Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 109 of 135
Found at i:40220821 original size:100 final size:100
Alignment explanation
Indices: 40220696--40221416 Score: 870
Period size: 100 Copynumber: 7.1 Consensus size: 100
40220686 GATTCACCAT
* * * * * *
40220696 CTTCAATTTGTTTAACTACAATGTCGAGGAAATAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* * * ** *
40220761 CTGCACTGCCAGTGAAGTAAGATTTGCTATTGTAG
66 CTACACTGCCAGGGAAGTAAGATTCGCCGTTGTGG
* * *
40220796 CTTCAATCTATTTAACTTCAATGTCGGGGAAAGAAGATTCGCTGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* * *
40220861 TTACACCGCCAGGGAAGTATGATTCGCCGTTGTGG
66 CTACACTGCCAGGGAAGTAAGATTCGCCGTTGTGG
* * * *
40220896 CTCCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTTGCCGTCGTAGCTTTAATTTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* * *
40220961 TTACACCGCCAGAGAAGTAAGATTCGCCGTTGTGG
66 CTACACTGCCAGGGAAGTAAGATTCGCCGTTGTGG
* * * *
40220996 GTTCAATCTATTTAACTGCAATGTTGGGGAAACAAGATTCGTCGTCGTAGCTTCAATTTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* * *
40221061 CCACACTGCCAGGGAAGTAAGGGAAGTAAGATTCACCATTGTGG
66 CTACACTGCC---------AGGGAAGTAAGATTCGCCGTTGTGG
* * * *
40221105 GTTCAATCTATTTAACTACAATGTCGGGGGAACAAGATTCGCCGTCATAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
40221170 CTACACTGCCAGGGAAGTAAGATTCGCCGTTGTGG
66 CTACACTGCCAGGGAAGTAAGATTCGCCGTTGTGG
* * * *
40221205 GTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGA-TCTACCATCGTAGCTTTAATCTGTTCC
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC-GCCGTCGTAGCTTCAATCTGTTCC
* * * *
40221269 ACTACA-TCGCTAGGGAAGTAAGGTTCACCGTTATGG
65 ACTACACT-GCCAGGGAAGTAAGATTCGCCGTTGTGG
* * * * * *
40221305 CTTCAATTTATTTAACTGCAATGTTGGGGAAACATGATCCACCGTCGTAGCTTCAATCTATTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
*
40221370 CTACATTGCCAGGGAAGTAAGATTCGCCGTTGTGG
66 CTACACTGCCAGGGAAGTAAGATTCGCCGTTGTGG
40221405 CTTCAATCTATT
1 CTTCAATCTATT
40221417 CCACTTAATG
Statistics
Matches: 539, Mismatches: 69, Indels: 26
0.85 0.11 0.04
Matches are distributed among these distances:
99 3 0.01
100 444 0.82
101 2 0.00
109 90 0.17
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (100 bp):
CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
CTACACTGCCAGGGAAGTAAGATTCGCCGTTGTGG
Found at i:40221256 original size:309 final size:309
Alignment explanation
Indices: 40220696--40221390 Score: 913
Period size: 309 Copynumber: 2.3 Consensus size: 309
40220686 GATTCACCAT
* * * * * * * *
40220696 CTTCAATTTGTTTAACTACAATGTCGAGGAAATAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTTGGGGAAACAAGATCCACCGTCGTAGCTTCAATCTATTCCA
** ** * *
40220761 CTGCACTGCC-----AGT----GAAGTAAGATTTGCTATTGTAGCTTCAATCTATTTAACTTCAA
66 CCACACTGCCAGGGAAGTAAGGGAAGTAAGATTCACCATTGTAGCTTCAATCTATTTAACTACAA
* * * * *
40220817 TGTCGGGGAAAGAAGATTCGCTGTCGTAGCTTCAATCTGTTCCATTACACCGCCAGGGAAGTATG
131 TGTCGGGGAAACAAGATTCGCCGTCATAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAG
* * *
40220882 ATTCGCCGTTGTGGCTCCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTTGCCGTCGTAGC
196 ATTCGCCGTTGTGGCTCCAATCTATTTAACTGCAATGTCGGGGAAACAAGATCTACCATCGTAGC
* * * *
40220947 TTTAATTTGTTCCATTACACCGCCAGAGAAGTAAGATTCGCCGTTGTGG
261 TTTAATCTGTTCCACTACACCGCCAGAGAAGTAAGATTCACCGTTATGG
* * ** * *
40220996 GTTCAATCTATTTAACTGCAATGTTGGGGAAACAAGATTCGTCGTCGTAGCTTCAATTTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTTGGGGAAACAAGATCCACCGTCGTAGCTTCAATCTATTCCA
* *
40221061 CCACACTGCCAGGGAAGTAAGGGAAGTAAGATTCACCATTGTGGGTTCAATCTATTTAACTACAA
66 CCACACTGCCAGGGAAGTAAGGGAAGTAAGATTCACCATTGTAGCTTCAATCTATTTAACTACAA
* *
40221126 TGTCGGGGGAACAAGATTCGCCGTCATAGCTTCAATCTGTTCCACTACACTGCCAGGGAAGTAAG
131 TGTCGGGGAAACAAGATTCGCCGTCATAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAG
* *
40221191 ATTCGCCGTTGTGGGTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATCTACCATCGTAGC
196 ATTCGCCGTTGTGGCTCCAATCTATTTAACTGCAATGTCGGGGAAACAAGATCTACCATCGTAGC
* * * *
40221256 TTTAATCTGTTCCACTACATCGCTAGGGAAGTAAGGTTCACCGTTATGG
261 TTTAATCTGTTCCACTACACCGCCAGAGAAGTAAGATTCACCGTTATGG
* *
40221305 CTTCAATTTATTTAACTGCAATGTTGGGGAAACATGATCCACCGTCGTAGCTTCAATCTATTCCA
1 CTTCAATCTATTTAACTGCAATGTTGGGGAAACAAGATCCACCGTCGTAGCTTCAATCTATTCCA
* *
40221370 CTACATTGCCAGGGAAGTAAG
66 CCACACTGCCAGGGAAGTAAG
40221391 ATTCGCCGTT
Statistics
Matches: 338, Mismatches: 48, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
300 63 0.19
305 3 0.01
309 272 0.80
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (309 bp):
CTTCAATCTATTTAACTGCAATGTTGGGGAAACAAGATCCACCGTCGTAGCTTCAATCTATTCCA
CCACACTGCCAGGGAAGTAAGGGAAGTAAGATTCACCATTGTAGCTTCAATCTATTTAACTACAA
TGTCGGGGAAACAAGATTCGCCGTCATAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAG
ATTCGCCGTTGTGGCTCCAATCTATTTAACTGCAATGTCGGGGAAACAAGATCTACCATCGTAGC
TTTAATCTGTTCCACTACACCGCCAGAGAAGTAAGATTCACCGTTATGG
Found at i:40222962 original size:15 final size:14
Alignment explanation
Indices: 40222937--40222990 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 14
40222927 CACCTTAGCC
*
40222937 TTTCCAATTTTACTT
1 TTTCCATTTTTA-TT
40222952 TTTCCATTTTTTATT
1 TTTCCA-TTTTTATT
*
40222967 TTT-CATTTTCATT
1 TTTCCATTTTTATT
*
40222980 TTTTCATTTTT
1 TTTCCATTTTT
40222991 TTCATTTCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 10 0.29
14 8 0.24
15 11 0.32
16 5 0.15
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTCCATTTTTATT
Found at i:40222967 original size:21 final size:21
Alignment explanation
Indices: 40222943--40222989 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
40222933 AGCCTTTCCA
*
40222943 ATTTTACTTTTTCCATTTTTT-
1 ATTTTACATTTT-CATTTTTTC
*
40222964 ATTTTTCATTTTCATTTTTTC
1 ATTTTACATTTTCATTTTTTC
40222985 ATTTT
1 ATTTT
40222990 TTTCATTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (21 bp):
ATTTTACATTTTCATTTTTTC
Found at i:40222983 original size:8 final size:8
Alignment explanation
Indices: 40222950--40222997 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
40222940 CCAATTTTAC
*
40222950 TTTTTCCA
1 TTTTTTCA
40222958 TTTTTT-A
1 TTTTTTCA
40222965 -TTTTTCA
1 TTTTTTCA
40222972 --TTTTCA
1 TTTTTTCA
40222978 TTTTTTCA
1 TTTTTTCA
40222986 TTTTTTTCA
1 -TTTTTTCA
40222995 TTT
1 TTT
40222998 CATTTTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
6 11 0.31
7 2 0.06
8 14 0.40
9 8 0.23
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTTCA
Found at i:40222991 original size:22 final size:21
Alignment explanation
Indices: 40222951--40223005 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
40222941 CAATTTTACT
40222951 TTTTCCATTTTTTA-TTTTTCA
1 TTTT-CATTTTTTATTTTTTCA
40222972 TTTTCATTTTTTCATTTTTTTCA
1 TTTTCATTTTTT-A-TTTTTTCA
40222995 -TTTCATTTTTT
1 TTTTCATTTTTT
40223006 TACGACTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.26
21 5 0.16
22 11 0.35
23 7 0.23
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTCATTTTTTATTTTTTCA
Found at i:40222998 original size:28 final size:28
Alignment explanation
Indices: 40222950--40223003 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
40222940 CCAATTTTAC
*
40222950 TTTTTCCATTTTTTATTTTTCATTTTCA
1 TTTTTCCATTTTTTATATTTCATTTTCA
*
40222978 TTTTTTCATTTTTT-TCATTTCATTTT
1 TTTTTCCATTTTTTAT-ATTTCATTTT
40223004 TTTACGACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (28 bp):
TTTTTCCATTTTTTATATTTCATTTTCA
Found at i:40229100 original size:29 final size:30
Alignment explanation
Indices: 40229058--40229115 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
40229048 TTGGTTTAAT
*
40229058 GTATAATTCGATATATG-AATTTTAATTTG
1 GTATAATTAGATATATGAAATTTTAATTTG
* *
40229087 GTATAATTATATATATGAAATTTTGATTT
1 GTATAATTAGATATATGAAATTTTAATTT
40229116 TGATTCAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (30 bp):
GTATAATTAGATATATGAAATTTTAATTTG
Found at i:40229596 original size:2 final size:2
Alignment explanation
Indices: 40229589--40229630 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
40229579 TAATTCCTTA
*
40229589 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40229631 CATGTCAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40245527 original size:13 final size:12
Alignment explanation
Indices: 40245503--40245535 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
40245493 GAAGTGAAAG
40245503 AATAAT-AAATA
1 AATAATAAAATA
40245514 AATAGATAAAATA
1 AATA-ATAAAATA
40245527 AATAATAAA
1 AATAATAAA
40245536 TAACATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 7 0.35
13 9 0.45
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
AATAATAAAATA
Found at i:40246689 original size:19 final size:18
Alignment explanation
Indices: 40246665--40246706 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
40246655 AAATCTTTGA
40246665 TTTTTTTTGTATTCAATCT
1 TTTTTTTTGTATTCAAT-T
*
40246684 TTTTTTTTGTATTCGATT
1 TTTTTTTTGTATTCAATT
40246702 TTTTT
1 TTTTT
40246707 CTCTCAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.74
Consensus pattern (18 bp):
TTTTTTTTGTATTCAATT
Found at i:40248395 original size:17 final size:16
Alignment explanation
Indices: 40248364--40248408 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
40248354 AAAAAATTGT
*
40248364 TAAAAAATATAAAAATGG
1 TAAAAAAT-TTAAAAT-G
40248382 TAAAAAATTTAAAATG
1 TAAAAAATTTAAAATG
40248398 TATAAAAATTT
1 TA-AAAAATTT
40248409 TATAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 3 0.12
17 14 0.56
18 8 0.32
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (16 bp):
TAAAAAATTTAAAATG
Found at i:40248403 original size:18 final size:18
Alignment explanation
Indices: 40248364--40248450 Score: 52
Period size: 18 Copynumber: 4.6 Consensus size: 18
40248354 AAAAAATTGT
* *
40248364 TAAAAAATATAAAAATG-G
1 TAAAAAAT-TTAAAATGTA
40248382 TAAAAAATTTAAAATGTA
1 TAAAAAATTTAAAATGTA
* * *
40248400 TAAAAATTTTATAATATTTG
1 TAAAAAATTTA-AA-ATGTA
40248420 T-AAAAATTATAAGAATGATA
1 TAAAAAATT-TAA-AATG-TA
*
40248440 TAATAAATTTA
1 TAAAAAATTTA
40248451 TTTGAAATCT
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
17 7 0.13
18 18 0.34
19 11 0.21
20 11 0.21
21 6 0.11
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (18 bp):
TAAAAAATTTAAAATGTA
Found at i:40253364 original size:80 final size:80
Alignment explanation
Indices: 40253221--40253382 Score: 216
Period size: 80 Copynumber: 2.0 Consensus size: 80
40253211 GAATATTTGA
* * *
40253221 AATGGTTATATGAATTTATTCTATGGAAACATATACACGAAATGGTTATATGAATTGATTATATG
1 AATGGTTATATGAATTGATTCTATGGAAACAAATACACGAAATGGTTATATGAATTGACTATATG
40253286 GAAATAGATATATGG
66 GAAATAGATATATGG
* * * * * * * *
40253301 AATGGTTATGTGAATTGATTGTATGGAAATAAATATATGAAATGTTTATATGATTTGGCTATATG
1 AATGGTTATATGAATTGATTCTATGGAAACAAATACACGAAATGGTTATATGAATTGACTATATG
