Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 122 of 145
Found at i:40667042 original size:15 final size:15
Alignment explanation
Indices: 40667022--40667060 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
40667012 TTTTCTCACA
*
40667022 ACCACCGCAGTATGT
1 ACCACCGCAGTATGC
40667037 ACCACCGCAGTATGC
1 ACCACCGCAGTATGC
40667052 ACCACCGCA
1 ACCACCGCA
40667061 CGTCCCTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.28, C:0.41, G:0.18, T:0.13
Consensus pattern (15 bp):
ACCACCGCAGTATGC
Found at i:40670550 original size:45 final size:48
Alignment explanation
Indices: 40670487--40670588 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 48
40670477 AAATTTATCT
*
40670487 TTTTCTCTAAAAAACCCTAAATTAAA-CC-CCA-AATCCATTCTTCTCC
1 TTTTCT-TAAAAAACCCTAAAATAAACCCTCCATAATCCATTCTTCTCC
* * *
40670533 TTTTCTTAAAAATCCCTAAAATAAACCCTCCATAGTCCATTCTTCTTC
1 TTTTCTTAAAAAACCCTAAAATAAACCCTCCATAATCCATTCTTCTCC
40670581 TTCTTCTT
1 TT-TTCTT
40670589 CTTCTTCTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
45 17 0.35
46 8 0.17
47 3 0.06
48 15 0.31
49 5 0.10
ACGTcount: A:0.30, C:0.30, G:0.01, T:0.38
Consensus pattern (48 bp):
TTTTCTTAAAAAACCCTAAAATAAACCCTCCATAATCCATTCTTCTCC
Found at i:40670580 original size:3 final size:3
Alignment explanation
Indices: 40670572--40670597 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40670562 CCATAGTCCA
40670572 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
40670598 TTGCATCAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:40671788 original size:27 final size:27
Alignment explanation
Indices: 40671758--40671815 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
40671748 CAACCCTTTG
40671758 GGAATTGGGACTACCAACGACCCTCTA
1 GGAATTGGGACTACCAACGACCCTCTA
*
40671785 GGAATTGGGACTACCAACGACCCTCTG
1 GGAATTGGGACTACCAACGACCCTCTA
40671812 GGAA
1 GGAA
40671816 CTAACAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.17
Consensus pattern (27 bp):
GGAATTGGGACTACCAACGACCCTCTA
Found at i:40672782 original size:9 final size:9
Alignment explanation
Indices: 40672768--40672798 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40672758 GTTAAACGAA
40672768 TCGAGTTAT
1 TCGAGTTAT
*
40672777 TCGAGTTAA
1 TCGAGTTAT
40672786 TCGAGTTAT
1 TCGAGTTAT
40672795 TCGA
1 TCGA
40672799 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:40672877 original size:18 final size:18
Alignment explanation
Indices: 40672851--40672885 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40672841 TGAGTTTTTG
*
40672851 AATTTGAATAACTCGAAC
1 AATTCGAATAACTCGAAC
*
40672869 AATTCGAATAATTCGAA
1 AATTCGAATAACTCGAA
40672886 TATCAAACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (18 bp):
AATTCGAATAACTCGAAC
Found at i:40673277 original size:17 final size:18
Alignment explanation
Indices: 40673238--40673293 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
40673228 ACTCCCCTTA
40673238 TTTACTTTCCCTC-AAAC-T
1 TTTA-TTTCCC-CAAAACTT
40673256 TTTA-TTCCCCAAAACTT
1 TTTATTTCCCCAAAACTT
*
40673273 TTTATTTTCCCCTAAACTT
1 TTTA-TTTCCCCAAAACTT
40673292 TT
1 TT
40673294 ACTTCTCACC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
15 1 0.03
16 9 0.27
17 5 0.15
18 4 0.12
19 14 0.42
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTATTTCCCCAAAACTT
Found at i:40680032 original size:50 final size:50
Alignment explanation
Indices: 40679923--40680164 Score: 231
Period size: 50 Copynumber: 4.7 Consensus size: 50
40679913 TGGGTAAATA
* * *
40679923 TCCCATGTAAGACCATGTATGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAAG
* *
40679979 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGATG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAG
* * * *
40680029 TCCC-TCGTAAGACCATGTCTGGGATATGGCATGGGCACCGATATGAGAAC
1 TCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAG
* * * * * *
40680079 TCCCATGTAAGACCATATCTGGGATATGGCATTGG-A-AGTACAAGA-AACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAA-G
*
40680128 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
40680165 TGTTATAATC
Statistics
Matches: 162, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
48 3 0.02
49 38 0.23
50 81 0.50
51 1 0.01
53 3 0.02
55 1 0.01
56 35 0.22
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAG
Found at i:40682913 original size:19 final size:19
Alignment explanation
Indices: 40682889--40682927 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
40682879 ATTAACTGAT
40682889 AAAGGTTTTGTAAGGCCTA
1 AAAGGTTTTGTAAGGCCTA
40682908 AAAGGTTTTGTAAGGCCTA
