Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 129 of 207
Found at i:39395345 original size:70 final size:71
Alignment explanation
Indices: 39395213--39395362 Score: 248
Period size: 70 Copynumber: 2.1 Consensus size: 71
39395203 TCATTGGTGG
* *
39395213 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCG
39395278 AGGGGT
66 AGGGGT
***
39395284 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCG
39395348 AGGGGT
66 AGGGGT
39395354 TGCTAAGTG
1 TGCTAAGTG
39395363 ATGATTCCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 44 0.59
71 30 0.41
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (71 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCG
AGGGGT
Found at i:39395358 original size:26 final size:26
Alignment explanation
Indices: 39395323--39395374 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
39395313 AAATGAAAAG
* *
39395323 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGATGATTCCCCGA
39395349 GGGGTTGCTAAGTGATGATTCCCCGA
1 GGGGTTGCTAAGTGATGATTCCCCGA
39395375 TTCAGTGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.15, C:0.21, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGATGATTCCCCGA
Found at i:39402805 original size:104 final size:104
Alignment explanation
Indices: 39402625--39402848 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
39402615 TTGTATATAA
** * *
39402625 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
39402690 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
39402729 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
39402793 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
39402833 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
39402849 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:39402900 original size:71 final size:72
Alignment explanation
Indices: 39402767--39402918 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
39402757 TCATTGGTGG
* *
39402767 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
39402832 GAGGGGT
66 GAGGGGT
***
39402839 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
39402903 GAGGGGT
66 GAGGGGT
39402910 TGCTAAGTG
1 TGCTAAGTG
39402919 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:39415093 original size:17 final size:17
Alignment explanation
Indices: 39415067--39415100 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39415057 AGGGTCAATA
*
39415067 TACCATATAAGGCCTTC
1 TACCACATAAGGCCTTC
39415084 TACCACATAAGGCCTTC
1 TACCACATAAGGCCTTC
39415101 CAACTATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.26
Consensus pattern (17 bp):
TACCACATAAGGCCTTC
Found at i:39419086 original size:40 final size:40
Alignment explanation
Indices: 39418937--39419122 Score: 218
Period size: 40 Copynumber: 4.7 Consensus size: 40
39418927 TTGAATGATG
* * * *
39418937 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
39418977 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
39419017 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
39419057 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
39419098 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39419123 AACGAGGAGC
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.01
40 119 0.92
41 10 0.08
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:39419140 original size:80 final size:79
Alignment explanation
Indices: 39418990--39419155 Score: 187
Period size: 80 Copynumber: 2.1 Consensus size: 79
39418980 GGACTAAGAT
** *
39418990 CCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTA
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTGACTA
*
39419055 AATCCGGGTTAAGTC
66 AATCC-GGTTAAATC
* *
39419070 CCGAAGGCATTTGTGCGA-ATTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTGAACGAG-GA
1 CCGAAGGCATTTGTGCGAGA-TACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTGA
* *
39419131 GCTATATCCGGTTAAATT
63 -CTAAATCCGGTTAAATC
39419149 CCGAAGG
1 CCGAAGG
39419156 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
79 17 0.23
80 55 0.74
81 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTGACTA
AATCCGGTTAAATC
Found at i:39424631 original size:40 final size:40
Alignment explanation
Indices: 39424577--39424687 Score: 123
Period size: 40 Copynumber: 2.8 Consensus size: 40
39424567 TGTCTAACTG
* * * *
39424577 CACATGCGTACCCCTGTTTGTACTTTGGTACCCCTAAATG
1 CACATACGTGCCCCTGTTTGTACTTCGGTACCCCTAAATA
* * * *
39424617 TACATACGTGCCCCTATTTATACTTCGGTACCCCTGAATA
1 CACATACGTGCCCCTGTTTGTACTTCGGTACCCCTAAATA
* * *
39424657 CACATACGTGCCCTTGTTGGTACCTCGGTAC
1 CACATACGTGCCCCTGTTTGTACTTCGGTAC
39424688 TCCTGAAGGC
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.32
Consensus pattern (40 bp):
CACATACGTGCCCCTGTTTGTACTTCGGTACCCCTAAATA
Found at i:39431622 original size:56 final size:56
Alignment explanation
Indices: 39431536--39431711 Score: 352
Period size: 56 Copynumber: 3.1 Consensus size: 56
39431526 ACGAGGGATG
39431536 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
39431592 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
39431648 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
39431704 ATGGGCAA
1 ATGGGCAA
39431712 TAAACTAATA
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 120 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:39431746 original size:112 final size:112
Alignment explanation
Indices: 39431536--39431751 Score: 269
Period size: 112 Copynumber: 1.9 Consensus size: 112
39431526 ACGAGGGATG
39431536 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAA
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAA
* * * ** ** *** *
39431601 ACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
66 ACATCTAATGAAAAATGAAGTGAGAAAACAAAAAAAAAATAAGAAGC
39431648 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAT
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAA-
39431713 AA-A-CTAAT-AAGAAATGGAAG-GAAGAAAACAAAAAAAAAA
65 AACATCTAATGAA-AAAT-GAAGTG-AGAAAACAAAAAAAAAA
39431752 GGAATGTGTG
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
110 2 0.02
111 7 0.08
112 78 0.88
113 2 0.02
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.20
Consensus pattern (112 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAA
ACATCTAATGAAAAATGAAGTGAGAAAACAAAAAAAAAATAAGAAGC
Found at i:39440568 original size:50 final size:50
Alignment explanation
Indices: 39440469--39440619 Score: 176
Period size: 50 Copynumber: 2.9 Consensus size: 50
39440459 AATGAGATGC
*
39440469 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTCA
*
39440525 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCA
*** * * *
39440575 CCCATAAGACCGTGTCTGGGACATGGCATGGGCACCGATATGAGA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGA
39440620 ACTTCCATTG
Statistics
Matches: 87, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
50 49 0.56
53 3 0.03
55 1 0.01
56 34 0.39
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCA
Found at i:39447670 original size:50 final size:53
Alignment explanation
Indices: 39447567--39447759 Score: 175
Period size: 50 Copynumber: 3.7 Consensus size: 53
39447557 GGGAATGAGA
*
39447567 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCATCA-CGAG--TATGAGAGG
* * *
39447623 TCCCATGTAATACCATGTCTGGGACATGGCGTTGGCA-C-CGAG-ATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCATCACGAGTATGAGAGG
* * **
39447673 TCCCCCGCAAGACCATGTCTGGGACATGGCA-TGG--TCATCGA-TATGAGAAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCATCA-CGAGTATGAGAGG
*** * * *
39447723 TCCTTTGTAAGACCATATCTGGGATATGGAATTGGCA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
39447760 GTACAGGAAA
Statistics
Matches: 112, Mismatches: 18, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
48 1 0.01
49 3 0.03
50 67 0.60
51 3 0.03
53 3 0.03
55 1 0.01
56 34 0.30
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (53 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCATCACGAGTATGAGAGG
Found at i:39449341 original size:40 final size:40
Alignment explanation
Indices: 39449292--39449537 Score: 316
Period size: 40 Copynumber: 6.1 Consensus size: 40
39449282 TAATTAATGT
* *
39449292 CTGAATGCACATATGTGCCCCTGTTTGTACTTTGGTACCC
1 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
* *
39449332 CT-AAGTGCACATACGTGCCCTTGTTTGTACTTCGATACCC
1 CTGAA-TGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
* * * *
39449372 TTGAATGCACATATGTGCCCTTGTTTGTACTTTGGTACCC
1 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
* *
39449412 CTAAATGCACATACATGCCCCTGTTTGTACTTCGGTACCC
1 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
* *
39449452 CTGAATGCACATATGTGCCCCTATTTGTACTTCGGTACCCC
1 CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTA-CCC
* * *
39449493 CTGAATGCACATGCGTGCCCCTGTTAGTACCTTC-GTACTC
1 CTGAATGCACATACGTGCCCCTGTTTGTA-CTTCGGTACCC
39449533 CTGAA
1 CTGAA
39449538 GGCATATTCA
Statistics
Matches: 179, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
39 2 0.01
40 140 0.78
41 33 0.18
42 4 0.02
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (40 bp):
CTGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
Found at i:39449386 original size:80 final size:79
Alignment explanation
Indices: 39449292--39449537 Score: 350
Period size: 80 Copynumber: 3.1 Consensus size: 79
39449282 TAATTAATGT
*
39449292 CTGAATGCACATATGTGCCCCTGTTTGTACTTTGGTACCCCTAAGTGCACATACGTGCCCTTGTT
1 CTGAATGCACATATGTGCCCCTGTTTGTACTTTGGTACCCCTAA-TGCACATACGTGCCCCTGTT
39449357 TGTACTTCGATACCC
65 TGTACTTCGATACCC
* * *
39449372 TTGAATGCACATATGTGCCCTTGTTTGTACTTTGGTACCCCTAAATGCACATACATGCCCCTGTT
1 CTGAATGCACATATGTGCCCCTGTTTGTACTTTGGTACCCCT-AATGCACATACGTGCCCCTGTT
*
39449437 TGTACTTCGGTACCC
65 TGTACTTCGATACCC
* * *
39449452 CTGAATGCACATATGTGCCCCTATTTGTACTTCGGTACCCCCTGAATGCACATGCGTGCCCCTGT
1 CTGAATGCACATATGTGCCCCTGTTTGTACTTTGGTA-CCCCT-AATGCACATACGTGCCCCTGT
* *
39449517 TAGTACCTTCG-TACTC
64 TTGTA-CTTCGATACCC
39449533 CTGAA
1 CTGAA
39449538 GGCATATTCA
Statistics
Matches: 149, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
80 105 0.70
81 39 0.26
82 5 0.03
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (79 bp):
CTGAATGCACATATGTGCCCCTGTTTGTACTTTGGTACCCCTAATGCACATACGTGCCCCTGTTT
GTACTTCGATACCC
Found at i:39449452 original size:20 final size:20
Alignment explanation
Indices: 39449429--39449492 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 20
39449419 CACATACATG
39449429 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
** * * ** *
39449449 CCCCTGAATGCACATATGTG
1 CCCCTGTTTGTACTTCGGTA
*
39449469 CCCCTATTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
39449489 CCCC
1 CCCC
39449493 CTGAATGCAC
Statistics
Matches: 29, Mismatches: 15, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.16, C:0.34, G:0.17, T:0.33
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:39451652 original size:20 final size:20
Alignment explanation
Indices: 39451592--39451738 Score: 102
Period size: 20 Copynumber: 7.3 Consensus size: 20
39451582 TTGTACGAGA
* *
39451592 TTTGCACTTTGATGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
* *
39451612 GTTGCACTTCGATGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
39451632 TTTGCACTTCGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
* * ** *
39451652 TATACACTTCGGTGTTCCTA
1 TTTGCACTTCGGTGCCCCTG
* * *
39451672 TTCGCACTAT-GATGCTCCTG
1 TTTGCACT-TCGGTGCCCCTG
* *
39451692 TTTGCACATT-TGTG-CCCTT
1 TTTGCAC-TTCGGTGCCCCTG
*
39451711 TTCTACACTTCGGTGCCCCTG
1 TT-TGCACTTCGGTGCCCCTG
39451732 TTCTGCA
1 TT-TGCA
39451739 TCTATGATGC
Statistics
Matches: 98, Mismatches: 24, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