*
40253366 GAAATAGCTATATGG
66 GAAATAGATATATGG
40253381 AA
1 AA
40253383 ATAGTTTAAC
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
80 70 1.00
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (80 bp):
AATGGTTATATGAATTGATTCTATGGAAACAAATACACGAAATGGTTATATGAATTGACTATATG
GAAATAGATATATGG
Found at i:40253378 original size:40 final size:40
Alignment explanation
Indices: 40253213--40253384 Score: 191
Period size: 40 Copynumber: 4.3 Consensus size: 40
40253203 TGGAAAATGA
* * * * *
40253213 ATATTTGAAATGGTTATATGAATTTATTCTATGGAAACAT
1 ATATATGAAATGGTTATATGAATTGATTATATGGAAATAG
* *
40253253 ATACACGAAATGGTTATATGAATTGATTATATGGAAATAG
1 ATATATGAAATGGTTATATGAATTGATTATATGGAAATAG
* * * *
40253293 ATATATGGAATGGTTATGTGAATTGATTGTATGGAAATAA
1 ATATATGAAATGGTTATATGAATTGATTATATGGAAATAG
* * **
40253333 ATATATGAAATGTTTATATGATTTGGCTATATGGAAATAG
1 ATATATGAAATGGTTATATGAATTGATTATATGGAAATAG
*
40253373 CTATATGGAAAT
1 ATATAT-GAAAT
40253385 AGTTTAACAT
Statistics
Matches: 109, Mismatches: 22, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
40 104 0.95
41 5 0.05
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.38
Consensus pattern (40 bp):
ATATATGAAATGGTTATATGAATTGATTATATGGAAATAG
Found at i:40253525 original size:13 final size:13
Alignment explanation
Indices: 40253498--40253683 Score: 101
Period size: 13 Copynumber: 14.0 Consensus size: 13
40253488 TCGGGTGGAA
* *
40253498 AAATGAATATTTG
1 AAATGATTATATG
*
40253511 AAATGGTTATATG
1 AAATGATTATATG
*
40253524 AATTGATTATATGG
1 AAATGATTATAT-G
* *
40253538 AAA-CATATATACG
1 AAATGAT-TATATG
40253551 AAATGATTATATGG
1 AAATGATTATAT-G
40253565 AAATAGA-TATATG
1 AAAT-GATTATATG
* * *
40253578 GAATGGTTATGTG
1 AAATGATTATATG
* *
40253591 AATTGATTGTATGG
1 AAATGATTATAT-G
* *
40253605 AAATAAATATATG
1 AAATGATTATATG
*
40253618 AAATGTTTATATG
1 AAATGATTATATG
* **
40253631 -ATTCGGCTATATGG
1 AAAT-GATTATAT-G
40253645 AAAT-AGTTATATG
1 AAATGA-TTATATG
*
40253658 AAATGTTTATATG
1 AAATGATTATATG
*
40253671 AAATGTTTATATG
1 AAATGATTATATG
40253684 GATATAAATA
Statistics
Matches: 129, Mismatches: 32, Indels: 24
0.70 0.17 0.13
Matches are distributed among these distances:
12 3 0.02
13 88 0.68
14 34 0.26
15 4 0.03
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.38
Consensus pattern (13 bp):
AAATGATTATATG
Found at i:40253548 original size:27 final size:27
Alignment explanation
Indices: 40253518--40253587 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
40253508 TTGAAATGGT
* *
40253518 TATATGAATTGATTATATGGAAACATA
1 TATATGAAATGATTATATGGAAACAGA
* *
40253545 TATACGAAATGATTATATGGAAATAGA
1 TATATGAAATGATTATATGGAAACAGA
* *
40253572 TATATGGAATGGTTAT
1 TATATGAAATGATTAT
40253588 GTGAATTGAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.36
Consensus pattern (27 bp):
TATATGAAATGATTATATGGAAACAGA
Found at i:40253598 original size:40 final size:40
Alignment explanation
Indices: 40253545--40253694 Score: 158
Period size: 40 Copynumber: 3.8 Consensus size: 40
40253535 TGGAAACATA
* * * * *
40253545 TATACGAAATGATTATATGGAAATAGATATATGGAATGGT
1 TATATGAATTGATTATATGGAAATAAATATATGAAATGTT
* *
40253585 TATGTGAATTGATTGTATGGAAATAAATATATGAAATGTT
1 TATATGAATTGATTATATGGAAATAAATATATGAAATGTT
** **
40253625 TATATG-ATTCGGCTATATGGAAATAGTTATATGAAATGTT
1 TATATGAATT-GATTATATGGAAATAAATATATGAAATGTT
* * *
40253665 TATATGAAATGTTTATATGGATATAAATAT
1 TATATGAATTGATTATATGGAAATAAATAT
40253695 GTAAAAAGTG
Statistics
Matches: 89, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
39 3 0.03
40 84 0.94
41 2 0.02
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.39
Consensus pattern (40 bp):
TATATGAATTGATTATATGGAAATAAATATATGAAATGTT
Found at i:40253649 original size:278 final size:281
Alignment explanation
Indices: 40253093--40253666 Score: 881
Period size: 278 Copynumber: 2.0 Consensus size: 281
40253083 CAACATCGTG
* * *
40253093 TAGTTTAACATCCCGACCCATAGATCATGTGAGCATATACAGTTAATAGTCACAGCTTGTGTGAG
1 TAGTTTAACATCCCGACCCATAGATCATGTGAACACATACAGTTAACAGTCACAGCTTGTGTGAG
*
40253158 CATTATTCCCATGTAACCAATGTTATTTCATTGTGGTTCATTGGGTGGAAAATGAATATTTGAAA
66 CATTATTCCCATGTAACCAATGTTATTTCATTGTGGTTCATCGGGTGGAAAATGAATATTTGAAA
* *
40253223 TGGTTATATGAATTTATTCTATGGAAACATATACACGAAATGGTTATATGAATTGATTATATGGA
131 TGGTTATATGAATTGATTATATGGAAACATATACAC---A--G---TA-GAATTGATTATATGGA
40253288 AATAGATATATGGAATGGTTATGTGAATTGATTGTATGGAAATAAATATATGAAATGTTTATATG
187 AATAGATATATGGAATGGTTATGTGAATTGATTGTATGGAAATAAATATATGAAATGTTTATATG
*
40253353 ATTTGGCTATATGGAAATAGCTATATGGAAA
252 ATTCGGCTATATGGAAATAGCTATAT-GAAA
* * * *
40253384 TAGTTTAACATCTCGACCTATAGCTCGTGTGAACACATACAGTT-ACAGTCACAGCTTGTGTGAG
1 TAGTTTAACATCCCGACCCATAGATCATGTGAACACATACAGTTAACAGTCACAGCTTGTGTGAG
*
40253448 CATTATTCTCATGTAACCAATGTTATTTCATTGTGGTTCATCGGGTGGAAAAATGAATATTTGAA
66 CATTATTCCCATGTAACCAATGTTATTTCATTGTGGTTCATCGGGTGG-AAAATGAATATTTGAA
*
40253513 ATGGTTATATGAATTGATTATATGGAAACATATATAC-G-A-AA-TGATTATATGGAAATAGATA
130 ATGGTTATATGAATTGATTATATGGAAACATATACACAGTAGAATTGATTATATGGAAATAGATA
40253574 TATGGAATGGTTATGTGAATTGATTGTATGGAAATAAATATATGAAATGTTTATATGATTCGGCT
195 TATGGAATGGTTATGTGAATTGATTGTATGGAAATAAATATATGAAATGTTTATATGATTCGGCT
*
40253639 ATATGGAAATAGTTATATGAAA
260 ATATGGAAATAGCTATATGAAA
40253661 T-GTTTA
1 TAGTTTA
40253667 TATGAAATGT
Statistics
Matches: 268, Mismatches: 14, Indels: 17
0.90 0.05 0.06
Matches are distributed among these distances:
276 5 0.02
277 5 0.02
278 101 0.38
279 2 0.01
281 1 0.00
285 1 0.00
290 65 0.24
291 88 0.33
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (281 bp):
TAGTTTAACATCCCGACCCATAGATCATGTGAACACATACAGTTAACAGTCACAGCTTGTGTGAG
CATTATTCCCATGTAACCAATGTTATTTCATTGTGGTTCATCGGGTGGAAAATGAATATTTGAAA
TGGTTATATGAATTGATTATATGGAAACATATACACAGTAGAATTGATTATATGGAAATAGATAT
ATGGAATGGTTATGTGAATTGATTGTATGGAAATAAATATATGAAATGTTTATATGATTCGGCTA
TATGGAAATAGCTATATGAAA
Found at i:40253654 original size:67 final size:68
Alignment explanation
Indices: 40253510--40253670 Score: 184
Period size: 67 Copynumber: 2.4 Consensus size: 68
40253500 ATGAATATTT
*
40253510 GAAATGGTTATATGAATTGATTATATGGAAACATATATACGAAATGATTATATGGAAATAGATAT
1 GAAATGGTTATATGAATTGATTATATGGAAACAAATATACGAAATGATTATATGGAAATAGATAT
40253575 ATG
66 ATG
* * * * * * * *
40253578 G-AATGGTTATGTGAATTGATTGTATGGAAATAAATATATGAAATGTTTATAT-G-ATTCGGCTA
1 GAAATGGTTATATGAATTGATTATATGGAAACAAATATACGAAATGATTATATGGAAAT-AGATA
40253640 TATG
65 TATG
* * *
40253644 GAAATAGTTATATGAAATGTTTATATG
1 GAAATGGTTATATGAATTGATTATATG
40253671 AAATGTTTAT
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
65 2 0.03
66 9 0.12
67 65 0.84
68 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.20, T:0.37
Consensus pattern (68 bp):
GAAATGGTTATATGAATTGATTATATGGAAACAAATATACGAAATGATTATATGGAAATAGATAT
ATG
Found at i:40254870 original size:25 final size:25
Alignment explanation
Indices: 40254833--40254975 Score: 144
Period size: 25 Copynumber: 5.8 Consensus size: 25
40254823 AACACACCAC
* * *
40254833 AGCTCTCAAGAGCTTCCCAATATTT
1 AGCTCGCATGAGCTTCCCGATATTT
*
40254858 AGCTCGCATGAGCTTCCCGAT-TTC
1 AGCTCGCATGAGCTTCCCGATATTT
** *
40254882 AGCTCTTATGAGCTTCCCGATATAT
1 AGCTCGCATGAGCTTCCCGATATTT
* *
40254907 AGCTCGCATGAGCTTCCTGTTATTT
1 AGCTCGCATGAGCTTCCCGATATTT
* * * *
40254932 AGCTCACATGAGCTTTCCGTTATAT
1 AGCTCGCATGAGCTTCCCGATATTT
* *
40254957 AGCTCGGAAGAGCTTCCCG
1 AGCTCGCATGAGCTTCCCG
40254976 TTTACATGCT
Statistics
Matches: 96, Mismatches: 21, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
24 21 0.22
25 75 0.78
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (25 bp):
AGCTCGCATGAGCTTCCCGATATTT
Found at i:40254956 original size:50 final size:49
Alignment explanation
Indices: 40254832--40254994 Score: 168
Period size: 50 Copynumber: 3.3 Consensus size: 49
40254822 GAACACACCA
* * * *
40254832 CAGCTCTCAAGAGCTTCCCAATATTTAGCTCGCATGAGCTTCCCGATTT
1 CAGCTCACATGAGCTTCCCGATATATAGCTCGCATGAGCTTCCCGATTT
** *
40254881 CAGCTCTTATGAGCTTCCCGATATATAGCTCGCATGAGCTTCCTGTTATTT
1 CAGCTCACATGAGCTTCCCGATATATAGCTCGCATGAGCTTCCCG--ATTT
* * * *
40254932 -AGCTCACATGAGCTTTCCGTTATATAGCTCGGAAGAGCTTCCCG-TTT
1 CAGCTCACATGAGCTTCCCGATATATAGCTCGCATGAGCTTCCCGATTT
*
40254979 ACATGCTCATATGAGC
1 -CA-GCTCACATGAGC
40254995 ATACATGTAC
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
47 3 0.03
49 41 0.43
50 48 0.50
51 4 0.04
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (49 bp):
CAGCTCACATGAGCTTCCCGATATATAGCTCGCATGAGCTTCCCGATTT
Found at i:40254994 original size:25 final size:25
Alignment explanation
Indices: 40254833--40254994 Score: 114
Period size: 25 Copynumber: 6.5 Consensus size: 25
40254823 AACACACCAC
* * ** *
40254833 AGCTCTCAAGAGCTTCCCAATATTT
1 AGCTCACATGAGCTTCCCGTTATAT
* *
40254858 AGCTCGCATGAGCTTCCCGATT-T-C
1 AGCTCACATGAGCTTCCCG-TTATAT
** *
40254882 AGCTCTTATGAGCTTCCCGATATAT
1 AGCTCACATGAGCTTCCCGTTATAT
* * *
40254907 AGCTCGCATGAGCTTCCTGTTATTT
1 AGCTCACATGAGCTTCCCGTTATAT
*
40254932 AGCTCACATGAGCTTTCCGTTATAT
1 AGCTCACATGAGCTTCCCGTTATAT
** * *
40254957 AGCTCGGAAGAGCTTCCCGTT-TAC
1 AGCTCACATGAGCTTCCCGTTATAT
*
40254981 ATGCTCATATGAGC
1 A-GCTCACATGAGC
40254995 ATACATGTAC
Statistics
Matches: 107, Mismatches: 26, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
23 1 0.01
24 21 0.20
25 84 0.79
26 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.33
Consensus pattern (25 bp):
AGCTCACATGAGCTTCCCGTTATAT
Found at i:40265948 original size:31 final size:32
Alignment explanation
Indices: 40265904--40265976 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
40265894 AAAAAACATG
* * * *
40265904 AATTCAACTCTTTTTGAAAGGTTG-ATGGTCA
1 AATTTAACTCTTTTTAAAAGATTGAATAGTCA
* *
40265935 AATTTGACTCTTTTTAAAATATTGAATAGTCA
1 AATTTAACTCTTTTTAAAAGATTGAATAGTCA
40265967 AATTTAACTC
1 AATTTAACTC
40265977 ATAAAAAGAG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 19 0.56
32 15 0.44
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (32 bp):
AATTTAACTCTTTTTAAAAGATTGAATAGTCA
Found at i:40267835 original size:15 final size:15
Alignment explanation
Indices: 40267811--40267848 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
40267801 AAATAGTTTT
40267811 AAAA-AATAATGATA
1 AAAATAATAATGATA
40267825 AAAATAATAATGATA
1 AAAATAATAATGATA
*
40267840 ATAATAATA
1 AAAATAATA
40267849 GTAATTGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (15 bp):
AAAATAATAATGATA
Found at i:40269742 original size:9 final size:9
Alignment explanation
Indices: 40269728--40269770 Score: 68
Period size: 9 Copynumber: 4.7 Consensus size: 9
40269718 ATAGATTTGC
40269728 AAAATAAAT
1 AAAATAAAT
40269737 AAAATAAAT
1 AAAATAAAT
40269746 AAAATAAGAT
1 AAAATAA-AT
*
40269756 CAAATAAAT