1 AAAGGTTTTGTAAGGCCTA
40682927 A
1 A
40682928 TTGTTCTCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (19 bp):
AAAGGTTTTGTAAGGCCTA
Found at i:40686468 original size:50 final size:50
Alignment explanation
Indices: 40686357--40686603 Score: 232
Period size: 50 Copynumber: 4.8 Consensus size: 50
40686347 ATTTGGGTAA
*
40686357 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
* *
40686413 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
40686463 AGAGGTCTCC-TGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGATC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * * * * *
40686513 AGA-ACTCCCACGTAAGACCATATCTAGGATATGACTTTGGCA--GTACAAG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* * *
40686562 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
40686604 TGTTATTATC
Statistics
Matches: 164, Mismatches: 22, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
48 1 0.01
49 39 0.24
50 78 0.48
51 2 0.01
53 3 0.02
55 1 0.01
56 40 0.24
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:40691835 original size:32 final size:32
Alignment explanation
Indices: 40691789--40691850 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
40691779 ATTAATCGGT
* *
40691789 ATGAGTTATCAAATTGAATTAATTAATTTATC
1 ATGAGTTATCAAATTCAAGTAATTAATTTATC
*
40691821 ATGAGTTATTAAATTCAAGTAATTAATTTA
1 ATGAGTTATCAAATTCAAGTAATTAATTTA
40691851 AAAGTTTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.44
Consensus pattern (32 bp):
ATGAGTTATCAAATTCAAGTAATTAATTTATC
Found at i:40693396 original size:14 final size:14
Alignment explanation
Indices: 40693379--40693406 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40693369 GTTTAAAATT
40693379 TTTATTTAATTAAA
1 TTTATTTAATTAAA
40693393 TTTATTTAATTAAA
1 TTTATTTAATTAAA
40693407 AATCTATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATTTAATTAAA
Found at i:40694178 original size:29 final size:29
Alignment explanation
Indices: 40694141--40694197 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
40694131 CCAAAATTAG
*
40694141 CCTATTCCGATAAATTTTG-TAAAAATCGA
1 CCTAATCCGAT-AATTTTGTTAAAAATCGA
*
40694170 CCTAATCCGGTAATTTTGTTTAAAAATC
1 CCTAATCCGATAATTTTG-TTAAAAATC
40694198 AACATATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.29
29 9 0.38
30 8 0.33
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (29 bp):
CCTAATCCGATAATTTTGTTAAAAATCGA
Found at i:40701243 original size:34 final size:35
Alignment explanation
Indices: 40701171--40701245 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 35
40701161 AACAATACGG
* * *
40701171 TAGC-AATCAATATGCTTATAACAGTTTGATACAG
1 TAGCAAATCAATATGCTTATAACAGATTAATACAA
*
40701205 TAGCAAAT-AATATGCTTATAACAGATTAATTCAA
1 TAGCAAATCAATATGCTTATAACAGATTAATACAA
40701239 TAGCAAA
1 TAGCAAA
40701246 AGACGTGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
34 33 0.92
35 3 0.08
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (35 bp):
TAGCAAATCAATATGCTTATAACAGATTAATACAA
Found at i:40702625 original size:9 final size:9
Alignment explanation
Indices: 40702613--40702786 Score: 70
Period size: 9 Copynumber: 18.3 Consensus size: 9
40702603 GTTTTATGAT
40702613 TTTTTATAA
1 TTTTTATAA
40702622 TTTTTATAA
1 TTTTTATAA
*
40702631 -GTTTAT-A
1 TTTTTATAA
40702638 TTAATTT-TAA
1 TT--TTTATAA
* *
40702648 TTTTTTTAT
1 TTTTTATAA
40702657 TTTTTATAA
1 TTTTTATAA
40702666 TTTTTATAGAA
1 TTTTTAT--AA
* *
40702677 TTTTAATACG
1 TTTTTATA-A
40702687 TTTTTATAAA
1 TTTTTAT-AA
* *
40702697 ATTTTAAATA
1 TTTTTATA-A
*
40702707 TATTTTATTA
1 T-TTTTATAA
* *
40702717 GTTTTATTA
1 TTTTTATAA
*
40702726 TTTTTTTAA
1 TTTTTATAA
*
40702735 TTTATTA-GA
1 TTT-TTATAA
40702744 TGTTTTAT-A
1 T-TTTTATAA
*
40702753 TTTTTGGTAA
1 TTTTT-ATAA
40702763 TTTTTGATAAA
1 TTTTT-AT-AA
40702774 TTTTTTATAA
1 -TTTTTATAA
40702784 TTT
1 TTT
40702787 ATGTCAATTT
Statistics
Matches: 125, Mismatches: 22, Indels: 36
0.68 0.12 0.20
Matches are distributed among these distances:
7 1 0.01
8 12 0.10
9 56 0.45
10 33 0.26
11 18 0.14
12 5 0.04
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:40702661 original size:35 final size:36
Alignment explanation
Indices: 40702611--40702683 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 36
40702601 AAGTTTTATG
*
40702611 ATTTTTTATAATTTTTATAAGTTTATAT-TAATTTTA
1 ATTTTTTATAATTTTTATAA-TTTATATAGAATTTTA
* *
40702647 ATTTTTT-TATTTTTTATAATTTTTATAGAATTTTA
1 ATTTTTTATAATTTTTATAATTTATATAGAATTTTA
40702682 AT
1 AT
40702684 ACGTTTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 6 0.18
35 20 0.61
36 7 0.21