19 7 0.07
20 79 0.81
21 12 0.12
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.37
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCCCTG
Found at i:39451692 original size:60 final size:62
Alignment explanation
Indices: 39451622--39451749 Score: 154
Period size: 60 Copynumber: 2.1 Consensus size: 62
39451612 GTTGCACTTC
**
39451622 GATGCCCCTGTTTGCAC-TTCGGTGCCCCTGTATACACTTCGGTGTTCCTATTC-GCA-CTAT
1 GATGCCCCTGTTTGCACATT-GGTGCCCCTGTATACACTTCGGTGCCCCTATTCTGCATCTAT
* * * * * *
39451682 GATGCTCCTGTTTGCACATTTGTGCCCTTTTCTACACTTCGGTGCCCCTGTTCTGCATCTAT
1 GATGCCCCTGTTTGCACATTGGTGCCCCTGTATACACTTCGGTGCCCCTATTCTGCATCTAT
39451744 GATGCC
1 GATGCC
39451750 TCTGGTGTGA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 42 0.75
61 5 0.09
62 9 0.16
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.37
Consensus pattern (62 bp):
GATGCCCCTGTTTGCACATTGGTGCCCCTGTATACACTTCGGTGCCCCTATTCTGCATCTAT
Found at i:39456444 original size:50 final size:50
Alignment explanation
Indices: 39456337--39456516 Score: 180
Period size: 50 Copynumber: 3.5 Consensus size: 50
39456327 GGGAATGAGA
* * *
39456337 TCCCATGTAAGACCATGTATGGGACATGGCATTGGCATCATTGAGATTGCAAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAGA-TG--AGAGG
39456393 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * * **
39456443 TCCCCCGTAAGGCCATGTCTAGCACATGGCATGGGCACCGATATGAGAAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * *
39456493 TCCCATGTAAGACTATATCTGGGA
1 TCCCACGTAAGACCATGTCTGGGA
39456517 TATGACATCG
Statistics
Matches: 106, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
50 64 0.60
52 2 0.02
53 4 0.04
55 1 0.01
56 35 0.33
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:39457033 original size:169 final size:169
Alignment explanation
Indices: 39456754--39457092 Score: 651
Period size: 169 Copynumber: 2.0 Consensus size: 169
39456744 CAGTAAGTGA
39456754 AGAGTAAGTTATAATTGTGAGTTATTTAAGCAAGCAAGTAGGTAAACAAGTAAGTGAGTAAGTAA
1 AGAGTAAGTTATAATTGTGAGTTATTTAAGCAAGCAAGTAGGTAAACAAGTAAGTGAGTAAGTAA
*
39456819 AGAATAAAGTAAAGATCCTAGTGCTTGATGAAAATTTATGAGTATGATGGTTTATGATAAATGTT
66 AGAAGAAAGTAAAGATCCTAGTGCTTGATGAAAATTTATGAGTATGATGGTTTATGATAAATGTT
*
39456884 GTTATTTATTTACTTGTAAACTTACTAAGCTTTATGCTG
131 GTTATTTATTTACATGTAAACTTACTAAGCTTTATGCTG
*
39456923 AGAGTAAGTTATAATTGTGAGTTATTTAAGCAAGCAAGTAGGTAAACAAGTACGTGAGTAAGTAA
1 AGAGTAAGTTATAATTGTGAGTTATTTAAGCAAGCAAGTAGGTAAACAAGTAAGTGAGTAAGTAA
39456988 AGAAGAAAGTAAAGATCCTAGTGCTTGATGAAAATTTATGAGTATGATGGTTTATGATAAATGTT
66 AGAAGAAAGTAAAGATCCTAGTGCTTGATGAAAATTTATGAGTATGATGGTTTATGATAAATGTT
39457053 GTTATTTATTTACATGTAAACTTACTAAGCTTTATGCTG
131 GTTATTTATTTACATGTAAACTTACTAAGCTTTATGCTG
39457092 A
1 A
39457093 CCTTCTTTAT
Statistics
Matches: 167, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
169 167 1.00
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (169 bp):
AGAGTAAGTTATAATTGTGAGTTATTTAAGCAAGCAAGTAGGTAAACAAGTAAGTGAGTAAGTAA
AGAAGAAAGTAAAGATCCTAGTGCTTGATGAAAATTTATGAGTATGATGGTTTATGATAAATGTT
GTTATTTATTTACATGTAAACTTACTAAGCTTTATGCTG
Found at i:39463211 original size:22 final size:22
Alignment explanation
Indices: 39463183--39463304 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
39463173 TTCCACATCC
39463183 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
39463205 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
39463229 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
39463252 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
39463276 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
39463299 ATCACA
1 ATCACA
39463305 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:39463218 original size:47 final size:47
Alignment explanation
Indices: 39463155--39463657 Score: 753
Period size: 47 Copynumber: 10.6 Consensus size: 47
39463145 CCCTTCGGGA
* * *
39463155 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
39463202 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39463249 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
39463296 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
39463343 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
39463390 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
39463437 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39463486 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
39463533 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
39463582 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
39463631 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
39463658 TGTTCAAATA
Statistics
Matches: 428, Mismatches: 22, Indels: 12
0.93 0.05 0.03
Matches are distributed among these distances:
46 1 0.00
47 288 0.67
49 138 0.32
50 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:39465166 original size:56 final size:56
Alignment explanation
Indices: 39465099--39465218 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
39465089 TATTAGTTTA
39465099 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
39465155 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
39465211 TTGCCCAT
1 TTGCCCAT
39465219 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:39474621 original size:23 final size:23
Alignment explanation
Indices: 39474514--39474616 Score: 111
Period size: 23 Copynumber: 4.5 Consensus size: 23
39474504 GAATAACATT
* * *
39474514 AATCACTTTAATATTTAAGAACA
1 AATCACATTAATATTTAAGCATA
*
39474537 AATCACATTAATATTTAAGAATA
1 AATCACATTAATATTTAAGCATA
39474560 AATC-CAATTAATATTTAAGCATA
1 AATCAC-ATTAATATTTAAGCATA
* * *
39474583 AAGCACATTGACT-TTTCAGCATA
1 AATCACATT-AATATTTAAGCATA
39474606 AATCACATTAA
1 AATCACATTAA
39474617 CTTTTAACAC
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
22 2 0.03
23 64 0.93
24 3 0.04
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.33
Consensus pattern (23 bp):
AATCACATTAATATTTAAGCATA
Found at i:39478555 original size:154 final size:154
Alignment explanation
Indices: 39478270--39478573 Score: 475
Period size: 154 Copynumber: 2.0 Consensus size: 154
39478260 ACCCTCCCAT
*
39478270 TGTGACAAAGCACCCTACACTGTTGATCGTTTGCAGGTCTACTATTAGGAGTTGGTTCTAGAACC
1 TGTGACAAAGCACCCTACACTGTTGATCGTTTGCAGGTCTACTATTAAGAGTTGGTTCTAGAACC
* *
39478335 ATCTTCGTAGGATTTTATATATTTCCTGAAATTTCCTCGAGTACGTCTTTACTCCGAGATTGGAA
66 ATCTTCGTAGGATTTTATATATTTCCTGAAAGTTCCTCAAGTACGTCTTTACTCCGAGATTGGAA
*
39478400 GTTATTCATGTAATTTCCTCTTAC
131 GTCATTCATGTAATTTCCTCTTAC
* * * *
39478424 TGTGACAGAGCACCCTACGCTGTTGATCGTTTGCAGGTCTACTATTAAGAGTTGGTTTTAGAAGC
1 TGTGACAAAGCACCCTACACTGTTGATCGTTTGCAGGTCTACTATTAAGAGTTGGTTCTAGAACC
* * * * *
39478489 ATTTTCGTATGG-TTTTATATATTTCCTGAAAGTTCCTCAAGTACTTCTTTACTCTGAGGTTTGA
66 ATCTTCGTA-GGATTTTATATATTTCCTGAAAGTTCCTCAAGTACGTCTTTACTCCGAGATTGGA
39478553 AGTCATTCATGTAATTTCCTC
130 AGTCATTCATGTAATTTCCTC
39478574 AAATAAAGTA
Statistics
Matches: 136, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
154 134 0.99
155 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (154 bp):
TGTGACAAAGCACCCTACACTGTTGATCGTTTGCAGGTCTACTATTAAGAGTTGGTTCTAGAACC
ATCTTCGTAGGATTTTATATATTTCCTGAAAGTTCCTCAAGTACGTCTTTACTCCGAGATTGGAA
GTCATTCATGTAATTTCCTCTTAC
Found at i:39485571 original size:9 final size:9
Alignment explanation
Indices: 39485557--39485616 Score: 52
Period size: 10 Copynumber: 6.6 Consensus size: 9
39485547 TTTTGATGTA
39485557 TTTTATAAT
1 TTTTATAAT
39485566 TTTTATATAT
1 TTTTATA-AT
**
39485576 TTTTACGA-
1 TTTTATAAT
39485584 TTTTATATAT
1 TTTTATA-AT
39485594 TTTTAT-AT
1 TTTTATAAT
*
39485602 TTTTAATAAA
1 TTTT-ATAAT
39485612 TTTTA
1 TTTTA
39485617 AATGCTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
8 11 0.27
9 12 0.29
10 18 0.44
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:39485576 original size:18 final size:18
Alignment explanation
Indices: 39485555--39485606 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
39485545 CTTTTTGATG
39485555 TATTTTATA-ATTTTTATA
1 TATTTT-TACATTTTTATA
39485573 TATTTTTACGA-TTTTATA
1 TATTTTTAC-ATTTTTATA
*
39485591 TATTTTTATATTTTTA
1 TATTTTTACATTTTTA
39485607 ATAAATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 3 0.10
18 26 0.87
19 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TATTTTTACATTTTTATA
Found at i:39485577 original size:10 final size:10
Alignment explanation
Indices: 39485557--39485637 Score: 57
Period size: 9 Copynumber: 8.6 Consensus size: 10
39485547 TTTTGATGTA
39485557 TTTTATA-AT
1 TTTTATATAT
39485566 TTTTATATAT
1 TTTTATATAT
**
39485576 TTTTA-CGA-
1 TTTTATATAT
39485584 TTTTATATAT
1 TTTTATATAT
39485594 TTTTATAT-T
1 TTTTATATAT
* *
39485603 TTTAATA-AA
1 TTTTATATAT
* *
39485612 TTTTAAATGCT
1 TTTTATAT-AT
39485623 TTTT-TATAT
1 TTTTATATAT
39485632 TTTTAT
1 TTTTAT
39485638 TAAAGTTTAA
Statistics
Matches: 53, Mismatches: 12, Indels: 13
0.68 0.15 0.17
Matches are distributed among these distances:
8 5 0.09
9 26 0.49
10 18 0.34
11 4 0.08
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTATATAT
Found at i:39485957 original size:95 final size:93
Alignment explanation
Indices: 39485827--39485999 Score: 220
Period size: 95 Copynumber: 1.8 Consensus size: 93
39485817 AAACAAAAAC
** * * *
39485827 TTAATTGTTTTTTTTTTTAAAGTTTGATAGTATTTTTGGTGTATTTTAACAATTCAAGTACTCAA
1 TTAATTGTTTTTTTTTAAAAAGTTTGATAATATTTTTGATATATTTTAACAATTCAAGTACTCAA
*
39485892 TTGAGTGCAAAAAGACAACAACAGTGAT
66 TTGAATGCAAAAAGACAACAACAGTGAT
* * * **
39485920 TTAATTGCTTTTTTTTTGAAAAAGTTTGATAATATTTTTTATATATTTTGACAGTTTGAGTACTC
1 TTAATTG-TTTTTTTTT-AAAAAGTTTGATAATATTTTTGATATATTTTAACAATTCAAGTACTC
*
39485985 AATTGAATGTAAAAA
64 AATTGAATGCAAAAA
39486000 AACCATAATG
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
93 7 0.11
94 9 0.14
95 50 0.76
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.46
Consensus pattern (93 bp):
TTAATTGTTTTTTTTTAAAAAGTTTGATAATATTTTTGATATATTTTAACAATTCAAGTACTCAA
TTGAATGCAAAAAGACAACAACAGTGAT
Found at i:39490663 original size:19 final size:19
Alignment explanation
Indices: 39490639--39490675 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
39490629 TTACTTTCTA
39490639 TTTTT-GTTGATTTTCTTGC
1 TTTTTGGTTG-TTTTCTTGC
39490658 TTTTTGGTTGTTTTCTTG
1 TTTTTGGTTGTTTTCTTG
39490676 TATGGTGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.03, C:0.08, G:0.19, T:0.70
Consensus pattern (19 bp):
TTTTTGGTTGTTTTCTTGC
Found at i:39492412 original size:18 final size:17
Alignment explanation
Indices: 39492386--39492421 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39492376 TTTGGTTATA
39492386 TTTAATTTTCGATATGTT
1 TTTAATTTT-GATATGTT
*
39492404 TTTATTTTTGATATGTT
1 TTTAATTTTGATATGTT
39492421 T
1 T
39492422 CATTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTAATTTTGATATGTT
Found at i:39503686 original size:51 final size:50
Alignment explanation
Indices: 39503551--39503845 Score: 301
Period size: 51 Copynumber: 5.8 Consensus size: 50
39503541 ACTTTTATCA
* * *
39503551 TTCGATACACGTAGTAACTTTCACATAGTACTACACACGTGATCAAG-TT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTT
* * *
39503600 CTACGGTTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
1 -TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAGCTT
* * * *
39503652 TTCGATACACATAGTAGCCTTCACTTAGTACTACACATGTGACC-ATCATT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGC-TT
* * *
39503702 TATCGATTCACGTAGTAGCCTTCACACAGTACTACACACATGACCAAAGCTT
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAGCTT
* * * * * *
39503754 CTCGGTACACATTA-TAGCCTTCACTTAGTACTACACATGTGACC-ATCATT
1 TTCGATACAC-GTAGTAGCCTTCACATAGTACTACACACGTGACCAAGC-TT
* *
39503804 TATCGATACACGTAGTAGCCTTCACACAGTACTATACACGTG