1 AAAATAAAT
40269765 AAAATA
1 AAAATA
40269771 GAAAGAGACG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (9 bp):
AAAATAAAT
Found at i:40269762 original size:19 final size:18
Alignment explanation
Indices: 40269728--40269770 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
40269718 ATAGATTTGC
40269728 AAAATAAATAAAATAAAT
1 AAAATAAATAAAATAAAT
*
40269746 AAAATAAGATCAAATAAAT
1 AAAATAA-ATAAAATAAAT
40269765 AAAATA
1 AAAATA
40269771 GAAAGAGACG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAATAAATAAAATAAAT
Found at i:40270868 original size:44 final size:44
Alignment explanation
Indices: 40270755--40270994 Score: 252
Period size: 44 Copynumber: 5.5 Consensus size: 44
40270745 NNNNNNNNNN
* *
40270755 ACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAAT
1 ACATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAAT
*** *
40270800 ATGGGAAGACAAGATCTGC-ATCTTCGAT-TCACTTCACGCCAAT
1 ACATGAAGACAAGATCTGCTATCTTCGATCT-ACTTCACACCAAT
* * *
40270843 ACATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCCACCAAT
1 ACATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAAT
*** * *
40270888 ATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCACTCCAAT
1 ACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAAT
* * * * *
40270931 ACATGAAGATAGGACCTGCTATCTTTGATCTACTTCACGCCAAT
1 ACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAAT
*
40270975 GCATGAAGACAAGATCTGCT
1 ACATGAAGACAAGATCTGCT
40270995 TTAATAACTT
Statistics
Matches: 156, Mismatches: 34, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
43 41 0.26
44 77 0.49
45 38 0.24
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (44 bp):
ACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAAT
Found at i:40270904 original size:88 final size:88
Alignment explanation
Indices: 40270755--40270966 Score: 352
Period size: 88 Copynumber: 2.4 Consensus size: 88
40270745 NNNNNNNNNN
40270755 ACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCA
1 ACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCA
*
40270820 TCTTCGATTCACTTCACGCCAAT
66 TCTTCGATCCACTTCACGCCAAT
*
40270843 ACATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCA
1 ACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCA
*
40270908 TCTTCGATCCACTTCACTCCAAT
66 TCTTCGATCCACTTCACGCCAAT
* * * * *
40270931 ACATGAAGATAGGACCTGCTATCTTTGATCTACTTC
1 ACATGAAGACAAGATCTGCTTTCTTCGATCTACTTC
40270967 ACGCCAATGC
Statistics
Matches: 115, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 115 1.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (88 bp):
ACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCA
TCTTCGATCCACTTCACGCCAAT
Found at i:40285467 original size:107 final size:107
Alignment explanation
Indices: 40285281--40285525 Score: 490
Period size: 107 Copynumber: 2.3 Consensus size: 107
40285271 NNNNNNNNNN
40285281 GATTTTCCAAACGCGAAATATTGCCTTATTTTAAAAGTTTAAAAAGGATATTTGGCTATTTGGTC
1 GATTTTCCAAACGCGAAATATTGCCTTATTTTAAAAGTTTAAAAAGGATATTTGGCTATTTGGTC
40285346 GAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTT
66 GAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTT
40285388 GATTTTCCAAACGCGAAATATTGCCTTATTTTAAAAGTTTAAAAAGGATATTTGGCTATTTGGTC
1 GATTTTCCAAACGCGAAATATTGCCTTATTTTAAAAGTTTAAAAAGGATATTTGGCTATTTGGTC
40285453 GAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTT
66 GAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTT
40285495 GATTTTCCAAACGCGAAATATTGCCTTATTT
1 GATTTTCCAAACGCGAAATATTGCCTTATTT
40285526 AGAAAAAACT
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 138 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (107 bp):
GATTTTCCAAACGCGAAATATTGCCTTATTTTAAAAGTTTAAAAAGGATATTTGGCTATTTGGTC
GAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTT
Found at i:40285994 original size:7 final size:7
Alignment explanation
Indices: 40285978--40286007 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
40285968 GAATATAAAG
40285978 AATATAA
1 AATATAA
*
40285985 AATATGA
1 AATATAA
40285992 AATATAA
1 AATATAA
40285999 AATATAA
1 AATATAA
40286006 AA
1 AA
40286008 AGTATATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (7 bp):
AATATAA
Found at i:40287742 original size:12 final size:11
Alignment explanation
Indices: 40287723--40287752 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
40287713 AAAAATGAAG
40287723 AATAATAGACA
1 AATAATAGACA
40287734 AATTAATAGACA
1 AA-TAATAGACA
40287746 AATAATA
1 AATAATA
40287753 AAATAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (11 bp):
AATAATAGACA
Found at i:40291050 original size:27 final size:28
Alignment explanation
Indices: 40291014--40291078 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
40291004 ATAAAAAATA
40291014 ACCAAAATATTAT-AATTTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTTATTT
*
40291041 ATCAAAATATTATAAATTTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTTATTT
40291069 ACCAAAATAT
1 ACCAAAATAT
40291079 ACCAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 12 0.34
28 23 0.66
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.51
Consensus pattern (28 bp):
ACCAAAATATTATAAATTTTTTTTATTT
Found at i:40291170 original size:27 final size:27
Alignment explanation
Indices: 40291136--40291214 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 27
40291126 GGCCAATCAC
*
40291136 ATTGGCGGCACCAAAGGTGCCAAAGAT-
1 ATTGGCGGCACCAATGGTGCCAAAG-TG
* *
40291163 ATTTGCGGCACCAATGGTGCCAATGTG
1 ATTGGCGGCACCAATGGTGCCAAAGTG
40291190 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAATGGTGCCAAAG
40291215 GACTAAAATG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.28, C:0.23, G:0.30, T:0.19
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGTG
Found at i:40291545 original size:19 final size:19
Alignment explanation
Indices: 40291521--40291586 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
40291511 ATTAAAATAG
40291521 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
40291540 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
40291558 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
40291577 TTTAATTTAA
1 TTTAATTTAA
40291587 AAAAATTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:40292115 original size:198 final size:188
Alignment explanation
Indices: 40291731--40292116 Score: 585
Period size: 198 Copynumber: 2.0 Consensus size: 188
40291721 AAATAGAGTT
40291731 ATTAAATAAAAAAGTGAGTTGAAGGGGAATAAAAAGAAAATAATAAATAAGGAGGGCTTAGAAGG
1 ATTAAATAAAAAAGTGAGTTGAAGGGGAATAAAAAGAAAATAATAAATAAGGAGGGCTTAGAAGG
* *
40291796 CAATTAGTCATATTTCAATTTAGTGCGCACAGCAGCCGCAATTAACTTTCAAAATTCAAAATAGT
66 CAATTAGCCACATTTCAATTTAGTGCGCACAGCAGCCGCAATTAACTTTCAAAATTCAAAATAGT
* *
40291861 AAACTTGCATGTCAGGTCCTTGAAACTACCCTTAACTAACATTTTAGTCCTTTGGCAC
131 AAACTTGCATGTCAGGTCCTTAAAACTACCCTCAACTAACATTTTAGTCCTTTGGCAC
40291919 ATTAAATAAAAAAGTGAGTTGAAGGGGAATAAAAAGAAAATAATAAATAAAGGAGGGCTT-GAAG
1 ATTAAATAAAAAAGTGAGTTGAAGGGGAATAAAAAGAAAATAATAAAT-AAGGAGGGCTTAGAAG
* *
40291983 GCAATTAGCCACATTTCAATTTTAGTGCGCCCCACACGCACAGCACCATCAATTCACTTTCAAAA
65 GCAATTAGCCACATTTCAA-TTTAGTGCG---CACA-G--CAG--CC-GCAATTAACTTTCAAAA
* * *
40292048 TTTAAAATGGTAAATTTGCATGTCAGGTCCTTAAAACTACCCTCAACTAACATTTTAGTCCTTTG
120 TTCAAAATAGTAAACTTGCATGTCAGGTCCTTAAAACTACCCTCAACTAACATTTTAGTCCTTTG
40292113 GCAC
185 GCAC
40292117 CATTGGTGCC
Statistics
Matches: 178, Mismatches: 9, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
188 69 0.39
189 20 0.11
192 4 0.02
193 1 0.01
195 3 0.02
197 2 0.01
198 79 0.44
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (188 bp):
ATTAAATAAAAAAGTGAGTTGAAGGGGAATAAAAAGAAAATAATAAATAAGGAGGGCTTAGAAGG
CAATTAGCCACATTTCAATTTAGTGCGCACAGCAGCCGCAATTAACTTTCAAAATTCAAAATAGT
AAACTTGCATGTCAGGTCCTTAAAACTACCCTCAACTAACATTTTAGTCCTTTGGCAC
Found at i:40292148 original size:27 final size:27
Alignment explanation
Indices: 40292110--40292186 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
40292100 TTTTAGTCCT
40292110 TTGGCACCATTGGTGCCGCCAATCA-CA
1 TTGGCACCATTGGTGCCGCCAAT-ATCA
* * *
40292137 TTGGCACCATTGGCGCCACCAATATCT
1 TTGGCACCATTGGTGCCGCCAATATCA
*
40292164 TTGGCA-CATTTGGTGCTGCCAAT
1 TTGGCACCA-TTGGTGCCGCCAAT
40292187 GTGATTGGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
26 3 0.07
27 39 0.93
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATATCA
Found at i:40292286 original size:28 final size:28
Alignment explanation
Indices: 40292250--40292315 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
40292240 TGTTTTTGGT
*
40292250 ATATTTTGGTAAATAAAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
40292278 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
40292306 ATATTTTGGT
1 ATATTTTGGT
40292316 TATTTTTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:40293362 original size:21 final size:20
Alignment explanation
Indices: 40293332--40293390 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
40293322 TCCCATTTTT
* *
40293332 ATTAGAAAAATTAAAATGAA
1 ATTAAAAAAAATAAAATGAA
* *
40293352 TTCTAAAAAAAACAAAA-GAA
1 AT-TAAAAAAAATAAAATGAA
40293372 ATTAAAAAAAATAAAATGA
1 ATTAAAAAAAATAAAATGA
40293391 TTATTCCTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
19 13 0.42
20 7 0.23
21 11 0.35
ACGTcount: A:0.69, C:0.03, G:0.07, T:0.20
Consensus pattern (20 bp):
ATTAAAAAAAATAAAATGAA
Found at i:40293448 original size:20 final size:21
Alignment explanation
Indices: 40293423--40293470 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
40293413 TTTATCCCTG
*
40293423 TAAAAAGCCAACA-TTTCCTA
1 TAAAAACCCAACATTTTCCTA
*
40293443 TAAAAACCCAATATTTTCCTA
1 TAAAAACCCAACATTTTCCTA
40293464 TAAAAAC
1 TAAAAAC
40293471 TTAGATTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (21 bp):
TAAAAACCCAACATTTTCCTA
Found at i:40295960 original size:2 final size:2
Alignment explanation
Indices: 40295913--40295949 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
40295903 CTACTGAGCA
*
40295913 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40295950 ACTTATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:40300528 original size:43 final size:43
Alignment explanation
Indices: 40300467--40300691 Score: 308
Period size: 43 Copynumber: 5.3 Consensus size: 43
40300457 NNNNNNNNNN
* *
40300467 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGAAAAAACGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGTAAAAGCGCCGC
* **
40300510 TAAAGGTCATAGTCTTTAGCGGCGTTTGTGGTAAAAGCATCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGTAAAAGCGCCGC
* * * **
40300553 TAAAGATCGTGGTCTATAGCGGCGTTTGTGGTAAAAGCGCCAT
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGTAAAAGCGCCGC
* *