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (36 bp):
ATTTTTTATAATTTTTATAATTTATATAGAATTTTA
Found at i:40702751 original size:25 final size:25
Alignment explanation
Indices: 40702710--40702757 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
40702700 TTAAATATAT
* *
40702710 TTTATTAGTTTTATTATTTTTTTAA
1 TTTATTAGTGTTATTATATTTTTAA
40702735 TTTATTAGATGTT-TTATATTTTT
1 TTTATTAG-TGTTATTATATTTTT
40702758 GGTAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (25 bp):
TTTATTAGTGTTATTATATTTTTAA
Found at i:40702814 original size:10 final size:9
Alignment explanation
Indices: 40702798--40702828 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
40702788 TGTCAATTTC
40702798 ATATTTTTA
1 ATATTTTTA
40702807 ATATTTTTA
1 ATATTTTTA
40702816 ATACTTTTTA
1 ATA-TTTTTA
40702826 ATA
1 ATA
40702829 ACTTTTTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (9 bp):
ATATTTTTA
Found at i:40706248 original size:20 final size:20
Alignment explanation
Indices: 40706223--40706262 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40706213 CCCTCATAAA
40706223 GGCACCAACAGTAAGATATT
1 GGCACCAACAGTAAGATATT
40706243 GGCACCAACAGTAAGATATT
1 GGCACCAACAGTAAGATATT
40706263 ATTTCAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
GGCACCAACAGTAAGATATT
Found at i:40710852 original size:51 final size:51
Alignment explanation
Indices: 40710776--40710876 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
40710766 ATGTCTTCAT
*
40710776 CCTGATCTGTTGAAGTTTTTTCTTCATCAGATTGTTTCTTAAATAATTCTA
1 CCTGATCTGCTGAAGTTTTTTCTTCATCAGATTGTTTCTTAAATAATTCTA
40710827 CCTGATCTGCTGAAGTTTTTTCTTCATCAGATTGTTTCTTAAATAATTCT
1 CCTGATCTGCTGAAGTTTTTTCTTCATCAGATTGTTTCTTAAATAATTCT
40710877 GTNNNNNNNN
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.49
Consensus pattern (51 bp):
CCTGATCTGCTGAAGTTTTTTCTTCATCAGATTGTTTCTTAAATAATTCTA
Found at i:40716750 original size:165 final size:165
Alignment explanation
Indices: 40716465--40716794 Score: 561
Period size: 165 Copynumber: 2.0 Consensus size: 165
40716455 TTTAGTTTTT
* *
40716465 TCTCTTGTAAAGCCTTTCCGTTTTGTTAATAAAAGAGTCTATATTCCCTTCCGCTCATACTCAAA
1 TCTCTTGTAAAGCCTTTCCGTTTTGTTAAAAAAAGAGTCTATATTCCCTTCCACTCATACTCAAA
* * * *
40716530 GATACCCTCTACTCTCCCTTCCCCCTCACTTTTGGTAACAGAGTTGCCGGTGTAACGAGTTTCTG
66 GATACCCTCTACTCTCCCTTCCCCCTCACTTTTGGTAACAGAGGTACCAGTGTAACGACTTTCTG
40716595 GAGAAATAATATCGTAATATTCATTGTAAGATTTC
131 GAGAAATAATATCGTAATATTCATTGTAAGATTTC
*
40716630 TCTCTTGTAAAGCCTTTCCTTTTTGTTAAAAAAAGAGTCTATATTCCCTTCCACTCATACTCAAA
1 TCTCTTGTAAAGCCTTTCCGTTTTGTTAAAAAAAGAGTCTATATTCCCTTCCACTCATACTCAAA
* **
40716695 GATACCCTCTACTCTCCCTTCCCCCTCGCTTTTGGTATTAGAGGTACCAGTGTAACGACTTTCTG
66 GATACCCTCTACTCTCCCTTCCCCCTCACTTTTGGTAACAGAGGTACCAGTGTAACGACTTTCTG
*
40716760 GAGAAATAATATCGTAATATTCATTGTAAGTTTTC
131 GAGAAATAATATCGTAATATTCATTGTAAGATTTC
40716795 ATCTTTGATT
Statistics
Matches: 154, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
165 154 1.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (165 bp):
TCTCTTGTAAAGCCTTTCCGTTTTGTTAAAAAAAGAGTCTATATTCCCTTCCACTCATACTCAAA
GATACCCTCTACTCTCCCTTCCCCCTCACTTTTGGTAACAGAGGTACCAGTGTAACGACTTTCTG
GAGAAATAATATCGTAATATTCATTGTAAGATTTC
Found at i:40721007 original size:9 final size:9
Alignment explanation
Indices: 40720987--40721021 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
40720977 TCGTCTATGT
40720987 TAAAAAATTA
1 TAAAAAA-TA
40720997 TAAAAAATA
1 TAAAAAATA
*
40721006 TAAAAAATG
1 TAAAAAATA
40721015 TAAAAAA
1 TAAAAAA
40721022 GATGATAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 17 0.71
10 7 0.29
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (9 bp):
TAAAAAATA
Found at i:40729488 original size:17 final size:16
Alignment explanation
Indices: 40729454--40729499 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
40729444 TATAGACTCT
40729454 AGAAATGAAAACAAGGTC
1 AGAAATG-AAA-AAGGTC
*
40729472 AGTAATGTAAAAAGGTC
1 AGAAATG-AAAAAGGTC
40729489 AGAAATGAAAA
1 AGAAATGAAAA
40729500 CTTGTAAGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 4 0.16
17 12 0.48
18 9 0.36
ACGTcount: A:0.57, C:0.07, G:0.22, T:0.15
Consensus pattern (16 bp):
AGAAATGAAAAAGGTC
Found at i:40729726 original size:32 final size:33
Alignment explanation
Indices: 40729685--40729750 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
40729675 AGATGTAAAT
40729685 TTAGGTCCTTTATATTACGGTAATA-CAAGATC
1 TTAGGTCCTTTATATTACGGTAATAGCAAGATC
40729717 TTAGGTCCTTTATATTACGGTAATAGTCAAGATC
1 TTAGGTCCTTTATATTACGGTAATAG-CAAGATC