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTG
39503846 TTCATCGATA
Statistics
Matches: 199, Mismatches: 36, Indels: 19
0.78 0.14 0.07
Matches are distributed among these distances:
49 4 0.02
50 45 0.23
51 142 0.71
52 6 0.03
53 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (50 bp):
TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTT
Found at i:39503740 original size:102 final size:102
Alignment explanation
Indices: 39503551--39503845 Score: 418
Period size: 102 Copynumber: 2.9 Consensus size: 102
39503541 ACTTTTATCA
* * * * * * *
39503551 TTCGATACACGTAGTAACTTTCACATAGTACTACACACGTGATCA--AGTTCTA-CGGTTCACGT
1 TTCGATACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCA-TT-TATCGATTCACGT
*
39503613 AGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
64 AGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
39503652 TTCGATACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
1 TTCGATACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
*
39503717 TAGCCTTCACACAGTACTACACACATGACCAAAGCTT
66 TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
* * *
39503754 CTCGGTACACATTA-TAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATACACGTA
1 TTCGATACACA-TAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTA
*
39503818 GTAGCCTTCACACAGTACTATACACGTG
65 GTAGCCTTCACACAGTACTACACACGTG
39503846 TTCATCGATA
Statistics
Matches: 176, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
101 41 0.23
102 132 0.75
103 3 0.02
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (102 bp):
TTCGATACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAG
TAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
Found at i:39503827 original size:153 final size:151
Alignment explanation
Indices: 39503552--39503837 Score: 371
Period size: 153 Copynumber: 1.9 Consensus size: 151
39503542 CTTTTATCAT
* * * * *
39503552 TCGATACACGTAGTAACTTTCACATAGTACTACACACGTGATCAAGTTCTACGGTTCACGTAGTA
1 TCGATACACGTAGTAACCTTCACACAGTACTACACACATGACCAAGTTCTACGGTACACGTAGTA
**
39503617 GCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGATACACATAGTAGCCTTCACTTAGTA
66 GCCTTCACATAGTACTACACACGTGACCAAA-CTTTTCGATACACATAGTAGCCTTCACACAGTA
39503682 CTACACATGTGACCATCATTTA
130 CTACACATGTGACCATCATTTA
* * *
39503704 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACATGACCAAAGCTTCT-CGGTACACATTA
1 TCGATACACGTAGTAACCTTCACACAGTACTACACACATGACC-AAG-TTCTACGGTACAC-GTA
* * * *
39503768 -TAGCCTTCACTTAGTACTACACATGTGACC-ATCATTTATCGATACACGTAGTAGCCTTCACAC
63 GTAGCCTTCACATAGTACTACACACGTGACCAAAC-TTT-TCGATACACATAGTAGCCTTCACAC
39503831 AGTACTA
126 AGTACTA
39503838 TACACGTGTT
Statistics
Matches: 115, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
151 1 0.01
152 41 0.36
153 67 0.58
154 6 0.05
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (151 bp):
TCGATACACGTAGTAACCTTCACACAGTACTACACACATGACCAAGTTCTACGGTACACGTAGTA
GCCTTCACATAGTACTACACACGTGACCAAACTTTTCGATACACATAGTAGCCTTCACACAGTAC
TACACATGTGACCATCATTTA
Found at i:39505006 original size:249 final size:249
Alignment explanation
Indices: 39504565--39505052 Score: 906
Period size: 249 Copynumber: 2.0 Consensus size: 249
39504555 TTCCTAGCTT
* *
39504565 CATATTCTACCATAAAACAGCAAAATAAACATATTTCACCTATGGGTATTTTTCCAAATGTGAAC
1 CATATTCTACCATAAAACAGCAAAATAAAAACATTTCACCTATGGGTATTTTTCCAAATGTGAAC
*
39504630 CCTAACATGAATTAATGGTAGAAATAGCTAAACCGAGCTTCGAGGATCTCAAAAATGCAAAGAAC
66 CCTAACATGAATTAATGGTAGAAATAGCTAAACCGAGCTACGAGGATCTCAAAAATGCAAAGAAC
* *
39504695 ATTAAAAACGGGGCTAAGATGCACTTACTATGAGCTTGAGAAAGTGAAGAAACCCTAGCTATGGT
131 ATTAAAAACGGGGCTAAGATGCACTTACTATGAGCTTAAGAAAGTGAAGAAACCCCAGCTATGGT
39504760 GTCTTCCAAAATTTGGCAGCAACTAATGAAGATGAACACCATTTCATATTCTAC
196 GTCTTCCAAAATTTGGCAGCAACTAATGAAGATGAACACCATTTCATATTCTAC
39504814 CATATTCTACCATAAAACAGCAAAATAAAAACATTTCACCTATGGGTATTTTTCCAAATGTGAAC
1 CATATTCTACCATAAAACAGCAAAATAAAAACATTTCACCTATGGGTATTTTTCCAAATGTGAAC
39504879 CCTAACATGAATTAATGGTAGAAATAGCTAAACCGAGCTACG-GCGATCTCAAAAATGCAAAGAA
66 CCTAACATGAATTAATGGTAGAAATAGCTAAACCGAGCTACGAG-GATCTCAAAAATGCAAAGAA
39504943 CATTAAAAACGGGGCTAAGATGCACTTACTATGAGCTTAAGAAAGTGAAGAAACCCCAGCTATGG
130 CATTAAAAACGGGGCTAAGATGCACTTACTATGAGCTTAAGAAAGTGAAGAAACCCCAGCTATGG
*
39505008 TGTCTTCCAAAATTTGGCAGCAACTAATGAAGATTAACACCATTT
195 TGTCTTCCAAAATTTGGCAGCAACTAATGAAGATGAACACCATTT
39505053 TTTCATCTTT
Statistics
Matches: 232, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
248 1 0.00
249 231 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (249 bp):
CATATTCTACCATAAAACAGCAAAATAAAAACATTTCACCTATGGGTATTTTTCCAAATGTGAAC
CCTAACATGAATTAATGGTAGAAATAGCTAAACCGAGCTACGAGGATCTCAAAAATGCAAAGAAC
ATTAAAAACGGGGCTAAGATGCACTTACTATGAGCTTAAGAAAGTGAAGAAACCCCAGCTATGGT
GTCTTCCAAAATTTGGCAGCAACTAATGAAGATGAACACCATTTCATATTCTAC
Found at i:39508865 original size:16 final size:16
Alignment explanation
Indices: 39508844--39508875 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39508834 GTTTTGTTGC
*
39508844 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
39508860 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
39508876 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:39509166 original size:51 final size:51
Alignment explanation
Indices: 39509093--39509296 Score: 245
Period size: 51 Copynumber: 4.0 Consensus size: 51
39509083 ATTAATGATA
* * * *
39509093 CCGGTTCACATAGTAGCTTGCACATAGTACTACACATGTGACCATCACTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
* *
39509144 CCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTAT
* ** * * *
39509195 CTGGTATGCATAGTAGCCTGCACATAGTACTACACATGAGACCTATCA-T-T
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTAT
39509245 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
39509296 C
1 C
39509297 ACTTTCACAT
Statistics
Matches: 126, Mismatches: 20, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
49 4 0.03
50 41 0.33
51 78 0.62
52 2 0.02
53 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (51 bp):
CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
Found at i:39509269 original size:101 final size:102
Alignment explanation
Indices: 39509101--39509285 Score: 320
Period size: 101 Copynumber: 1.8 Consensus size: 102
39509091 TACCGGTTCA
* *
39509101 CATAGTAGCTTGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGAGACCATCACTATCCGATACACGTAGTAGCCTGCA
39509166 CATAGTACTACACACGTGATCGAAGCTATCTGGTATG
66 CATAGTACTACACACGTGATCGAAGCTATCTGGTATG
*
39509203 CATAGTAGCCTGCACATAGTACTACACATGAGACCTATCA-T-TCCGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGAGACC-ATCACTATCCGATACACGTAGTAGCCTGC
39509266 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
39509286 CCATCACTAT
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
101 41 0.52
102 34 0.43
103 4 0.05
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGAGACCATCACTATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAGCTATCTGGTATG
Found at i:39509308 original size:101 final size:103
Alignment explanation
Indices: 39509097--39509319 Score: 287
Period size: 101 Copynumber: 2.2 Consensus size: 103
39509087 ATGATACCGG
* *
39509097 TTCACATAGTAGCTTGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCC
1 TTCACATAGTAGCCTGCACATAGTACTACACATGAGACCATCACTATCCGATACACGTAGTAGCC
* **
39509162 TGCACATAGTACTACACACGTGATCGAAGCTATCTGGT
66 TGCACATAGTACTACACACGTGATCCAAGCTATCTACT
* * *
39509200 AT-GCATAGTAGCCTGCACATAGTACTACACATGAGACCTATCA-T-TCCGGTACACGTAGTAGC
1 TTCACATAGTAGCCTGCACATAGTACTACACATGAGACC-ATCACTATCCGATACACGTAGTAGC
39509262 CTGCACATAGTACTACACACGTGA-CCATCA-CTATC-ACT
65 CTGCACATAGTACTACACACGTGATCCA--AGCTATCTACT
* *
39509300 TTCACATAGTGGCCTACACA
1 TTCACATAGTAGCCTGCACA
39509320 CAGTCCATGC
Statistics
Matches: 104, Mismatches: 12, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
100 4 0.04
101 60 0.58
102 35 0.34
103 5 0.05
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (103 bp):
TTCACATAGTAGCCTGCACATAGTACTACACATGAGACCATCACTATCCGATACACGTAGTAGCC
TGCACATAGTACTACACACGTGATCCAAGCTATCTACT
Found at i:39524385 original size:49 final size:49
Alignment explanation
Indices: 39524317--39524416 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
39524307 AGCACAATGG
39524317 AGGTACCATTCTTAACAAGACTAGAGGACAAGCAAAAGGGGGACAAGGT
1 AGGTACCATTCTTAACAAGACTAGAGGACAAGCAAAAGGGGGACAAGGT
39524366 AGGTACCATTCTTAACAAGACTAGAGGACAAGCAAAAGGGGGACAAGGT
1 AGGTACCATTCTTAACAAGACTAGAGGACAAGCAAAAGGGGGACAAGGT
39524415 AG
1 AG
39524417 ATTTTATAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (49 bp):
AGGTACCATTCTTAACAAGACTAGAGGACAAGCAAAAGGGGGACAAGGT
Found at i:39529407 original size:39 final size:39
Alignment explanation
Indices: 39529301--39529416 Score: 164
Period size: 38 Copynumber: 3.0 Consensus size: 39
39529291 TATTATAGTT
*
39529301 TGAGTCTTTAATTATGTCTTAATTTGAACATTATTAATA
1 TGAGTCTTTAATTATGTCATAATTTGAACATTATTAATA
*
39529340 TGAGT-TTTAATTATATCATAATTTGAACATTATTAATA
1 TGAGTCTTTAATTATGTCATAATTTGAACATTATTAATA
* * *
39529378 TGGGTCTTTAATTATGTCATAGTTCGAACATGT-TTAATA
1 TGAGTCTTTAATTATGTCATAATTTGAACAT-TATTAATA
39529417 CTTGTTTTCA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
38 35 0.51
39 33 0.48
40 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.47
Consensus pattern (39 bp):
TGAGTCTTTAATTATGTCATAATTTGAACATTATTAATA
Found at i:39535757 original size:24 final size:24
Alignment explanation
Indices: 39535730--39535777 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
39535720 ACTCTGTTAG
39535730 TTGTCATAGTCGAGTTATAGTCTT
1 TTGTCATAGTCGAGTTATAGTCTT
* *
39535754 TTGTCATTGTTGAGTTATAGTCTT
1 TTGTCATAGTCGAGTTATAGTCTT
39535778 ACACCTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.10, G:0.21, T:0.50
Consensus pattern (24 bp):
TTGTCATAGTCGAGTTATAGTCTT
Found at i:39539672 original size:29 final size:29
Alignment explanation
Indices: 39539639--39539696 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
39539629 AAATTAAGTA
39539639 TAAATTCAAGAAATTTTCCATTAAACCAG
1 TAAATTCAAGAAATTTTCCATTAAACCAG
39539668 TAAATTCAAGAAATTTTCCATTAAACCAG
1 TAAATTCAAGAAATTTTCCATTAAACCAG
39539697 CCCCTAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (29 bp):
TAAATTCAAGAAATTTTCCATTAAACCAG
Found at i:39542342 original size:24 final size:25
Alignment explanation
Indices: 39542290--39542377 Score: 99
Period size: 25 Copynumber: 3.6 Consensus size: 25
39542280 ATACATGTAT
* * *
39542290 GCTCATACTAGCTCTAAATCGGTAT
1 GCTCATACGAGCTGTAAATCGGTAA
*
39542315 GCTCTTACGAGCTGTAAA-CGGTAA
1 GCTCATACGAGCTGTAAATCGGTAA
*
39542339 GCTCATATGAGCTG-AATATCGGTAA
1 GCTCATACGAGCTGTAA-ATCGGTAA
*
39542364 GCTCATGCGAGCTG
1 GCTCATACGAGCTG
39542378 AAGATCTATA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
23 2 0.04
24 18 0.34
25 33 0.62
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (25 bp):
GCTCATACGAGCTGTAAATCGGTAA
Found at i:39542389 original size:25 final size:25
Alignment explanation
Indices: 39542315--39542392 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
39542305 AAATCGGTAT
* *
39542315 GCTCTTACGAGCTGTAA-A-CGGTAA
1 GCTCATACGAGCTG-AAGATCGATAA
* * *
39542339 GCTCATATGAGCTGAATATCGGTAA
1 GCTCATACGAGCTGAAGATCGATAA
* *
39542364 GCTCATGCGAGCTGAAGATCTATAA
1 GCTCATACGAGCTGAAGATCGATAA
39542389 GCTC
1 GCTC
39542393 TCTTGATCTG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
23 2 0.04
24 13 0.29
25 30 0.67
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (25 bp):
GCTCATACGAGCTGAAGATCGATAA
Found at i:39551385 original size:55 final size:55
Alignment explanation
Indices: 39551297--39551427 Score: 131
Period size: 55 Copynumber: 2.3 Consensus size: 55
39551287 AACATGCCAG
* * * * * *
