Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 9 of 186
Found at i:2741735 original size:27 final size:27
Alignment explanation
Indices: 2741713--2741776 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
2741703 TGCCAGAAAC
*
2741713 AGTAAATGTGGCAAAGCCACCAGTATT
1 AGTAAATGTGGCAAAGCCACCAGTAAT
* *
2741740 AGTAATTGTGGCATAGCCACCAGTAAT
1 AGTAAATGTGGCAAAGCCACCAGTAAT
*
2741767 AGTGAATGTG
1 AGTAAATGTG
2741777 ACTTAGTCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (27 bp):
AGTAAATGTGGCAAAGCCACCAGTAAT
Found at i:2741787 original size:27 final size:27
Alignment explanation
Indices: 2741713--2741791 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
2741703 TGCCAGAAAC
* * * *
2741713 AGTAAATGTGGCAAAGCCACCAGTATT
1 AGTAATTGTGACATAGCCACCAGTAAT
*
2741740 AGTAATTGTGGCATAGCCACCAGTAAT
1 AGTAATTGTGACATAGCCACCAGTAAT
* *
2741767 AGTGAA-TGTGACTTAGTCACCAGTA
1 AGT-AATTGTGACATAGCCACCAGTA
2741792 CAGTACTTCC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 43 0.96
28 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (27 bp):
AGTAATTGTGACATAGCCACCAGTAAT
Found at i:2741963 original size:27 final size:27
Alignment explanation
Indices: 2741932--2742065 Score: 153
Period size: 27 Copynumber: 5.0 Consensus size: 27
2741922 GGGCATAATC
* *
2741932 GTCATATTACCATACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
* * * **
2741959 GTCATTTTACCCTATA-TGGAATTATA
1 GTCATTTTACCCTACAGGGGTATTACG
*
2741985 GTCATTTTACCCTATAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
*
2742012 GTCATTTTACCCTACAGGGGTATTACA
1 GTCATTTTACCCTACAGGGGTATTACG
* * *
2742039 ATCATTTTACCTTACAGGGGTGTTACG
1 GTCATTTTACCCTACAGGGGTATTACG
2742066 ATCAGATAAC
Statistics
Matches: 89, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
26 22 0.25
27 67 0.75
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGTATTACG
Found at i:2744714 original size:46 final size:46
Alignment explanation
Indices: 2744664--2744836 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
2744654 TGGTTGAGCA
2744664 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
2744710 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
2744755 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
2744803 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
2744837 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:2744820 original size:93 final size:93
Alignment explanation
Indices: 2744661--2744831 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
2744651 GGATGGTTGA
* *
2744661 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
2744726 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
2744754 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
2744819 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
2744832 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:2751441 original size:55 final size:55
Alignment explanation
Indices: 2751357--2751472 Score: 205
Period size: 55 Copynumber: 2.1 Consensus size: 55
2751347 TTAGTCAAAG
*
2751357 TCTCCCAAGTTGCAGGGATCGACTACACTGACCTTTGCCCATTACTACTTGGATA
1 TCTCCCAAGTTGCAGGGATCGACTACACTGACCTTTGCCCATTACGACTTGGATA
* *
2751412 TCTCCCATGTTGCAGGGGTCGACTACACTGACCTTTGCCCATTACGACTTGGATA
1 TCTCCCAAGTTGCAGGGATCGACTACACTGACCTTTGCCCATTACGACTTGGATA
2751467 TCTCCC
1 TCTCCC
2751473 TACACGGGGC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.29
Consensus pattern (55 bp):
TCTCCCAAGTTGCAGGGATCGACTACACTGACCTTTGCCCATTACGACTTGGATA
Found at i:2752543 original size:27 final size:27
Alignment explanation
Indices: 2752513--2752691 Score: 198
Period size: 27 Copynumber: 6.6 Consensus size: 27
2752503 ATATTGAGTC
* * * *
2752513 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* * *
2752540 CGCACATTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
2752567 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
2752595 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
2752622 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
2752649 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
2752676 CGCACACTTAGTGCTA
1 CGCACACTTAGTGCTA
2752692 TACAACATAG
Statistics
Matches: 129, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:2763627 original size:51 final size:51
Alignment explanation
Indices: 2763568--2763669 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
2763558 AATCAGAACA
2763568 GTAGTTTTGGGACCACAAATCTGAGATTAAAATATTTATTTTATTATTATT
1 GTAGTTTTGGGACCACAAATCTGAGATTAAAATATTTATTTTATTATTATT
2763619 GTAGTTTTGGGACCACAAATCTGAGATTAAAATATTTATTTTATTATTATT
1 GTAGTTTTGGGACCACAAATCTGAGATTAAAATATTTATTTTATTATTATT
2763670 TTAATGTCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (51 bp):
GTAGTTTTGGGACCACAAATCTGAGATTAAAATATTTATTTTATTATTATT
Found at i:2766268 original size:50 final size:50
Alignment explanation
Indices: 2766193--2766297 Score: 176
Period size: 50 Copynumber: 2.1 Consensus size: 50
2766183 TCCTTTCTTT
**
2766193 TCTTTTCTGAAACCTGTTCACTATTCCCTCCCGCTT-ATCTACTACTTCTA
1 TCTTTTCCAAAACCTGTTCACTATTCCCTCCCG-TTCATCTACTACTTCTA
2766243 TCTTTTCCAAAACCTGTTCACTATTCCCTCCCGTTCATCTACTACTTCTA
1 TCTTTTCCAAAACCTGTTCACTATTCCCTCCCGTTCATCTACTACTTCTA
2766293 TCTTT
1 TCTTT
2766298 ACTTTTTCTG
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
49 2 0.04
50 50 0.96
ACGTcount: A:0.18, C:0.34, G:0.05, T:0.43
Consensus pattern (50 bp):
TCTTTTCCAAAACCTGTTCACTATTCCCTCCCGTTCATCTACTACTTCTA
Found at i:2767411 original size:11 final size:10
Alignment explanation
Indices: 2767379--2767433 Score: 60
Period size: 11 Copynumber: 5.5 Consensus size: 10
2767369 CATGAGATTT
2767379 TGATAT-ACA
1 TGATATGACA
*
2767388 TGATTTGACA
1 TGATATGACA
2767398 TGATATGCACA
1 TGATATG-ACA
*
2767409 TGATATG-TA
1 TGATATGACA
2767418 TGATATGCACA
1 TGATATG-ACA
2767429 TGATA
1 TGATA
2767434 AATTCATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 13 0.34
10 9 0.24
11 16 0.42
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (10 bp):
TGATATGACA
Found at i:2767584 original size:24 final size:25
Alignment explanation
Indices: 2767477--2767571 Score: 163
Period size: 25 Copynumber: 3.8 Consensus size: 25
2767467 GATGAAGTGC
2767477 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
*
2767502 AAAAGGGTTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
* *
2767527 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCG
2767552 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
2767572 ATTAAAAGAG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 66 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:2767826 original size:31 final size:31
Alignment explanation
Indices: 2767791--2767874 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
2767781 CGTTTACAGT
2767791 AAAGGCTTCGGCCCAGTGATATGAATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
* *
2767822 AAAGGCTTCGGCCCAGTGACATGAATAATGT
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
*
2767853 AAAGGCTTCTGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
2767875 CTGAGATTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 4 0.08
31 45 0.92
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:2774877 original size:55 final size:55
Alignment explanation
Indices: 2774800--2774908 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 55
2774790 TCGCGTAGGG
2774800 GATCTCATCGAGGAATACCGCAAATCAGGTGTGTAACGAACCCTCTTTCGTAGCA
1 GATCTCATCGAGGAATACCGCAAATCAGGTGTGTAACGAACCCTCTTTCGTAGCA
* * *
2774855 GATCTCGTCGAGGAATATCGCAAATCATGTGTGTAACGAACCCTCTTTCGTAGC
1 GATCTCATCGAGGAATACCGCAAATCAGGTGTGTAACGAACCCTCTTTCGTAGC
2774909 TTAACTCGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.26
Consensus pattern (55 bp):
GATCTCATCGAGGAATACCGCAAATCAGGTGTGTAACGAACCCTCTTTCGTAGCA
Found at i:2776459 original size:46 final size:46
Alignment explanation
Indices: 2776406--2776496 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
2776396 TATATATACA
* * *
2776406 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATATC
* * *
2776452 CATCTCATACACATTTCGCATTAACCATTCGGCTTTCCCACATAT
1 CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATAT
2776497 ATACACATCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.27, C:0.32, G:0.07, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATATC
Found at i:2776772 original size:47 final size:47
Alignment explanation
Indices: 2776506--2776770 Score: 386
Period size: 47 Copynumber: 5.6 Consensus size: 47
2776496 TATACACATC
* * **
2776506 CACATTCATCACTTTGGCCATTCTGCCTTATCACATGTATGCATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTT
* *
2776553 CACATTTATCACATTGGCCATTCGGCCTTATCACATATATGCATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTT
* * *
2776600 CATATTCTTCACATTGGCCATTCGGCCTTATCACACATATACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTT
* *
2776647 CACATTCATCACATTGGCCATTCGGTCTTATCACACAAATGCATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTT
* * *
2776694 CACATTCATCACATTTGCCATTCGGCCTTAGCACACAAATGCATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTT
* *
2776741 CACATTCATGACATTTGCCATTCGGCCTTA
1 CACATTCATCACATTGGCCATTCGGCCTTA
2776771 GCTCATGTAT
Statistics
Matches: 200, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 200 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.34
Consensus pattern (47 bp):
CACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTT
Found at i:2776782 original size:141 final size:141
Alignment explanation
Indices: 2776476--2776801 Score: 409
Period size: 141 Copynumber: 2.3 Consensus size: 141
2776466 TTCGCATTAA
* ** * * * *
2776476 CCATTCGGCTTTCCCACATATATACACATCCACATTCATCACTTTGGCCATTCTGCCTTATCACA
1 CCATTCGGCCTTAGCACACATATACACATTCACATTCATCACATTGGCCATTCGGCCTTATCACA
*** * * * * *
2776541 TGTATGCATGTTCACATTTATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATT
66 CAAATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTAGCACACAAATGCATGTTCACATT
*
2776606 CTTCACATTGG
131 CATCACATTGG
* ** *
2776617 CCATTCGGCCTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGTCTTATCACA
1 CCATTCGGCCTTAGCACACATATACACATTCACATTCATCACATTGGCCATTCGGCCTTATCACA
*
2776682 CAAATGCATGTTCACATTCATCACATTTGCCATTCGGCCTTAGCACACAAATGCATGTTCACATT
66 CAAATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTAGCACACAAATGCATGTTCACATT
* *
2776747 CATGACATTTG
131 CATCACATTGG
* ** *
2776758 CCATTCGGCCTTAGCTCATGTATACACATTCACATCCATCACAT