40300596 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCTGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGTAAAAGCGCCGC
* * *
40300639 TAAAGGTCATGGTCTATAGCGGCGTTTGTGG-GAAAGTGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGTAAAAGCGCCGC
40300681 TAAAGGTCATG
1 TAAAGGTCATG
40300692 ACTTTTAGCG
Statistics
Matches: 158, Mismatches: 24, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 19 0.12
43 139 0.88
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (43 bp):
TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGTAAAAGCGCCGC
Found at i:40300902 original size:2 final size:2
Alignment explanation
Indices: 40300895--40300922 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40300885 ATATAGACAC
40300895 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40300923 GTGTTCTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40302229 original size:11 final size:11
Alignment explanation
Indices: 40302215--40302281 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
40302205 ATTTTTATTT
40302215 TTTTAAAATAC
1 TTTTAAAATAC
40302226 TTTTAAAATAC
1 TTTTAAAATAC
*
40302237 TTTTTTTAAAT--
1 --TTTTAAAATAC
*
40302248 TTTTTAAA-A-
1 TTTTAAAATAC
*
40302257 -TTTAAAATAT
1 TTTTAAAATAC
40302267 TTTTAAAATAC
1 TTTTAAAATAC
40302278 TTTT
1 TTTT
40302282 TTTAATTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
8 6 0.13
9 9 0.19
11 24 0.51
13 8 0.17
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:40302261 original size:41 final size:39
Alignment explanation
Indices: 40302216--40302296 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 39
40302206 TTTTTATTTT
40302216 TTTAAAATACTTTTAAAATACTTTTTTTAAATTTTTTAAAA
1 TTTAAAATACTTTTAAAATACTTTTTTT-AA-TTTTTAAAA
*
40302257 TTTAAAATATTTTTAAAATACTTTTTTTAATTTTTAAAA
1 TTTAAAATACTTTTAAAATACTTTTTTTAATTTTTAAAA
40302296 T
1 T
40302297 AAATTTTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 10 0.26
40 2 0.05
41 27 0.69
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (39 bp):
TTTAAAATACTTTTAAAATACTTTTTTTAATTTTTAAAA
Found at i:40302303 original size:20 final size:21
Alignment explanation
Indices: 40302265--40302312 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
40302255 AATTTAAAAT
**
40302265 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATACAATTTTTA
40302286 ATTTTTAAAATA-AATTTTTA
1 ATTTTTAAAATACAATTTTTA
*
40302306 ATATTTA
1 ATTTTTA
40302313 TTAAAAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTTTTAAAATACAATTTTTA
Found at i:40302303 original size:21 final size:22
Alignment explanation
Indices: 40302262--40302318 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
40302252 TAAAATTTAA
**
40302262 AATATTTTTAAAATACTTTTTT
1 AATATTTTTAAAATAAATTTTT
*
40302284 TA-ATTTTTAAAATAAATTTTT
1 AATATTTTTAAAATAAATTTTT
40302305 AATATTTATTAAAA
1 AATATTT-TTAAAA
40302319 AATGGGCCGG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 18 0.62
22 5 0.17
23 6 0.21
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
AATATTTTTAAAATAAATTTTT
Found at i:40313118 original size:12 final size:12
Alignment explanation
Indices: 40313101--40313125 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40313091 TTACATGCAA
40313101 ACCATGAAGCAG
1 ACCATGAAGCAG
40313113 ACCATGAAGCAG
1 ACCATGAAGCAG
40313125 A
1 A
40313126 TCAAGTTGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.24, T:0.08
Consensus pattern (12 bp):
ACCATGAAGCAG
Found at i:40319110 original size:6 final size:6
Alignment explanation
Indices: 40319090--40319124 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
40319080 TAAAAACAAC
* *
40319090 TAAAAA TAACAA TAAACA TAAAAA TAAAAA TAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
40319125 CAAATAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:40319110 original size:12 final size:12
Alignment explanation
Indices: 40319076--40319122 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
40319066 TAAGAAAGTG
*
40319076 ACAATAAAAACA
1 ACAATAAAAATA
40319088 AC--TAAAAATA
1 ACAATAAAAATA
*
40319098 ACAATAAACATA
1 ACAATAAAAATA
*
40319110 AAAATAAAAATA
1 ACAATAAAAATA
40319122 A
1 A
40319123 AACAAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 9 0.31
12 20 0.69
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.15
Consensus pattern (12 bp):
ACAATAAAAATA
Found at i:40325519 original size:18 final size:20
Alignment explanation
Indices: 40325478--40325520 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
40325468 AGAGAAACGG
*
40325478 AAGAAATAAGAAGGAAGCAG
1 AAGAAATAAGAAGGAAGCAA
*
40325498 AAGAAA-AA-AAGGAAGGAA
1 AAGAAATAAGAAGGAAGCAA
40325516 AAGAA
1 AAGAA
40325521 GGGAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 13 0.62
19 2 0.10
20 6 0.29
ACGTcount: A:0.67, C:0.02, G:0.28, T:0.02
Consensus pattern (20 bp):
AAGAAATAAGAAGGAAGCAA
Found at i:40329009 original size:16 final size:15
Alignment explanation
Indices: 40328978--40329019 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
40328968 ACAAAATCAA
*
40328978 ATAAAATTTAATTAT
1 ATAAAAGTTAATTAT
40328993 ATAAAAGTTACATTAT
1 ATAAAAGTTA-ATTAT
*
40329009 ATAAAAATTAA
1 ATAAAAGTTAA
40329020 ATGAGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAAAGTTAATTAT
Found at i:40329354 original size:19 final size:19
Alignment explanation
Indices: 40329323--40329393 Score: 88
Period size: 19 Copynumber: 3.5 Consensus size: 19
40329313 AAATTTAATT
40329323 ATAAAATAATTACAATATTC
1 ATAAAA-AATTACAATATTC
40329343 ATAAAAAATTACAATATTC
1 ATAAAAAATTACAATATTC
*
40329362 ATACAAAAAAATTAGAATATTC
1 AT---AAAAAATTACAATATTC
*
40329384 ATACAAAATT
1 ATAAAAAATT
40329394 CTAATCCAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
19 22 0.48
20 6 0.13
22 18 0.39
ACGTcount: A:0.58, C:0.10, G:0.01, T:0.31
Consensus pattern (19 bp):
ATAAAAAATTACAATATTC
Found at i:40329370 original size:22 final size:22
Alignment explanation
Indices: 40329325--40329391 Score: 95
Period size: 22 Copynumber: 3.2 Consensus size: 22
40329315 ATTTAATTAT
*
40329325 AAAATAATTACAATATTCAT--
1 AAAAAAATTACAATATTCATAC
40329345 -AAAAAATTACAATATTCATAC
1 AAAAAAATTACAATATTCATAC
*
40329366 AAAAAAATTAGAATATTCATAC
1 AAAAAAATTACAATATTCATAC
40329388 AAAA
1 AAAA
40329392 TTCTAATCCA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.43
22 24 0.57
ACGTcount: A:0.60, C:0.10, G:0.01, T:0.28
Consensus pattern (22 bp):
AAAAAAATTACAATATTCATAC
Found at i:40329477 original size:12 final size:12
Alignment explanation
Indices: 40329460--40329485 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40329450 AAAAGTTCAC
40329460 AATATCTTCTAA
1 AATATCTTCTAA
40329472 AATATCTTCTAA
1 AATATCTTCTAA
40329484 AA
1 AA
40329486 AATTCACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATCTTCTAA
Found at i:40329792 original size:27 final size:27
Alignment explanation
Indices: 40329717--40329781 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
40329707 AGAAGGCCAC
40329717 CATTGGCGCCTCTCTATGAGGCACCTT
1 CATTGGCGCCTCTCTATGAGGCACCTT
40329744 CATTGGCGCCTCTCTATGAGGCACCTT
1 CATTGGCGCCTCTCTATGAGGCACCTT
*
40329771 TATTGGCGCCT
1 CATTGGCGCCT
40329782 ACCTGATAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.14, C:0.32, G:0.23, T:0.31
Consensus pattern (27 bp):
CATTGGCGCCTCTCTATGAGGCACCTT
Found at i:40329881 original size:17 final size:18
Alignment explanation
Indices: 40329859--40329892 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40329849 AAAATATATA
40329859 AAAAAAATATT-TTATTC
1 AAAAAAATATTATTATTC
*
40329876 AAAAAATTATTATTATT
1 AAAAAAATATTATTATT
40329893 TTTTATTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAAAAATATTATTATTC
Found at i:40336156 original size:6 final size:6
Alignment explanation
Indices: 40336145--40336200 Score: 103
Period size: 6 Copynumber: 9.3 Consensus size: 6
40336135 TGGAGCTGGT
*
40336145 GCAGGA GCAGGA GCAGGA GCAGGA GCAGAA GCAGGA GCAGGA GCAGGA
1 GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA GCAGGA
40336193 GCAGGA GC
1 GCAGGA GC
40336201 CACAACCGCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.34, C:0.18, G:0.48, T:0.00
Consensus pattern (6 bp):
GCAGGA
Found at i:40338413 original size:2 final size:2
Alignment explanation
Indices: 40338406--40339246 Score: 1655
Period size: 2 Copynumber: 420.5 Consensus size: 2
40338396 ATCTTCCTAT
40338406 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40338448 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40338490 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40338532 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40338574 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40338616 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40338658 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40338700 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40338742 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40338784 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40338826 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40338868 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40338910 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40338952 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40338994 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40339036 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40339078 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40339120 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40339162 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
40339204 TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC CC TC TC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40339246 T
1 T
40339247 AACAAAATAT
Statistics
Matches: 833, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
2 833 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:40348138 original size:6 final size:6
Alignment explanation
Indices: 40348127--40348180 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
40348117 GAGCTCGTGG
* * *
40348127 AGGAGC AGGAGC AGCAGC AGCAGC AGGAGC AGGAGC AGAAGC AGGAGC
1 AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC
40348175 AGGAGC
1 AGGAGC
40348181 CACAACCGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.35, C:0.20, G:0.44, T:0.00
Consensus pattern (6 bp):
AGGAGC
Found at i:40350393 original size:2 final size:2
Alignment explanation
Indices: 40350386--40351226 Score: 1655
Period size: 2 Copynumber: 420.5 Consensus size: 2
40350376 ATCTTCCTAT