39551297 GAAAAAGAAAGCCTTTGTAGTGATCTAAGAAAAAGGGAGCCTTTGTGGCGATCTAC
1 GAAAAAG-GAGCCTTTGTGGTGACCTAAGAAAAAGGAAGCCTTTGTGGCAACCTAC
** *
39551353 GAAAAATGG-GCCTTTGTGGTGACCTATA-AAAAAGGAAGTGTTTGTGGCAACCTAT
1 GAAAAA-GGAGCCTTTGTGGTGACCTA-AGAAAAAGGAAGCCTTTGTGGCAACCTAC
39551408 GAAAAAGGAAGCCTTTGTGG
1 GAAAAAGG-AGCCTTTGTGG
39551428 CAATCTATGA
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
54 2 0.03
55 42 0.68
56 17 0.27
57 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.24
Consensus pattern (55 bp):
GAAAAAGGAGCCTTTGTGGTGACCTAAGAAAAAGGAAGCCTTTGTGGCAACCTAC
Found at i:39551428 original size:28 final size:28
Alignment explanation
Indices: 39551297--39551451 Score: 143
Period size: 28 Copynumber: 5.6 Consensus size: 28
39551287 AACATGCCAG
* * * *
39551297 GAAAAAGAAAGCCTTTGTAGTGATCTAA
1 GAAAAAGGAAGCCTTTGTGGCGATCTAT
* *
39551325 GAAAAAGGGAGCCTTTGTGGCGATCTAC
1 GAAAAAGGAAGCCTTTGTGGCGATCTAT
* *
39551353 GAAAAATGG--GCCTTTGTGGTGACCTAT
1 GAAAAA-GGAAGCCTTTGTGGCGATCTAT
* ** * *
39551380 AAAAAAGGAAGTGTTTGTGGCAACCTAT
1 GAAAAAGGAAGCCTTTGTGGCGATCTAT
*
39551408 GAAAAAGGAAGCCTTTGTGGCAATCTAT
1 GAAAAAGGAAGCCTTTGTGGCGATCTAT
* *
39551436 GAAAATGAAAGCCTTT
1 GAAAAAGGAAGCCTTT
39551452 TATGGTGATT
Statistics
Matches: 105, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
26 2 0.02
27 20 0.19
28 81 0.77
29 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (28 bp):
GAAAAAGGAAGCCTTTGTGGCGATCTAT
Found at i:39558315 original size:29 final size:29
Alignment explanation
Indices: 39558282--39558666 Score: 292
Period size: 29 Copynumber: 13.2 Consensus size: 29
39558272 GCACCGATTA
* *
39558282 ATGAAAAAGGATGGTGACGACCATTGAAT
1 ATGAAAAGGGATGGTGACGACCATCGAAT
* * *** * *
39558311 ATGAAAATGAATGGTTTTGACTATCGACT
1 ATGAAAAGGGATGGTGACGACCATCGAAT
*
39558340 ATGAAAAGGGATGGTGATGACCATC-AACT
1 ATGAAAAGGGATGGTGACGACCATCGAA-T
*
39558369 ATGAAAAGGGATGGTGATGACCATCGAAT
1 ATGAAAAGGGATGGTGACGACCATCGAAT
* ** * *
39558398 ATGAAAAGGGATAGTTTCGACTATCGACT
1 ATGAAAAGGGATGGTGACGACCATCGAAT
*
39558427 ATGAAAAGGGATGGTGACGACCATTGAAT
1 ATGAAAAGGGATGGTGACGACCATCGAAT
* *** * *
39558456 ATGAAAAGGGATAGTTTTGACTATCGACT
1 ATGAAAAGGGATGGTGACGACCATCGAAT
* * *
39558485 ATGAAAAGGGATAGTGATGACCATCAAAT
1 ATGAAAAGGGATGGTGACGACCATCGAAT
* **** * *
39558514 AT-AAAATGGGATAGCT-TTTTCTATCGACT
1 ATGAAAA-GGGAT-GGTGACGACCATCGAAT
* *
39558543 ATGAAAAGGGATGGCGATGACCATC-AACT
1 ATGAAAAGGGATGGTGACGACCATCGAA-T
* * * *
39558572 ATGAAAACGGATTGTGATGACCATCGATT
1 ATGAAAAGGGATGGTGACGACCATCGAAT
* **
39558601 AATGAAAAGGGCTGGTTTCGACCATCGAAT
1 -ATGAAAAGGGATGGTGACGACCATCGAAT
* *
39558631 ATGAAAAGGGATGGTGACGAACAACGAAT
1 ATGAAAAGGGATGGTGACGACCATCGAAT
*
39558660 ATAAAAA
1 ATGAAAA
39558667 TGAATGGTTT
Statistics
Matches: 277, Mismatches: 70, Indels: 18
0.76 0.19 0.05
Matches are distributed among these distances:
28 7 0.03
29 240 0.87
30 30 0.11
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.24
Consensus pattern (29 bp):
ATGAAAAGGGATGGTGACGACCATCGAAT
Found at i:39562523 original size:17 final size:18
Alignment explanation
Indices: 39562493--39562526 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
39562483 AGCAACTCAT
39562493 TTATTAATCTAAGATGAG
1 TTATTAATCTAAGATGAG
39562511 TTATTAA-CTAAGATGA
1 TTATTAATCTAAGATGA
39562527 ACTCAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (18 bp):
TTATTAATCTAAGATGAG
Found at i:39565825 original size:30 final size:30
Alignment explanation
Indices: 39565791--39565913 Score: 133
Period size: 29 Copynumber: 4.2 Consensus size: 30
39565781 AATAACATTA
* *
39565791 ACCATCGATTAATGAAAAGGGATGGTGAGG
1 ACCATCAATTAATGAAAAGGGATGGTGACG
* * *
39565821 ACCATCAACT-ATGAAAAGGGGTGGCGACG
1 ACCATCAATTAATGAAAAGGGATGGTGACG
***
39565850 ACCATCAATTAATGAAAAGGGATGGTTTTG
1 ACCATCAATTAATGAAAAGGGATGGTGACG
* **
39565880 ACCATCGA-GGATGAAAAGGGATGGTGACG
1 ACCATCAATTAATGAAAAGGGATGGTGACG
39565909 ACCAT
1 ACCAT
39565914 TGTTTAGTAC
Statistics
Matches: 75, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
29 46 0.61
30 29 0.39
ACGTcount: A:0.36, C:0.15, G:0.30, T:0.20
Consensus pattern (30 bp):
ACCATCAATTAATGAAAAGGGATGGTGACG
Found at i:39565883 original size:59 final size:59
Alignment explanation
Indices: 39565791--39565913 Score: 165
Period size: 59 Copynumber: 2.1 Consensus size: 59
39565781 AATAACATTA
* * *
39565791 ACCATCGATTAATGAAAAGGGATGGTGAGGACCATCAACTATGAAAAGGGGTGGCGACG
1 ACCATCAATTAATGAAAAGGGATGGTGAGGACCATCAACGATGAAAAGGGATGGCGACG
*** * * *
39565850 ACCATCAATTAATGAAAAGGGATGGTTTTGACCATCGAGGATGAAAAGGGATGGTGACG
1 ACCATCAATTAATGAAAAGGGATGGTGAGGACCATCAACGATGAAAAGGGATGGCGACG
39565909 ACCAT
1 ACCAT
39565914 TGTTTAGTAC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.36, C:0.15, G:0.30, T:0.20
Consensus pattern (59 bp):
ACCATCAATTAATGAAAAGGGATGGTGAGGACCATCAACGATGAAAAGGGATGGCGACG
Found at i:39568851 original size:27 final size:27
Alignment explanation
Indices: 39568820--39568997 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
39568810 TAAATTGTAC
*
39568820 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
39568847 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
39568873 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
39568901 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
39568928 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * * *
39568956 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
39568983 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39568998 GACTTAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:39568881 original size:54 final size:55
Alignment explanation
Indices: 39568820--39568997 Score: 236
Period size: 54 Copynumber: 3.3 Consensus size: 55
39568810 TAAATTGTAC
* **
39568820 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* * * *
39568875 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* *
39568928 AGCACTAAGTGTGCGAGTTTGATTATGTGGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
*
39568983 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39568998 GACTTAATAT
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:39576872 original size:30 final size:30
Alignment explanation
Indices: 39576836--39576897 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
39576826 TCGGTTATTT
39576836 TACCCAACATAAAGTAAGTCATTAAGCATG
1 TACCCAACATAAAGTAAGTCATTAAGCATG
39576866 TACCCAACATAAAGTAAGTCATTAAGCATG
1 TACCCAACATAAAGTAAGTCATTAAGCATG
39576896 TA
1 TA
39576898 GTTGGTATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (30 bp):
TACCCAACATAAAGTAAGTCATTAAGCATG
Found at i:39577147 original size:27 final size:27
Alignment explanation
Indices: 39577116--39577293 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
39577106 TAAATTGTAC
*
39577116 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
39577143 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
39577169 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
39577197 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
39577224 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * * *
39577252 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
39577279 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39577294 GACTTAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:39577177 original size:54 final size:55
Alignment explanation
Indices: 39577116--39577293 Score: 236
Period size: 54 Copynumber: 3.3 Consensus size: 55
39577106 TAAATTGTAC
* **
39577116 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* * * *
39577171 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* *
39577224 AGCACTAAGTGTGCGAGTTTGATTATGTGGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
*
39577279 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39577294 GACTTAATAT
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:39583000 original size:40 final size:39
Alignment explanation
Indices: 39582956--39583077 Score: 145
Period size: 40 Copynumber: 3.1 Consensus size: 39
39582946 ATATTATTTA
* * *
39582956 ATTCATGATTACCAAAGTACAAACAGGGGCATGTACGTGC
1 ATTCAGGA-TACCAAAGTACAAACAGGGGCACGTATGTGC
* *
39582996 ATTCAGGGATGCCAAAGTACAAACAGGGGCACATATGTGC
1 ATTCA-GGATACCAAAGTACAAACAGGGGCACGTATGTGC
* **
39583036 ATTCAGGGGTACTGAAGTACAAACAGGGGCACGTATGTGC
1 ATTCA-GGATACCAAAGTACAAACAGGGGCACGTATGTGC
39583076 AT
1 AT
39583078 CCATTGAATA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 69 0.97
41 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.20
Consensus pattern (39 bp):
ATTCAGGATACCAAAGTACAAACAGGGGCACGTATGTGC
Found at i:39586399 original size:16 final size:18
Alignment explanation
Indices: 39586365--39586419 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 18
39586355 CAAAAGGAGA
39586365 TTTAGAGGTTTTAAGGAT
1 TTTAGAGGTTTTAAGGAT
39586383 TTTAG-GGTTTT-AGGAT
1 TTTAGAGGTTTTAAGGAT
39586399 TTTA-AGAG-TTTAGAGGAT
1 TTTAGAG-GTTTTA-AGGAT
39586417 TTT
1 TTT
39586420 GAAAGAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 13 0.39
17 7 0.21
18 13 0.39
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.47
Consensus pattern (18 bp):
TTTAGAGGTTTTAAGGAT
Found at i:39597057 original size:44 final size:44
Alignment explanation
Indices: 39596994--39597082 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
39596984 CTTGTAACGC
* *
39596994 ATAGGTTTTTGCAAGTGTACACAGTCGTTATCAATTAATAAGTA
1 ATAGGTTTGTGCAAGTGTACACAGTCGTTATCAACTAATAAGTA
39597038 ATAGGTTTGTGCAAGTGTACACAGTCGTTATCAACTAATAAGTA
1 ATAGGTTTGTGCAAGTGTACACAGTCGTTATCAACTAATAAGTA
39597082 A
1 A
39597083 GTTTCAAGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (44 bp):
ATAGGTTTGTGCAAGTGTACACAGTCGTTATCAACTAATAAGTA
Found at i:39601414 original size:27 final size:27
Alignment explanation
Indices: 39601384--39601515 Score: 138
Period size: 27 Copynumber: 4.9 Consensus size: 27
39601374 TTTCATCTCC
** * *
39601384 TAGGGGTATAACAATTATTTTACCCAA
1 TAGGGGTATTTCAATCATTTTACCCTA
**
39601411 TAGGGGTATTTCGGTCATTTTACCCTA
1 TAGGGGTATTTCAATCATTTTACCCTA
*
39601438 TGGGGGTATTTCAATCATTTTACCCTA
1 TAGGGGTATTTCAATCATTTTACCCTA
***
39601465 TAGGGGTATTTTGGTCATTTTACCCTA
1 TAGGGGTATTTCAATCATTTTACCCTA
* * **
39601492 TGGGGGCATTTCGGTCATTTTACC
1 TAGGGGTATTTCAATCATTTTACC
39601516 TATTTTAGGG
Statistics
Matches: 89, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 89 1.00
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.39
Consensus pattern (27 bp):
TAGGGGTATTTCAATCATTTTACCCTA
Found at i:39601458 original size:54 final size:54
Alignment explanation
Indices: 39601386--39601515 Score: 188
Period size: 54 Copynumber: 2.4 Consensus size: 54
39601376 TCATCTCCTA
** *
39601386 GGGGTATAACAATTATTTTACCCAATAGGGGTATTTCGGTCATTTTACCCTATG
1 GGGGTATTTCAATCATTTTACCCAATAGGGGTATTTCGGTCATTTTACCCTATG
* *
39601440 GGGGTATTTCAATCATTTTACCCTATAGGGGTATTTTGGTCATTTTACCCTATG
1 GGGGTATTTCAATCATTTTACCCAATAGGGGTATTTCGGTCATTTTACCCTATG
* **
39601494 GGGGCATTTCGGTCATTTTACC
1 GGGGTATTTCAATCATTTTACC
39601516 TATTTTAGGG
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 68 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (54 bp):
GGGGTATTTCAATCATTTTACCCAATAGGGGTATTTCGGTCATTTTACCCTATG
Found at i:39609509 original size:17 final size:17
Alignment explanation
Indices: 39609487--39609519 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39609477 TTTTGATATA
39609487 AAACTA-TTAAATAACTT
1 AAACTACTT-AATAACTT
39609504 AAACTACTTAATAACT
1 AAACTACTTAATAACT
39609520 ATTAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (17 bp):
AAACTACTTAATAACTT
Found at i:39615580 original size:38 final size:39
Alignment explanation
Indices: 39615475--39615620 Score: 131