1 CCATTCGGCCTTAGCACACATATACACATTCACATTCATCACAT
2776802 AAAATCCTAA
Statistics
Matches: 156, Mismatches: 29, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
141 156 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.33
Consensus pattern (141 bp):
CCATTCGGCCTTAGCACACATATACACATTCACATTCATCACATTGGCCATTCGGCCTTATCACA
CAAATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTAGCACACAAATGCATGTTCACATT
CATCACATTGG
Found at i:2776800 original size:94 final size:94
Alignment explanation
Indices: 2776476--2776801 Score: 375
Period size: 94 Copynumber: 3.5 Consensus size: 94
2776466 TTCGCATTAA
* ** * *
2776476 CCATTCGGCTTTCCCACATATATACACATCCACATTCATCAC-TTTGGCCATTCTGCCTTATCAC
1 CCATTCGGCCTTATCACATATATACACATTCACATTCATCACATTT-GCCATTCGGCCTTATCAC
** *
2776540 ATGTATGCATGTTCACATTTATCACATTGG
65 ACATATGCATGTTCACATTCATCACATTGG
* ** * * *
2776570 CCATTCGGCCTTATCACATATATGCATGTTCATATTCTTCACATTGGCCATTCGGCCTTATCACA
1 CCATTCGGCCTTATCACATATATACACATTCACATTCATCACATTTGCCATTCGGCCTTATCACA
*
2776635 CATATACATGTTCACATTCATCACATTGG
66 CATATGCATGTTCACATTCATCACATTGG
* * * * ** *
2776664 CCATTCGGTCTTATCACACAAATGCATGTTCACATTCATCACATTTGCCATTCGGCCTTAGCACA
1 CCATTCGGCCTTATCACATATATACACATTCACATTCATCACATTTGCCATTCGGCCTTATCACA
* * *
2776729 CAAATGCATGTTCACATTCATGACATTTG
66 CATATGCATGTTCACATTCATCACATTGG
* * * *
2776758 CCATTCGGCCTTAGCTCATGTATACACATTCACATCCATCACAT
1 CCATTCGGCCTTATCACATATATACACATTCACATTCATCACAT
2776802 AAAATCCTAA
Statistics
Matches: 195, Mismatches: 36, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
94 193 0.99
95 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.33
Consensus pattern (94 bp):
CCATTCGGCCTTATCACATATATACACATTCACATTCATCACATTTGCCATTCGGCCTTATCACA
CATATGCATGTTCACATTCATCACATTGG
Found at i:2779167 original size:11 final size:11
Alignment explanation
Indices: 2779141--2779209 Score: 76
Period size: 11 Copynumber: 6.7 Consensus size: 11
2779131 ATTTTGATAT
*
2779141 ACATGATTTG-
1 ACATGATATGC
2779151 ACATGATATGC
1 ACATGATATGC
2779162 ACATGATATG-
1 ACATGATATGC
*
2779172 -TATGATATGC
1 ACATGATATGC
*
2779182 ACATGATATGT
1 ACATGATATGC
2779193 A-AT-ATATGC
1 ACATGATATGC
2779202 ACATGATA
1 ACATGATA
2779210 AATTCATATA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
9 14 0.29
10 13 0.27
11 22 0.45
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (11 bp):
ACATGATATGC
Found at i:2779178 original size:20 final size:21
Alignment explanation
Indices: 2779153--2779209 Score: 100
Period size: 20 Copynumber: 2.8 Consensus size: 21
2779143 ATGATTTGAC
2779153 ATGATATGCACATGATATGT-
1 ATGATATGCACATGATATGTA
2779173 ATGATATGCACATGATATGTA
1 ATGATATGCACATGATATGTA
2779194 AT-ATATGCACATGATA
1 ATGATATGCACATGATA
2779210 AATTCATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 34 0.94
21 2 0.06
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (21 bp):
ATGATATGCACATGATATGTA
Found at i:2779291 original size:25 final size:24
Alignment explanation
Indices: 2779257--2779326 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 24
2779247 GAGGAAGTGC
*
2779257 AAAAGGGCTTTGCTCCAGTTTACCG
1 AAAAGGGCTTTGC-CCAGTTTACCA
*
2779282 AAAAGGGCTTTGCCTCAGTTTATCA
1 AAAAGGGCTTTGCC-CAGTTTACCA
2779307 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTG-CCCAGTT
2779327 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
24 1 0.02
25 38 0.93
26 2 0.05
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCAGTTTACCA
Found at i:2779339 original size:24 final size:25
Alignment explanation
Indices: 2779256--2779339 Score: 86
Period size: 25 Copynumber: 3.4 Consensus size: 25
2779246 GGAGGAAGTG
* *
2779256 CAAAAG-GGCTTTGCTCCAGTTTAC
1 CAAAAGAGGCTTTGCCCCAGTTTAT
*
2779280 CGAAAAG-GGCTTTGCCTCAGTTTAT
1 C-AAAAGAGGCTTTGCCCCAGTTTAT
2779305 CAAAA-AGGGCTTTGCCCCAG-TTAT
1 CAAAAGA-GGCTTTGCCCCAGTTTAT
*
2779329 TAAAAGAGGCT
1 CAAAAGAGGCT
2779340 AGGCTTCCAG
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
24 17 0.33
25 34 0.67
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (25 bp):
CAAAAGAGGCTTTGCCCCAGTTTAT
Found at i:2779584 original size:31 final size:31
Alignment explanation
Indices: 2779546--2779629 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
2779536 CGTTTACAGT
2779546 AAAGGCTTCAGCCCAGTGATATGAATAATGA
1 AAAGGCTTCAGCCCAGTGATATGAATAATGA
* * *
2779577 AAAGGCTTCGGCCCAGTGACATGAATAATGT
1 AAAGGCTTCAGCCCAGTGATATGAATAATGA
2779608 AAAGGCTTCAGCCCAGT-ATATG
1 AAAGGCTTCAGCCCAGTGATATG
2779630 CTGAGATTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 4 0.08
31 44 0.92
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCAGCCCAGTGATATGAATAATGA
Found at i:2780954 original size:38 final size:38
Alignment explanation
Indices: 2780903--2780978 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
2780893 AAAAAGACAC
2780903 CATTTTAGGGCTTAAGCA-TGCAGCTAACTTGGGTAAGT
1 CATTTTAGGGCTTAAGCATTG-AGCTAACTTGGGTAAGT
2780941 CATTTTAGGGCTTAAGCATTGAGCTAACTTGGGTAAGT
1 CATTTTAGGGCTTAAGCATTGAGCTAACTTGGGTAAGT
2780979 GCATGTAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 35 0.95
39 2 0.05
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (38 bp):
CATTTTAGGGCTTAAGCATTGAGCTAACTTGGGTAAGT
Found at i:2785477 original size:56 final size:56
Alignment explanation
Indices: 2785390--2785524 Score: 189
Period size: 56 Copynumber: 2.4 Consensus size: 56
2785380 ATCATGGCAT
* * *
2785390 CGATATATGTGTGCGAGAAAGACCATATTTAATACGTTGGCATCGATATGTGAATC
1 CGATATATGTGTGCGAGTAAGACCACATTTAATACATTGGCATCGATATGTGAATC
** * * * *
2785446 CGATATATGTGTATGAGTAAGACCACGTTTAATGCATTGGCATCGATATGTGACTT
1 CGATATATGTGTGCGAGTAAGACCACATTTAATACATTGGCATCGATATGTGAATC
2785502 CGATATATGTGTGCGAGTAAGAC
1 CGATATATGTGTGCGAGTAAGAC
2785525 TCTATCTGGG
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 68 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (56 bp):
CGATATATGTGTGCGAGTAAGACCACATTTAATACATTGGCATCGATATGTGAATC
Found at i:2792054 original size:56 final size:56
Alignment explanation
Indices: 2791966--2792189 Score: 315
Period size: 56 Copynumber: 4.0 Consensus size: 56
2791956 GACCATGGCA
* * *
2791966 TCGATATTTGTGTGTGAGTAAGACCACCTTTAATACATTGGCATCGATATGTGATT
1 TCGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGATATGTGATT
2792022 TCGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGATATGTGATT
1 TCGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGATATGTGATT
* * * *
2792078 TCGATATATGTGTGTGAGTAAGACTACGTTTAATACGTTGGCATCGATATGTGACT
1 TCGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGATATGTGATT
* * *** *
2792134 TCGATATATGTCTGCGAGTAAGACC-CTGTCTGGGACAGTGGCATCGATATGTGATT
1 TCGATATATGTGTGCGAGTAAGACCAC-GTTTAATACATTGGCATCGATATGTGATT
2792190 ACGTGTAAGA
Statistics
Matches: 150, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
55 1 0.01
56 149 0.99
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (56 bp):
TCGATATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGATATGTGATT
Found at i:2801147 original size:30 final size:30
Alignment explanation
Indices: 2801107--2801166 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2801097 TTCCCGAGCC
*
2801107 TAGGGACAAAAGTGTAATTATGCAAAAGTT
1 TAGGGACAAAAATGTAATTATGCAAAAGTT
* * * *
2801137 TAGGGGCAAAAATGTATTTTTGCCAAAGTT
1 TAGGGACAAAAATGTAATTATGCAAAAGTT
2801167 CGTATTAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.30
Consensus pattern (30 bp):
TAGGGACAAAAATGTAATTATGCAAAAGTT
Found at i:2809613 original size:15 final size:17
Alignment explanation
Indices: 2809595--2809626 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2809585 TAGCATAATT
2809595 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
2809610 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
2809627 CAAGTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:2813580 original size:38 final size:38
Alignment explanation
Indices: 2813517--2813617 Score: 121
Period size: 38 Copynumber: 2.6 Consensus size: 38
2813507 ATTTGATGTG
*
2813517 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAAAA
1 TATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAAAA
* * **
2813557 TATCCGGGTTAAATCTCGCAGGCTTTGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAA
* *
2813595 TATCTGGGATAAATCCCGCAGGC
1 TATCCGGGTTAAATCCCGCAGGC
2813618 CTAGTGTTGG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 40 0.75
39 5 0.09
40 8 0.15
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.28
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAA
Found at i:2813629 original size:38 final size:38
Alignment explanation
Indices: 2813533--2813640 Score: 126
Period size: 38 Copynumber: 2.8 Consensus size: 38
2813523 GGCTTAAAGA
* ** *
2813533 CCCGCAGGCTTCGTGCTGGTAAAATATCCGGGTTAAAT
1 CCCGCAGGCTTAGTGCTGGTATTATATCCGGGATAAAT
* * *
2813571 CTCGCAGGCTTTGTGCTGGTATTATATCTGGGATAAAT
1 CCCGCAGGCTTAGTGCTGGTATTATATCCGGGATAAAT
* * *
2813609 CCCGCAGGCCTAGTGTTGGTATTATATTCGGG
1 CCCGCAGGCTTAGTGCTGGTATTATATCCGGG
2813641 CCTTCGTGCC
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 58 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31
Consensus pattern (38 bp):
CCCGCAGGCTTAGTGCTGGTATTATATCCGGGATAAAT
Found at i:2814015 original size:43 final size:43
Alignment explanation
Indices: 2813633--2814002 Score: 614
Period size: 43 Copynumber: 8.6 Consensus size: 43
2813623 GTTGGTATTA
*
2813633 TATTCGGGCCTTCGTGCCTAGCAAGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* *
2813676 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATATG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
2813719 TATTCGGGCCTTCGTGCATAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* *
2813762 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATATG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
2813805 TATTCGGGCCTTCGTGCATAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* *
2813848 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATATG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
2813891 TATTCGGGCCTTCGTGCATAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
2813934 TATTCGGGCCTTCGTGCCTAGCAGGCTTCATGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* * *
2813977 TATTCGAGCCTTCATGCCTAGTAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
2814003 GTAATGCCGG
Statistics
Matches: 304, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 304 1.00
ACGTcount: A:0.13, C:0.25, G:0.32, T:0.30
