 Score: 220
Period size: 88 Copynumber: 1.9 Consensus size: 88
20015367 TAAGTCCTAG
*
20015377 CTCCCT-GAGCAACAATGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGACGGCGAA
1 CTCCCTCG-GCAACAATGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAA
20015441 GCAGATCGAAGACACAAGCCTTGC
65 GCAGATCGAAGACACAAGCCTTGC
**** * * * * *
20015465 CTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGGTCTTGCCTTCTTGCATCGATAGTGAAG
1 CTCCCTCGGCAACAATGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAG
20015530 CAGATCGAAG
66 CAGATCGAAG
20015540 CCAATGGTCA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
88 63 0.98
89 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (88 bp):
CTCCCTCGGCAACAATGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAG
CAGATCGAAGACACAAGCCTTGC
Found at i:20015532 original size:45 final size:45
Alignment explanation
Indices: 20015395--20015532 Score: 120
Period size: 44 Copynumber: 3.1 Consensus size: 45
20015385 GCAACAATGG
* ** *
20015395 AGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGACGGCGA
1 AGCAGGTTGAAGATAGCAGGTCTTGCCTTCCTGCATCGATAGTGA
* * * * * * * * *
20015440 AGCAGATCGAAGACA-CAAGCCTTGCCTCCCT-CGGTTG-TAGTGG
1 AGCAGGTTGAAGATAGCAGGTCTTGCCTTCCTGC-ATCGATAGTGA
*
20015483 AGCAGGTTGAAGATAGCAGGTCTTGCCTTCTTGCATCGATAGTGA
1 AGCAGGTTGAAGATAGCAGGTCTTGCCTTCCTGCATCGATAGTGA
20015528 AGCAG
1 AGCAG
20015533 ATCGAAGCCA
Statistics
Matches: 66, Mismatches: 23, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
43 15 0.23
44 28 0.42
45 23 0.35
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (45 bp):
AGCAGGTTGAAGATAGCAGGTCTTGCCTTCCTGCATCGATAGTGA
Found at i:20025396 original size:21 final size:22
Alignment explanation
Indices: 20025370--20025410 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
20025360 GTTGATAATG
20025370 AAAGAAAATGAG-AGAAAAATA
1 AAAGAAAATGAGAAGAAAAATA
**
20025391 AAAGAATTTGAGAAGAAAAA
1 AAAGAAAATGAGAAGAAAAA
20025411 AGAAATAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.12
Consensus pattern (22 bp):
AAAGAAAATGAGAAGAAAAATA
Found at i:20036408 original size:41 final size:41
Alignment explanation
Indices: 20036358--20036452 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
20036348 GGCTCAGTGC
* * * * * *
20036358 CTAGTAGGCTTATTGCCGATGAAACCATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGATGAAACAATTCAAACTATAAGT
* *
20036399 CTAGCAGGCTAAATGCCGGTGAAACAATTCAAACTATAAGT
1 CTAGCAGGCTTAATGCCGATGAAACAATTCAAACTATAAGT
20036440 CTAGCAGGCTTAA
1 CTAGCAGGCTTAA
20036453 AGCAGGTGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGATGAAACAATTCAAACTATAAGT
Found at i:20047611 original size:19 final size:21
Alignment explanation
Indices: 20047561--20047617 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
20047551 GTGGATTAGA
* *
20047561 TCTTATGAGCTTCTTTTCAGC
1 TCTTACGAGCTTCTGTTCAGC
20047582 TCTTACGAGCTTCTGTTCAGC
1 TCTTACGAGCTTCTGTTCAGC
20047603 T-TT-CGAGCTTCTGTT
1 TCTTACGAGCTTCTGTT
20047618 GGTGTATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.35
20 2 0.06
21 20 0.59
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.46
Consensus pattern (21 bp):
TCTTACGAGCTTCTGTTCAGC
Found at i:20048594 original size:42 final size:42
Alignment explanation
Indices: 20048537--20048630 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 42
20048527 TTCAAATGCC
* * * *
20048537 CACACGGCCTGAGACACGGGCGTGTCTCCTGACCCTGTGAGT
1 CACACGGCCTAAGACACAGACGTGTCTCCTGACCATGTGAGT
*
20048579 CACACGGCCTAAGACACAGACTTGTCTCCTGACCATGTGAGT
1 CACACGGCCTAAGACACAGACGTGTCTCCTGACCATGTGAGT
20048621 CACACGGCCT
1 CACACGGCCT
20048631 GGCCACATGG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.19
Consensus pattern (42 bp):
CACACGGCCTAAGACACAGACGTGTCTCCTGACCATGTGAGT
Found at i:20048824 original size:11 final size:12
Alignment explanation
Indices: 20048808--20048841 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
20048798 AATTTCACGA
20048808 AAAAATTTCG-T
1 AAAAATTTCGTT