40729751 ATATTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 25 0.78
34 7 0.22
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (33 bp):
TTAGGTCCTTTATATTACGGTAATAGCAAGATC
Found at i:40731219 original size:131 final size:132
Alignment explanation
Indices: 40730985--40731248 Score: 521
Period size: 131 Copynumber: 2.0 Consensus size: 132
40730975 ATATAGACTC
40730985 TTTTATTAACAAAAAGGAAAGGCTTTACAAGAGAGAAAACTAAAAAGTAAAACTATTAGGTAATT
1 TTTTATTAACAAAAAGGAAAGGCTTTACAAGAGAGAAAACTAAAAAGTAAAACTATTAGGTAATT
40731050 ACAAGATGTCTATACAATTGATCTTTCCTCTCTATTTATAGAGGAGATTAAAAATT-TATACAAT
66 ACAAGATGTCTATACAATTGATCTTTCCTCTCTATTTATAGAGGAGATTAAAAATTCTATACAAT
40731114 TG
131 TG
40731116 TTTTATTAACAAAAAGGAAAGGCTTTACAAGAGAGAAAACTAAAAAGTAAAACTATTAGGTAATT
1 TTTTATTAACAAAAAGGAAAGGCTTTACAAGAGAGAAAACTAAAAAGTAAAACTATTAGGTAATT
40731181 ACAAGATGTCTATACAATTGATCTTTCCTCTCTATTTATAGAGGAGATTAAAAATTCTATACAAT
66 ACAAGATGTCTATACAATTGATCTTTCCTCTCTATTTATAGAGGAGATTAAAAATTCTATACAAT
40731246 TG
131 TG
40731248 T
1 T
40731249 CTTTTGAATC
Statistics
Matches: 132, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
131 121 0.92
132 11 0.08
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (132 bp):
TTTTATTAACAAAAAGGAAAGGCTTTACAAGAGAGAAAACTAAAAAGTAAAACTATTAGGTAATT
ACAAGATGTCTATACAATTGATCTTTCCTCTCTATTTATAGAGGAGATTAAAAATTCTATACAAT
TG
Found at i:40740947 original size:11 final size:11
Alignment explanation
Indices: 40740916--40740956 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
40740906 CGTTAACAAC
40740916 AAAATAGTAGT
1 AAAATAGTAGT
*
40740927 AACATAGTAGT
1 AAAATAGTAGT
* *
40740938 AAAATGGTAGC
1 AAAATAGTAGT
40740949 AAAATAGT
1 AAAATAGT
40740957 GGGAAAACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.24
Consensus pattern (11 bp):
AAAATAGTAGT
Found at i:40749494 original size:25 final size:25
Alignment explanation
Indices: 40749457--40749507 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
40749447 ATAAATACTA
* *
40749457 AAAAAATCGCAATAAAAAATTAATT
1 AAAAAACCACAATAAAAAATTAATT
*
40749482 AAAAAACCACAATACAAAATTAATT
1 AAAAAACCACAATAAAAAATTAATT
40749507 A
1 A
40749508 GGCTAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.65, C:0.12, G:0.02, T:0.22
Consensus pattern (25 bp):
AAAAAACCACAATAAAAAATTAATT
Found at i:40751615 original size:19 final size:19
Alignment explanation
Indices: 40751557--40751615 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
40751547 GAAAAGGAAA
40751557 AATATGTATAATTTAAATG
1 AATATGTATAATTTAAATG
* * ** **
40751576 AACA--AATTTTTTAAAAA
1 AATATGTATAATTTAAATG
40751593 AATATGTATAATTTAAATG
1 AATATGTATAATTTAAATG
40751612 AATA
1 AATA
40751616 ATAATTCAAA
Statistics
Matches: 26, Mismatches: 12, Indels: 4
0.62 0.29 0.10
Matches are distributed among these distances:
17 11 0.42
19 15 0.58
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.39
Consensus pattern (19 bp):
AATATGTATAATTTAAATG
Found at i:40760503 original size:30 final size:29
Alignment explanation
Indices: 40760449--40760505 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
40760439 GAGGCCTATC
40760449 TCATTTTCTAAACGGGTCTTTTTTTTTTT
1 TCATTTTCTAAACGGGTCTTTTTTTTTTT
*
40760478 TCATTTTTTAAACGGGTCTTTTTTTTTT
1 TCATTTTCTAAACGGGTCTTTTTTTTTT
40760506 GCCTAAGCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.14, C:0.12, G:0.11, T:0.63
Consensus pattern (29 bp):
TCATTTTCTAAACGGGTCTTTTTTTTTTT
Found at i:40784010 original size:24 final size:24
Alignment explanation
Indices: 40783983--40784031 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
40783973 TAAATACGAA
40783983 AAAAATTGCAATAAAAAATTAATT
1 AAAAATTGCAATAAAAAATTAATT
* *
40784007 AAAAATTGTAATACAAAATTAATT
1 AAAAATTGCAATAAAAAATTAATT
40784031 A
1 A
40784032 GGCTAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (24 bp):
AAAAATTGCAATAAAAAATTAATT
Found at i:40792422 original size:221 final size:223
Alignment explanation
Indices: 40792025--40792483 Score: 697
Period size: 221 Copynumber: 2.1 Consensus size: 223
40792015 AATTTTGTTA
* * * *
40792025 TTGGTCTCATGATATATGTAAGTTATAGGTTTAATCTATACTTTTTGAAAATTTAAATTTCAATT
1 TTGGT-TCGTGATTTATGTAAGTTATAGGTTTAATCTATACTTTTTGAAAATCTAAATTTCAATC
* * ** * * *
40792090 CTAATTGAAACGATAGTTGTTAAATCTATTTGTGACATGTTTATGGGTATTATGTGAAAATAACA
65 CCAATTCAAACGATAGTCATTAAATCCATTTGTGACATGTTTACGAGTATTATGTGAAAATAACA
*
40792155 AATTGACATGATATTATACTTGTGATAATCTATTTGTCACATACAATTTTAGAAATAGCAAAATA
130 AATTGACATGACATTATACTTGTGATAATCTATTTGTCACATACAATTTTAGAAATAGCAAAATA
* *
40792220 TAAC-T-TAATGAATGTAATGTCTACCAT