40350386 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40350428 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40350470 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40350512 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40350554 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40350596 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40350638 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40350680 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40350722 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40350764 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40350806 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40350848 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40350890 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40350932 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40350974 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40351016 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40351058 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40351100 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40351142 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
40351184 TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC CC TC TC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40351226 T
1 T
40351227 AACAAAATAT
Statistics
Matches: 833, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
2 833 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:40352424 original size:454 final size:459
Alignment explanation
Indices: 40351544--40352459 Score: 1653
Period size: 454 Copynumber: 2.0 Consensus size: 459
40351534 ACGACTTGCT
* *
40351544 TGTTTATAAAACTCCAGAATTGCTATTTGTCTTTTTTTTTTTAGTTAATTGTAAGTCACTATTAA
1 TGTTTATAAAACTCCAGAATTGCTATTTGTC-TTTTTTTTTCAGTTAATTGTAAGTCAATATTAA
*
40351609 GAAAATGTAAGTGACTGCCTTGGCAATTTTGAGCAGAATCCTCCTAATGCTCTTCCACATGTCCT
65 GAAAATGTAAGTGACTGCCTTGGCAATTTTGAGAAGAATCCTCCTAATGCTCTTCCACATGTCCT
40351674 CTCTCTCTCTATAAAAAGATCGTGGTTACCTCCCCCCCACAATATCGTTCAAGGTTAGTAATTAT
130 CTCTCTCTCTATAAAAAGATCGTGGTTACCTCCCCCCCACAATATCGTTCAAGGTTAGTAATTAT
*
40351739 ATAATATAGGGTTGATTGAATTGGTGTGTTTTTTTTTTTTTTTGTGGGAGGGGTATATGATGCTT
195 ATAACATAGGGTTGATTGAATTGGTGTG-TTTTTTTTTTTTTTGTGGGAGGGGTATATGATGCTT
40351804 TCATCCTTATCTTTTGCTAGTTCCTCCATGAAGACAAGAAGACCAAGCCAATTGGTTTAGTAAAT
259 TCATCCTTATCTTTTGCTAGTTCCTCCATGAAGACAAGAAGACCAAGCCAATTGGTTTAGTAAAT
*
40351869 TGACGTAGTGGTTAATTGTATAAGCATTTTAACACAAGTCTTGCTTGTTTATAAGACTCCAAAAT
324 TGACGTAGTGGTTAACTGTATAAGCATTTTAACACAAGTCTTGCTTGTTTATAAGACTCCAAAAT
*
40351934 TGTTACTTGTCCCTTCTATTTAAGCAAATTGTAAGTCGGTATTATGAAAGTATAAGTGATTCTCT
389 TGTTACTTGTCCCTTCTATTTAAGCAAATTGTAAGTCGATATTATGAAAGTATAAGTGATTCTCT
40351999 TGATAG
454 TGATAG
* *
40352005 TGTTTATAAGACTCCAGAATTGTTATTTGTC-TTTTTTTTCAGTTAATTGTAAGTCAATATTAAG
1 TGTTTATAAAACTCCAGAATTGCTATTTGTCTTTTTTTTTCAGTTAATTGTAAGTCAATATTAAG
* *
40352069 AAAATGTAAGTGACTGCCTTGGCAATTTTGTGAAGAATCCTTCTAATGCTCTTCCACATGTCCTC
66 AAAATGTAAGTGACTGCCTTGGCAATTTTGAGAAGAATCCTCCTAATGCTCTTCCACATGTCCTC
*
40352134 TCTCTCTCTATAAAAAGATCGTGGTTACCTCTCCCCCACAATATCGTTCAAGGTTAGTAATTATA
131 TCTCTCTCTATAAAAAGATCGTGGTTACCTCCCCCCCACAATATCGTTCAAGGTTAGTAATTATA
40352199 TAACATAGGGTTGATTGAATT-G-GTG-TTTTTTTTTTTTTGTGGG-GGGGTATATGATGCTTTC
196 TAACATAGGGTTGATTGAATTGGTGTGTTTTTTTTTTTTTTGTGGGAGGGGTATATGATGCTTTC
*
40352260 ATCCTTATCTTTTGCTGGTTCCTCCATGAAGACAAGAAGACCAAGCCAATTGGTTTAGTAAATTG
261 ATCCTTATCTTTTGCTAGTTCCTCCATGAAGACAAGAAGACCAAGCCAATTGGTTTAGTAAATTG
40352325 ACGTAGTGGTTAACTGTATAAGCATTTTAACACAAGTCTTGCTTGTTTATAAGACTCCAAAATTG
326 ACGTAGTGGTTAACTGTATAAGCATTTTAACACAAGTCTTGCTTGTTTATAAGACTCCAAAATTG
* *
40352390 TTACTTGTCTCTTCTATTTAAGCAAATTGTAAGTCGATATTATGAAAGTTTAAGTGATTCTCTTG
391 TTACTTGTCCCTTCTATTTAAGCAAATTGTAAGTCGATATTATGAAAGTATAAGTGATTCTCTTG
40352455 ATAG
456 ATAG
40352459 T
1 T
40352460 TTTGAGAAGA
Statistics
Matches: 441, Mismatches: 14, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
454 213 0.48
455 18 0.04
457 3 0.01
458 1 0.00
459 177 0.40
461 29 0.07
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.39
Consensus pattern (459 bp):
TGTTTATAAAACTCCAGAATTGCTATTTGTCTTTTTTTTTCAGTTAATTGTAAGTCAATATTAAG
AAAATGTAAGTGACTGCCTTGGCAATTTTGAGAAGAATCCTCCTAATGCTCTTCCACATGTCCTC
TCTCTCTCTATAAAAAGATCGTGGTTACCTCCCCCCCACAATATCGTTCAAGGTTAGTAATTATA
TAACATAGGGTTGATTGAATTGGTGTGTTTTTTTTTTTTTTGTGGGAGGGGTATATGATGCTTTC
ATCCTTATCTTTTGCTAGTTCCTCCATGAAGACAAGAAGACCAAGCCAATTGGTTTAGTAAATTG
ACGTAGTGGTTAACTGTATAAGCATTTTAACACAAGTCTTGCTTGTTTATAAGACTCCAAAATTG
TTACTTGTCCCTTCTATTTAAGCAAATTGTAAGTCGATATTATGAAAGTATAAGTGATTCTCTTG
ATAG
Found at i:40357353 original size:12 final size:12
Alignment explanation
Indices: 40357336--40357362 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40357326 TAGATGAAGC
40357336 TGCTACAGTTTG
1 TGCTACAGTTTG
40357348 TGCTACAGTTTG
1 TGCTACAGTTTG
40357360 TGC
1 TGC
40357363 AGTCTGAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.19, G:0.26, T:0.41
Consensus pattern (12 bp):
TGCTACAGTTTG
Found at i:40373802 original size:16 final size:16
Alignment explanation
Indices: 40373758--40373805 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
40373748 AAATTTCATT
40373758 AATAAAAAT-G-ATAA
1 AATAAAAATAGAATAA
*
40373772 AGTAAAAATAGAATAA
1 AATAAAAATAGAATAA
40373788 AATAATAAATA-AATAA
1 AATAA-AAATAGAATAA
40373804 AA
1 AA
40373806 AAACAGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 8 0.28
15 1 0.03
16 15 0.52
17 5 0.17
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (16 bp):
AATAAAAATAGAATAA
Found at i:40381827 original size:15 final size:16
Alignment explanation
Indices: 40381797--40381837 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
40381787 AAATCATTTG
*
40381797 AACCCAAAATGGCCCA
1 AACCCAAAATGACCCA
40381813 AACCC-AAATGACCCA
1 AACCCAAAATGACCCA
40381828 AACCCTAAAA
1 AACCC-AAAA
40381838 ACCTGAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 14 0.64
16 5 0.23
17 3 0.14
ACGTcount: A:0.49, C:0.37, G:0.07, T:0.07
Consensus pattern (16 bp):
AACCCAAAATGACCCA
Found at i:40382359 original size:18 final size:19
Alignment explanation
Indices: 40382312--40382359 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
40382302 TGTAACTAGT
*
40382312 GGTTTTATTTTCTTTTTAA
1 GGTTCTATTTTCTTTTTAA
*
40382331 GGTTTTATTTTCTTTTTAA
1 GGTTCTATTTTCTTTTTAA
*
40382350 -GTTCTCTTTT
1 GGTTCTATTTT
40382360 TCTAGGCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.12, C:0.08, G:0.10, T:0.69
Consensus pattern (19 bp):
GGTTCTATTTTCTTTTTAA
Found at i:40382362 original size:19 final size:19
Alignment explanation
Indices: 40382312--40382350 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
40382302 TGTAACTAGT
40382312 GGTTTTATTTTCTTTTTAA
1 GGTTTTATTTTCTTTTTAA
40382331 GGTTTTATTTTCTTTTTAA
1 GGTTTTATTTTCTTTTTAA
40382350 G
1 G
40382351 TTCTCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.05, G:0.13, T:0.67
Consensus pattern (19 bp):
GGTTTTATTTTCTTTTTAA
Found at i:40393626 original size:60 final size:60
Alignment explanation
Indices: 40393513--40393626 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
40393503 CGGCTTTCGT
** * * * *
40393513 TAATATTTTCAAGATGGTTTGTTTTGATCATTAAACTTTAAAAAAATATAATTTGGTGAC
1 TAATATTTTCAAGATAATCTGATTTGATCACTAAACTTTAAAAAAATACAATTTGGTGAC
**
40393573 TAATATTTTCAAGATAATCTGATTTGATCACTAAACTTTAAAAAGTTACAATTT
1 TAATATTTTCAAGATAATCTGATTTGATCACTAAACTTTAAAAAAATACAATTT
40393627 AATCACTTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.42
Consensus pattern (60 bp):
TAATATTTTCAAGATAATCTGATTTGATCACTAAACTTTAAAAAAATACAATTTGGTGAC
Found at i:40393639 original size:60 final size:60
Alignment explanation
Indices: 40393513--40393641 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 60
40393503 CGGCTTTCGT
** * * * * ** *
40393513 TAATATTTTCAAGATGGTTTGTTTTGATCATTAAACTTTAAAAAAATATAATTTGGTGAC
1 TAATATTTTCAAGATAATCTGATTTGATCACTAAACTTTAAAAAAATACAATTTAATCAC
**
40393573 TAATATTTTCAAGATAATCTGATTTGATCACTAAACTTTAAAAAGTTACAATTTAATCAC
1 TAATATTTTCAAGATAATCTGATTTGATCACTAAACTTTAAAAAAATACAATTTAATCAC
*
40393633 TTATATTTT
1 TAATATTTT
40393642 TAAAATGATT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.43
Consensus pattern (60 bp):
TAATATTTTCAAGATAATCTGATTTGATCACTAAACTTTAAAAAAATACAATTTAATCAC
Found at i:40394780 original size:2 final size:2
Alignment explanation
Indices: 40394773--40394805 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40394763 ATAATACTCA
40394773 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40394806 AAGTGAATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40412976 original size:86 final size:86
Alignment explanation
Indices: 40412836--40413007 Score: 335
Period size: 86 Copynumber: 2.0 Consensus size: 86
40412826 TAACATCTGG
*
40412836 GTATGAAGAAAGGGATTGATACCTTCGCCTATGGAGGCAAAGCCTTATATATATCCACTTTATGT
1 GTATGAAGAAAGGGATTGATACCTTCGCCTATGGAGGCAAAGCCGTATATATATCCACTTTATGT
40412901 AAAGAGATTTGTTTTCTAGTA
66 AAAGAGATTTGTTTTCTAGTA
40412922 GTATGAAGAAAGGGATTGATACCTTCGCCTATGGAGGCAAAGCCGTATATATATCCACTTTATGT
1 GTATGAAGAAAGGGATTGATACCTTCGCCTATGGAGGCAAAGCCGTATATATATCCACTTTATGT
40412987 AAAGAGATTTGTTTTCTAGTA
66 AAAGAGATTTGTTTTCTAGTA
40413008 AAGTTGTTGT
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (86 bp):
GTATGAAGAAAGGGATTGATACCTTCGCCTATGGAGGCAAAGCCGTATATATATCCACTTTATGT
AAAGAGATTTGTTTTCTAGTA
Found at i:40415799 original size:17 final size:17
Alignment explanation
Indices: 40415778--40415816 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
40415768 CAAAAAAGAG
*
40415778 CAAAAAAATAA-AAAAC
1 CAAAAAAAAAATAAAAC
*
40415794 CAAAAAAAAAATAAAAG
1 CAAAAAAAAAATAAAAC
40415811 CAAAAA
1 CAAAAA
40415817 CAAGAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.82, C:0.10, G:0.03, T:0.05
Consensus pattern (17 bp):
CAAAAAAAAAATAAAAC
Found at i:40416288 original size:18 final size:18
Alignment explanation
Indices: 40416265--40416301 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40416255 AATTCACTTG
40416265 AAAAAAGAAACA-AAAAGA
1 AAAAAAGAAA-AGAAAAGA
40416283 AAAAAAGAAAAGAAAAGA
1 AAAAAAGAAAAGAAAAGA
40416301 A
1 A
40416302 CAACAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.84, C:0.03, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAGAAAAGA
Found at i:40417650 original size:50 final size:50
Alignment explanation
Indices: 40417595--40418356 Score: 401
Period size: 50 Copynumber: 15.3 Consensus size: 50
40417585 CAAAGCTACG
* * * * * *
40417595 ACGGCGAATCTTGCTTCCCTGGTATTGCAATTAAAAAGATTGAAACCGCA
1 ACGGTGAATCTTACTTCCCTGGCATTGCAATTAAACAGATTGAAGCCACA
* * * ** * *
40417645 ACGGCGAATCTTACTTTCCTGGCGA-TGCAGTGGATCAGATTGAAGCTACA
1 ACGGTGAATCTTACTTCCCTGGC-ATTGCAATTAAACAGATTGAAGCCACA
* * * * * *
40417695 ACGGTGAATCTT-GTTCCCTGACATTACATTTAAAGATATTGAAGCCACA