20048819 AAAAATTTCGTT
1 AAAAATTTCGTT
20048831 AGAAAATTTCG
1 A-AAAATTTCG
20048842 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 2 0.10
13 9 0.43
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (12 bp):
AAAAATTTCGTT
Found at i:20049982 original size:33 final size:33
Alignment explanation
Indices: 20049940--20050223 Score: 172
Period size: 33 Copynumber: 7.8 Consensus size: 33
20049930 TCCCCCAAGG
*
20049940 GGTTGCTAAGTGCTGATTCCTCGATTCATTAGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTAGT
* * *
20049973 GGTTGCTAAGTGCTGATTCTACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTC-CCCG-A--TT-CAT-T---AGT
*
20050015 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTAGT
* * *
20050048 GGTTGCTAAGTGTTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---AGT
*
20050090 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTAGT
* * *
20050123 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---AGT
* * *
20050165 GGTTGCTAAGTGTTGATTCCTCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTAGT
*
20050198 GGTTGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
20050224 AACGGATAAC
Statistics
Matches: 194, Mismatches: 29, Indels: 55
0.70 0.10 0.20
Matches are distributed among these distances:
33 78 0.40
34 12 0.06
35 3 0.02
36 3 0.02
37 12 0.06
38 12 0.06
39 3 0.02
40 3 0.02
41 8 0.04
42 60 0.31
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTAGT
Found at i:20050020 original size:42 final size:41
Alignment explanation
Indices: 20049973--20050183 Score: 202
Period size: 42 Copynumber: 5.5 Consensus size: 41
20049963 ATTCATTAGT
20049973 GGTTGCTAAGTGCTGATTCTACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTC-ACCGTATCTTAAATGTGAAAGG
* * *
20050015 GGTTGCTAAGTGCTGATTCCCCG-A--TT-CAT-TG---GT
1 GGTTGCTAAGTGCTGATTCACCGTATCTTAAATGTGAAAGG
*
20050048 GGTTGCTAAGTGTTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATT-CACCGTATCTTAAATGTGAAAGG
* * *
20050090 GGTTGCTAAGTGCTGATTCCCCG-A--TT-CAT-TG---GT
1 GGTTGCTAAGTGCTGATTCACCGTATCTTAAATGTGAAAGG
*
20050123 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGAT-TCACCGTATCTTAAATGTGAAAGG
*
20050165 GGTTGCTAAGTGTTGATTC
1 GGTTGCTAAGTGCTGATTC
20050184 CTCGATTCAT
Statistics
Matches: 134, Mismatches: 17, Indels: 37
0.71 0.09 0.20
Matches are distributed among these distances:
33 36 0.27
34 8 0.06
35 2 0.01
36 4 0.03
37 8 0.06
38 8 0.06
39 4 0.03
40 2 0.01
41 8 0.06
42 54 0.40
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCACCGTATCTTAAATGTGAAAGG
Found at i:20050059 original size:75 final size:75
Alignment explanation
Indices: 20049936--20050221 Score: 500
Period size: 75 Copynumber: 3.8 Consensus size: 75
20049926 TGGTTCCCCC
* * *
20049936 AAGGGGTTGCTAAGTGCTGATTCCTCGATTCATTAGTGGTTGCTAAGTGCTGATTCTACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
20050001 TTAAATGTGA
66 TTAAATGTGA
*
20050011 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGTTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
20050076 TTAAATGTGA
66 TTAAATGTGA
*
20050086 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
20050151 TTAAATGTGA
66 TTAAATGTGA
* * *
20050161 AAGGGGTTGCTAAGTGTTGATTCCTCGATTCATTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
20050222 ATAACGGATA
Statistics
Matches: 201, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 201 1.00
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:20057919 original size:21 final size:21
Alignment explanation
Indices: 20057873--20057930 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
20057863 ATTGGGTGGG
* *
20057873 TCAGCTCTTATGAGCTT-CTT
1 TCAGCTCTTACGAGCTTCCGT
20057893 TCCAGCTCTTACGAGCTTCCGT
1 T-CAGCTCTTACGAGCTTCCGT
20057915 TCAGCT-TT-CGAGCTTC
1 TCAGCTCTTACGAGCTTC
20057931 TGTTAGTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 8 0.24
20 3 0.09
21 20 0.59
22 3 0.09
ACGTcount: A:0.14, C:0.31, G:0.17, T:0.38
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTCCGT
Done.