195 TAACTTATAATAAATGTAACGTCTACCAT
*
40792247 TTGGTTCGTGATTTATGTAAGTTATAGGTTTAATCTATACTTTTTGAATATCTAAATTTCAATCC
1 TTGGTTCGTGATTTATGTAAGTTATAGGTTTAATCTATACTTTTTGAAAATCTAAATTTCAATCC
* * * * *
40792312 CGATTCAAAGGGTAGTCATTAAATCCATTTGTGACATGTTTACGAGTATTGTGTGAAAATAATAA
66 CAATTCAAACGATAGTCATTAAATCCATTTGTGACATGTTTACGAGTATTATGTGAAAATAACAA
40792377 ATTGACATGACATTATACTTGTGATAATCTATTTGTCACATACAATTTTAGAAATAGCAAAATAT
131 ATTGACATGACATTATACTTGTGATAATCTATTTGTCACATACAATTTTAGAAATAGCAAAATAT
*
40792442 AACTTAATAATAAATGTAACGTTTACCAT
196 AACTT-ATAATAAATGTAACGTCTACCAT
40792471 TTGGTTCGTGATT
1 TTGGTTCGTGATT
40792484 GAAATTTAAA
Statistics
Matches: 213, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
221 175 0.82
222 6 0.03
224 32 0.15
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.40
Consensus pattern (223 bp):
TTGGTTCGTGATTTATGTAAGTTATAGGTTTAATCTATACTTTTTGAAAATCTAAATTTCAATCC
CAATTCAAACGATAGTCATTAAATCCATTTGTGACATGTTTACGAGTATTATGTGAAAATAACAA
ATTGACATGACATTATACTTGTGATAATCTATTTGTCACATACAATTTTAGAAATAGCAAAATAT
AACTTATAATAAATGTAACGTCTACCAT
Found at i:40798769 original size:25 final size:25
Alignment explanation
Indices: 40798731--40798781 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
40798721 ATAAATACGA
*
40798731 AAAAAATTGCAATAAAAAATTAATT
1 AAAAAATCGCAATAAAAAATTAATT
* *
40798756 AAAAAATCGTAATACAAAATTAATT
1 AAAAAATCGCAATAAAAAATTAATT
40798781 A
1 A
40798782 GGCTAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (25 bp):
AAAAAATCGCAATAAAAAATTAATT
Found at i:40801661 original size:19 final size:19
Alignment explanation
Indices: 40801604--40801661 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
40801594 GAAAAGGAAA
40801604 AATATGTATAATTTAAATG
1 AATATGTATAATTTAAATG
* * * **
40801623 AACA--AAT-TTTTAAAAA
1 AATATGTATAATTTAAATG
40801639 AATATGTATAATTTAAATG
1 AATATGTATAATTTAAATG
40801658 AATA
1 AATA
40801662 ATAATTCAAA
Statistics
Matches: 26, Mismatches: 10, Indels: 6
0.62 0.24 0.14
Matches are distributed among these distances:
16 9 0.35
17 2 0.08
18 2 0.08
19 13 0.50
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (19 bp):
AATATGTATAATTTAAATG
Found at i:40807476 original size:207 final size:208
Alignment explanation
Indices: 40807109--40807524 Score: 825
Period size: 207 Copynumber: 2.0 Consensus size: 208
40807099 TTATCTTAAT
40807109 ATTAAATTTAATTTAATGTTTATCTTGTAGATAAATTTTCTATTAATTAAATAAAATTTAATCTA
1 ATTAAATTTAATTTAATGTTTATCTTGTAGATAAATTTTCTATTAATTAAATAAAATTTAATCTA
40807174 ATATTTATCAAAATAAATATTAGATTAAATTTAGTATTAAAATGATTAAGTTTAATCATAGTTGA
66 ATATTTATCAAAATAAATATTAGATTAAATTTAGTATTAAAATGATTAAGTTTAATCATAGTTGA
40807239 ACTCTCTAAACTCCCCCTATATAAAGAGAGCTTTTGGTCATTATTTACACACACTTGAATTTAAG
131 ACTCTCTAAACTCCCCCTATATAAAGAGAGCTTTTGGTCATTATTTACACACACTTGAATTTAAG
40807304 AGAAAGTTGTAGA
196 AGAAAGTTGTAGA
40807317 ATTAAATTTAA-TTAATGTTTATCTTGTAGATAAATTTTCTATTAATTAAATAAAATTTAATCTA
1 ATTAAATTTAATTTAATGTTTATCTTGTAGATAAATTTTCTATTAATTAAATAAAATTTAATCTA
40807381 ATATTTATCAAAATAAATATTAGATTAAATTTAGTATTAAAATGATTAAGTTTAATCATAGTTGA
66 ATATTTATCAAAATAAATATTAGATTAAATTTAGTATTAAAATGATTAAGTTTAATCATAGTTGA
40807446 ACTCTCTAAACTCCCCCTATATAAAGAGAGCTTTTGGTCATTATTTACACACACTTGAATTTAAG
131 ACTCTCTAAACTCCCCCTATATAAAGAGAGCTTTTGGTCATTATTTACACACACTTGAATTTAAG
40807511 AGAAAGTTGTAGA
196 AGAAAGTTGTAGA
40807524 A
1 A
40807525 AGAAATTTTT
Statistics
Matches: 208, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
207 197 0.95
208 11 0.05
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.40
Consensus pattern (208 bp):
ATTAAATTTAATTTAATGTTTATCTTGTAGATAAATTTTCTATTAATTAAATAAAATTTAATCTA
ATATTTATCAAAATAAATATTAGATTAAATTTAGTATTAAAATGATTAAGTTTAATCATAGTTGA
ACTCTCTAAACTCCCCCTATATAAAGAGAGCTTTTGGTCATTATTTACACACACTTGAATTTAAG
AGAAAGTTGTAGA
Found at i:40812337 original size:22 final size:21
Alignment explanation
Indices: 40812293--40812333 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40812283 CAAAAATAAC
* *
40812293 TTTTAAGAAAAAAATTCGAAT
1 TTTTAAGAAAAAAAATAGAAT
*
40812314 TTTTCAGAAAAAAAATAGAA
1 TTTTAAGAAAAAAAATAGAA
40812334 ATTTAAAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.29
Consensus pattern (21 bp):
TTTTAAGAAAAAAAATAGAAT
Found at i:40815333 original size:27 final size:27
Alignment explanation
Indices: 40815303--40815358 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
40815293 AGTTCGAGAG
* *
40815303 CAATGAAGCGTCAACGAAGTGGACCAT
1 CAATGAAGCGTCAACGAAGCGGAACAT
**
40815330 CAATGATTCGTCAACGAAGCGGAACAT
1 CAATGAAGCGTCAACGAAGCGGAACAT
40815357 CA
1 CA