1 ACGGTGAATCTTACTTCCCTGGCATTGCAATTAAACAGATTGAAGCCACA
* * * * **** * * * **
40417744 ACGGCGAATCTCACTTCCCTGGCAATACAGCGGAGCAGATTAAAGCTATG
1 ACGGTGAATCTTACTTCCCTGGCATTGCAATTAAACAGATTGAAGCCACA
* * * * * *
40417794 ACAGTGAATCTTGCTTCCCTAGTATTGCAATTAAAAAGATTGAAGCCGCA
1 ACGGTGAATCTTACTTCCCTGGCATTGCAATTAAACAGATTGAAGCCACA
* * * * ** * *
40417844 ACGGTGAATCTTACTTTCCTAGCGA-TGTAGTGGATCAGATTGAAGCTACA
1 ACGGTGAATCTTACTTCCCTGGC-ATTGCAATTAAACAGATTGAAGCCACA
** * * * *
40417894 ACGGCAAATCTT-GTTCCCCGACATTGCAATTAAAGAGATTGAAGCCACA
1 ACGGTGAATCTTACTTCCCTGGCATTGCAATTAAACAGATTGAAGCCACA
* * * * * * * *
40417943 ACGGTGAATCTCACTTCCCTGGCAGTAC-AGTAGAGCAGATTAAAGCTACG
1 ACGGTGAATCTTACTTCCCTGGCATTGCAATTA-AACAGATTGAAGCCACA
* * * *
40417993 ACGGTGAATCTTACTTTCCTGGTATTGCAATTAAAAAGATTGAAGCCGCA
1 ACGGTGAATCTTACTTCCCTGGCATTGCAATTAAACAGATTGAAGCCACA
* * * * ** * *
40418043 ACGGTGAATCTTTCTTTCCTGGCGA-TGTAGTGGATCAGATTGAAGCTACA
1 ACGGTGAATCTTACTTCCCTGGC-ATTGCAATTAAACAGATTGAAGCCACA
* * * * * * *
40418093 ACGGCGGATCTT-GTTCCCCGACATTG-ATTTTAAAGAGATTGAAGCCACA
1 ACGGTGAATCTTACTTCCCTGGCATTGCA-ATTAAACAGATTGAAGCCACA
* * * ** * ** * * * *
40418142 ACGGCGAATCTCACTTCCCTGGCAGTATAGTGGAGCAGATTAAAGCTACG
1 ACGGTGAATCTTACTTCCCTGGCATTGCAATTAAACAGATTGAAGCCACA
* * * * *
40418192 ACGGTGAATCTTGCTTCCCTGGTATTGCAATTAAAAAGATTGAAGTCGCA
1 ACGGTGAATCTTACTTCCCTGGCATTGCAATTAAACAGATTGAAGCCACA
* * * ** * * *
40418242 ACAGTGAATCTTACTTTCCTGGCGA-TGCAGTGGATCAGATTTAAGCTACA
1 ACGGTGAATCTTACTTCCCTGGC-ATTGCAATTAAACAGATTGAAGCCACA
* * * * *
40418292 ACGGTGAATCTT-GTTCCCCGACATTGCAATTAAAGAGATCGAAGCCACA
1 ACGGTGAATCTTACTTCCCTGGCATTGCAATTAAACAGATTGAAGCCACA
**
40418341 ACGGCAAATCTTACTT
1 ACGGTGAATCTTACTT
40418357 TCCTTGGCGG
Statistics
Matches: 503, Mismatches: 193, Indels: 32
0.69 0.27 0.04
Matches are distributed among these distances:
48 5 0.01
49 135 0.27
50 355 0.71
51 8 0.02
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (50 bp):
ACGGTGAATCTTACTTCCCTGGCATTGCAATTAAACAGATTGAAGCCACA
Found at i:40417906 original size:199 final size:199
Alignment explanation
Indices: 40417558--40418412 Score: 1289
Period size: 199 Copynumber: 4.3 Consensus size: 199
40417548 ATGAAGTTAC
** *
40417558 CTTCCCTGGCAGTACAGTGGAGCAGACCAAAGCTACGACGGCGAATCTTGCTTCCCTGGTATTGC
1 CTTCCCTGGCAGTACAGTGGAGCAGATTAAAGCTACGACGGTGAATCTTGCTTCCCTGGTATTGC
* *
40417623 AATTAAAAAGATTGAAACCGCAACGGCGAATCTTACTTTCCTGGCGATGCAGTGGATCAGATTGA
66 AATTAAAAAGATTGAAGCCGCAACGGTGAATCTTACTTTCCTGGCGATGCAGTGGATCAGATTGA
* * * *
40417688 AGCTACAACGGTGAATCTTGTTCCCTGACATTACATTTAAAGATATTGAAGCCACAACGGCGAAT
131 AGCTACAACGGCGAATCTTGTTCCCCGACATTACAATTAAAGAGATTGAAGCCACAACGGCGAAT
40417753 CTCA
196 CTCA
* * * * *
40417757 CTTCCCTGGCAATACAGCGGAGCAGATTAAAGCTATGACAGTGAATCTTGCTTCCCTAGTATTGC
1 CTTCCCTGGCAGTACAGTGGAGCAGATTAAAGCTACGACGGTGAATCTTGCTTCCCTGGTATTGC
* *
40417822 AATTAAAAAGATTGAAGCCGCAACGGTGAATCTTACTTTCCTAGCGATGTAGTGGATCAGATTGA
66 AATTAAAAAGATTGAAGCCGCAACGGTGAATCTTACTTTCCTGGCGATGCAGTGGATCAGATTGA
* * *
40417887 AGCTACAACGGCAAATCTTGTTCCCCGACATTGCAATTAAAGAGATTGAAGCCACAACGGTGAAT
131 AGCTACAACGGCGAATCTTGTTCCCCGACATTACAATTAAAGAGATTGAAGCCACAACGGCGAAT
40417952 CTCA
196 CTCA
* * *
40417956 CTTCCCTGGCAGTACAGTAGAGCAGATTAAAGCTACGACGGTGAATCTTACTTTCCTGGTATTGC
1 CTTCCCTGGCAGTACAGTGGAGCAGATTAAAGCTACGACGGTGAATCTTGCTTCCCTGGTATTGC
* *
40418021 AATTAAAAAGATTGAAGCCGCAACGGTGAATCTTTCTTTCCTGGCGATGTAGTGGATCAGATTGA
66 AATTAAAAAGATTGAAGCCGCAACGGTGAATCTTACTTTCCTGGCGATGCAGTGGATCAGATTGA
* **
40418086 AGCTACAACGGCGGATCTTGTTCCCCGACATTGA-TTTTAAAGAGATTGAAGCCACAACGGCGAA
131 AGCTACAACGGCGAATCTTGTTCCCCGACATT-ACAATTAAAGAGATTGAAGCCACAACGGCGAA
40418150 TCTCA
195 TCTCA
*
40418155 CTTCCCTGGCAGTATAGTGGAGCAGATTAAAGCTACGACGGTGAATCTTGCTTCCCTGGTATTGC
1 CTTCCCTGGCAGTACAGTGGAGCAGATTAAAGCTACGACGGTGAATCTTGCTTCCCTGGTATTGC
* * *
40418220 AATTAAAAAGATTGAAGTCGCAACAGTGAATCTTACTTTCCTGGCGATGCAGTGGATCAGATTTA
66 AATTAAAAAGATTGAAGCCGCAACGGTGAATCTTACTTTCCTGGCGATGCAGTGGATCAGATTGA
* * * *
40418285 AGCTACAACGGTGAATCTTGTTCCCCGACATTGCAATTAAAGAGATCGAAGCCACAACGGCAAAT
131 AGCTACAACGGCGAATCTTGTTCCCCGACATTACAATTAAAGAGATTGAAGCCACAACGGCGAAT
*
40418350 CTTA
196 CTCA
* * ** * * * *
40418354 CTTTCCTTGGCGGTGTAGTGGAGCAGATTGAAGCTATGACGGCGAATCTTACTTCCCTG
1 C-TTCCCTGGCAGTACAGTGGAGCAGATTAAAGCTACGACGGTGAATCTTGCTTCCCTG
40418413 AGGTTGCAGT
Statistics
Matches: 594, Mismatches: 59, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
199 544 0.92
200 50 0.08
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (199 bp):
CTTCCCTGGCAGTACAGTGGAGCAGATTAAAGCTACGACGGTGAATCTTGCTTCCCTGGTATTGC
AATTAAAAAGATTGAAGCCGCAACGGTGAATCTTACTTTCCTGGCGATGCAGTGGATCAGATTGA
AGCTACAACGGCGAATCTTGTTCCCCGACATTACAATTAAAGAGATTGAAGCCACAACGGCGAAT
CTCA
Found at i:40421717 original size:27 final size:27
Alignment explanation
Indices: 40421687--40421740 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
40421677 AAAAACATTA
*
40421687 ACTCTGTATTAATATACTATAAATCCT
1 ACTCTATATTAATATACTATAAATCCT
40421714 ACTCTATATTAATATACTATAAATCCT
1 ACTCTATATTAATATACTATAAATCCT
40421741 TCTATTGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.41
Consensus pattern (27 bp):
ACTCTATATTAATATACTATAAATCCT
Found at i:40422796 original size:4 final size:4
Alignment explanation
Indices: 40422787--40422819 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
40422777 CTTAGATCTG
40422787 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
40422820 ATATAAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:40423962 original size:6 final size:6
Alignment explanation
Indices: 40423951--40423992 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
40423941 CATGATTTAA
40423951 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
40423993 TTCTAATTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:40425592 original size:30 final size:30
Alignment explanation
Indices: 40425553--40425632 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
40425543 GAGACATTTG
40425553 CAATTGTAGTTGCTGCA-TGTAAGAATATCA
1 CAATTGTAGTTGCTG-ATTGTAAGAATATCA
* *
40425583 CAATCGTAGTTGCTGATTGTAAGAATATCC
1 CAATTGTAGTTGCTGATTGTAAGAATATCA
40425613 CAATTGTAGTTGCTGATTGT
1 CAATTGTAGTTGCTGATTGT
40425633 TGACCAAGTC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 1 0.02
30 45 0.98
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (30 bp):
CAATTGTAGTTGCTGATTGTAAGAATATCA
Found at i:40434627 original size:22 final size:22
Alignment explanation
Indices: 40434602--40434644 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40434592 TTGAGAATTA
*
40434602 ATTTAAGATTTTTTGAATTATT
1 ATTTAAGATTTATTGAATTATT
*
40434624 ATTTAAGGTTTATTGAATTAT
1 ATTTAAGATTTATTGAATTAT
40434645 AATTAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (22 bp):
ATTTAAGATTTATTGAATTATT
Found at i:40447538 original size:18 final size:19
Alignment explanation
Indices: 40447515--40447552 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
40447505 GGCTGCAGGC
*
40447515 AATGATTGAAGA-AATCAG
1 AATGATTGAAAAGAATCAG
40447533 AATGATTGAAAAGAATCAG
1 AATGATTGAAAAGAATCAG
40447552 A
1 A
40447553 CCTGGAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGATTGAAAAGAATCAG
Found at i:40451502 original size:37 final size:39
Alignment explanation
Indices: 40451409--40451504 Score: 101
Period size: 39 Copynumber: 2.5 Consensus size: 39
40451399 CACTCCAGTA
* *
40451409 TGGCACGCAGTACCTCATCGGATAGTTCGAAGCAATAGT
1 TGGCACGCAGTACCTCATCGGAAAGCTCGAAGCAATAGT
**
40451448 TGGCATC-CAGTGTCTCATCGGCAAAGCT-GAAG-AA-AGT
1 TGGCA-CGCAGTACCTCATCGG-AAAGCTCGAAGCAATAGT
*
40451485 TGGTACGCAGTACCTCATCG
1 TGGCACGCAGTACCTCATCG
40451505 AATCTATTCG
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
36 1 0.02
37 18 0.38
38 2 0.04
39 21 0.45
40 5 0.11
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (39 bp):
TGGCACGCAGTACCTCATCGGAAAGCTCGAAGCAATAGT
Found at i:40459085 original size:23 final size:23
Alignment explanation
Indices: 40459057--40459101 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
40459047 AGGTTTTCCT
* *
40459057 TTTCTTTCTTTTTTTTTCCCAAC
1 TTTCTTTCTTTTTCTTCCCCAAC
40459080 TTTCTTTCTTTTTCTTCCCCAA
1 TTTCTTTCTTTTTCTTCCCCAA
40459102 TTCGTTTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.09, C:0.29, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTCTTTCTTTTTCTTCCCCAAC
Found at i:40463469 original size:2 final size:2
Alignment explanation
Indices: 40463464--40463489 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40463454 TCACACACAC
40463464 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
40463490 GCACGTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40466371 original size:20 final size:20
Alignment explanation
Indices: 40466346--40466386 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
40466336 CTCTTTCTAC
40466346 TTCATCACCTTTCAAAAATT
1 TTCATCACCTTTCAAAAATT
40466366 TTCATCACCTTTCAAAAATT
1 TTCATCACCTTTCAAAAATT
40466386 T
1 T
40466387 GTGAACCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.41
Consensus pattern (20 bp):
TTCATCACCTTTCAAAAATT
Found at i:40470212 original size:19 final size:21
Alignment explanation
Indices: 40470172--40470212 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
40470162 AAATAAAATG
*
40470172 ATTGTGTTAAACAAATATAAA
1 ATTGTGTTAAACAAATACAAA
40470193 ATTGTG-TAAA-AAATACAAA
1 ATTGTGTTAAACAAATACAAA
40470212 A
1 A
40470213 AGCAAGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 4 0.21
21 6 0.32
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.29
Consensus pattern (21 bp):
ATTGTGTTAAACAAATACAAA
Found at i:40472858 original size:14 final size:14
Alignment explanation
Indices: 40472839--40472868 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40472829 ATTCCAAACA
40472839 TACATACATATATG
1 TACATACATATATG
*
40472853 TACATATATATATG
1 TACATACATATATG
40472867 TA
1 TA
40472869 TATGATGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (14 bp):
TACATACATATATG
Found at i:40473284 original size:31 final size:31
Alignment explanation
Indices: 40473248--40473314 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
40473238 TATTCCATAT
40473248 AGAGAAAGAATGCAGTAAAATAGTTAAAAAG
1 AGAGAAAGAATGCAGTAAAATAGTTAAAAAG
40473279 AGAGAAAGAATGCAGTAAAATAGTTAAAAAG
1 AGAGAAAGAATGCAGTAAAATAGTTAAAAAG
40473310 AGAGA
1 AGAGA
40473315 CACTTCACCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.58, C:0.03, G:0.24, T:0.15
Consensus pattern (31 bp):
AGAGAAAGAATGCAGTAAAATAGTTAAAAAG
Found at i:40480707 original size:23 final size:23
Alignment explanation
Indices: 40480663--40480712 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
40480653 CAATTTTTTA
* *