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:2818028 original size:22 final size:22
Alignment explanation
Indices: 2818003--2818067 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
2817993 AGTACCACGA
2818003 ATACAAGATTATTCCACCACTG
1 ATACAAGATTATTCCACCACTG
* ** *
2818025 ATAC---CTTGGT--ACCACGG
1 ATACAAGATTATTCCACCACTG
2818042 ATACAAGATTATTCCACCACTG
1 ATACAAGATTATTCCACCACTG
2818064 ATAC
1 ATAC
2818068 GTTGTGTCTC
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 10 0.33
19 3 0.10
20 3 0.10
22 14 0.47
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (22 bp):
ATACAAGATTATTCCACCACTG
Found at i:2818037 original size:39 final size:39
Alignment explanation
Indices: 2817989--2818067 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
2817979 TAACTCTTTC
2817989 CCTTAGTACCACGAATACAAGATTATTCCACCACTGATA
1 CCTTAGTACCACGAATACAAGATTATTCCACCACTGATA
* *
2818028 CCTTGGTACCACGGATACAAGATTATTCCACCACTGATA
1 CCTTAGTACCACGAATACAAGATTATTCCACCACTGATA
2818067 C
1 C
2818068 GTTGTGTCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.25
Consensus pattern (39 bp):
CCTTAGTACCACGAATACAAGATTATTCCACCACTGATA
Found at i:2818450 original size:50 final size:50
Alignment explanation
Indices: 2818375--2818475 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
2818365 TTTGGAAGAA
2818375 AGCTTCTCTAGCCTCTCCTCCCTGACTAACCGTTACTGGTCAACTTTCAG
1 AGCTTCTCTAGCCTCTCCTCCCTGACTAACCGTTACTGGTCAACTTTCAG
2818425 AGCTTCTCTAGCCTCTCCTCCCTGACTAACCGTTACTGGTCAACTTTCAG
1 AGCTTCTCTAGCCTCTCCTCCCTGACTAACCGTTACTGGTCAACTTTCAG
2818475 A
1 A
2818476 TGGCGCTGTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.19, C:0.36, G:0.14, T:0.32
Consensus pattern (50 bp):
AGCTTCTCTAGCCTCTCCTCCCTGACTAACCGTTACTGGTCAACTTTCAG
Found at i:2831489 original size:14 final size:14
Alignment explanation
Indices: 2831470--2831498 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2831460 CAATTATTCT
2831470 CATCTTTGACATAC
1 CATCTTTGACATAC
2831484 CATCTTTGACATAC
1 CATCTTTGACATAC
2831498 C
1 C
2831499 CGTGAACCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.31, G:0.07, T:0.34
Consensus pattern (14 bp):
CATCTTTGACATAC
Found at i:2834370 original size:39 final size:39
Alignment explanation
Indices: 2834325--2834450 Score: 180
Period size: 39 Copynumber: 3.2 Consensus size: 39
2834315 TCTTTAACTA
* ** * *
2834325 GGATATTTTTCTAGCACGTAGCCTGCGGACCTCAAGTCC
1 GGATATTTTTCCAGCATATAGCCTGCGAACCTCATGTCC
** *
2834364 AAATATTTTTCCAGCATATAGCCTTCGAACCTCATGTCC
1 GGATATTTTTCCAGCATATAGCCTGCGAACCTCATGTCC
2834403 GGATATTTTTCCAGCATATAGCCTGCGAACCTCATGTCC
1 GGATATTTTTCCAGCATATAGCCTGCGAACCTCATGTCC
2834442 GGATATTTT
1 GGATATTTT
2834451 CAATCTCATA
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 76 1.00
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (39 bp):
GGATATTTTTCCAGCATATAGCCTGCGAACCTCATGTCC
Found at i:2836892 original size:48 final size:48
Alignment explanation
Indices: 2836821--2836918 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
2836811 ATCAGAGTAA
*
2836821 AAATTGGGTTCCAAAGTCAATTATGAAGAAGGTTTTAGCACGCTTGCG
1 AAATTGGGTTCCAAAGCCAATTATGAAGAAGGTTTTAGCACGCTTGCG
2836869 AAATTGGGTTCCAAAGCCAATTATGAAGAAGGTTTTAGCACGCTTGCG
1 AAATTGGGTTCCAAAGCCAATTATGAAGAAGGTTTTAGCACGCTTGCG
2836917 AA
1 AA
2836919 GTCCAAATTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (48 bp):
AAATTGGGTTCCAAAGCCAATTATGAAGAAGGTTTTAGCACGCTTGCG
Found at i:2837275 original size:25 final size:26
Alignment explanation
Indices: 2837246--2837294 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
2837236 TAATTATAAT
2837246 TTAATTAA-TATTATATTT-AATAAGA
1 TTAATTAATTATTAT-TTTGAATAAGA
2837271 TTAATTAATTATTATTTTGAATAA
1 TTAATTAATTATTATTTTGAATAA
2837295 TGTTACTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (26 bp):
TTAATTAATTATTATTTTGAATAAGA
Found at i:2840279 original size:22 final size:20
Alignment explanation
Indices: 2840232--2840280 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
2840222 GTACATTATC
* *
2840232 CTTCTTTTTTGTTCTCCTTT
1 CTTCTTTTTTCTTCTCCTAT
2840252 CGTTCTTTCTTTCTTCTCCCTAT
1 C-TTCTTT-TTTCTTCT-CCTAT
2840275 CTTCTT
1 CTTCTT
2840281 CCTTCCGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.04
21 6 0.25
22 12 0.50
23 5 0.21
ACGTcount: A:0.02, C:0.31, G:0.04, T:0.63
Consensus pattern (20 bp):
CTTCTTTTTTCTTCTCCTAT
Found at i:2840425 original size:27 final size:27
Alignment explanation
Indices: 2840369--2840436 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
2840359 CATTGGTGCT
* *
2840369 GCCTATCAGATAAGGGTCACCAGTGAC
1 GCCTATCAGATAGGGGTCACCAATGAC
* *
2840396 GCCTATCAGATAGGGGTTACCAATGGC
1 GCCTATCAGATAGGGGTCACCAATGAC
* *
2840423 GCCAACCAGATAGG
1 GCCTATCAGATAGG
2840437 CTCCACTCCC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.29, C:0.25, G:0.28, T:0.18
Consensus pattern (27 bp):
GCCTATCAGATAGGGGTCACCAATGAC
Found at i:2840569 original size:19 final size:17
Alignment explanation
Indices: 2840537--2840571 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
2840527 AGTACCATTA
2840537 ATAAAAAATATTAAAAG
1 ATAAAAAATATTAAAAG
2840554 ATAAAAGAATTATTAAAA
1 ATAAAA-AA-TATTAAAA
2840572 AATTGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (17 bp):
ATAAAAAATATTAAAAG
Found at i:2843139 original size:41 final size:43
Alignment explanation
Indices: 2843065--2843322 Score: 237
Period size: 45 Copynumber: 5.9 Consensus size: 43
2843055 TTTATCAAAT
* *
2843065 CACCGGCATTTAGCCTGCTAGGTTTTAAA--CCCGAAT-TCATC
1 CACCGGCATTTAGCCTGCTAGG-CTCAAAGGCCCGAATATCATC
* *
2843106 CACCGGCATTTCA-CCTGCTAGGCTCGAA-GCCCG-ATATCATTT
1 CACCGGCATTT-AGCCTGCTAGGCTCAAAGGCCCGAATATCA-TC
2843148 CACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGT-ATC
1 CACCGGCATT-TAGCCTGCTAGGCTCAAAGGCCCGAATA-TCATC
*
2843192 TCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGT-ATC
1 -CACCGGCAT-TTAGCCTGCTAGGCTCAAAGGCCCGAATA-TCATC
* * *
2843237 TCACCAGCATCATAGCCTGCTAGGCTCAAAGGCCCAAATAGT-ATC
1 -CACCGGCAT-TTAGCCTGCTAGGCTCAAAGGCCCGAATA-TCATC
* *
2843282 TCACCGACATCATAGCCTGCTAGGCTCAAAAGGCCCGAATA
1 -CACCGGCAT-TTAGCCTGCTAGGCTC-AAAGGCCCGAATA
2843323 GTACCGTAGA
Statistics
Matches: 193, Mismatches: 12, Indels: 19
0.86 0.05 0.08
Matches are distributed among these distances:
40 5 0.03
41 27 0.14
42 13 0.07
43 15 0.08
44 6 0.03
45 114 0.59
46 13 0.07
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (43 bp):
CACCGGCATTTAGCCTGCTAGGCTCAAAGGCCCGAATATCATC
Found at i:2843207 original size:45 final size:45
Alignment explanation
Indices: 2843119--2843325 Score: 321
Period size: 45 Copynumber: 4.6 Consensus size: 45
2843109 CGGCATTTCA
* * *
2843119 CCTGCTAGGCTCGAA-GCCCG-ATA-TCATTTCACCGGCATTATAG
1 CCTGCTAGGCTCAAAGGCCCGAATAGT-ATCTCACCGGCATCATAG
2843162 CCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGCATCATAG
1 CCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGCATCATAG
*
2843207 CCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCAGCATCATAG
1 CCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGCATCATAG
* *
2843252 CCTGCTAGGCTCAAAGGCCCAAATAGTATCTCACCGACATCATAG
1 CCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGCATCATAG
2843297 CCTGCTAGGCTCAAAAGGCCCGAATAGTA
1 CCTGCTAGGCTC-AAAGGCCCGAATAGTA
2843326 CCGTAGAATA
Statistics
Matches: 152, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
43 14 0.09
44 5 0.03
45 117 0.77
46 16 0.11
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (45 bp):
CCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGCATCATAG
Found at i:2848323 original size:31 final size:31
Alignment explanation
Indices: 2848285--2848433 Score: 176
Period size: 31 Copynumber: 4.8 Consensus size: 31
2848275 ACAAATGACA
*
2848285 AGTGAAAAGTGGTAGCTTCGACTACCTGATT
1 AGTGAAAAGTGGTAGCTTCGACTACCTGATC
* *
2848316 AGTGAAAAGTGGTAGCTTTTG-CTACTTGATC
1 AGTGAAAAGTGGTAGC-TTCGACTACCTGATC
* *
2848347 GGTGAAAAGTGGTAGCTCCGACTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGACTACCTGATC
* * *
2848378 AGTTAAAAATGGTAGC-TCCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGA-CTACCTGATC
* *
2848409 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGACTAC
2848434 AAGTGACAAG
Statistics
Matches: 97, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
30 4 0.04
31 88 0.91
32 5 0.05
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGACTACCTGATC
Found at i:2848537 original size:47 final size:46
Alignment explanation
Indices: 2848451--2848606 Score: 141
Period size: 47 Copynumber: 3.3 Consensus size: 46
2848441 AAGTGATTTC
* * * *
2848451 CGTATAAGACCATATCTGGGATATGACATCGGTGTGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * * *
2848497 CTGTATAAGACCATATCTAGGATATGGCATTAGTGAGATATGTGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * * * * *
2848544 CGTGTAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTA
1 CGTATAAGACCATATCTGGGATATGGCATC-A-GTGAGATATATGA-TA
*
2848593 CGTGTAAGACCATA
1 CGTATAAGACCATA
2848607 GTTGGGCTAT
Statistics
Matches: 90, Mismatches: 16, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
46 25 0.28
47 39 0.43
48 11 0.12
49 15 0.17
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
Found at i:2848569 original size:46 final size:47
Alignment explanation
Indices: 2848502--2848626 Score: 146
Period size: 49 Copynumber: 2.6 Consensus size: 47
2848492 TGCTACTGTA
* * *
2848502 TAAGACCATATCTAGGATATGGCAT-TAGTGAGATATGTGATT-CGTG
1 TAAGACCATAGCTGGGCTATGGCATATA-TGAGATATGTGATTACGTG
*
2848548 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGCTATGGCAT--ATATGAGATATGTGATTACGTG
* *
2848597 TAAGACCATAGTTGGGCTATGACATGATAT
1 TAAGACCATAGCTGGGCTATGGCAT-ATAT
2848627 ATGAAGATGT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
46 22 0.32
48 18 0.26
49 29 0.42
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (47 bp):
TAAGACCATAGCTGGGCTATGGCATATATGAGATATGTGATTACGTG
Found at i:2848603 original size:49 final size:47
Alignment explanation
Indices: 2848533--2848626 Score: 152
Period size: 49 Copynumber: 2.0 Consensus size: 47
2848523 GCATTAGTGA
*
2848533 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATGT
1 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGACAT-GATATGT
*
2848581 GATATGTGATTACGTGTAAGACCATAGTTGGGCTATGACATGATAT
1 GATATGTGATT-CGTGTAAGACCATAGCTGGGCTATGACATGATAT
2848627 ATGAAGATGT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
48 16 0.37
49 27 0.63