40815359 TCGAAACACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (27 bp):
CAATGAAGCGTCAACGAAGCGGAACAT
Found at i:40824938 original size:44 final size:44
Alignment explanation
Indices: 40824888--40824972 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
40824878 GCCCAATCGG
* * *
40824888 CCCAAAACAGTTCCTAGTCCAACATTACAAAATTAAACAGACGA
1 CCCAAAACAGTCCCTAGCCCAACACTACAAAATTAAACAGACGA
* * * *
40824932 CCCAAAACGGTCCCTGGCCCAACACTACAAAGTTAAGCAGA
1 CCCAAAACAGTCCCTAGCCCAACACTACAAAATTAAACAGA
40824973 AAAACCCTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.41, C:0.31, G:0.13, T:0.15
Consensus pattern (44 bp):
CCCAAAACAGTCCCTAGCCCAACACTACAAAATTAAACAGACGA
Found at i:40827846 original size:16 final size:16
Alignment explanation
Indices: 40827825--40827868 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
40827815 TTTTGTTTTG
40827825 ATTGCATGACATCATA
1 ATTGCATGACATCATA
40827841 ATTGCATGACATCATA
1 ATTGCATGACATCATA
40827857 ATTGCATGACAT
1 ATTGCATGACAT
40827869 TTCATTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (16 bp):
ATTGCATGACATCATA
Found at i:40837836 original size:89 final size:89
Alignment explanation
Indices: 40837736--40837931 Score: 261
Period size: 89 Copynumber: 2.2 Consensus size: 89
40837726 ATGTACCGAC
* ** * *
40837736 GTGAAACAGATCAAAGATAGTAGGTCCTGTCCTCCTATATCTG-TAGCGAAGTGGATCGAATATA
1 GTGAAGCAGATCAAAGATAACAGGTCCTGTCCTCCTATATC-GATAGCGAAATGGATCAAATATA
*
40837800 CAGATTTTATCTTCCCGTACTGATG
65 CAGATTTTATCTTCCCATACTGATG
*
40837825 GTGAAGCAGATCAAATG-TAACAGGTCCTGTCTTCCTATATCGATAGCGAAATGGATCAAATATA
1 GTGAAGCAGATCAAA-GATAACAGGTCCTGTCCTCCTATATCGATAGCGAAATGGATCAAATATA
*
40837889 CAGATTTTATCTTCCCATACTGGTG
65 CAGATTTTATCTTCCCATACTGATG
* * *
40837914 GCGAAGTAGATCGAAGAT
1 GTGAAGCAGATCAAAGAT
40837932 TACGGATCTT
Statistics
Matches: 93, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
88 2 0.02
89 90 0.97
90 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (89 bp):
GTGAAGCAGATCAAAGATAACAGGTCCTGTCCTCCTATATCGATAGCGAAATGGATCAAATATAC
AGATTTTATCTTCCCATACTGATG
Found at i:40837918 original size:44 final size:44
Alignment explanation
Indices: 40837781--40837925 Score: 130
Period size: 44 Copynumber: 3.3 Consensus size: 44
40837771 TATATCTGTA
* *
40837781 GCGAAGTGGATCGAATATACAGATTTTATCTTCCCGTACTGATG
1 GCGAAGTGGATCAAATATACAGATTTTATCTTCCCATACTGATG
* ** * * ** * * *
40837825 GTGAAGCAGATCAAATGTAACAGGTCCTGTCTTCCTATA-TCGATA
1 GCGAAGTGGATCAAATAT-ACAGATTTTATCTTCCCATACT-GATG
* *
40837870 GCGAAATGGATCAAATATACAGATTTTATCTTCCCATACTGGTG
1 GCGAAGTGGATCAAATATACAGATTTTATCTTCCCATACTGATG
*
40837914 GCGAAGTAGATC
1 GCGAAGTGGATC
40837926 GAAGATTACG
Statistics
Matches: 72, Mismatches: 26, Indels: 6
0.69 0.25 0.06
Matches are distributed among these distances:
44 41 0.57
45 31 0.43
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (44 bp):
GCGAAGTGGATCAAATATACAGATTTTATCTTCCCATACTGATG
Found at i:40839875 original size:15 final size:15
Alignment explanation
Indices: 40839855--40839892 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
40839845 TTATTCTATC
40839855 TTTTAT-CCTTTATAT
1 TTTTATACC-TTATAT
40839870 TTTTATACCTTATAT
1 TTTTATACCTTATAT
40839885 TTTATATA
1 TTT-TATA
40839893 TATGTGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTATACCTTATAT
Found at i:40849782 original size:32 final size:32
Alignment explanation
Indices: 40849712--40849788 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
40849702 TTCAATAAAT
* *
40849712 AAAAAAT-ATATAAAATTTTATTAAATATTAA
1 AAAAAATCATATAAAATTTTATAAAAAATTAA
40849743 AATAAAATCATATAAATATTTT-TAAAAAAATT-A
1 AA-AAAATCATATAAA-ATTTTAT-AAAAAATTAA
40849776 AAAAAATCATATA
1 AAAAAATCATATA
40849789 GGTGAGCCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
31 2 0.05
32 16 0.40
33 11 0.28
34 11 0.28
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (32 bp):
AAAAAATCATATAAAATTTTATAAAAAATTAA
Found at i:40861844 original size:30 final size:30
Alignment explanation
Indices: 40861779--40861849 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
40861769 ACCAATGCAC
*
40861779 TATTTTTTAATCAATTTAGCCCTTGTACTT
1 TATTTTTTAATCAATTTAGCCCTTATACTT
* *
40861809 TATTTTTT-ATCAGTTTAGCTCC-TATCCTT
1 TATTTTTTAATCAATTTAGC-CCTTATACTT
*
40861838 TCATTTTGTAAT
1 T-ATTTTTTAAT
40861850 TCTTGTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 16 0.47
30 16 0.47
31 2 0.06
ACGTcount: A:0.21, C:0.17, G:0.07, T:0.55
Consensus pattern (30 bp):
TATTTTTTAATCAATTTAGCCCTTATACTT
Found at i:40868130 original size:13 final size:13