Period size: 38 Copynumber: 3.8 Consensus size: 39
39615465 TAAACACATG
* * * **
39615475 TATTAAAGATG-TCTAAACTAGGACAT-ATTTAAAACATA
1 TATTAAAGATGTTC-AAATTATGACATAATTAAAAACCCA
* * *
39615513 TATTTAAA-ATGTCCTAAACTATGACATAATTAAAAACCCT
1 TA-TTAAAGATGTTC-AAATTATGACATAATTAAAAACCCA
* *
39615553 TATTAAAGATG-TCAGATTATGACATAATT-AAAACTCA
1 TATTAAAGATGTTCAAATTATGACATAATTAAAAACCCA
*
39615590 TATTAATGATGTTCAAATTATGACATAATTA
1 TATTAAAGATGTTCAAATTATGACATAATTA
39615621 TAGACTTAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 11
0.79 0.12 0.10
Matches are distributed among these distances:
37 16 0.18
38 36 0.40
39 24 0.27
40 13 0.15
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (39 bp):
TATTAAAGATGTTCAAATTATGACATAATTAAAAACCCA
Found at i:39618203 original size:112 final size:112
Alignment explanation
Indices: 39618006--39618234 Score: 395
Period size: 112 Copynumber: 2.0 Consensus size: 112
39617996 GCATAACCAA
* *
39618006 CCACTCGTACAAACCGTGCTTTGTCTTAAATTTCATTTTCCACTAATCTCCTTCTCGCATTCATA
1 CCACTCGTACAAACCGTGCTTTGTCTTAAATGTCATTTTCCACTAATCTCCTTCTCGCATTCAGA
39618071 TCTCATGATAACCACTTTTGAGATCTATTTTGGAGAAGAGTTGGGCT
66 TCTCATGATAACCACTTTTGAGATCTATTTTGGAGAAGAGTTGGGCT
* * *
39618118 CCACTCGTACAAACTGTGCTTTGTCTTAAATGTCGTTTTCCACTAATCTCCTTCTCGCATTCGGA
1 CCACTCGTACAAACCGTGCTTTGTCTTAAATGTCATTTTCCACTAATCTCCTTCTCGCATTCAGA
**
39618183 TCTGGTGATAACCACTTTTGAGATCTATTTTGGAGAAGAGTTGGGCT
66 TCTCATGATAACCACTTTTGAGATCTATTTTGGAGAAGAGTTGGGCT
39618230 CCACT
1 CCACT
39618235 TAGTTCATCC
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 110 1.00
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.37
Consensus pattern (112 bp):
CCACTCGTACAAACCGTGCTTTGTCTTAAATGTCATTTTCCACTAATCTCCTTCTCGCATTCAGA
TCTCATGATAACCACTTTTGAGATCTATTTTGGAGAAGAGTTGGGCT
Found at i:39618817 original size:22 final size:21
Alignment explanation
Indices: 39618781--39618840 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
39618771 TCTCTTTATT
*
39618781 CTTTTCCCTTGTTTTTACCTCTTG
1 CTTTT-CCTTTTTTTTA-CT-TTG
*
39618805 C-TTTCCTTTTTTTTAGTTTG
1 CTTTTCCTTTTTTTTACTTTG
39618825 CTTTTCCTTTTCTTTT
1 CTTTTCCTTTT-TTTT
39618841 TCAATCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 4 0.12
21 10 0.31
22 14 0.44
23 3 0.09
24 1 0.03
ACGTcount: A:0.03, C:0.23, G:0.07, T:0.67
Consensus pattern (21 bp):
CTTTTCCTTTTTTTTACTTTG
Found at i:39622061 original size:38 final size:39
Alignment explanation
Indices: 39622014--39622102 Score: 121
Period size: 38 Copynumber: 2.3 Consensus size: 39
39622004 TGTCCTAAAC
* *
39622014 TATGACATAATTAAAAACCCTTATTAAA-GATG-TCATAT
1 TATGACATAATTAAAAACCCATA-TAAATGATGTTCAAAT
*
39622052 TATGACATAATT-AAAACTCATATAAATGATGTTCAAAT
1 TATGACATAATTAAAAACCCATATAAATGATGTTCAAAT
39622090 TATGACATAATTA
1 TATGACATAATTA
39622103 TAGACTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
36 4 0.09
37 12 0.27
38 29 0.64
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (39 bp):
TATGACATAATTAAAAACCCATATAAATGATGTTCAAAT
Found at i:39626574 original size:104 final size:104
Alignment explanation
Indices: 39626394--39626617 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
39626384 TGTATATAAA
** * *
39626394 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
39626459 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
39626498 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
39626562 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
39626602 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
39626618 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:39626669 original size:71 final size:72
Alignment explanation
Indices: 39626536--39626687 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
39626526 TCATTGGTGG
* *
39626536 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
39626601 GAGGGGT
66 GAGGGGT
***
39626608 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
39626672 GAGGGGT
66 GAGGGGT
39626679 TGCTAAGTG
1 TGCTAAGTG
39626688 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:39634059 original size:26 final size:26
Alignment explanation
Indices: 39634024--39634074 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
39634014 AATGTGAAAG
*
39634024 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
39634050 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
39634075 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:39634112 original size:103 final size:103
Alignment explanation
Indices: 39633947--39634168 Score: 367
Period size: 103 Copynumber: 2.2 Consensus size: 103
39633937 TGTATATAAA
** * *
39633947 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGTGGTGCTATGTGCGTGATCCACCATATCTTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
39634012 GAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
66 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
39634049 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCA-TGGTGGTGCTAAGTGCG-TGATCCACCATATCT
39634113 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
64 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
39634153 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
39634169 GATATCCATT
Statistics
Matches: 112, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
102 27 0.24
103 63 0.56
104 22 0.20
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.32
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:39634220 original size:71 final size:72
Alignment explanation
Indices: 39634087--39634238 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
39634077 TCATTGGTGG
* *
39634087 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
39634152 GAGGGGT
66 GAGGGGT
***
39634159 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
39634223 GAGGGGT
66 GAGGGGT
39634230 TGCTAAGTG
1 TGCTAAGTG
39634239 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:39639856 original size:17 final size:17
Alignment explanation
Indices: 39639836--39639870 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
39639826 TGATTCAATA
*
39639836 TCTAGCGTTTCTTGGTT
1 TCTAGAGTTTCTTGGTT
*
39639853 TCTAGAGTTTCTTTGTT
1 TCTAGAGTTTCTTGGTT
39639870 T
1 T
39639871 AGGCCTAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.14, G:0.20, T:0.57
Consensus pattern (17 bp):
TCTAGAGTTTCTTGGTT
Found at i:39640798 original size:31 final size:31
Alignment explanation
Indices: 39640757--39640829 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
39640747 GTTTCAAAAA
* * *
39640757 TTTTCATTTAAATCATTAAACTATT-TACAAT
1 TTTTTATTTAAATCACTAAACTATTCGA-AAT
*
39640788 TTTTTATTTAAATCACTAAATTATTCGAAAT
1 TTTTTATTTAAATCACTAAACTATTCGAAAT
39640819 TTTTTATTTAA
1 TTTTTATTTAA
39640830 GTTGCGCATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 36 0.97
32 1 0.03
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.52
Consensus pattern (31 bp):
TTTTTATTTAAATCACTAAACTATTCGAAAT
Found at i:39643964 original size:9 final size:9
Alignment explanation
Indices: 39643947--39643983 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
39643937 TATAGTTTGA
*
39643947 TATTAGAAT
1 TATTCGAAT
39643956 TATTCGAAT
1 TATTCGAAT
*
39643965 TATTCGAGT
1 TATTCGAAT
39643974 TATTCGAAT
1 TATTCGAAT
39643983 T
1 T
39643984 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:39647140 original size:24 final size:26
Alignment explanation
Indices: 39647113--39647163 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 26
39647103 ATATACATAT
*
39647113 ACATGTAGATATTT-ATA-TTTTATA
1 ACATATAGATATTTCATATTTTTATA
* *
39647137 ACATATATATTTTTCATATTTTTATA
1 ACATATAGATATTTCATATTTTTATA
39647163 A
1 A
39647164 TTTTATGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 11 0.50
25 3 0.14
26 8 0.36
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (26 bp):
ACATATAGATATTTCATATTTTTATA
Found at i:39647730 original size:108 final size:108
Alignment explanation
Indices: 39647443--39647854 Score: 560
Period size: 108 Copynumber: 3.8 Consensus size: 108
39647433 TCTAATTGAT
* * * * *
39647443 GCAATATTTAGCGTTTGGAAACTCGAGAAACATGCCCTAAGGTGCTGGGTGTCGGTCTTTCTCGT
1 GCAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGT
** * *
39647508 TCAACCAAACGGCTTAATATCTTTTTCAAAAATTT-CAAAATAAG
66 TCAACCAAATAGCTAAATATC-CTTTC-AAAATTTACAAAATAAG
* * * *
39647552 GTAATGTTCTACGTTTGGAAATTCGAGAAAACATGCCCTAAAGTGCTGGGTGTCGATTTTTCTCG
1 GCAATGTTTTGCGTTTGGAAATTCGAG-AAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCG
39647617 TTCAACCAAATAGCTAAATATCCTTTCAAAATTTACAAAATAAG
65 TTCAACCAAATAGCTAAATATCCTTTCAAAATTTACAAAATAAG
* * *
39647661 GCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGTTGGGTGTCGATTTTTCTCGT
1 GCAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGT
*
39647726 TCAACCAAATAGCTAAATATCCTTTCAAAAATTACAAAATAAG
66 TCAACCAAATAGCTAAATATCCTTTCAAAATTTACAAAATAAG
* * * *
39647769 GCAATGTTTTGCGTTTGGAAATTTGAGGAACGTGCCCTAAGGTGCTGGGTTTCGA--TTTCTCGT
1 GCAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGT
* * *
39647832 TTAACCAAATTGCCAAATATCCT
66 TCAACCAAATAGCTAAATATCCT
39647855 CTTGAATTTT
Statistics
Matches: 274, Mismatches: 27, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
106 28 0.10
108 135 0.49
109 58 0.21
110 53 0.19
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (108 bp):
GCAATGTTTTGCGTTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGT
TCAACCAAATAGCTAAATATCCTTTCAAAATTTACAAAATAAG
Found at i:39658962 original size:41 final size:42
Alignment explanation
Indices: 39658909--39659177 Score: 193
Period size: 41 Copynumber: 6.3 Consensus size: 42
39658899 AAATAAAAGA
* * *
39658909 TCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGGA-TCAGG
1 TCTTATCTCCCTGAGGTTACAGTAGAGCAGATCGGATTCAGG
* * * * *
39658950 TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTAGAGCAGATCG--G-A-TTCAGG
* * * **
39658996 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAG
1 TCTTATCTCCCTGAGGTTACAGTAGAGCAGATCGGATTCAG-G
* * * *
39659039 ATCTTATCTCCCTGAGATTACAGTAAAGCAGATCGCA-TCAAG
1 -TCTTATCTCCCTGAGGTTACAGTAGAGCAGATCGGATTCAGG
*** **
39659081 TCTTATCTCCCTGAGGTTACAGTAGAGCAGATTAAAGCCAGAG
1 TCTTATCTCCCTGAGGTTACAGTAGAGCAGATCGGATTCAG-G
* * * * * *
39659124 ATCTTATCTTCTTGAGATTACAGTGGAGCAGATCGCA-TCAAG
1 -TCTTATCTCCCTGAGGTTACAGTAGAGCAGATCGGATTCAGG
39659166 TCTTATCTCCCT
1 TCTTATCTCCCT
39659178 AAGCAGTAGT
Statistics
Matches: 181, Mismatches: 37, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
41 72 0.40
42 7 0.04
43 7 0.04
44 61 0.34
46 34 0.19
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (42 bp):
TCTTATCTCCCTGAGGTTACAGTAGAGCAGATCGGATTCAGG
Found at i:39659053 original size:44 final size:44
Alignment explanation
Indices: 39658817--39659177 Score: 283
Period size: 44 Copynumber: 8.4 Consensus size: 44
39658807 GGTGAATATT
* * * *
39658817 AGAGATCTTATCTCCCTGAGATTACGGCGGAGCAGATCGAAGAC
1 AGAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGTC
** * * * ** * *
39658861 A-CTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATA
1 AGAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGTC
* * * * * *
39658904 AAAGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGGA-TC
1 AGAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGTC
* * * *
39658947 AG-G-TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATT
1 AGAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAG--TC
** * *
39658991 TCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCC
1 AGAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGTC
* ** *
39659035 AGAGATCTTATCTCCCTGAGATTACAGTAAAGCAGATCGCA-TC
1 AGAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGTC
* ** *