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.32
Consensus pattern (47 bp):
GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGACATGATATGT
Found at i:2848637 original size:49 final size:48
Alignment explanation
Indices: 2848536--2848637 Score: 143
Period size: 49 Copynumber: 2.1 Consensus size: 48
2848526 TTAGTGAGAT
* * *
2848536 ATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATGTGAT
1 ATGTGATTCGTGTAAGACCATAGCTGGGCTATGACATCGATATATGAG
*
2848584 ATGTGATTACGTGTAAGACCATAGTTGGGCTATGACAT-GATATATGAAG
1 ATGTGATT-CGTGTAAGACCATAGCTGGGCTATGACATCGATATATG-AG
2848633 ATGTG
1 ATGTG
2848638 TAAGACCATA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
48 15 0.31
49 33 0.69
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.31
Consensus pattern (48 bp):
ATGTGATTCGTGTAAGACCATAGCTGGGCTATGACATCGATATATGAG
Found at i:2857722 original size:16 final size:16
Alignment explanation
Indices: 2857701--2857731 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2857691 TATTTATATT
*
2857701 GAAATTTTATTAATAG
1 GAAATTTAATTAATAG
2857717 GAAATTTAATTAATA
1 GAAATTTAATTAATA
2857732 ATAATTTTTA
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:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
GAAATTTAATTAATAG
Found at i:2867526 original size:39 final size:41
Alignment explanation
Indices: 2867431--2867614 Score: 199
Period size: 40 Copynumber: 4.6 Consensus size: 41
2867421 TTGAATGATG
*
2867431 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATA
*
2867470 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTAATA
2867510 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATA
* *
2867549 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
* * *
2867589 ACCGGGATATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
2867615 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
39 54 0.43
40 61 0.48
41 11 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
Found at i:2867566 original size:79 final size:81
Alignment explanation
Indices: 2867431--2867614 Score: 213
Period size: 79 Copynumber: 2.3 Consensus size: 81
2867421 TTGAATGATG
2867431 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
2867494 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * **
2867509 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGTTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
2867570 ATTTGTGCGAATTACTATA
63 ATTTGTGCGAATTACTATA
* * *
2867589 ACCGGGATATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
2867615 AACGAGGAGC
Statistics
Matches: 91, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
78 11 0.12
79 57 0.63
80 23 0.25
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:2867636 original size:79 final size:79
Alignment explanation
Indices: 2867483--2867637 Score: 183
Period size: 79 Copynumber: 2.0 Consensus size: 79
2867473 GGACTAAGAT
* * ** *
2867483 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGATAAGCCCGAAGGCATTTGAACGAGTGACTAA
2867548 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
*
2867562 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGATATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGATAAG-CCCGAAGGCATTTGAACGAGTGA-
*
2867624 CTATATCC-GGTTAA
62 CTAAATCCGGGTTAA
2867638 ATTCTGAAGG
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
78 3 0.05
79 37 0.57
80 25 0.38
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGATAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAGTC
Found at i:2873612 original size:28 final size:28
Alignment explanation
Indices: 2873580--2873663 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
2873570 AACTTCGATC
2873580 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
2873608 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
2873630 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
2873658 ACGTGT
1 ACGTGT
2873664 ATAGGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:2873653 original size:50 final size:49
Alignment explanation
Indices: 2873532--2873706 Score: 219
Period size: 50 Copynumber: 3.5 Consensus size: 49
2873522 TGAGGTCGCA
* * * * *
2873532 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAA-TT-GGTCACG
**
2873583 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATT-GGTCACG
* *
2873633 TGTGTAGTACTAAGTGCAGGCTACTACGTGTAT-AGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCA-GATAATTGGTCACG
2873682 TGTGTAGTACTAAGTGCA-GCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
2873707 TTCGTACCAG
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
48 7 0.06
49 24 0.22
50 46 0.41
51 34 0.31
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAATTGGTCACG
Found at i:2875551 original size:14 final size:12
Alignment explanation
Indices: 2875522--2875552 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2875512 ACTCCTTAAT
*
2875522 TCTCTTCCTAAA
1 TCTCTCCCTAAA
2875534 TCTCTCCCTAAA
1 TCTCTCCCTAAA
2875546 TCTCTCC
1 TCTCTCC
2875553 TCTTCTCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.42, G:0.00, T:0.39
Consensus pattern (12 bp):
TCTCTCCCTAAA
Found at i:2881084 original size:40 final size:40
Alignment explanation
Indices: 2881001--2881303 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
2880991 TTGAATGCTG
* * * * * *
2881001 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
* * * *
2881041 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
2881081 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
*
2881121 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
2881161 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
2881201 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
2881241 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
2881280 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
2881304 TGAACGAGGA
Statistics
Matches: 239, Mismatches: 21, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
39 35 0.15
40 196 0.82
41 8 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:2889196 original size:39 final size:40
Alignment explanation
Indices: 2888992--2889214 Score: 245
Period size: 40 Copynumber: 5.6 Consensus size: 40
2888982 TTGAATGCTG
* * * * * *
2888992 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
* * * *
2889032 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
2889072 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
2889112 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
2889152 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
2889191 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
2889215 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 35 0.22
40 118 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:2889234 original size:79 final size:80
Alignment explanation
Indices: 2889067--2889249 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
2889057 GTGCGAGATA
* * *
2889067 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
2889132 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
2889147 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
2889211 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
2889226 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
2889250 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:2891534 original size:196 final size:195
Alignment explanation
Indices: 2891197--2891587 Score: 710
Period size: 196 Copynumber: 2.0 Consensus size: 195
2891187 TTACAGTAAG
2891197 CCACCACTGATAGGCTTCATCTTGCAACAACGACACTGCACCTTTCAGTTTCTGCTCTAGGGTGC
1 CCACCACTGATAGGCTTCATCTTGCAACAACGACACTGCACCTTTCAGTTTCTGCTCTAGGGTGC
2891262 AGTCGAGATCATCCATGATCCTCTCTGTGGCCTCAATCCAATATTCAGCCACATTAGGGACAACC
66 AGTCGAGATCATCCATGATCCTCTCTGTGGCCTCAATCCAATATTCAGCCACATTAGGGACAACC
*
2891327 CCAGTGATACCCTTAAAGATCTCAGCCCCATTAGACCTGAGTTGCTCCGTTACCGACCCACGACC
131 CCAGCGATACCC-TAAAGATCTCAGCCCCATTAGACCTGAGTTGCTCCGTTACCGACCCACGACC
2891392 T
195 T
* *
2891393 CCACCACTGATAGGCTTCATCTTGCAACAACGACACTGCACCTTTCAGTTTCTGCTTTAGGGTGT
1 CCACCACTGATAGGCTTCATCTTGCAACAACGACACTGCACCTTTCAGTTTCTGCTCTAGGGTGC
* *
2891458 AGTCGAGATCATCCATGGTCCTCTCTGTGGCCTCAATCCAATATTCAGCCACATTAGGGACAGCC
66 AGTCGAGATCATCCATGATCCTCTCTGTGGCCTCAATCCAATATTCAGCCACATTAGGGACAACC
* *
2891523 CCAGCGATACCCTAAAGATCTCAGCCCCATTAGACCTGAGTTGTTCTGTTACCGACCCACGACCT
131 CCAGCGATACCCTAAAGATCTCAGCCCCATTAGACCTGAGTTGCTCCGTTACCGACCCACGACCT
2891588 ACAGTACCAG
Statistics
Matches: 188, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
195 51 0.27
196 137 0.73
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (195 bp):
CCACCACTGATAGGCTTCATCTTGCAACAACGACACTGCACCTTTCAGTTTCTGCTCTAGGGTGC
AGTCGAGATCATCCATGATCCTCTCTGTGGCCTCAATCCAATATTCAGCCACATTAGGGACAACC
CCAGCGATACCCTAAAGATCTCAGCCCCATTAGACCTGAGTTGCTCCGTTACCGACCCACGACCT
Found at i:2892845 original size:34 final size:34
Alignment explanation
Indices: 2892749--2892845 Score: 124
Period size: 34 Copynumber: 2.9 Consensus size: 34
2892739 TATAGTGTTG
* * **
2892749 ATCAGTCTGGGCCTAAGCCCAAACCAGTAGCAAT
1 ATCAGTGTGGGCCTTAGCCCAATTCAGTAGCAAT
* *
2892783 ATCAGTGTGGGCTTTAGCCC-ATTACAGTAGCAGT
1 ATCAGTGTGGGCCTTAGCCCAATT-CAGTAGCAAT
2892817 ATCAGTGTGGGCCTTAGCCCAATTCAGTA
1 ATCAGTGTGGGCCTTAGCCCAATTCAGTA
2892846 TAGAATCAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
33 1 0.02
34 50 0.93
35 3 0.06
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.25
Consensus pattern (34 bp):
ATCAGTGTGGGCCTTAGCCCAATTCAGTAGCAAT
Found at i:2895908 original size:27 final size:27
Alignment explanation
Indices: 2895878--2895931 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
2895868 CTTCTGCTAC
*
2895878 TACTTTAGCAGACCTACCTGAGCGGTT
1 TACTTGAGCAGACCTACCTGAGCGGTT
*
2895905 TACTTGAGCAGGCCTACCTGAGCGGTT
1 TACTTGAGCAGACCTACCTGAGCGGTT
2895932 CACTCGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (27 bp):
TACTTGAGCAGACCTACCTGAGCGGTT
Found at i:2896106 original size:12 final size:12
Alignment explanation
Indices: 2896086--2896116 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2896076 TTTGTTTATC
*
2896086 TTATTTTTATTT
1 TTATGTTTATTT
2896098 TTATGTTTATTT
1 TTATGTTTATTT
2896110 TTATGTT
1 TTATGTT
2896117 CTTAGACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.77
Consensus pattern (12 bp):
TTATGTTTATTT
Found at i:2896762 original size:11 final size:10
Alignment explanation