Alignment explanation
Indices: 40868112--40868137 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40868102 GTCTTTTACA
40868112 AATATAGACAAAT
1 AATATAGACAAAT
40868125 AATATAGACAAAT
1 AATATAGACAAAT
40868138 TTAAACAAAA
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:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (13 bp):
AATATAGACAAAT
Found at i:40876191 original size:12 final size:12
Alignment explanation
Indices: 40876174--40876198 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40876164 ATGATAAACG
40876174 ATGAAAATTTAA
1 ATGAAAATTTAA
40876186 ATGAAAATTTAA
1 ATGAAAATTTAA
40876198 A
1 A
40876199 AACATGTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATGAAAATTTAA
Found at i:40884620 original size:9 final size:9
Alignment explanation
Indices: 40884599--40884654 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
40884589 TATTTTAGAA
40884599 TTTTATA-T
1 TTTTATATT
40884607 TTTTATATT
1 TTTTATATT
40884616 TTTTATATCAAT
1 TTTTATAT---T
* *
40884628 TTTCATAAT
1 TTTTATATT
40884637 TTTTAT-TT
1 TTTTATATT
40884645 TTTTATATT
1 TTTTATATT
40884654 T
1 T
40884655 AATATTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
8 14 0.36
9 18 0.46
12 7 0.18
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTATATT
Found at i:40884649 original size:29 final size:28
Alignment explanation
Indices: 40884597--40884670 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 28
40884587 AATATTTTAG
40884597 AATTTTATATTTTTATATTTTTTATATC
1 AATTTTATATTTTTATATTTTTTATATC
*
40884625 AATTTTCATAATTTTTAT-TTTTTTATATTT
1 AATTTT-AT-ATTTTTATATTTTTTATA-TC
40884655 AATATTTAATATTTTT
1 AAT-TTT-ATATTTTT
40884671 TAATTATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
28 6 0.15
29 11 0.28
30 18 0.45
31 5 0.12
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (28 bp):
AATTTTATATTTTTATATTTTTTATATC
Found at i:40891009 original size:21 final size:21
Alignment explanation
Indices: 40890983--40891039 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
40890973 ACACGAGCTG
40890983 CTCACATGGGCGTGTGCGGCC
1 CTCACATGGGCGTGTGCGGCC
* * *
40891004 CTCACACGGGCATGTGTGGCC
1 CTCACATGGGCGTGTGCGGCC
*
40891025 TTCACATGGGCGTGT
1 CTCACATGGGCGTGT
40891040 AGACCCCAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.12, C:0.30, G:0.35, T:0.23
Consensus pattern (21 bp):
CTCACATGGGCGTGTGCGGCC
Found at i:40891738 original size:21 final size:20
Alignment explanation
Indices: 40891702--40891743 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
40891692 CTGAATATAC
40891702 GTCTGTTTGTCAGAACATTTT
1 GTCTGTTTGTCAGAAC-TTTT
**
40891723 GTCTGTTTGTGTGAACTTTT
1 GTCTGTTTGTCAGAACTTTT
40891743 G
1 G
40891744 GTTATTGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.24, T:0.50
Consensus pattern (20 bp):
GTCTGTTTGTCAGAACTTTT
Found at i:40892581 original size:32 final size:32
Alignment explanation
Indices: 40892540--40892604 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
40892530 CATTAGCAAA
40892540 GTTAGCAACTATTAACTTTTCCATCCATTTTG
1 GTTAGCAACTATTAACTTTTCCATCCATTTTG
40892572 GTTAGCAACTATTAACTTTTCCATCCATTTTG
1 GTTAGCAACTATTAACTTTTCCATCCATTTTG
40892604 G
1 G
40892605 GGTGATTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.43
Consensus pattern (32 bp):
GTTAGCAACTATTAACTTTTCCATCCATTTTG
Found at i:40895210 original size:697 final size:698
Alignment explanation
Indices: 40893863--40895258 Score: 2785
Period size: 697 Copynumber: 2.0 Consensus size: 698
40893853 TATATTTTGT
40893863 TTTTATTTTTTAATTTTAAAATATTTTTAAAATACTTTTATTTTTATTTTCTTTATTTTTAAAAT
1 TTTTATTTTTTAATTTTAAAATATTTTTAAAATACTTTTATTTTTATTTTCTTTATTTTTAAAAT
40893928 ATTTTTTTGGTGTTTATTAAAAAATGGGCCGAGCCAGGCCGGGCTCGGGCTTAGGATTTTATTCC
66 ATTTTTTTGGTGTTTATTAAAAAATGGGCCGAGCCAGGCCGGGCTCGGGCTTAGGATTTTATTCC
40893993 CGGGTCGGGCCTAGACAAAATTTCAGGCCCATATTTCGGGCCGGTCTGGGCCCGGGCCTAGGAGG
131 CGGGTCGGGCCTAGACAAAATTTCAGGCCCATATTTCGGGCCGGTCTGGGCCCGGGCCTAGGAGG
40894058 CGGGCCAAAATTTTTTCTGGGCTCGACTCGAACCTGGCCCGACCCGGCCCATGGACACCTCTATT
196 CGGGCCAAAATTTTTTCTGGGCTCGACTCGAACCTGGCCCGACCCGGCCCATGGACACCTCTATT
40894123 ACTACCGTTTGAGTCAAGACTAAAATATCAAAATTTGAAAAGTATAGAGATTAAAATTGACCGAT
261 ACTACCGTTTGAGTCAAGACTAAAATATCAAAATTTGAAAAGTATAGAGATTAAAATTGACCGAT
40894188 TCAAAAAGCACATGGATTGAAATCTGCAAATTTCATAACGCTCAAGGACTAATAGCAGAATTTAC
326 TCAAAAAGCACATGGATTGAAATCTGCAAATTTCATAACGCTCAAGGACTAATAGCAGAATTTAC
40894253 CCAAAACTAAAATTTTAAGACTTAAAATTACTACTTTATTAGTTAATTTAGGATCATGTATTAAG
391 CCAAAACTAAAATTTTAAGACTTAAAATTACTACTTTATTAGTTAATTTAGGATCATGTATTAAG