39659078 A-AG-TCTTATCTCCCTGAGGTTACAGTAGAGCAGATTAAAGCC
1 AGAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGTC
* * * *
39659120 AGAGATCTTATCTTCTTGAGATTACAGTGGAGCAGATCGCA-TC
1 AGAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGTC
39659163 A-AG-TCTTATCTCCCT
1 AGAGATCTTATCTCCCT
39659178 AAGCAGTAGT
Statistics
Matches: 246, Mismatches: 62, Indels: 21
0.75 0.19 0.06
Matches are distributed among these distances:
41 73 0.30
42 7 0.03
43 38 0.15
44 94 0.38
45 1 0.00
46 33 0.13
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (44 bp):
AGAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGTC
Found at i:39659060 original size:131 final size:131
Alignment explanation
Indices: 39658868--39659103 Score: 339
Period size: 131 Copynumber: 1.8 Consensus size: 131
39658858 GACACTATCC
* * *
39658868 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAAGATCTTATCTCCCTGAAGTTACAGTA
* * * * *
39658933 GAGTAGATCGGATCAGGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATC
66 AAGCAGATCGCATCAAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATC
39658998 T
131 T
* * * * *
39658999 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTG-AGATTACAGT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAAGATCTTATCTCCCTGAAG-TTACAGT
39659063 AAAGCAGATCGCATCAAGTCTTATCTCCCTGAGGTTACAGT
65 AAAGCAGATCGCATCAAGTCTTATCTCCCTGAGGTTACAGT
39659104 AGAGCAGATT
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
130 2 0.02
131 89 0.98
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (131 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAAGATCTTATCTCCCTGAAGTTACAGTA
AAGCAGATCGCATCAAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATC
T
Found at i:39659101 original size:85 final size:85
Alignment explanation
Indices: 39658996--39659177 Score: 310
Period size: 85 Copynumber: 2.1 Consensus size: 85
39658986 GAATTTCAGA
* *
39658996 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGGTTACAGTAGAGCAGATTAAAGCCAGAGATCTTATCTCCCTGAGATTACA
39659061 GTAAAGCAGATCGCATCAAG
66 GTAAAGCAGATCGCATCAAG
* *
39659081 TCTTATCTCCCTGAGGTTACAGTAGAGCAGATTAAAGCCAGAGATCTTATCTTCTTGAGATTACA
1 TCTTATCTCCCTGAGGTTACAGTAGAGCAGATTAAAGCCAGAGATCTTATCTCCCTGAGATTACA
**
39659146 GTGGAGCAGATCGCATCAAG
66 GTAAAGCAGATCGCATCAAG
39659166 TCTTATCTCCCT
1 TCTTATCTCCCT
39659178 AAGCAGTAGT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 91 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (85 bp):
TCTTATCTCCCTGAGGTTACAGTAGAGCAGATTAAAGCCAGAGATCTTATCTCCCTGAGATTACA
GTAAAGCAGATCGCATCAAG
Found at i:39661148 original size:24 final size:26
Alignment explanation
Indices: 39661121--39661171 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 26
39661111 ATATACATAT
*
39661121 ACATGTAGATATTT-ATA-TTTTATA
1 ACATATAGATATTTCATATTTTTATA
* *
39661145 ACATATATATTTTTCATATTTTTATA
1 ACATATAGATATTTCATATTTTTATA
39661171 A
1 A
39661172 TTTTATGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 11 0.50
25 3 0.14
26 8 0.36
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (26 bp):
ACATATAGATATTTCATATTTTTATA
Found at i:39661736 original size:108 final size:108
Alignment explanation
Indices: 39661464--39661862 Score: 554
Period size: 108 Copynumber: 3.7 Consensus size: 108
39661454 ATATTTAGCA
* * * * *
39661464 TTTGGAAACTCAAGAAACATGCCCTAAGGTGCTGGGTGTCGGTCTTTCTCGTTCAACCAAA-CGA
1 TTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAG-
* * * *
39661528 CTTAATATCTTTTTCAAAAATTT-CAAAATAAGGTAATGTTCTGCG
65 CTAAATATC-CTTTC-AAAATTTACAAAATAAGGCAATGTTTTGCG
*
39661573 TTTGGAAATTCGAGAAAACATGCCCTAAAGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAG
1 TTTGGAAATTCGAG-AAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAG
39661638 CTAAATATCCTTTCAAAATTTACAAAATAAGGCAATGTTTTGCG
65 CTAAATATCCTTTCAAAATTTACAAAATAAGGCAATGTTTTGCG
* *
39661682 TTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGC
1 TTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGC
*
39661747 TAAATATCCTTTCAAAAATTACAAAATAAGGCAATGTTTTGCG
66 TAAATATCCTTTCAAAATTTACAAAATAAGGCAATGTTTTGCG
* * * * * *
39661790 TTTGGAAATTTGAGGAACGTGCCCTAAGGTGCTGGGTTTCGA--TTTCTCGTTTAACCAAATTGC
1 TTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGC
*
39661853 CAAATATCCT
66 TAAATATCCT
39661863 CTTGAATTTT
Statistics
Matches: 268, Mismatches: 19, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
106 28 0.10
108 137 0.51
109 50 0.19
110 52 0.19
111 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (108 bp):
TTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGC
TAAATATCCTTTCAAAATTTACAAAATAAGGCAATGTTTTGCG
Found at i:39667257 original size:21 final size:21
Alignment explanation
Indices: 39667233--39667274 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
39667223 TTTGCTCTTT
39667233 GCTGGTTCCCTCTGCTGCTAC
1 GCTGGTTCCCTCTGCTGCTAC
*
39667254 GCTGGTTCTCTCTGCTGCTAC
1 GCTGGTTCCCTCTGCTGCTAC
39667275 ACTACTCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.05, C:0.36, G:0.24, T:0.36
Consensus pattern (21 bp):
GCTGGTTCCCTCTGCTGCTAC
Found at i:39668427 original size:16 final size:16
Alignment explanation
Indices: 39668403--39668433 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39668393 TAAAATTTTT
39668403 ATACCGTTTTTTGTTA
1 ATACCGTTTTTTGTTA
*
39668419 ATACTGTTTTTTGTT
1 ATACCGTTTTTTGTT
39668434 CATGTATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.10, G:0.13, T:0.61
Consensus pattern (16 bp):
ATACCGTTTTTTGTTA
Found at i:39669756 original size:72 final size:72
Alignment explanation
Indices: 39669639--39669802 Score: 233
Period size: 72 Copynumber: 2.3 Consensus size: 72
39669629 CGAAGTATGT
* * * * *
39669639 TTTTATCAATAGTTATTTATGTTTAGTTTTTAGATATTGAATTTATGTTCTACTTATTTATGT-G
1 TTTTATTAATAGTTGTTTATGTTTAGTCTTTAGATATTGAATTTATGTTCCACTTATTT-TGTAC
39669703 T-AATCTAG
65 TAAAT-TAG
* *
39669711 TTTTATTAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCCACTTATTTTTTACT
1 TTTTATTAATAGTTGTTTATGTTTAGTCTTTAGATATTGAATTTATGTTCCACTTATTTTGTACT
39669776 AAATTAG
66 AAATTAG
39669783 TTTTATTAATAGTTGTTTAT
1 TTTTATTAATAGTTGTTTAT
39669803 ATGTGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
71 2 0.02
72 78 0.94
73 3 0.04
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57
Consensus pattern (72 bp):
TTTTATTAATAGTTGTTTATGTTTAGTCTTTAGATATTGAATTTATGTTCCACTTATTTTGTACT
AAATTAG
Found at i:39671874 original size:13 final size:13
Alignment explanation
Indices: 39671853--39671916 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
39671843 ACACTCAAAA
39671853 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
39671866 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
*
39671879 TTTTCCACAA-CAC
1 TTTT-CAAAAGCAC
39671892 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
39671905 TTTTTAAAAGCA
1 TTTTCAAAAGCA
39671917 ATGAAGAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
12 4 0.09
13 36 0.82
14 4 0.09
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:39672281 original size:11 final size:11
Alignment explanation
Indices: 39672265--39672293 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
39672255 GGTATTAAAA
39672265 TATTTTTATTC
1 TATTTTTATTC
39672276 TA-TTTTATTC
1 TATTTTTATTC
39672286 TATTTTTA
1 TATTTTTA
39672294 ATTCCCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTTTTATTC
Found at i:39674580 original size:35 final size:35
Alignment explanation
Indices: 39674532--39674696 Score: 222
Period size: 35 Copynumber: 4.7 Consensus size: 35
39674522 TGTCTTAGAT
* *
39674532 GAGTCTATCCCAACCTTTTTAAGGTTGCCTTAAAC
1 GAGTCTATCCCAACCCTTTTAAGGTTGACTTAAAC
* * *
39674567 GTGTCTATCCCAACCCATTTAAGGTTGACTTAGAC
1 GAGTCTATCCCAACCCTTTTAAGGTTGACTTAAAC
* *
39674602 GAGTCTATCCCAACCCTTTTCAGGTTGACTTAAAT
1 GAGTCTATCCCAACCCTTTTAAGGTTGACTTAAAC
* * *
39674637 GAGTCTATCCCAACCCTTCTAAGGTTGCCTTAGAC
1 GAGTCTATCCCAACCCTTTTAAGGTTGACTTAAAC
* *
39674672 GAGCCTATCCCAACACTTTTAAGGT
1 GAGTCTATCCCAACCCTTTTAAGGT
39674697 CACTTTTGAC
Statistics
Matches: 112, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 112 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (35 bp):
GAGTCTATCCCAACCCTTTTAAGGTTGACTTAAAC
Found at i:39674627 original size:70 final size:70
Alignment explanation
Indices: 39674525--39674696 Score: 247
Period size: 70 Copynumber: 2.5 Consensus size: 70
39674515 ACAAATTTGT
* * * *
39674525 CTTAGATGAGTCTATCCCAACCTTTTTAAGGTTGCCTTAAACGTGTCTATCCCAACCCATT-TAA
1 CTTAGACGAGTCTATCCCAACCCTTTTAAGGTTGACTTAAACGAGTCTATCCCAACCC-TTCTAA
39674589 GGTTGA
65 GGTTGA
* *
39674595 CTTAGACGAGTCTATCCCAACCCTTTTCAGGTTGACTTAAATGAGTCTATCCCAACCCTTCTAAG
1 CTTAGACGAGTCTATCCCAACCCTTTTAAGGTTGACTTAAACGAGTCTATCCCAACCCTTCTAAG
*
39674660 GTTGC
66 GTTGA
* *
39674665 CTTAGACGAGCCTATCCCAACACTTTTAAGGT
1 CTTAGACGAGTCTATCCCAACCCTTTTAAGGT
39674697 CACTTTTGAC
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
69 2 0.02
70 89 0.98
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.32
Consensus pattern (70 bp):
CTTAGACGAGTCTATCCCAACCCTTTTAAGGTTGACTTAAACGAGTCTATCCCAACCCTTCTAAG
GTTGA
Found at i:39676899 original size:12 final size:13
Alignment explanation
Indices: 39676873--39676904 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
39676863 TCATTAAATG
39676873 TAAATTTTCTTTT
1 TAAATTTTCTTTT
39676886 TAAATTTT-TTTT
1 TAAATTTTCTTTT
39676898 TAAATTT
1 TAAATTT
39676905 CAACTACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (13 bp):
TAAATTTTCTTTT
Found at i:39677132 original size:21 final size:21
Alignment explanation
Indices: 39677075--39677133 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
39677065 TAATGATAAA
*
39677075 TTTAGTAGTTAATATTTATATT
1 TTTATTAGTTAA-ATTTATATT
* * * *
39677097 TTTATCAATTTAATTTTTATT
1 TTTATTAGTTAAATTTATATT
39677118 TTTATTAGTTAAATTT
1 TTTATTAGTTAAATTT
39677134 GGTTGTTACT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.63
Consensus pattern (21 bp):
TTTATTAGTTAAATTTATATT
Found at i:39678603 original size:28 final size:30
Alignment explanation
Indices: 39678538--39678604 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
39678528 TGTGTGTTTT
* * **
39678538 TATTATTAAATCTTAATTTCTAAATAATGG
1 TATTATTTATTCTTAATTTCTAAATAATAA
39678568 TATT-TTTATTCTT-ATTTCTAAA-AATAA
1 TATTATTTATTCTTAATTTCTAAATAATAA
39678595 TATTATTTAT
1 TATTATTTAT
39678605 CAAGAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 7 0.22
28 14 0.44
29 7 0.22
30 4 0.12
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (30 bp):
TATTATTTATTCTTAATTTCTAAATAATAA
Found at i:39687546 original size:10 final size:11
Alignment explanation
Indices: 39687497--39687543 Score: 87
Period size: 11 Copynumber: 4.4 Consensus size: 11
39687487 TTGTAAAATC
39687497 CAAAA-ATTTT
1 CAAAATATTTT
39687507 CAAAATATTTT
1 CAAAATATTTT
39687518 CAAAATATTTT
1 CAAAATATTTT
39687529 CAAAATATTTT
1 CAAAATATTTT
39687540 CAAA
1 CAAA
39687544 TATCCTTGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 5 0.14
11 31 0.86
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (11 bp):
CAAAATATTTT
Found at i:39688344 original size:13 final size:13
Alignment explanation
Indices: 39688326--39688351 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39688316 CCGTCAATGA
39688326 ATAAATGAACCAG
1 ATAAATGAACCAG
39688339 ATAAATGAACCAG
1 ATAAATGAACCAG
39688352 CAATCTATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (13 bp):
ATAAATGAACCAG
Found at i:39706807 original size:15 final size:16
Alignment explanation
Indices: 39706776--39706809 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
39706766 TAGTTTGCAT
*
39706776 AATATTTAGATTTTTA
1 AATATTTAGATTATTA
39706792 AATATTT-GATTATTA