Indices: 2896742--2896780 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
2896732 AATGATGATG
2896742 AAAA-AAAGA
1 AAAAGAAAGA
2896751 AAAGAGAAAGA
1 AAA-AGAAAGA
*
2896762 AAAAGAAAAA
1 AAAAGAAAGA
2896772 AAAAGAAAG
1 AAAAGAAAG
2896781 GCTCTCATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 3 0.12
10 15 0.58
11 8 0.31
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAGAAAGA
Found at i:2898094 original size:40 final size:40
Alignment explanation
Indices: 2898038--2898255 Score: 280
Period size: 40 Copynumber: 5.5 Consensus size: 40
2898028 TGGATGATAA
* * *
2898038 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
* *
2898078 CCGGGCTAAGTTCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
2898118 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
2898158 CCAGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
2898198 CCTGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
2898238 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
2898256 TACTTGGCTT
Statistics
Matches: 160, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 16 0.10
40 144 0.90
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:2904860 original size:16 final size:17
Alignment explanation
Indices: 2904828--2904869 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
2904818 TGATGATGAA
*
2904828 AAAAAGAAAAGAGAAAG
1 AAAAAGAAAAGAAAAAG
2904845 AAAAAGAAAA-AAAAAG
1 AAAAAGAAAAGAAAAAG
*
2904861 AAGAAGAAA
1 AAAAAGAAA
2904870 GGCTCTCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAAG
Found at i:2907098 original size:27 final size:27
Alignment explanation
Indices: 2907064--2907241 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
2907054 AAAATTGTAC
2907064 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
2907091 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2907117 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
2907145 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
2907173 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2907200 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2907227 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2907242 GACTCAATAT
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 108 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:2907178 original size:82 final size:81
Alignment explanation
Indices: 2907065--2907220 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
2907055 AAATTGTACA
*
2907065 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
2907129 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
2907146 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
2907211 TGCGAGTTGA
65 TGCGAATTGA
2907221 TTATATAGCA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:2907232 original size:82 final size:81
Alignment explanation
Indices: 2907061--2907241 Score: 238
Period size: 82 Copynumber: 2.2 Consensus size: 81
2907051 ATTAAAATTG
*
2907061 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
2907126 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
2907142 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
2907206 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
2907224 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
2907242 GACTCAATAT
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 18 0.21
82 67 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:2908244 original size:150 final size:150
Alignment explanation
Indices: 2907973--2908273 Score: 593
Period size: 150 Copynumber: 2.0 Consensus size: 150
2907963 GCAGCAGCAG
2907973 TGTCATGAGATTGAAAAATCACTAAAAATAGTAGGAGTGGAATTAATTGATGAATAAATTATGTA
1 TGTCATGAGATTGAAAAATCACTAAAAATAGTAGGAGTGGAATTAATTGATGAATAAATTATGTA
2908038 ATCGAAGCTCGATGAGTCTGTTTTCATGAGGAAGTAACGATAAGATCATATGGGCAGTGTCTGGA
66 ATCGAAGCTCGATGAGTCTGTTTTCATGAGGAAGTAACGATAAGATCATATGGGCAGTGTCTGGA
*
2908103 AAATAAATTTTGTAAGGGGT
131 AAATAAATTTTATAAGGGGT
2908123 TGTCATGAGATTGAAAAATCACTAAAAATAGTAGGAGTGGAATTAATTGATGAATAAATTATGTA
1 TGTCATGAGATTGAAAAATCACTAAAAATAGTAGGAGTGGAATTAATTGATGAATAAATTATGTA
2908188 ATCGAAGCTCGATGAGTCTGTTTTCATGAGGAAGTAACGATAAGATCATATGGGCAGTGTCTGGA
66 ATCGAAGCTCGATGAGTCTGTTTTCATGAGGAAGTAACGATAAGATCATATGGGCAGTGTCTGGA
2908253 AAATAAATTTTATAAGGGGT
131 AAATAAATTTTATAAGGGGT
2908273 T
1 T
2908274 AAAGTCAGTT
Statistics
Matches: 150, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 150 1.00
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (150 bp):
TGTCATGAGATTGAAAAATCACTAAAAATAGTAGGAGTGGAATTAATTGATGAATAAATTATGTA
ATCGAAGCTCGATGAGTCTGTTTTCATGAGGAAGTAACGATAAGATCATATGGGCAGTGTCTGGA
AAATAAATTTTATAAGGGGT
Found at i:2910277 original size:47 final size:47
Alignment explanation
Indices: 2910224--2910316 Score: 159
Period size: 47 Copynumber: 2.0 Consensus size: 47
2910214 TTCAATTATG
* *
2910224 ATAACTTAGACAAAGAGCACTCATCCAATCCTCATACGAATGATACT
1 ATAACTTAGACAAAAAGCACTCATCCAATCCTCATACGAACGATACT
*
2910271 ATAACTTAGACAAAAAGCACTCATCCAATCCTCATAGGAACGATAC
1 ATAACTTAGACAAAAAGCACTCATCCAATCCTCATACGAACGATAC
2910317 CCACTCATCA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.22
Consensus pattern (47 bp):
ATAACTTAGACAAAAAGCACTCATCCAATCCTCATACGAACGATACT
Found at i:2912378 original size:50 final size:50
Alignment explanation
Indices: 2912296--2912390 Score: 163
Period size: 50 Copynumber: 1.9 Consensus size: 50
2912286 GCCAAGTTTA
2912296 TGAAAGACATACTTTCAAAGAAAAGACAATTGTGAGAATTTGAAACAATT
1 TGAAAGACATACTTTCAAAGAAAAGACAATTGTGAGAATTTGAAACAATT
* **
2912346 TGAAGGACATACTTTCAAAGAAAAGATGATTGTGAGAATTTGAAA
1 TGAAAGACATACTTTCAAAGAAAAGACAATTGTGAGAATTTGAAA
2912391 TAATCACACT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.26
Consensus pattern (50 bp):
TGAAAGACATACTTTCAAAGAAAAGACAATTGTGAGAATTTGAAACAATT
Found at i:2914964 original size:45 final size:45
Alignment explanation
Indices: 2914899--2915076 Score: 184
Period size: 45 Copynumber: 4.0 Consensus size: 45
2914889 TAGGATTCCG
*
2914899 ATATGTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATTGAT
1 ATATGTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT
* * *
2914944 ATATGTGATTTCGTGAAAGACCACGTCTGGGACATTGACATCGAT
1 ATATGTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT
* ** * * * *
2914989 GTATACGGTTACGTGTAAGACCATGTATGGGACATCGGCATCG-T
1 ATATGTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT
* * * * *
2915033 AT-T-TGA-TTCATGTAAGACCCTGTCTGGGATAGTGGCATCAAT
1 ATATGTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT
2915075 AT
1 AT
2915077 GAGATAGCAT
Statistics
Matches: 107, Mismatches: 25, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
41 26 0.24
42 4 0.04
43 1 0.01
44 2 0.02
45 74 0.69
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (45 bp):
ATATGTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT
Found at i:2924010 original size:18 final size:18
Alignment explanation
Indices: 2923980--2924014 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2923970 TCTGACCTTG
2923980 TCTCATAAAAATTCAAATA
1 TCTCATAAAAATT-AAATA
2923999 TCTCAT-AAAATTAAAT
1 TCTCATAAAAATTAAAT
2924015 TCTTTTGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 6 0.38
19 6 0.38
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (18 bp):
TCTCATAAAAATTAAATA
Found at i:2925544 original size:42 final size:42
Alignment explanation
Indices: 2925472--2925579 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
2925462 TGGATCTTAT
* * *
2925472 GCCATATCCCGGATATGGTCTTACATGAAAT-ATCATA-TCGAC
1 GCCATATCCCAGATATGGTCTTATACGAAATCA-CATACT-GAC
* * * *
2925514 GCCATGTCCCTGACATGGTCTTATACGAAATCACATACTGAT
1 GCCATATCCCAGATATGGTCTTATACGAAATCACATACTGAC
2925556 GCCATATCCCAGATATGGTCTTAT
1 GCCATATCCCAGATATGGTCTTAT
2925580 TCGGAATCTC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
42 53 0.96
43 2 0.04
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (42 bp):
GCCATATCCCAGATATGGTCTTATACGAAATCACATACTGAC
Found at i:2932200 original size:40 final size:40
Alignment explanation
Indices: 2932163--2932387 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
2932153 GCTACTCGTT
*
2932163 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
2932203 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
2932243 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * *
2932283 CAAATGCCTTTGGG-CTTAGCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
2932322 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
2932363 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
2932388 CATCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.01
39 33 0.21
40 107 0.68
41 15 0.10
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:2932335 original size:79 final size:81
Alignment explanation
Indices: 2932163--2932380 Score: 277
Period size: 79 Copynumber: 2.7 Consensus size: 81
2932153 GCTACTCGTT
* *
2932163 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTC-GGATCTTAGTCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCC
* *
2932226 GGATTTAGTAACTCGCA
65 AGAATTAGTAACTCGCA
* * *
2932243 CAAATGCCTTCGGATCTTAGTCCGGATT-TAGTAACTCGTACAAATGCCTTTGGG-CTTAGCCCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCA
*
2932306 GAATTAGTATCTCGCA
66 GAATTAGTAACTCGCA
* * *
2932322 CAAATGCCTTCGGATCTTAGTCCGGA-TATGGTCACTTAGCACAAA-GCCTTCGGGACTTA
1 CAAATGCCTTCGGATCTTAGTCCGGATTATAGTAAC-TCGCACAAATGCCTTCGGGACTTA
2932381 GCCCGGACAT
Statistics
Matches: 120, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 63 0.52
80 54 0.45
81 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (81 bp):
CAAATGCCTTCGGATCTTAGTCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCA
GAATTAGTAACTCGCA
Found at i:2938407 original size:50 final size:49
Alignment explanation
Indices: 2938279--2938456 Score: 203
Period size: 50 Copynumber: 3.6 Consensus size: 49
2938269 TGTGAGGTTG
* * * * *
2938279 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCGATAACTTCGATCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATAA-TT-GGTCA
*
2938330 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATGATTAGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATAATT-GGTCA
* * ** **
2938380 CGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCGGATAATTGGTTG
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATAATTGGTCA
* *
2938429 TATGTGTAGTACTATGTGCAGGCTACTA
1 CATGTGTAGTACTAAGTGCAGGCTACTA
2938457 TGCGTACCAG
Statistics