40480663 AATATATTTTAAAGAAACAATAT
1 AATATATTGTAAAGAAACAATAC
*
40480686 AATATATTGTAATAGATA-AATAC
1 AATATATTGTAA-AGAAACAATAC
40480709 AATA
1 AATA
40480713 AGCCTGCGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (23 bp):
AATATATTGTAAAGAAACAATAC
Found at i:40480769 original size:14 final size:14
Alignment explanation
Indices: 40480752--40480778 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40480742 AGCTTTTTCA
40480752 AATAATAATATTTT
1 AATAATAATATTTT
40480766 AATAATAATATTT
1 AATAATAATATTT
40480779 AATTCTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATAATAATATTTT
Found at i:40483246 original size:83 final size:83
Alignment explanation
Indices: 40483127--40483292 Score: 323
Period size: 83 Copynumber: 2.0 Consensus size: 83
40483117 GAAGAAAAAG
*
40483127 AAGGTTAAAATGAGATACACGCACACTTAGATGAAAAGAAAAGAAAAATTGCAAAACAAGCAACA
1 AAGGTTAAAATGAGATACACACACACTTAGATGAAAAGAAAAGAAAAATTGCAAAACAAGCAACA
40483192 CGAAACAAACTTTCAGAC
66 CGAAACAAACTTTCAGAC
40483210 AAGGTTAAAATGAGATACACACACACTTAGATGAAAAGAAAAGAAAAATTGCAAAACAAGCAACA
1 AAGGTTAAAATGAGATACACACACACTTAGATGAAAAGAAAAGAAAAATTGCAAAACAAGCAACA
40483275 CGAAACAAACTTTCAGAC
66 CGAAACAAACTTTCAGAC
40483293 TACTAGAGAC
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.54, C:0.17, G:0.15, T:0.14
Consensus pattern (83 bp):
AAGGTTAAAATGAGATACACACACACTTAGATGAAAAGAAAAGAAAAATTGCAAAACAAGCAACA
CGAAACAAACTTTCAGAC
Found at i:40486893 original size:7 final size:6
Alignment explanation
Indices: 40486853--40486892 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
40486843 CTCTTAGGGG
40486853 TTTTA- TTTTATT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTA-T TTTTAT TTTTAT TTTTAT TTTTAT TTTT
40486893 TTGTCTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.15
6 23 0.70
7 5 0.15
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:40491795 original size:57 final size:58
Alignment explanation
Indices: 40491696--40491816 Score: 147
Period size: 57 Copynumber: 2.1 Consensus size: 58
40491686 TCATTTTCAT
* * * * *
40491696 TTTTCGTTTTCATTTTTGAGAAAGCTACATTCATTTCTAAATGATTC-AATTTCTCCA
1 TTTTCATTTTCATTTTAGAGAAAGCCACAATAATTTCTAAATGATTCTAATTTCTCCA
* * *
40491753 TTTTCATTTTCATTTTAGAGAAAGCCATAATAA-TTCTCAAATGTTTCTCATTTCTCCA
1 TTTTCATTTTCATTTTAGAGAAAGCCACAATAATTTCT-AAATGATTCTAATTTCTCCA
40491811 TTTTCA
1 TTTTCA
40491817 CCATTTCTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
56 4 0.07
57 35 0.65
58 15 0.28
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.47
Consensus pattern (58 bp):
TTTTCATTTTCATTTTAGAGAAAGCCACAATAATTTCTAAATGATTCTAATTTCTCCA
Found at i:40496703 original size:15 final size:15
Alignment explanation
Indices: 40496683--40496712 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40496673 TTTACTTTAT
40496683 TTAATAATAATAATA
1 TTAATAATAATAATA
*
40496698 TTAATATTAATAATA
1 TTAATAATAATAATA
40496713 AAAGACCATA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAATAATAATAATA
Found at i:40503568 original size:25 final size:25
Alignment explanation
Indices: 40503538--40503619 Score: 118
Period size: 25 Copynumber: 3.4 Consensus size: 25
40503528 GGAGTTTAGC
40503538 GTGCTCTCTGATATTTAGCACGTTA
1 GTGCTCTCTGATATTTAGCACGTTA
*
40503563 GTGCTCTCTG---TTTAGCACATCT-
1 GTGCTCTCTGATATTTAGCACGT-TA
40503585 GTGCTCTCTGATATTTAGCACGTTA
1 GTGCTCTCTGATATTTAGCACGTTA
40503610 GTGCTCTCTG
1 GTGCTCTCTG
40503620 TCTAGCACAT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
22 19 0.38
23 1 0.02
24 1 0.02
25 29 0.58
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.40
Consensus pattern (25 bp):
GTGCTCTCTGATATTTAGCACGTTA
Found at i:40503607 original size:47 final size:47
Alignment explanation
Indices: 40503538--40503653 Score: 207
Period size: 47 Copynumber: 2.5 Consensus size: 47
40503528 GGAGTTTAGC
*
40503538 GTGCTCTCTGATATTTAGCACGTTAGTGCTCTCTGTTTAGCACATCT
1 GTGCTCTCTGATATTTAGCACGTTAGTGCTCTCTGTCTAGCACATCT
40503585 GTGCTCTCTGATATTTAGCACGTTAGTGCTCTCTGTCTAGCACATCT
1 GTGCTCTCTGATATTTAGCACGTTAGTGCTCTCTGTCTAGCACATCT
40503632 GTGCTCTCTGAT-TATTAGCACG
1 GTGCTCTCTGATAT-TTAGCACG
40503654 CTCTCTGATC
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
46 1 0.01
47 66 0.99
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (47 bp):
GTGCTCTCTGATATTTAGCACGTTAGTGCTCTCTGTCTAGCACATCT
Found at i:40503650 original size:25 final size:24
Alignment explanation
Indices: 40503538--40503707 Score: 125
Period size: 22 Copynumber: 7.4 Consensus size: 24
40503528 GGAGTTTAGC
*
40503538 GTGCTCTCTGATATTTAGCACGTTA
1 GTGCTCTCTGATA-TTAGCACATTA
40503563 GTGCTCTCTG-T-TTAGCACATCT-
1 GTGCTCTCTGATATTAGCACAT-TA
*
40503585 GTGCTCTCTGATATTTAGCACGTTA
1 GTGCTCTCTGATA-TTAGCACATTA
*
40503610 GTGCTCTCTG-T-CTAGCACATCT-
1 GTGCTCTCTGATATTAGCACAT-TA
40503632 GTGCTCTCTGATTATTAGCAC----
1 GTGCTCTCTGA-TATTAGCACATTA
* *
40503653 --GCTCTCTGATCACTAGCACGTTA
1 GTGCTCTCTGAT-ATTAGCACATTA
* *
40503676 GTGCTCTCCG-T-TTAGCACATTT
1 GTGCTCTCTGATATTAGCACATTA
40503698 GTGCTCTCTG
1 GTGCTCTCTG
40503708 TATAGTCCCG
Statistics
Matches: 118, Mismatches: 11, Indels: 35
0.72 0.07 0.21
Matches are distributed among these distances:
18 1 0.01
19 16 0.14
22 52 0.44
23 3 0.03
24 5 0.04
25 41 0.35
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.38
Consensus pattern (24 bp):
GTGCTCTCTGATATTAGCACATTA
Found at i:40503658 original size:19 final size:19
Alignment explanation
Indices: 40503634--40503672 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
40503624 GCACATCTGT
* *
40503634 GCTCTCTGATTATTAGCAC
1 GCTCTCTGATCACTAGCAC
40503653 GCTCTCTGATCACTAGCAC
1 GCTCTCTGATCACTAGCAC
40503672 G
1 G
40503673 TTAGTGCTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.31, G:0.18, T:0.31
Consensus pattern (19 bp):
GCTCTCTGATCACTAGCAC
Found at i:40504638 original size:13 final size:13
Alignment explanation
Indices: 40504622--40504649 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40504612 CGATTTCTTC
40504622 TGGGTATTCTATA
1 TGGGTATTCTATA
40504635 TGGGTATTCTATA
1 TGGGTATTCTATA
40504648 TG
1 TG
40504650 CTCTTTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.25, T:0.46
Consensus pattern (13 bp):
TGGGTATTCTATA
Found at i:40504964 original size:12 final size:12
Alignment explanation
Indices: 40504949--40504988 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
40504939 TTCTTCTTTT
40504949 GGATTTTCTCTG
1 GGATTTTCTCTG
* * *
40504961 GGATATTCTTTT
1 GGATTTTCTCTG
40504973 GGATTTTCTCTG
1 GGATTTTCTCTG
40504985 GGAT
1 GGAT
40504989 ATCATCGATC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (12 bp):
GGATTTTCTCTG
Found at i:40504974 original size:24 final size:24
Alignment explanation
Indices: 40504942--40504990 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
40504932 AGTGATATTC
40504942 TTCTTTTGGATTTTCTCTGGGATA
1 TTCTTTTGGATTTTCTCTGGGATA
40504966 TTCTTTTGGATTTTCTCTGGGATA
1 TTCTTTTGGATTTTCTCTGGGATA
40504990 T
1 T
40504991 CATCGATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.55
Consensus pattern (24 bp):
TTCTTTTGGATTTTCTCTGGGATA
Found at i:40509949 original size:113 final size:115
Alignment explanation
Indices: 40509803--40510033 Score: 412
Period size: 113 Copynumber: 2.0 Consensus size: 115
40509793 AGTGAGCTTA
*
40509803 GTAAATGGTTAGGATATGTATGGCATGTCATTAGGGTTATACTCATATTTGATCAGGGATTTACA
1 GTAAATGGTTAGGATATGTATGGCATGTCATTAGGGTTATACTCATATTTGATCACGGATTTACA
*
40509868 TGTTATTATGAGATCCAACATTTGTTGCAGATTCTCAAGTTAAATTTATT
66 TGTTATTATGAGATCCAACATTTGTTGCAGATTCTCAAGTTAAATGTATT
*
40509918 GTAAA-GGTTAGGATAT-TATGGCATGTCATTAGGGTTATACTCGTATTTGATCACGGATTTACA
1 GTAAATGGTTAGGATATGTATGGCATGTCATTAGGGTTATACTCATATTTGATCACGGATTTACA
*
40509981 TGTTATTATGAGATCCAGCATTTGTTGCAGATTCTCAAGTTAAATGTATT
66 TGTTATTATGAGATCCAACATTTGTTGCAGATTCTCAAGTTAAATGTATT
40510031 GTA
1 GTA
40510034 GGTTTAGTCA
Statistics
Matches: 112, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
113 96 0.86
114 11 0.10
115 5 0.04
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (115 bp):
GTAAATGGTTAGGATATGTATGGCATGTCATTAGGGTTATACTCATATTTGATCACGGATTTACA
TGTTATTATGAGATCCAACATTTGTTGCAGATTCTCAAGTTAAATGTATT
Found at i:40510085 original size:30 final size:30
Alignment explanation
Indices: 40510049--40510140 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 30
40510039 AGTCAGGACA
40510049 AGTAACCTCA-ATATAATGACAACTTGTGTG
1 AGTAACC-CAGATATAATGACAACTTGTGTG
* * *
40510079 AGTAACCCAGTTATAATGTCAGCTTGTGTG
1 AGTAACCCAGATATAATGACAACTTGTGTG
* * * * * *
40510109 AGCAATCCTGATATACTGTCAGCTTGTGTG
1 AGTAACCCAGATATAATGACAACTTGTGTG
40510139 AG
1 AG
40510141 CATTACATTC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 2 0.04
30 51 0.96
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (30 bp):
AGTAACCCAGATATAATGACAACTTGTGTG
Found at i:40510141 original size:30 final size:30
Alignment explanation
Indices: 40510059--40510142 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
40510049 AGTAACCTCA
* * *
40510059 ATATAATGACAACTTGTGTGAGTAACCCAG
1 ATATAATGTCAGCTTGTGTGAGCAACCCAG
* * *
40510089 TTATAATGTCAGCTTGTGTGAGCAATCCTG
1 ATATAATGTCAGCTTGTGTGAGCAACCCAG
*
40510119 ATATACTGTCAGCTTGTGTGAGCA
1 ATATAATGTCAGCTTGTGTGAGCA
40510143 TTACATTCTC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.32
Consensus pattern (30 bp):
ATATAATGTCAGCTTGTGTGAGCAACCCAG
Found at i:40516248 original size:14 final size:15
Alignment explanation
Indices: 40516231--40516259 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40516221 CGAACCAAAA
40516231 AGAAAAGAGA-AGTT
1 AGAAAAGAGAGAGTT
40516245 AGAAAAGAGAGAGTT
1 AGAAAAGAGAGAGTT
40516260 CGAGCACCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.00, G:0.31, T:0.14
Consensus pattern (15 bp):
AGAAAAGAGAGAGTT
Found at i:40519062 original size:3 final size:3
Alignment explanation
Indices: 40519042--40519131 Score: 53
Period size: 3 Copynumber: 30.7 Consensus size: 3
40519032 CCCATTTTAT
* * * * * * *
40519042 TTA TTA TT- TTT TTA -TA TTA TTA CTA CTA CTA TTA CTA TTA CTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
40519088 TTA -TA TTTA TTA TTA TTA CTTA CT- TTA TTA TTA TTA TAA TTA TT
1 TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT
40519132 TACTCATTCG
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
2 7 0.10
3 57 0.83
4 5 0.07
ACGTcount: A:0.31, C:0.08, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:40519115 original size:24 final size:25
Alignment explanation
Indices: 40519071--40519135 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 25
40519061 TTACTACTAC
* *
40519071 TATTACTATTAC-TAGTATTA-TATT
1 TATTATTATTACTTACTATTATTA-T
40519095 TATTATTATTACTTACT-TTATTAT
1 TATTATTATTACTTACTATTATTAT
* *