1 AATATTTAGATTATTA
39706807 AAT
1 AAT
39706810 TCCTGTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
AATATTTAGATTATTA
Found at i:39711382 original size:22 final size:22
Alignment explanation
Indices: 39711354--39711397 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39711344 TCTTGAAAAC
39711354 AAATGCTAAACGATGAATCCAA
1 AAATGCTAAACGATGAATCCAA
*
39711376 AAATGCTAAATGATGAATCCAA
1 AAATGCTAAACGATGAATCCAA
39711398 CTCACTAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (22 bp):
AAATGCTAAACGATGAATCCAA
Found at i:39722415 original size:13 final size:13
Alignment explanation
Indices: 39722397--39722424 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39722387 AACTTGCGTC
39722397 TAATGGTTGTTGT
1 TAATGGTTGTTGT
39722410 TAATGGTTGTTGT
1 TAATGGTTGTTGT
39722423 TA
1 TA
39722425 CAACCTTTTA
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:0.18, C:0.00, G:0.29, T:0.54
Consensus pattern (13 bp):
TAATGGTTGTTGT
Found at i:39725038 original size:27 final size:27
Alignment explanation
Indices: 39725007--39725184 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39724997 TAAATTGTAC
39725007 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
39725034 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39725060 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
39725088 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
39725116 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39725143 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
39725170 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39725185 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:39725121 original size:82 final size:81
Alignment explanation
Indices: 39725008--39725163 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39724998 AAATTGTACA
* *
39725008 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
39725072 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
39725089 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
39725154 TGCGAGTTGA
65 TGCGAATTGA
39725164 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:39725175 original size:82 final size:81
Alignment explanation
Indices: 39725004--39725184 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
39724994 GATTAAATTG
* *
39725004 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
39725069 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
39725085 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
39725149 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
39725167 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
39725185 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:39729916 original size:20 final size:20
Alignment explanation
Indices: 39729852--39729917 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
39729842 CGAGGTTCAG
* *
39729852 GGTTTGTGTTCAAGATTTAA
1 GGTTTGGGTTCAAGGTTTAA
*
39729872 -GTTTAGGGTTC-AGG-TTCA
1 GGTTT-GGGTTCAAGGTTTAA
*
39729890 GATTTTGGGTTCAAGGTTTAA
1 G-GTTTGGGTTCAAGGTTTAA
39729911 GGTTTGG
1 GGTTTGG
39729918 AGTTATGGGT
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
18 3 0.09
19 12 0.34
20 16 0.46
21 4 0.11
ACGTcount: A:0.20, C:0.06, G:0.32, T:0.42
Consensus pattern (20 bp):
GGTTTGGGTTCAAGGTTTAA
Found at i:39730686 original size:28 final size:29
Alignment explanation
Indices: 39730654--39730728 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 29
39730644 CTCAAACTTC
39730654 AAACCCTTAAACCTTAAACAAG-AATCCT
1 AAACCCTTAAACCTTAAACAAGTAATCCT
* ** * *
39730682 GAACCC-CGAA-CTTGTAACTAGTAATCCT
1 AAACCCTTAAACCTT-AAACAAGTAATCCT
39730710 AAACCCTTAAACCTTAAAC
1 AAACCCTTAAACCTTAAAC
39730729 CTAAACCTCG
Statistics
Matches: 34, Mismatches: 9, Indels: 7
0.68 0.18 0.14
Matches are distributed among these distances:
26 3 0.09
27 7 0.21
28 16 0.47
29 5 0.15
30 3 0.09
ACGTcount: A:0.41, C:0.29, G:0.07, T:0.23
Consensus pattern (29 bp):
AAACCCTTAAACCTTAAACAAGTAATCCT
Found at i:39730742 original size:28 final size:28
Alignment explanation
Indices: 39730711--39730798 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 28
39730701 AGTAATCCTA
*
39730711 AACCCTTAAACCTTAAACCTAAACCTCG
1 AACCCTTAAACCTTAAACCTAAAACTCG
** * * * *
39730739 AACCCTTGGACTTTGAACCCAAAACTTG
1 AACCCTTAAACCTTAAACCTAAAACTCG
*
39730767 AACCC--AAACCTTAAACCTTAAATCTCG
1 AACCCTTAAACCTTAAACC-TAAAACTCG
39730794 AACCC
1 AACCC
39730799 AAACCCTGAA
Statistics
Matches: 45, Mismatches: 14, Indels: 3
0.73 0.23 0.05
Matches are distributed among these distances:
26 8 0.18
27 11 0.24
28 26 0.58
ACGTcount: A:0.38, C:0.34, G:0.07, T:0.22
Consensus pattern (28 bp):
AACCCTTAAACCTTAAACCTAAAACTCG
Found at i:39730769 original size:13 final size:13
Alignment explanation
Indices: 39730751--39730815 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
39730741 CCCTTGGACT
*
39730751 TTGAACCCAAAAC
1 TTGAACCCAAACC
39730764 TTGAACCCAAACC
1 TTGAACCCAAACC
* * *
39730777 TTAAACCTTAAATC
1 TTGAACC-CAAACC
*
39730791 TCGAACCCAAACC
1 TTGAACCCAAACC
*
39730804 CTGAACCTCAAA
1 TTGAACC-CAAA
39730816 GTTTAGGATT
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
13 27 0.68
14 13 0.32
ACGTcount: A:0.42, C:0.34, G:0.06, T:0.18
Consensus pattern (13 bp):
TTGAACCCAAACC
Found at i:39732262 original size:24 final size:25
Alignment explanation
Indices: 39732221--39732273 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
39732211 ATAGGAAAGG
* *
39732221 GGTTACAAGAAGAAGAAATGTTAAA
1 GGTTACAAGAAGAAGAAAGGTGAAA
* *
39732246 GGTTA-AATAAGATGAAAGGTGAAA
1 GGTTACAAGAAGAAGAAAGGTGAAA
39732270 GGTT
1 GGTT
39732274 GAACATCCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.47, C:0.02, G:0.28, T:0.23
Consensus pattern (25 bp):
GGTTACAAGAAGAAGAAAGGTGAAA
Found at i:39739994 original size:8 final size:8
Alignment explanation
Indices: 39739983--39740036 Score: 63
Period size: 8 Copynumber: 6.8 Consensus size: 8
39739973 AGAGTAGGCC
*
39739983 CATGATCC
1 CATGATCT
39739991 CATGATCT
1 CATGATCT
*
39739999 CATGGTCT
1 CATGATCT
*
39740007 CATAATCT
1 CATGATCT
*
39740015 CATAATCT
1 CATGATCT
*
39740023 CATGATCC
1 CATGATCT
39740031 CATGAT
1 CATGAT
39740037 TTTTTCCTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 40 1.00
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (8 bp):
CATGATCT
Found at i:39743754 original size:33 final size:34
Alignment explanation
Indices: 39743702--39743778 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 34
39743692 AAATTTAATA
* * *
39743702 TAAATATAAGTAGTTCCTTAAC-AAACTTTCAAG
1 TAAACATAAGTAATCCCTTAACAAAACTTTCAAG
39743735 TAAACATAAGTAATCCCTTAACAAAACTTTCAAG
1 TAAACATAAGTAATCCCTTAACAAAACTTTCAAG
*
39743769 CATAACATAA
1 TA-AACATAA
39743779 CAGGAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 19 0.50
34 12 0.32
35 7 0.18
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (34 bp):
TAAACATAAGTAATCCCTTAACAAAACTTTCAAG
Found at i:39744228 original size:24 final size:24
Alignment explanation
Indices: 39744194--39744248 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
39744184 AAGAACATGA
39744194 AAGGTTTAAGGAAGATGAAAGGTGG
1 AAGG-TTAAGGAAGATGAAAGGTGG
* *
39744219 AAGGTTAAGGGAGATTAAAGGTGG
1 AAGGTTAAGGAAGATGAAAGGTGG
39744243 AAGGTT
1 AAGGTT
39744249 GAACATCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.22
Consensus pattern (24 bp):
AAGGTTAAGGAAGATGAAAGGTGG
Found at i:39744725 original size:24 final size:24
Alignment explanation
Indices: 39744679--39744725 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
39744669 CTACTTTTTT
* *
39744679 TTTAAAAAAATTAATCAACTTAGC
1 TTTAAAAAAAGTAATCAAATTAGC
39744703 TTTAAAAAAAGTAAT-ATAATTAG
1 TTTAAAAAAAGTAATCA-AATTAG
39744726 ATTAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (24 bp):
TTTAAAAAAAGTAATCAAATTAGC
Found at i:39756846 original size:14 final size:14
Alignment explanation
Indices: 39756827--39756856 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39756817 TGGATGTGTT
39756827 ATAATCTAATATAA
1 ATAATCTAATATAA
*
39756841 ATAATCTAGTATAA
1 ATAATCTAATATAA
39756855 AT
1 AT
39756857 TAATTCAAGT
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:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (14 bp):
ATAATCTAATATAA
Found at i:39764813 original size:44 final size:44
Alignment explanation
Indices: 39764763--39765480 Score: 253
Period size: 44 Copynumber: 16.5 Consensus size: 44
39764753 CACTCTACTG
**
39764763 CAACTTCAGATTGATAAGATCTATTACTTTAATCCGCTCCACTA
1 CAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTA
* * ** * ** *
39764807 CAACTTCAGGGAGATAGGAT-TATCGGCTTCAATCTACTCCACTG
1 CAACTTCAGAGAGATAAGATCTAT-TACTTTAATCCGCTCCACTA
*
39764851 CAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTA
1 CAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTA
* * * * * *** **
39764895 CAACTTTAGGGAGATAGGAT-TATCGACTTCAATATACTCCACCG
1 CAACTTCAGAGAGATAAGATCTAT-TACTTTAATCCGCTCCACTA
* * * * ** * * *
39764939 CAACCTCAGGGAGATAAGATTTGCTT-CTTTGGTCTGCCCCACTG
1 CAACTTCAGAGAGATAAGATCT-ATTACTTTAATCCGCTCCACTA
** * * * * *
39764983 TGACTTCA-AGGGGATAAGA-CT-TGT-TTTCTCAGTCTGCTCCACTG
1 CAACTTCAGA-GAGATAAGATCTAT-TACTT-T-AATCCGCTCCACTA
* * * * * * *
39765027 CAACCTT-AGGGAGATAAGACCTGA-TGC---GATCCACTCTACTG
1 CAA-CTTCAGAGAGATAAGATCT-ATTACTTTAATCCGCTCCACTA
39765068 CAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTA
1 CAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTA
* * * * * * *
39765112 TAACTTCAGGGAGATAGGAT-TATCAGCTTCAATCTGCTCCTCTGA
1 CAACTTCAGAGAGATAAGATCTATTA-CTTTAATCCGCTCCACT-A
*
39765157 -AACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTA
1 CAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTA
* * * ** **
39765200 CAACTTCAGGGAGATAGGAT-TATCGACTTTAATCTACTCCACCG
1 CAACTTCAGAGAGATAAGATCTAT-TACTTTAATCCGCTCCACTA
* * * * ** * *
39765244 CAACCTCAGGGAGATAAGATTTGCTT-CTTTGGTCTGC-CCTACTG
1 CAACTTCAGAGAGATAAGATCT-ATTACTTTAATCCGCTCC-ACTA
** * * * * * *
39765288 TGACTTCAGGGGGATAAGA-CT-TGT-TTTCTCAGTCTGCTCCACTG
1 CAACTTCAGAGAGATAAGATCTAT-TACTT-T-AATCCGCTCCACTA
* * * * * * *
39765332 CAACCTCAGGGAGATAAGACCTGA-TAC---GATCCTCTCTACTG
1 CAACTTCAGAGAGATAAGATCT-ATTACTTTAATCCGCTCCACTA
* *
39765373 CAACTTCAGAGAGATATGATCTATTACTTTAATCCACTCCACTA
1 CAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTA
* * ** * * * *
39765417 CAACTTCAGGGAGATAGGAT-TATCGGCTTCAATCTGCTCGACTG
1 CAACTTCAGAGAGATAAGATCTAT-TACTTTAATCCGCTCCACTA
*
39765461 CAACTTCAGGGAGATAAGAT
1 CAACTTCAGAGAGATAAGAT
39765481 TTGCCATCTT
Statistics
Matches: 500, Mismatches: 133, Indels: 82
0.70 0.19 0.11
Matches are distributed among these distances:
40 5 0.01
41 59 0.12
42 6 0.01
43 23 0.05
44 384 0.77
45 21 0.04
46 2 0.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (44 bp):
CAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTA
Found at i:39764945 original size:217 final size:218
Alignment explanation
Indices: 39764519--39764957 Score: 490
Period size: 217 Copynumber: 2.0 Consensus size: 218
39764509 TCTAGTCGGC
* * *
39764519 AAGACTTGATGCGATCTATTTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCT
1 AAGACCTGATGCGATCCATCTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCT
* * *
39764584 CTACTACAAATTTAGGGAGATAGGATTATCGACTTCAATCTACTCCACCGCAACCTCAGGGAGAT
66 CCACTACAAATTCAGGGAGATAGGATTATCGACTTCAATCTACTCCACCGCAACCTCAGAGAGAT
* * *** * *** * * *** * * *
39764649 AAGATTTGCTTCTTTGGTCTGCCCCACTGTGACTTCAATGGGATAAGACTTGTTTTCTCAGTCTG
131 AAGATCTGATTCTTTAACCCGCCCCACTACAACTTCAAGGGGATAAGACTTATCGACTCAATATA
** *
39764714 CTTTACTACAACCTCAGGGAGAT
196 CTCCACCACAACCTCAGGGAGAT
** *
39764737 AAGACCTGATGCGATCCA-CTCTACTGCAACTTCAGATTGATAAGATCTATTACTTTAATCCGCT
1 AAGACCTGATGCGATCCATCTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCT
* * * *
39764801 CCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTACTCCACTGCAACTTCAGAGAGAT
66 CCACTACAAATTCAGGGAGATAGGATTATCGACTTCAATCTACTCCACCGCAACCTCAGAGAGAT
* * *
39764866 AAGATCT-ATTACTTTAACCCGCTCCACTACAACTT-TAGGGAGATAGGA-TTATCGACTTCAAT
131 AAGATCTGATT-CTTTAACCCGCCCCACTACAACTTCAAGGG-GATAAGACTTATCGAC-TCAAT
*
39764928 ATACTCCACCGCAACCTCAGGGAGAT
193 ATACTCCACCACAACCTCAGGGAGAT
39764954 AAGA
1 AAGA
39764958 TTTGCTTCTT
Statistics
Matches: 181, Mismatches: 37, Indels: 7
0.80 0.16 0.03
Matches are distributed among these distances:
216 9 0.05
217 156 0.86
218 16 0.09
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (218 bp):
AAGACCTGATGCGATCCATCTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCT
CCACTACAAATTCAGGGAGATAGGATTATCGACTTCAATCTACTCCACCGCAACCTCAGAGAGAT
AAGATCTGATTCTTTAACCCGCCCCACTACAACTTCAAGGGGATAAGACTTATCGACTCAATATA
CTCCACCACAACCTCAGGGAGAT
Found at i:39765093 original size:305 final size:305
Alignment explanation
Indices: 39764542--39765480 Score: 1653
Period size: 305 Copynumber: 3.1 Consensus size: 305
39764532 ATCTATTTCT
* *
39764542 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCTACTACAAATTTAGGGAGATAG
1 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTTAGGGAGATAG
39764607 GATTATCGACTTCAATCTACTCCACCGCAACCTCAGGGAGATAAGATTTGCTTCTTTGGTCTGCC
66 GATTATCGACTTCAATCTACTCCACCGCAACCTCAGGGAGATAAGATTTGCTTCTTTGGTCTGCC
* ** *
39764672 CCACTGTGACTTCAATGGGATAAGACTTGTTTTCTCAGTCTGCTTTACTACAACCTCAGGGAGAT
131 CCACTGTGACTTCAAGGGGATAAGACTTGTTTTCTCAGTCTGCTCCACTGCAACCTCAGGGAGAT
**
39764737 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGATTGATAAGATCTATTACTTTAATCCGCTC
196 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
*
39764802 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTACTCC
261 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCC
39764847 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTTAGGGAGATAG
1 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTTAGGGAGATAG
*
39764912 GATTATCGACTTCAATATACTCCACCGCAACCTCAGGGAGATAAGATTTGCTTCTTTGGTCTGCC
66 GATTATCGACTTCAATCTACTCCACCGCAACCTCAGGGAGATAAGATTTGCTTCTTTGGTCTGCC
*
39764977 CCACTGTGACTTCAAGGGGATAAGACTTGTTTTCTCAGTCTGCTCCACTGCAACCTTAGGGAGAT
131 CCACTGTGACTTCAAGGGGATAAGACTTGTTTTCTCAGTCTGCTCCACTGCAACCTCAGGGAGAT
39765042 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
196 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
* *
39765107 CACTATAACTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCC
261 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCC
* * *
39765152 TCTGAAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTCAGGGAGATAG
1 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTTAGGGAGATAG
*
39765217 GATTATCGACTTTAATCTACTCCACCGCAACCTCAGGGAGATAAGATTTGCTTCTTTGGTCTGCC
66 GATTATCGACTTCAATCTACTCCACCGCAACCTCAGGGAGATAAGATTTGCTTCTTTGGTCTGCC
* *
39765282 CTACTGTGACTTCAGGGGGATAAGACTTGTTTTCTCAGTCTGCTCCACTGCAACCTCAGGGAGAT
131 CCACTGTGACTTCAAGGGGATAAGACTTGTTTTCTCAGTCTGCTCCACTGCAACCTCAGGGAGAT
* * * *
39765347 AAGACCTGATACGATCCTCTCTACTGCAACTTCAGAGAGATATGATCTATTACTTTAATCCACTC
196 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
*
39765412 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCG
261 CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCC
*
39765457 ACTGCAACTTCAGGGAGATAAGAT
1 ACTGCAACTTCAGAGAGATAAGAT
39765481 TTGCCATCTT
Statistics
Matches: 603, Mismatches: 31, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
305 603 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (305 bp):
ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTTAGGGAGATAG
GATTATCGACTTCAATCTACTCCACCGCAACCTCAGGGAGATAAGATTTGCTTCTTTGGTCTGCC
CCACTGTGACTTCAAGGGGATAAGACTTGTTTTCTCAGTCTGCTCCACTGCAACCTCAGGGAGAT
AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
CACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCC
Found at i:39765249 original size:217 final size:217
Alignment explanation
Indices: 39764842--39765262 Score: 501
Period size: 217 Copynumber: 1.9 Consensus size: 217
39764832 GCTTCAATCT
*
39764842 ACTCCACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTTAGGGA
1 ACTCCACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTCAGGGA
* * * * ***
39764907 GATAGGATTATCGACTTCAATATACTCCACCGCAACCTCAGGGAGATAAGATTTGCTTCTTTGGT
66 GATAGGATTATCGACTTCAATATACTCCACCGAAACCTCAGAGAGATAAGATCTGATTCTTTAAC
* *** ** * * * *
39764972 CTGCCCCACTGTGACTTCAAGGGGATAAGACTTGTTTTCTCAGTCTGCTCCACTGCAACCTTAGG
131 CCGCCCCACTACAACTTCAAGGGGATAAGACTTGACTTCTCAATCTACTCCACCGCAACCTCAGG
39765037 GAGATAAGACCTGATGCGATCC
196 GAGATAAGACCTGATGCGATCC
* * *
39765059 ACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTATAACTTCAGGGA
1 ACTCCACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTCAGGGA
* * * * *
39765124 GATAGGATTATC-AGCTTCAATCTGCTCCTCTGAAACTTCAGAGAGATAAGATCT-ATTACTTTA
66 GATAGGATTATCGA-CTTCAATATACTCCACCGAAACCTCAGAGAGATAAGATCTGATT-CTTTA
* * *
39765187 ACCCGCTCCACTACAACTTC-AGGGAGATAGGATTATCGACTT-T-AATCTACTCCACCGCAACC
129 ACCCGCCCCACTACAACTTCAAGGG-GATAAGACT-T-GACTTCTCAATCTACTCCACCGCAACC
39765249 TCAGGGAGATAAGA
191 TCAGGGAGATAAGA
39765263 TTTGCTTCTT
Statistics
Matches: 170, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
216 7 0.04
217 158 0.93
218 2 0.01
219 3 0.02
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (217 bp):
ACTCCACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTCAGGGA
GATAGGATTATCGACTTCAATATACTCCACCGAAACCTCAGAGAGATAAGATCTGATTCTTTAAC
CCGCCCCACTACAACTTCAAGGGGATAAGACTTGACTTCTCAATCTACTCCACCGCAACCTCAGG
GAGATAAGACCTGATGCGATCC
Found at i:39765475 original size:88 final size:88
Alignment explanation
Indices: 39764759--39765480 Score: 410
Period size: 88 Copynumber: 8.3 Consensus size: 88
39764749 GATCCACTCT
*** *
39764759 ACTGCAACTTCAGATTGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAG
1 ACTGCAACTTCAGGGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAA
** *
39764824 GATTATCGGCTTCAATCTACTCC
66 GATTATCTACTTCAATCTGCTCC
* * * *
39764847 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTTAGGGAGATAG
1 ACTGCAACTTCAGGGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAA
* * *
39764912 GATTATCGACTTCAATATACTCC
66 GATTATCTACTTCAATCTGCTCC
* * * * ** * * ***
39764935 ACCGCAACCTCAGGGAGATAAGATTTGCTT-CTTTGGTCTGCCCCACTGTGACTTCAAGGG-GAT
1 ACTGCAACTTCAGGGAGATAAGATCT-ATTACTTTAATCCGCTCCACTACAACTTC-AGGGAGAT
* * * *
39764998 AAGACTTGTTTTC-TCAGTCTGCTCC
64 AAGA-TTATCTACTTCAATCTGCTCC
* * * * * * *
39765023 ACTGCAACCTT-AGGGAGATAAGACCTGA-TGC---GATCCACTCTACTGCAACTTCAGAGAGAT
1 ACTGCAA-CTTCAGGGAGATAAGATCT-ATTACTTTAATCCGCTCCACTACAACTTCAGGGAGAT
* *
39765083 AAGATCTAT-TACTTTAATCCGCTCC
64 AAGAT-TATCTACTTCAATCTGCTCC
** * * * * * *
39765108 ACTATAACTTCAGGGAGATAGGAT-TATCAGCTTCAATCTGCTCCTCTGA-AACTTCAGAGAGAT
1 ACTGCAACTTCAGGGAGATAAGATCTATTA-CTTTAATCCGCTCCACT-ACAACTTCAGGGAGAT
* * *
39765171 AAGATCTAT-TACTTTAACCCGCTCC
64 AAGAT-TATCTACTTCAATCTGCTCC
* * * ** ** *
39765196 ACTACAACTTCAGGGAGATAGGAT-TATCGACTTTAATCTACTCCACCGCAACCTCAGGGAGATA
1 ACTGCAACTTCAGGGAGATAAGATCTAT-TACTTTAATCCGCTCCACTACAACTTCAGGGAGATA
* ***
39765260 AGATT-TGCTTCTTTGGTCTGC-CC
65 AGATTAT-CTACTTCAATCTGCTCC
** * * * * * *
39765283 TACTGTGACTTCAGGGGGATAAGA-CT-TGT-TTTCTCAGTCTGCTCCACTGCAACCTCAGGGAG
1 -ACTGCAACTTCAGGGAGATAAGATCTAT-TACTT-T-AATCCGCTCCACTACAACTTCAGGGAG
* * * *
39765345 ATAAG---ACCTGA-TACGATCCT-CTCT
62 ATAAGATTATCT-ACTTCAAT-CTGCTCC
* * * *
39765369 ACTGCAACTTCAGAGAGATATGATCTATTACTTTAATCCACTCCACTACAACTTCAGGGAGATAG
1 ACTGCAACTTCAGGGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAA
** *
39765434 GATTATCGGCTTCAATCTGCTCG
66 GATTATCTACTTCAATCTGCTCC
39765457 ACTGCAACTTCAGGGAGATAAGAT
1 ACTGCAACTTCAGGGAGATAAGAT
39765481 TTGCCATCTT
Statistics
Matches: 489, Mismatches: 110, Indels: 70
0.73 0.16 0.10
Matches are distributed among these distances:
83 1 0.00
84 10 0.02
85 99 0.20
86 10 0.02
87 11 0.02
88 345 0.71
89 13 0.03
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (88 bp):
ACTGCAACTTCAGGGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAA
GATTATCTACTTCAATCTGCTCC
Found at i:39765626 original size:127 final size:128
Alignment explanation
Indices: 39765472--39765808 Score: 541
Period size: 127 Copynumber: 2.6 Consensus size: 128
39765462 AACTTCAGGG
* * *
39765472 AGATAAGATTTGCCATCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTCCA
39765537 ACCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATAT-CTTCCTTACACTTGA
66 ACCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATATACTTCCTTACACTTGA
* * * * *
39765599 AGATAAGATTCACCGTCTTCAATCTGCTCCGCTACTGCTTAGAGAGAAAAGATTTGTAATTTCCC
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTCCA
** * *
39765664 ACCTATTCCACTATTGACCAGGGATATAGGACTTGTGGCTTAAATCTACTTCCTTACACTTGA
66 ACCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATATACTTCCTTACACTTGA
*
39765727 AGATAAGATTCGCCGTCTTTGATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTCCC
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTT-CC
39765792 AACCTATTCCACTGCTG
65 AACCTATTCCACTGCTG
39765809 GTCAGAGAGC
Statistics
Matches: 188, Mismatches: 20, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
127 100 0.53
128 72 0.38
129 16 0.09
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.31
Consensus pattern (128 bp):
AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTCCA
ACCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATATACTTCCTTACACTTGA
Found at i:39767114 original size:7 final size:7
Alignment explanation
Indices: 39767102--39767135 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
39767092 AGCCTCTCCA
39767102 TTTTCAT
1 TTTTCAT
39767109 TTTTCA-
1 TTTTCAT
39767115 TTTTCATT
1 TTTTCA-T
39767123 TTTTCAT
1 TTTTCAT
39767130 TTTTCA
1 TTTTCA
39767136 CACATTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.24
7 13 0.52
8 6 0.24
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTCAT
Found at i:39767118 original size:13 final size:14
Alignment explanation
Indices: 39767100--39767132 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
39767090 TTAGCCTCTC
39767100 CATTTTCA-TTTTT
1 CATTTTCATTTTTT
39767113 CATTTTCATTTTTT
1 CATTTTCATTTTTT
39767127 CATTTT
1 CATTTT
39767133 TCACACATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (14 bp):
CATTTTCATTTTTT
Found at i:39767954 original size:13 final size:13
Alignment explanation
Indices: 39767936--39767960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39767926 TGGCCTCTCC
39767936 TTTTTATTTTTTA
1 TTTTTATTTTTTA
39767949 TTTTTATTTTTT
1 TTTTTATTTTTT
39767961 GTTTCAACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:39774449 original size:23 final size:23
Alignment explanation
Indices: 39774423--39774470 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
39774413 ATTGGGCTAG
*
39774423 GGTTTAATGGGTAATTCGGGTTA
1 GGTTTAATGAGTAATTCGGGTTA
* * *
39774446 GGTTTAGTTAGTATTTCGGGTTA
1 GGTTTAATGAGTAATTCGGGTTA
39774469 GG
1 GG
39774471 GTATTTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.19, C:0.04, G:0.35, T:0.42
Consensus pattern (23 bp):
GGTTTAATGAGTAATTCGGGTTA
Found at i:39783704 original size:21 final size:20
Alignment explanation
Indices: 39783674--39783712 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
39783664 CAAGATAAAA
39783674 AAATAGATTAAATTTAATATT
1 AAATAGATTAAA-TTAATATT
*
39783695 AAATATATTAAATTAATA
1 AAATAGATTAAATTAATA
39783713 GAATATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
AAATAGATTAAATTAATATT
Done.