Matches: 110, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 28 0.25
50 45 0.41
51 37 0.34
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.32
Consensus pattern (49 bp):
CATGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATAATTGGTCA
Found at i:2945799 original size:23 final size:26
Alignment explanation
Indices: 2945749--2945801 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 26
2945739 ATACAAATTA
*
2945749 CATGAGAGATATTGGCATGGGAATAT
1 CATGAGAGATATTGGCATGGGAAAAT
*
2945775 CATGAGA-AT-TT-GCATGGTAAAAT
1 CATGAGAGATATTGGCATGGGAAAAT
2945798 CATG
1 CATG
2945802 GGTATGAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 14 0.56
24 2 0.08
25 2 0.08
26 7 0.28
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.28
Consensus pattern (26 bp):
CATGAGAGATATTGGCATGGGAAAAT
Found at i:2955372 original size:43 final size:43
Alignment explanation
Indices: 2955323--2955449 Score: 159
Period size: 43 Copynumber: 3.0 Consensus size: 43
2955313 GGTTATCAAG
* *
2955323 ATGTGATTTCATGTAAGACCATATCTGGGACATTGGCATTGTAT
1 ATGTGATTACATGTAAGACCATATCTGGGATA-TGGCATTGTAT
* * * *
2955367 -TGTGATTACGTGTAAGACCCTGTCTGGGATAGTGGCA-TCTAT
1 ATGTGATTACATGTAAGACCATATCTGGGATA-TGGCATTGTAT
*
2955409 ATGTGATAACATGTAAGACCATATCTGGGATATGGCATTGT
1 ATGTGATTACATGTAAGACCATATCTGGGATATGGCATTGT
2955450 TCGAGCTTTA
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
42 9 0.13
43 60 0.87
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (43 bp):
ATGTGATTACATGTAAGACCATATCTGGGATATGGCATTGTAT
Found at i:2980761 original size:17 final size:18
Alignment explanation
Indices: 2980739--2980772 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2980729 CACATTGAAG
2980739 TGTTTT-AGTGAAAACCT
1 TGTTTTCAGTGAAAACCT
*
2980756 TGTTTTCATTGAAAACC
1 TGTTTTCAGTGAAAACC
2980773 CTTCCTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (18 bp):
TGTTTTCAGTGAAAACCT
Found at i:2981275 original size:142 final size:142
Alignment explanation
Indices: 2981019--2981302 Score: 568
Period size: 142 Copynumber: 2.0 Consensus size: 142
2981009 ACTTAATAAG
2981019 CTAGAAACTATATGCTTTCTTTAAAAAAAAACAAGTCCAAGTCATCTTGCTAGCTGGCCACCTCC
1 CTAGAAACTATATGCTTTCTTTAAAAAAAAACAAGTCCAAGTCATCTTGCTAGCTGGCCACCTCC
2981084 GAGTCCCACCAAACATCGAACCTCCTACTGAGCATCACCTAAGAAAAATAAAAGAGGGGGTGAGT
66 GAGTCCCACCAAACATCGAACCTCCTACTGAGCATCACCTAAGAAAAATAAAAGAGGGGGTGAGT
2981149 TTTTGAAAACTT
131 TTTTGAAAACTT
2981161 CTAGAAACTATATGCTTTCTTTAAAAAAAAACAAGTCCAAGTCATCTTGCTAGCTGGCCACCTCC
1 CTAGAAACTATATGCTTTCTTTAAAAAAAAACAAGTCCAAGTCATCTTGCTAGCTGGCCACCTCC
2981226 GAGTCCCACCAAACATCGAACCTCCTACTGAGCATCACCTAAGAAAAATAAAAGAGGGGGTGAGT
66 GAGTCCCACCAAACATCGAACCTCCTACTGAGCATCACCTAAGAAAAATAAAAGAGGGGGTGAGT
2981291 TTTTGAAAACTT
131 TTTTGAAAACTT
2981303 AGTGTGTACA
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 142 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (142 bp):
CTAGAAACTATATGCTTTCTTTAAAAAAAAACAAGTCCAAGTCATCTTGCTAGCTGGCCACCTCC
GAGTCCCACCAAACATCGAACCTCCTACTGAGCATCACCTAAGAAAAATAAAAGAGGGGGTGAGT
TTTTGAAAACTT
Found at i:2984559 original size:28 final size:29
Alignment explanation
Indices: 2984521--2984583 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 29
2984511 AAGTCTGCAT
*
2984521 ACATGCATATGGCCCATTAGGCCC-AATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
*
2984549 TCATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
2984578 ACATTC
1 ACATTC
2984584 GTATACATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 22 0.71
29 9 0.29
ACGTcount: A:0.29, C:0.32, G:0.14, T:0.25
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:2984839 original size:16 final size:18
Alignment explanation
Indices: 2984798--2984840 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
2984788 GTAGCCAAAC
2984798 TTTCGGC-TTTTCGACAT
1 TTTCGGCATTTTCGACAT
2984815 TTT-GGCATTTT-GAC-T
1 TTTCGGCATTTTCGACAT
2984830 TTTCGGCATTT
1 TTTCGGCATTT
2984841 CGGGATTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.17
16 13 0.54
17 7 0.29
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.51
Consensus pattern (18 bp):
TTTCGGCATTTTCGACAT
Found at i:2994316 original size:47 final size:47
Alignment explanation
Indices: 2994238--2994648 Score: 750
Period size: 47 Copynumber: 8.7 Consensus size: 47
2994228 CCCTTCGGGA
* * * * * *
2994238 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
2994285 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2994332 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2994379 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2994426 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2994473 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2994520 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2994567 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2994614 CTTATCACATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
2994649 AGAATCCTAA
Statistics
Matches: 354, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 354 1.00
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:2996738 original size:56 final size:56
Alignment explanation
Indices: 2996652--2996883 Score: 446
Period size: 56 Copynumber: 4.1 Consensus size: 56
2996642 TATTAGTTTA
* *
2996652 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTGATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
2996708 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
2996764 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
2996820 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
2996876 TTGCCCAT
1 TTGCCCAT
2996884 CATCCCTTGT
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 174 1.00
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.46
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:2997631 original size:44 final size:44
Alignment explanation
Indices: 2997534--2997624 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
2997524 ATTCATATGT
* * *
2997534 ATGAATGTTTTTAAAAAGAATAAAATTTTATGGCTTAGATTTGT
1 ATGAATGTTTTTAAAAAGAATAAAATTTTATGGCTCAGAATTGC
2997578 ATGAATGTTTTTAAAAAGAATAAAATTTTATGGCTCAGAATTGC
1 ATGAATGTTTTTAAAAAGAATAAAATTTTATGGCTCAGAATTGC
2997622 ATG
1 ATG
2997625 TGTGTTTACA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (44 bp):
ATGAATGTTTTTAAAAAGAATAAAATTTTATGGCTCAGAATTGC
Found at i:3001746 original size:46 final size:47
Alignment explanation
Indices: 3001693--3001951 Score: 164
Period size: 46 Copynumber: 5.5 Consensus size: 47
3001683 TTTGTGCACT
3001693 AGTGTAAGA-CATGTCTGGGACATGCATTGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATTGGCCACATTATGAGAGCC
* * * *
3001739 AGTGTAAGACCATGTCTAGGACATGGCA-T--CGACATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATTGGCCACATT---ATGAGAGCC
* * ** *
3001787 AGTGTAAGACACA--TCTGGGACATGAATCGGCCTTGA-GATGTA-AGCC
1 AGTGTAAGAC-CATGTCTGGGACATGCATTGGCC-ACATTATG-AGAGCC
* * * *
3001833 AGTGTAAGA-CATGTCTGGGACATGCATTGG-C-TATGA-GATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGCATTGGCCACATTATGA-GAGCC
* * * * * *
3001877 AGTGTAAGATCATGTCTAGGACATGGCATCGGCACAGATATGTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATTGGC-CACAT-TATGAGAGCC
3001927 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
3001952 GTGTCGGCCT
Statistics
Matches: 162, Mismatches: 28, Indels: 43
0.70 0.12 0.18
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 15 0.09
45 20 0.12
46 46 0.28
47 24 0.15
48 21 0.13
49 6 0.04
50 25 0.15
51 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGCATTGGCCACATTATGAGAGCC
Found at i:3002854 original size:42 final size:42
Alignment explanation
Indices: 3002795--3002878 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
3002785 ACACACGGGT
* *
3002795 GTGTGTCTAGGTCGTGTGTGATACACGGTCAGCCCCATGGGC
1 GTGTGTCTAGGCCGTGTGTGACACACGGTCAGCCCCATGGGC
*
3002837 GTGTGTCTAGGCCGTGTGTGACACACGGTCAGCTCCATGGGC
1 GTGTGTCTAGGCCGTGTGTGACACACGGTCAGCCCCATGGGC
3002879 ATGTTGTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.14, C:0.25, G:0.36, T:0.25
Consensus pattern (42 bp):
GTGTGTCTAGGCCGTGTGTGACACACGGTCAGCCCCATGGGC
Found at i:3013090 original size:46 final size:44
Alignment explanation
Indices: 3013006--3013105 Score: 139
Period size: 46 Copynumber: 2.2 Consensus size: 44
3012996 GACAAAAACT
3013006 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGT--GCC
* * *
3013052 AGTGTAAGATATGTCTGGGACATGCATCGG-CTATGAGATGTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGTGCC
3013096 AGTGTAAGAC
1 AGTGTAAGAC
3013106 CATATCTAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
44 11 0.22
45 2 0.04
46 36 0.73
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTGCC
Found at i:3024512 original size:42 final size:43
Alignment explanation
Indices: 3024413--3024527 Score: 119
Period size: 43 Copynumber: 2.7 Consensus size: 43
3024403 AATGCCAACA
* * *
3024413 TCCCAGACGTGGTCTTACATGAAATCAAACATCGATGCCACTG
1 TCCCAGACATGGTCTTACACGAAATCAGACATCGATGCCACTG
* * *
3024456 TCCTTA-ACAGGGTCTTACACGAAATCAGATA-CGATGCCGA-TG
1 TCC-CAGACATGGTCTTACACGAAATCAGACATCGATGCC-ACTG
*
3024498 TCCCAGACATGGTCTTACACGTAAAACAGA
1 TCCCAGACATGGTCTTACACG-AAATCAGA
3024528 AGTTAATGCT
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
41 1 0.02
42 26 0.44
43 31 0.53
44 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGAAATCAGACATCGATGCCACTG
Found at i:3031403 original size:23 final size:25
Alignment explanation
Indices: 3031353--3031405 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
3031343 ATGTCATAAA
*
3031353 CATAACTTCATCATATAACTTATAC
1 CATAACTTCATCATATAACATATAC
3031378 CATAAC-TCATTCATA-AACATAT-C
1 CATAACTTCA-TCATATAACATATAC
3031401 CATAA
1 CATAA
3031406 TCAAGCCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 6 0.23
24 9 0.35
25 11 0.42
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.32
Consensus pattern (25 bp):
CATAACTTCATCATATAACATATAC
Found at i:3033299 original size:50 final size:50
Alignment explanation
Indices: 3033211--3033421 Score: 201
Period size: 50 Copynumber: 4.2 Consensus size: 50
3033201 ATGACCTTTA
* * * * * *
3033211 ATATTCGACCACATAGGTATGTACATATATGATGTTATATTGGATCTTGT
1 ATATTCGGCCATAAAGGTATGCACATATGTGATATTATATTGGATCTTGT
* * *
3033261 ATATTCGGCTATAAAGGTATGCACAAATGTGATATTATATTTGAAT-TTGT
1 ATATTCGGCCATAAAGGTATGCACATATGTGATATTATA-TTGGATCTTGT
* * * * *
3033311 ATATTCAGCCATATAA-GTAAGCACATATGTGATGTTATATTTGATCTTGC