40519119 TATTATAATTATTTACT
1 TATTATTATTACTTACT
40519136 CATTCGTATC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
24 30 0.86
25 5 0.14
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (25 bp):
TATTATTATTACTTACTATTATTAT
Found at i:40536380 original size:14 final size:14
Alignment explanation
Indices: 40536361--40536388 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40536351 TTGAATCTAT
40536361 ACTTTGCTTGCTCA
1 ACTTTGCTTGCTCA
40536375 ACTTTGCTTGCTCA
1 ACTTTGCTTGCTCA
40536389 GAAGACAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (14 bp):
ACTTTGCTTGCTCA
Found at i:40549977 original size:73 final size:73
Alignment explanation
Indices: 40549858--40550004 Score: 240
Period size: 73 Copynumber: 2.0 Consensus size: 73
40549848 TTCTTCGCAT
* *
40549858 TCTTCGTCATGTCTAATAGTCAACTCCAATTCCGCATAAGATATTTCTTAAACTTGTGAAAATCA
1 TCTTCGTCATGTCTAATAGTCAACTCCAATTCCGCATAAGATATTTCTTAAACATGTGAAAACCA
40549923 TATTATTC
66 TATTATTC
* * * *
40549931 TCTTCGTCGTGTCTAATGGTCAACTCCAATTTCGTATAAGATATTTCTTAAACATGTGAAAACCA
1 TCTTCGTCATGTCTAATAGTCAACTCCAATTCCGCATAAGATATTTCTTAAACATGTGAAAACCA
40549996 TATTATTC
66 TATTATTC
40550004 T
1 T
40550005 AATGATCCTA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.39
Consensus pattern (73 bp):
TCTTCGTCATGTCTAATAGTCAACTCCAATTCCGCATAAGATATTTCTTAAACATGTGAAAACCA
TATTATTC
Found at i:40551836 original size:20 final size:19
Alignment explanation
Indices: 40551793--40551836 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
40551783 CAACAAAAAC
40551793 AAAAATGAAAAAGAGAAAG
1 AAAAATGAAAAAGAGAAAG
* * *
40551812 GAAAATAGAAAGAGAGAATG
1 AAAAAT-GAAAAAGAGAAAG
40551832 AAAAA
1 AAAAA
40551837 AATGACAGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (19 bp):
AAAAATGAAAAAGAGAAAG
Found at i:40551857 original size:18 final size:18
Alignment explanation
Indices: 40551824--40551863 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
40551814 AAATAGAAAG
40551824 AGAGAATGAAAAAAATGA
1 AGAGAATGAAAAAAATGA
*
40551842 CAGAGAA-GAAATAAATGA
1 -AGAGAATGAAAAAAATGA
40551860 AGAG
1 AGAG
40551864 CCACGCACGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 10 0.50
19 6 0.30
ACGTcount: A:0.62, C:0.03, G:0.25, T:0.10
Consensus pattern (18 bp):
AGAGAATGAAAAAAATGA
Found at i:40577537 original size:40 final size:41
Alignment explanation
Indices: 40577493--40577581 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
40577483 TAATAAAATA
*
40577493 ATATTAACTTTA-AATAATAGTT-AAAAAATATTGAAA-TTAG
1 ATATTAAATTTATAATAATA-TTAAAAAAATATT-AAATTTAG
* *
40577533 ATATTAAATTTATATTAATATTAAAAAAATATTAAATTTAT
1 ATATTAAATTTATAATAATATTAAAAAAATATTAAATTTAG
40577574 ATATTAAA
1 ATATTAAA
40577582 GTCATTAACG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
40 16 0.37
41 27 0.63
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (41 bp):
ATATTAAATTTATAATAATATTAAAAAAATATTAAATTTAG
Found at i:40577877 original size:197 final size:198
Alignment explanation
Indices: 40577533--40577928 Score: 785
Period size: 197 Copynumber: 2.0 Consensus size: 198
40577523 TTGAAATTAG
40577533 ATATTAAATTTATATTAATATTAAAAAAATATTAAATTTATATATTAAAGTCATTAACGTTTACG
1 ATATTAAATTTATATTAATATTAAAAAAATATTAAATTTATATATTAAAGTCATTAACGTTTACG
40577598 AATCTTACATATGCATATTTTTTAACATTAGTCTTATTACAGATTCTTATCATATTTGCTCTTTT
66 AATCTTACATATGCATATTTTTTAACATTAGTCTTATTACAGATTCTTATCATATTTGCTCTTTT
40577663 TGACACAATGCTTAGAACCACCTATAGCCCCTCTCCAACCCATAAATAGGAGTATAATACACTCC
131 TGACACAATGCTTAGAACCACCTATAGCCCCTCTCCAACCCATAAATAGGAGTATAATACACTCC
40577728 GGC
196 GGC
40577731 ATATTAAA-TTATATTAATATTAAAAAAATATTAAATTTATATATTAAAGTCATTAACGTTTACG
1 ATATTAAATTTATATTAATATTAAAAAAATATTAAATTTATATATTAAAGTCATTAACGTTTACG
40577795 AATCTTACATATGCATATTTTTTAACATTAGTCTTATTACAGATTCTTATCATATTTGCTCTTTT
66 AATCTTACATATGCATATTTTTTAACATTAGTCTTATTACAGATTCTTATCATATTTGCTCTTTT
40577860 TGACACAATGCTTAGAACCACCTATAGCCCCTCTCCAACCCATAAATAGGAGTATAATACACTCC
131 TGACACAATGCTTAGAACCACCTATAGCCCCTCTCCAACCCATAAATAGGAGTATAATACACTCC
40577925 GGC
196 GGC
40577928 A
1 A
40577929 CACTTGAACC
Statistics
Matches: 198, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
197 190 0.96
198 8 0.04
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.38
Consensus pattern (198 bp):
ATATTAAATTTATATTAATATTAAAAAAATATTAAATTTATATATTAAAGTCATTAACGTTTACG
AATCTTACATATGCATATTTTTTAACATTAGTCTTATTACAGATTCTTATCATATTTGCTCTTTT
TGACACAATGCTTAGAACCACCTATAGCCCCTCTCCAACCCATAAATAGGAGTATAATACACTCC
GGC
Found at i:40582033 original size:33 final size:33
Alignment explanation
Indices: 40581991--40582185 Score: 111
Period size: 33 Copynumber: 5.4 Consensus size: 33
40581981 AAAGGGGGTA
*
40581991 GCTAAGTGTTGATTCCCCGAATTATTGGTGGTT
1 GCTAAGTGCTGATTCCCCGAATTATTGGTGGTT
* * *
40582024 GCTAAGTGTTGATTCCACCGTATTTTAAATGTGAATGGGGTT
1 GCTAAGTGCTGATTCC-CCG-A-ATT--AT-TG---GTGGTT
* * *
40582066 GCTAAGTGCTGATTCCTCGACTCATTGGTGGTT
1 GCTAAGTGCTGATTCCCCGAATTATTGGTGGTT
* * *
40582099 GCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTT
1 GCTAAGTGCTGATTCC-CCG-A-ATT--AT-TG---GTGGTT
* * *
40582141 GCTAAGTGCTGATTCCTCGAATCACTGGTGGTT
1 GCTAAGTGCTGATTCCCCGAATTATTGGTGGTT
40582174 GCTAAGTGCTGA
1 GCTAAGTGCTGA
40582186 ATCCACCAAT
Statistics
Matches: 127, Mismatches: 17, Indels: 36
0.71 0.09 0.20
Matches are distributed among these distances:
33 53 0.42
34 5 0.04
35 2 0.02
36 8 0.06
37 3 0.02
38 4 0.03
39 6 0.05
40 2 0.02
41 4 0.03
42 40 0.31
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.34
Consensus pattern (33 bp):
GCTAAGTGCTGATTCCCCGAATTATTGGTGGTT
Found at i:40582079 original size:42 final size:40
Alignment explanation
Indices: 40582020--40582156 Score: 135
Period size: 42 Copynumber: 3.5 Consensus size: 40
40582010 AATTATTGGT
*
40582020 GGTTGCTAAGTGTTGATTCCACCGTATTTTAAATGTGAATGG
1 GGTTGCTAAGTGCTGATTCCACCGTA-TTTAAATGTGAA-GG
* * * *
40582062 GGTTGCTAAGTGCTGATTCC-TCG-A-CT-CAT-TG--GT
1 GGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTGAAGG
*
40582095 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTAT-TTAAATGTG-AAGG
40582137 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
40582157 TCGAATCACT
Statistics
Matches: 75, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
33 20 0.27
34 2 0.03
35 1 0.01
36 2 0.03
37 3 0.04
38 3 0.04
39 2 0.03
40 1 0.01
41 2 0.03
42 39 0.52
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (40 bp):
GGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTGAAGG
Found at i:40582117 original size:75 final size:75
Alignment explanation
Indices: 40581985--40582185 Score: 312
Period size: 75 Copynumber: 2.7 Consensus size: 75
40581975 GAATATAAAG
* * * * * * *
40581985 GGGGTAGCTAAGTGTTGATTCCCCGAATTATTGGTGGTTGCTAAGTGTTGATTCCACCGTATTTT
1 GGGGTTGCTAAGTGCTGATTCCTCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
*
40582050 AAATGTGAAT
66 AAATGTGAAA
*
40582060 GGGGTTGCTAAGTGCTGATTCCTCGACTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
1 GGGGTTGCTAAGTGCTGATTCCTCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
40582125 AAATGTGAAA
66 AAATGTGAAA
*
40582135 GGGGTTGCTAAGTGCTGATTCCTCGAATCACTGGTGGTTGCTAAGTGCTGA
1 GGGGTTGCTAAGTGCTGATTCCTCGAATCATTGGTGGTTGCTAAGTGCTGA
40582186 ATCCACCAAT
Statistics
Matches: 115, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 115 1.00
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (75 bp):
GGGGTTGCTAAGTGCTGATTCCTCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
AAATGTGAAA
Found at i:40589890 original size:46 final size:46
Alignment explanation
Indices: 40589823--40589961 Score: 233
Period size: 46 Copynumber: 3.0 Consensus size: 46
40589813 CATGGCAAAA
*
40589823 TGTGAAACGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
*
40589869 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATATTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
* * *
40589915 TGTGAAAAGTAGGTATGGTATTTCCGTGAGGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
40589961 T
1 T
40589962 ATAGCAATGT
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
Found at i:40592105 original size:33 final size:33
Alignment explanation
Indices: 40592063--40592257 Score: 131
Period size: 33 Copynumber: 5.4 Consensus size: 33
40592053 TCCCCCAAGG
40592063 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
40592096 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--AT-CAT-T---GGT
* *
40592138 GGTTGCTAAGTGCTGATTGCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
40592171 GGTTGCTAAGTGCTGA-TCCCATTGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCC--CGAATC----AT-TG---GT
*
40592213 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
40592246 GGTTGCTAAGTG
1 GGTTGCTAAGTG
40592258 TTGAATCCAC
Statistics
Matches: 126, Mismatches: 16, Indels: 40
0.69 0.09 0.22
Matches are distributed among these distances:
32 3 0.02
33 51 0.40
34 6 0.05
35 1 0.01
36 3 0.02
37 4 0.03
38 5 0.04
39 3 0.02
40 1 0.01
41 7 0.06
42 38 0.30
43 4 0.03
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:40592150 original size:75 final size:75
Alignment explanation
Indices: 40592059--40592269 Score: 332
Period size: 75 Copynumber: 2.8 Consensus size: 75
40592049 TGATTCCCCC
*
40592059 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
40592124 TTAAATGTGA
66 TTAAATGTGA
* * * * **
40592134 AGGGGGTTGCTAAGTGCTGATTGCCCGACTCATTGGTGGTTGCTAAGTGCTGATCCCATTGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
40592199 TTAAATGTGA
66 TTAAATGTGA
* * *
40592209 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGTTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCG
40592270 ATAACGGACA
Statistics
Matches: 120, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 120 1.00
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.32
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:40592155 original size:42 final size:41
Alignment explanation
Indices: 40592096--40592232 Score: 128
Period size: 42 Copynumber: 3.5 Consensus size: 41
40592086 AATCATTGGT
40592096 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTA-TTTAAATGTGAAGGG
* * * *
40592138 GGTTGCTAAGTGCTGATTGC-CCG-A-CT-CAT-T---GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTGAAGGG
* ** *
40592171 GGTTGCTAAGTGCTGATCCCATTGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTAT-TTAAATGTGAAGGG
40592213 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
40592233 CCGAATCACT
Statistics
Matches: 73, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
33 20 0.27
34 1 0.01
35 1 0.01
36 1 0.01
37 3 0.04
38 3 0.04
39 1 0.01
40 1 0.01
41 3 0.04
42 39 0.53
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTATTTAAATGTGAAGGG
Done.