1 ATATTCGGCCATA-AAGGTATGCACATATGTGATATTATATTGGATCTTGT
* * * ** * *
3033361 ATATTTGGCCACATAGGTATGCTTATATGTGATATTATATTTGATCTCGT
1 ATATTCGGCCATAAAGGTATGCACATATGTGATATTATATTGGATCTTGT
3033411 ATATTCGGCCA
1 ATATTCGGCCA
3033422 AATGAGTGAT
Statistics
Matches: 129, Mismatches: 28, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
49 5 0.04
50 117 0.91
51 7 0.05
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (50 bp):
ATATTCGGCCATAAAGGTATGCACATATGTGATATTATATTGGATCTTGT
Found at i:3033391 original size:100 final size:100
Alignment explanation
Indices: 3033233--3033421 Score: 254
Period size: 100 Copynumber: 1.9 Consensus size: 100
3033223 ATAGGTATGT
* * *
3033233 ACATATATGATGTTATATTGGATCTTGTATATTCGGCTATAAAGGTATGCACAAATGTGATATTA
1 ACATATATGATGTTATATTGGATCTTGCATATTCGGCCACAAAGGTATGCACAAATGTGATATTA
*
3033298 TATTTGAAT-TTGTATATTCAGCCATATAAGTAAGC
66 TATTTG-ATCTCGTATATTCAGCCATATAAGTAAGC
* * * * ** *
3033333 ACATATGTGATGTTATATTTGATCTTGCATATTTGGCCACATAGGTATGCTTATATGTGATATTA
1 ACATATATGATGTTATATTGGATCTTGCATATTCGGCCACAAAGGTATGCACAAATGTGATATTA
*
3033398 TATTTGATCTCGTATATTCGGCCA
66 TATTTGATCTCGTATATTCAGCCA
3033422 AATGAGTGAT
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
99 2 0.03
100 74 0.97
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (100 bp):
ACATATATGATGTTATATTGGATCTTGCATATTCGGCCACAAAGGTATGCACAAATGTGATATTA
TATTTGATCTCGTATATTCAGCCATATAAGTAAGC
Found at i:3037479 original size:43 final size:43
Alignment explanation
Indices: 3037432--3037519 Score: 99
Period size: 42 Copynumber: 2.0 Consensus size: 43
3037422 TCTTACATGC
3037432 AATCAAACATCGATGC-CATCGTCCCAGACAGGGCCTTACAC-TA
1 AATCAAACA-CGATGCTCAT-GTCCCAGACAGGGCCTTACACATA
* * * * *
3037475 AATCAGATACGATGCTGATGTCCCAGACATGGTCTTACACATA
1 AATCAAACACGATGCTCATGTCCCAGACAGGGCCTTACACATA
3037518 AA
1 AA
3037520 ATAGAAGTCG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
42 25 0.66
43 13 0.34
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (43 bp):
AATCAAACACGATGCTCATGTCCCAGACAGGGCCTTACACATA
Found at i:3039812 original size:17 final size:17
Alignment explanation
Indices: 3039790--3039825 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3039780 AATTAATATT
*
3039790 AAAATGAAAATAAAATG
1 AAAATGAAAAGAAAATG
*
3039807 AAAATGATAAGAAAATG
1 AAAATGAAAAGAAAATG
3039824 AA
1 AA
3039826 GGAAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (17 bp):
AAAATGAAAAGAAAATG
Found at i:3042005 original size:47 final size:47
Alignment explanation
Indices: 3041951--3042080 Score: 161
Period size: 47 Copynumber: 2.8 Consensus size: 47
3041941 GTGCGAATAA
* *
3041951 TACCTTGATTTGGCTATGGGCCATGGTATAAGTATTCAAAGATGAGT
1 TACCTTGATTTGGCTATGGGCCATGGTATAAGTACTCAAAGATAAGT
* * * *** *
3041998 TACCTTGATTTGGCTACGGGGCATGGTATAGGTACTCCGGGGTAAGT
1 TACCTTGATTTGGCTATGGGCCATGGTATAAGTACTCAAAGATAAGT
* *
3042045 TACCTTGATTTGGTTATGGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTATGGGCCATGGTATAAGTACT
3042081 TATCGATTGT
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (47 bp):
TACCTTGATTTGGCTATGGGCCATGGTATAAGTACTCAAAGATAAGT
Found at i:3042098 original size:47 final size:48
Alignment explanation
Indices: 3041948--3042099 Score: 129
Period size: 47 Copynumber: 3.2 Consensus size: 48
3041938 TGGGTGCGAA
* *
3041948 TAATACCTTGATTTGGCTATGGGCCATGGTATAAGTA-TTCAAAGATGAG
1 TAATACCTTGATTTGGCTATGGGCCATGGTATAGGTACTT-AACGAT-AG
* * * **
3041997 T--TACCTTGATTTGGCTACGGGGCATGGTATAGGTAC-T-CCG-GGG
1 TAATACCTTGATTTGGCTATGGGCCATGGTATAGGTACTTAACGATAG
* * *
3042040 TAAGTTACCTTGATTTGGTTATGGGCCATGGTATAGGTACTTATCGATTG
1 TAA--TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTTAACGATAG
3042090 TAAT-CCTTGA
1 TAATACCTTGA
3042100 GTATTTGATT
Statistics
Matches: 82, Mismatches: 13, Indels: 18
0.73 0.12 0.16
Matches are distributed among these distances:
43 2 0.02
45 1 0.01
47 70 0.85
48 2 0.02
49 3 0.04
50 4 0.05
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (48 bp):
TAATACCTTGATTTGGCTATGGGCCATGGTATAGGTACTTAACGATAG
Found at i:3043078 original size:21 final size:21
Alignment explanation
Indices: 3043038--3043079 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3043028 CCCCTCTAGA
*
3043038 TTTCAAATGGCCTAATTATAC
1 TTTCAAATGCCCTAATTATAC
3043059 TTTCAAATGACCCTAA-TATAC
1 TTTCAAATG-CCCTAATTATAC
3043080 CTCATTGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (21 bp):
TTTCAAATGCCCTAATTATAC
Found at i:3045826 original size:37 final size:37
Alignment explanation
Indices: 3045776--3045847 Score: 128
Period size: 37 Copynumber: 1.9 Consensus size: 37
3045766 TGGAGATACT
3045776 TTCAAGAATACTTTATCTCTGACCTAGG-ACTCAATCA
1 TTCAAGAATACTTTATCTCTGACCT-GGAACTCAATCA
3045813 TTCAAGAATACTTTATCTCTGACCTGGAACTCAAT
1 TTCAAGAATACTTTATCTCTGACCTGGAACTCAAT
3045848 TTCTTTTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
36 2 0.06
37 32 0.94
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (37 bp):
TTCAAGAATACTTTATCTCTGACCTGGAACTCAATCA
Found at i:3054357 original size:48 final size:48
Alignment explanation
Indices: 3054194--3054522 Score: 259
Period size: 49 Copynumber: 6.7 Consensus size: 48
3054184 CCTATTGTGA
* * *
3054194 GGTCACGTGTGTAGTACTAAGAGCAGGTTACTACGTGTACCAGATTA-TT-
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGT--CAGA-TAGTTG
* * * * * ** * * *
3054243 GGTCGCATGTGTACTTCTAAGTGCAGGCTACTATGCGTACCCGATAACTTC
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTA--CATGTCAGAT-AGTTG
* * *
3054294 GATCACGTGTGTAGTACTAAATGCAGGCTACTACATGTCAGATGGTTG
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTCAGATAGTTG
* * ** * * *
3054342 GGTCACGCGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTC
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTA--CATGTCAGAT-AGTTG
* * *
3054393 GATCACGTGTGTAGTACTAAATGCAGGCTACTACATGTCAGATGGTTG
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTCAGATAGTTG
* * * *
3054441 GGTCACGCGTGTAGTACTAAGTGCAAGCTACTACGTGTATCAGATAATT-
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATG--TCAGATAGTTG
*
3054490 GGTCACATGTGTAGTACTAAGTGCAGGCTACTA
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTA
3054523 TGCATACCAG
Statistics
Matches: 218, Mismatches: 52, Indels: 20
0.75 0.18 0.07
Matches are distributed among these distances:
48 67 0.31
49 73 0.33
50 16 0.07
51 62 0.28
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (48 bp):
GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTCAGATAGTTG
Found at i:3054381 original size:99 final size:99
Alignment explanation
Indices: 3054196--3054522 Score: 446
Period size: 99 Copynumber: 3.3 Consensus size: 99
3054186 TATTGTGAGG
* * ** * ** * *
3054196 TCACGTGTGTAGTACTAAGA-GCAGGTTACTACGTGTACCAGATTATT-GGTCGCATGTGTACTT
1 TCACGTGTGTAGTACTAA-ATGCAGGCTACTACATGT--CAGATGGTTGGGTCACGCGTGTAGTA
3054259 CTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGA
63 CTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGA
3054296 TCACGTGTGTAGTACTAAATGCAGGCTACTACATGTCAGATGGTTGGGTCACGCGTGTAGTACTA
1 TCACGTGTGTAGTACTAAATGCAGGCTACTACATGTCAGATGGTTGGGTCACGCGTGTAGTACTA
3054361 AGTGCAGGCTACTATGCGTACCCGATAACTTCGA
66 AGTGCAGGCTACTATGCGTACCCGATAACTTCGA
3054395 TCACGTGTGTAGTACTAAATGCAGGCTACTACATGTCAGATGGTTGGGTCACGCGTGTAGTACTA
1 TCACGTGTGTAGTACTAAATGCAGGCTACTACATGTCAGATGGTTGGGTCACGCGTGTAGTACTA
* * * * * *
3054460 AGTGCAAGCTACTACGTGTATCAGATAA-TT-GG
66 AGTGCAGGCTACTATGCGTACCCGATAACTTCGA
* *
3054492 TCACATGTGTAGTACTAAGTGCAGGCTACTA
1 TCACGTGTGTAGTACTAAATGCAGGCTACTA
3054523 TGCATACCAG
Statistics
Matches: 208, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
97 30 0.14
98 9 0.04
99 137 0.66
100 32 0.15
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (99 bp):
TCACGTGTGTAGTACTAAATGCAGGCTACTACATGTCAGATGGTTGGGTCACGCGTGTAGTACTA
AGTGCAGGCTACTATGCGTACCCGATAACTTCGA
Found at i:3060124 original size:42 final size:43
Alignment explanation
Indices: 3060034--3060136 Score: 120
Period size: 42 Copynumber: 2.4 Consensus size: 43
3060024 GTCCTGGACG
* ** *
3060034 TGGTCTTATATGTAATTCAATATCGATGCCTTTGTCCCAAATA
1 TGGTCTTATATGTAAATCAATATCGATGCCAATGTCCCAAACA
* * *
3060077 GGGTCTTACATG-AAATCAGATAT-GATGCCAATGTCCCAGACA
1 TGGTCTTATATGTAAATCA-ATATCGATGCCAATGTCCCAAACA
3060119 TGGTCTTATATGTAAATC
1 TGGTCTTATATGTAAATC
3060137 TCAATCGAGG
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 30 0.61
43 19 0.39
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (43 bp):
TGGTCTTATATGTAAATCAATATCGATGCCAATGTCCCAAACA
Found at i:3067438 original size:38 final size:38
Alignment explanation
Indices: 3067377--3067489 Score: 145
Period size: 38 Copynumber: 2.9 Consensus size: 38
3067367 ATTTGATGTG
*
3067377 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAAAA
1 TATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAAAA
**
3067417 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAA
* * * *
3067455 TATCCGGGATAAATCCCACAGGCCTAGTGCTGGTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTA
3067490 TTATATTCGG
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 53 0.80
39 5 0.08
40 8 0.12
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.26
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAAA
Found at i:3067490 original size:38 final size:38
Alignment explanation
Indices: 3067405--3067500 Score: 129
Period size: 38 Copynumber: 2.5 Consensus size: 38
3067395 CGCAGGCTTC
** * * * *
3067405 GTGCTGGTAAAATATCCGGGTTAAATCCCGCAGGCTTC
1 GTGCTGGTATTATATCCGGGATAAATCCCACAGGCCTA
3067443 GTGCTGGTATTATATCCGGGATAAATCCCACAGGCCTA
1 GTGCTGGTATTATATCCGGGATAAATCCCACAGGCCTA
*
3067481 GTGCTGGTATTATATTCGGG
1 GTGCTGGTATTATATCCGGG
3067501 CCTTCGTGCC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (38 bp):
GTGCTGGTATTATATCCGGGATAAATCCCACAGGCCTA
Found at i:3067570 original size:43 final size:43
Alignment explanation
Indices: 3067493--3067574 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
3067483 GCTGGTATTA
* **
3067493 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGATGTG
3067536 TATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGA
1 TATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGA
3067575 AATGATATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.12, C:0.26, G:0.34, T:0.28
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGATGTG
Found at i:3083602 original size:20 final size:20
Alignment explanation
Indices: 3083577--3083616 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3083567 GGATTAAACT
*
3083577 GAACTTATTCAGAAT-TTTCA
1 GAACTTAATCA-AATATTTCA
3083597 GAACTTAATCAAATATTTCA
1 GAACTTAATCAAATATTTCA
3083617 AAGCTGTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (20 bp):
GAACTTAATCAAATATTTCA
Found at i:3086642 original size:30 final size:30
Alignment explanation
Indices: 3086608--3086668 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3086598 TCCTTAACTC
3086608 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
3086638 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
3086668 A
1 A
3086669 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:3088232 original size:43 final size:43
Alignment explanation
Indices: 3088185--3088286 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 43
3088175 TCCCAGACGT
* ** *
3088185 GGTCTTATATGTAATTCA-ATATCGATGCCTTTGTCCCAAATAG
1 GGTCTTATATGTAAATCAGATA-CGATGCCAATGTCCCAAACAG
* * * *
3088228 GGTCTTACACG-AAATCAGATACGATGCCAATGTCCCAGACAT
1 GGTCTTATATGTAAATCAGATACGATGCCAATGTCCCAAACAG
3088270 GGTCTTATATGTAAATC
1 GGTCTTATATGTAAATC
3088287 TAAATCGAGG
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
42 30 0.64
43 17 0.36
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (43 bp):
GGTCTTATATGTAAATCAGATACGATGCCAATGTCCCAAACAG
Found at i:3088274 original size:42 final size:43
Alignment explanation
Indices: 3088174--3088323 Score: 110
Period size: 43 Copynumber: 3.5 Consensus size: 43
3088164 CAATGCCGAC
* * * * **
3088174 GTCCCAGACGTGGTCTTATATGTAATTCAATATCGATGCCTTT
1 GTCCCAGACATGGTCTTACACGTAAATCAATATCGATGCCAAT
* * *
3088217 GTCCCAAATAGGGTCTTACACG-AAATCAGATA-CGATGCCAAT
1 GTCCCAGACATGGTCTTACACGTAAATCA-ATATCGATGCCAAT
* * * *
3088259 GTCCCAGACATGGTCTTATATGTAAATCTAA-ATCGA-GGCATGT
1 GTCCCAGACATGGTCTTACACGTAAATC-AATATCGATGCCA-AT
* *
3088302 GTCCCACACAAGGTCTTACACG
1 GTCCCAGACATGGTCTTACACG
3088324 ATGTCGCAGA
Statistics
Matches: 82, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
42 34 0.41
43 47 0.57
44 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGTAAATCAATATCGATGCCAAT
Found at i:3100981 original size:47 final size:49
Alignment explanation
Indices: 3100857--3100985 Score: 147
Period size: 49 Copynumber: 2.7 Consensus size: 49
3100847 AGGGTATAAT
*
3100857 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTATTGAAATCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTATTGAAATCGAA
* * * **
3100906 GCCGACGCCATCTCCCAAACATGGTCTTACACTGACTCA-T-CCATC-AA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACT-ATTGAAATCGAA
** *
3100953 GTTGATGCCATGTCCTAGACATGGTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
3100986 AGCTCACAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
47 28 0.42
48 3 0.04
49 35 0.52
50 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (49 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTATTGAAATCGAA
Found at i:3105519 original size:23 final size:23
Alignment explanation
Indices: 3105467--3105564 Score: 80
Period size: 22 Copynumber: 4.3 Consensus size: 23
3105457 GCAGACAAAC
* *
3105467 GGTAAGCTCAATTA-AGCTGAACA
1 GGTAAGCTCCA-TAGAGCTGAAAA
*
3105490 -GTAAGCTCCATAGTGCTGAAAA
1 GGTAAGCTCCATAGAGCTGAAAA
* *
3105512 GGTAAGCTTCGA-AGAGCT-AAAC
1 GGTAAGC-TCCATAGAGCTGAAAA
*
3105534 GGTAAGCT-CATAAGAGCTGAAAC
1 GGTAAGCTCCAT-AGAGCTGAAAA
3105557 GGTAAGCT
1 GGTAAGCT
3105565 TGTACGAGCT
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
20 1 0.02
21 3 0.05
22 32 0.52
23 23 0.37
24 3 0.05
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (23 bp):
GGTAAGCTCCATAGAGCTGAAAA
Found at i:3105540 original size:22 final size:24
Alignment explanation
Indices: 3105504--3105565 Score: 85
Period size: 22 Copynumber: 2.7 Consensus size: 24
3105494 GCTCCATAGT
*
3105504 GCTGAAAAGGTAAGCTTC-GAAGA
1 GCTGAAACGGTAAGCTTCAGAAGA
*
3105527 GCT-AAACGGTAAGC-TCATAAGA
1 GCTGAAACGGTAAGCTTCAGAAGA
3105549 GCTGAAACGGTAAGCTT
1 GCTGAAACGGTAAGCTT
3105566 GTACGAGCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 2 0.06
22 17 0.50
23 14 0.41
24 1 0.03
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.19
Consensus pattern (24 bp):
GCTGAAACGGTAAGCTTCAGAAGA
Found at i:3105573 original size:23 final size:23
Alignment explanation
Indices: 3105504--3105575 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
3105494 GCTCCATAGT
*
3105504 GCTGAAAAGGTAAGCTTCG-AAGA
1 GCTGAAACGGTAAGCTT-GTAAGA
**
3105527 GCT-AAACGGTAAGCTCATAAGA
1 GCTGAAACGGTAAGCTTGTAAGA
*
3105549 GCTGAAACGGTAAGCTTGTACGA
1 GCTGAAACGGTAAGCTTGTAAGA
3105572 GCTG
1 GCTG
3105576 TGGTGAGTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 18 0.44
23 23 0.56
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (23 bp):
GCTGAAACGGTAAGCTTGTAAGA
Found at i:3112724 original size:129 final size:129
Alignment explanation
Indices: 3112492--3112745 Score: 280
Period size: 129 Copynumber: 2.0 Consensus size: 129
3112482 TCATATAGGC
** * * *
3112492 ATGTGACCCACTCACACAGCCATATGGCCTATCTTATACGAGCATGGCTCTTCTACACGGTTTAC
1 ATGTGACCCACTCACACAGCCATATGGCCTATCACACACGAGCATGGCTCTTCTAAAAGGTTTAC
**
3112557 CAACATAGTTGTGTGGTTAATCCCACACAAGCTAAGCTTTCA-CACACGGCCAAGGGACACGGGA
66 CAACATAGCAGTGTGGTTAATCCCACACAAGCTAAGCTTT-AGCACACGGCCAAGGGACACGGGA
* * * *
3112621 ATGTGACCCACTCACACGGCCATGTGGCCTATCACACATGAGCATGGCTCTTGTAAAAGGTTTAT
1 ATGTGACCCACTCACACAGCCATATGGCCTATCACACACGAGCATGGCTCTTCTAAAAGGTTTA-
* * * *** * * *
3112686 CGATACA-A-CAGTGTGGTTAATTCCTCATGGGCTGAGCTTTAGTACATGGCCAAGGGACAC
65 CCA-ACATAGCAGTGTGGTTAATCCCACACAAGCTAAGCTTTAGCACACGGCCAAGGGACAC
3112746 AGTCATGTAA
Statistics
Matches: 102, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
128 1 0.01
129 95 0.93
130 3 0.03
131 3 0.03
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (129 bp):
ATGTGACCCACTCACACAGCCATATGGCCTATCACACACGAGCATGGCTCTTCTAAAAGGTTTAC
CAACATAGCAGTGTGGTTAATCCCACACAAGCTAAGCTTTAGCACACGGCCAAGGGACACGGGA
Found at i:3116398 original size:24 final size:23
Alignment explanation
Indices: 3116354--3116398 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
3116344 TACATCAGTG
3116354 AAAGATTTATTGATTAGAAGCGT
1 AAAGATTTATTGATTAGAAGCGT
*
3116377 AAAGAGTTTCTTGAATTA-AAGC
1 AAAGA-TTTATTG-ATTAGAAGC
3116399 AGGGGAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 10 0.53
25 4 0.21
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (23 bp):
AAAGATTTATTGATTAGAAGCGT
Found at i:3120791 original size:21 final size:21
Alignment explanation
Indices: 3120766--3120807 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3120756 GAGATCGTTT
3120766 AGTTGAGACCGAGTTCACTTA
1 AGTTGAGACCGAGTTCACTTA
*
3120787 AGTTGAGTCCGAGTTCACTTA
1 AGTTGAGACCGAGTTCACTTA
3120808 TGGGCGGGTT
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:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (21 bp):
AGTTGAGACCGAGTTCACTTA
Found at i:3124609 original size:29 final size:29
Alignment explanation
Indices: 3124570--3124648 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
3124560 CTTAATAATC
*
3124570 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
3124600 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
3124629 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
3124649 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:3133754 original size:29 final size:29
Alignment explanation
Indices: 3133715--3133793 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
3133705 CTTAATAATC
*
3133715 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
3133745 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
3133774 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
3133794 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:3135910 original size:13 final size:13
Alignment explanation
Indices: 3135892--3135917 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3135882 CAGAAAACAT
3135892 GAAAAATTTTGAA
1 GAAAAATTTTGAA
3135905 GAAAAATTTTGAA
1 GAAAAATTTTGAA
3135918 AATAAGGGTC
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:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
GAAAAATTTTGAA
Found at i:3151322 original size:25 final size:25
Alignment explanation
Indices: 3151288--3151337 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3151278 CTTATAGATT
3151288 GTCTCAAGGCCGAATGCATTCTTAC
1 GTCTCAAGGCCGAATGCATTCTTAC
3151313 GTCTCAAGGCCGAATGCATTCTTAC
1 GTCTCAAGGCCGAATGCATTCTTAC
3151338 TTCCAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (25 bp):
GTCTCAAGGCCGAATGCATTCTTAC
Found at i:3155542 original size:132 final size:129
Alignment explanation
Indices: 3155172--3155677 Score: 566
Period size: 129 Copynumber: 3.9 Consensus size: 129
3155162 ATGAAATTCT
*
3155172 AAAGGAATATTCGATTATTTTGAACAAAC-AGGAGATTGCAACCCAGCACGATAGGGCACGATTC
1 AAAGGAATATTCGATTATTTTGAACAAACGA-GAAATTGCAACCCAGCACGATAGGGCACGATTC
* * * * *** * *
3155236 CCGAATTGCTAAACACCTAGTATTACCTTCGTTTTGGGGAGTTTTTAAAAGCATGAGTGAAACCC
65 CCGAATTGCCAAACACCGAATATTGCCTTCGTTTTAAAGAATTTTTAAAAGCATGAATGAAACCC
* * **
3155301 AAAGGAATATTCGATTGTTTTGAACAAACAAGAAATCACAACCCAGCACGATAGGGCACGATTCC
1 AAAGGAATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAGCACGATAGGGCACGATTCC
* * *
3155366 CGACTTGCCAAACACCGAGTATTGCCTTCATTTTAAAGAATTTTTAAAAGCATGAAT-AAACAAC
66 CGAATTGCCAAACACCGAATATTGCCTTCGTTTTAAAGAATTTTTAAAAGCATGAATGAAAC--C
3155430 C
129 C
* * * * * *
3155431 AGAGGAATATTCGATTGTTTTGAAAAAACGAGAGATTGCAACCCAAACACGATAGGGCACTATTC
1 AAAGGAATATTCGATTATTTTGAACAAACGAGAAATTGCAACCC-AGCACGATAGGGCACGATT-
* * * * *
3155496 CCCGAATTGCCAATCATCGAATATTTCCTTCGTTTTAAAGAGTTTTTAGAAAACATGAATGAAAT
64 CCCGAATTGCCAAACACCGAATATTGCCTTCGTTTTAAAGAATTTTTA-AAAGCATGAATGAAA-
* *
3155561 TCT
127 CCC
* * * *
3155564 AAAGGGACATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGTTAGGGCACGATTCC
1 AAAGGAATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAGCACGATAGGGCACGATTCC
* *** * *
3155629 GTGAATTGCCAAATGTCGAACATCGCCTTCGTTTTAAAGAATTTTTAAA
66 -CGAATTGCCAAACACCGAATATTGCCTTCGTTTTAAAGAATTTTTAAA
3155678 TGAATAATCA
Statistics
Matches: 318, Mismatches: 50, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
128 4 0.01
129 106 0.33
130 41 0.13
131 21 0.07
132 95 0.30
133 48 0.15
134 3 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (129 bp):
AAAGGAATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAGCACGATAGGGCACGATTCC
CGAATTGCCAAACACCGAATATTGCCTTCGTTTTAAAGAATTTTTAAAAGCATGAATGAAACCC
Done.