40894318 ATTTACTACATATATCAAATAATATTTTGGTATGTAATTAGACAAATTGTTGTAATTATAAATTA
456 ATTTACTACATATATCAAATAATATTTTGGTATGTAATTAGACAAATTGTTGTAATTATAAATTA
40894383 TGGATTTATTTAAGAGCAAGAGGAAAATGATGTTCTAAAAACCTCATTTTCTTATTAGTCTTGTC
521 TGGATTTATTTAAGAGCAAGAGGAAAATGATGTTCTAAAAACCTCATTTTCTTATTAGTCTTGTC
40894448 ACTATCAAATCTTATAAAACTCACCATAAATTGGAATTTAAAATGGAAGGTAGAGTTGAATTATT
586 ACTATCAAATCTTATAAAACTCACCATAAATTGGAATTTAAAATGGAAGGTAGAGTTGAATTATT
40894513 CATGCAATTATATTTATAAAAAAATTCCAACATCTCAATAATTCACAA
651 CATGCAATTATATTTATAAAAAAATTCCAACATCTCAATAATTCACAA
40894561 TTTTATTTTTT-ATTTTAAAATATTTTTAAAATACTTTTATTTTTATTTTCTTTATTTTTAAAAT
1 TTTTATTTTTTAATTTTAAAATATTTTTAAAATACTTTTATTTTTATTTTCTTTATTTTTAAAAT
40894625 ATTTTTTTGGTGTTTATTAAAAAATGGGCCGAGCCAGGCCGGGCTCGGGCTTAGGATTTTATTCC
66 ATTTTTTTGGTGTTTATTAAAAAATGGGCCGAGCCAGGCCGGGCTCGGGCTTAGGATTTTATTCC
40894690 CGGGTCGGGCCTAGACAAAATTTCAGGCCCATATTTCGGGCCGGTCTGGGCCCGGGCCTAGGAGG
131 CGGGTCGGGCCTAGACAAAATTTCAGGCCCATATTTCGGGCCGGTCTGGGCCCGGGCCTAGGAGG
40894755 CGGGCCAAAATTTTTTCTGGGCTCGACTCGAACCTGGCCCGACCCGGCCCATGGACACCTCTATT
196 CGGGCCAAAATTTTTTCTGGGCTCGACTCGAACCTGGCCCGACCCGGCCCATGGACACCTCTATT
40894820 ACTACCGTTTGAGTCAAGACTAAAATATCAAAATTTGAAAAGTATAGAGATTAAAATTGACCGAT
261 ACTACCGTTTGAGTCAAGACTAAAATATCAAAATTTGAAAAGTATAGAGATTAAAATTGACCGAT
40894885 TCAAAAAGCACATGGATTGAAATCTGCAAATTTCATAACGCTCAAGGACTAATAGCAGAATTTAC
326 TCAAAAAGCACATGGATTGAAATCTGCAAATTTCATAACGCTCAAGGACTAATAGCAGAATTTAC
40894950 CCAAAACTAAAATTTTAAGACTTAAAATTACTACTTTATTAGTTAATTTAGGATCATGTATTAAG
391 CCAAAACTAAAATTTTAAGACTTAAAATTACTACTTTATTAGTTAATTTAGGATCATGTATTAAG
40895015 ATTTACTACATATATCAAATAATATTTTGGTATGTAATTAGACAAATTGTTGTAATTATAAATTA
456 ATTTACTACATATATCAAATAATATTTTGGTATGTAATTAGACAAATTGTTGTAATTATAAATTA
40895080 TGGATTTATTTAAGAGCAAGAGGAAAATGATGTTCTAAAAACCTCATTTTCTTATTAGTCTTGTC
521 TGGATTTATTTAAGAGCAAGAGGAAAATGATGTTCTAAAAACCTCATTTTCTTATTAGTCTTGTC
40895145 ACTATCAAATCTTATAAAACTCACCATAAATTGGAATTTAAAATGGAAGGTAGAGTTGAATTATT
586 ACTATCAAATCTTATAAAACTCACCATAAATTGGAATTTAAAATGGAAGGTAGAGTTGAATTATT
40895210 CATGCAATTATATTTATAAAAAAATTCCAACATCTCAATAATTCACAA
651 CATGCAATTATATTTATAAAAAAATTCCAACATCTCAATAATTCACAA
40895258 T
1 T
40895259 AATTTCACAA
Statistics
Matches: 698, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
697 687 0.98
698 11 0.02
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Consensus pattern (698 bp):
TTTTATTTTTTAATTTTAAAATATTTTTAAAATACTTTTATTTTTATTTTCTTTATTTTTAAAAT
ATTTTTTTGGTGTTTATTAAAAAATGGGCCGAGCCAGGCCGGGCTCGGGCTTAGGATTTTATTCC
CGGGTCGGGCCTAGACAAAATTTCAGGCCCATATTTCGGGCCGGTCTGGGCCCGGGCCTAGGAGG
CGGGCCAAAATTTTTTCTGGGCTCGACTCGAACCTGGCCCGACCCGGCCCATGGACACCTCTATT
ACTACCGTTTGAGTCAAGACTAAAATATCAAAATTTGAAAAGTATAGAGATTAAAATTGACCGAT
TCAAAAAGCACATGGATTGAAATCTGCAAATTTCATAACGCTCAAGGACTAATAGCAGAATTTAC
CCAAAACTAAAATTTTAAGACTTAAAATTACTACTTTATTAGTTAATTTAGGATCATGTATTAAG
ATTTACTACATATATCAAATAATATTTTGGTATGTAATTAGACAAATTGTTGTAATTATAAATTA
TGGATTTATTTAAGAGCAAGAGGAAAATGATGTTCTAAAAACCTCATTTTCTTATTAGTCTTGTC
ACTATCAAATCTTATAAAACTCACCATAAATTGGAATTTAAAATGGAAGGTAGAGTTGAATTATT
CATGCAATTATATTTATAAAAAAATTCCAACATCTCAATAATTCACAA
Found at i:40897011 original size:75 final size:74
Alignment explanation
Indices: 40896916--40897073 Score: 264
Period size: 75 Copynumber: 2.1 Consensus size: 74
40896906 ATATTTTATT
*
40896916 TATAACTTTCTATTTGTTTAACATGTGCAAGATTTAATTAGTTTAT-AAACTTTTTATTCGAACA
1 TATAA-TTTCTATTTGTTTAACATGTGCAAGATTTAATTAGTTTATAAAACTTTTTA--AGAACA
40896980 ATATTTATTTAA
63 ATATTTATTTAA
40896992 TATAATTTCTATTTGTTTAACATGTGCAAGATTTAATTAGTTTATAAAAACTTTTTAAGAACAAT
1 TATAATTTCTATTTGTTTAACATGTGCAAGATTTAATTAGTTTAT-AAAACTTTTTAAGAACAAT
40897057 ATTTATTTAA
65 ATTTATTTAA
40897067 TATAATT
1 TATAATT
40897074 ATTATATATA
Statistics
Matches: 79, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
75 64 0.81
76 5 0.06
77 10 0.13
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.48
Consensus pattern (74 bp):
TATAATTTCTATTTGTTTAACATGTGCAAGATTTAATTAGTTTATAAAACTTTTTAAGAACAATA
TTTATTTAA
Found at i:40897556 original size:18 final size:18
Alignment explanation
Indices: 40897533--40897584 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
40897523 TTGGGTTATA
40897533 AAAAAATTATTATTTTTT
1 AAAAAATTATTATTTTTT
* *
40897551 AAAAAA-TACT-TTCTTT
1 AAAAAATTATTATTTTTT
40897567 AAAATAATT-TTATTTTTT
1 AAAA-AATTATTATTTTTT
40897585 CTCATTTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 9 0.33
17 6 0.22
18 12 0.44
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (18 bp):
AAAAAATTATTATTTTTT
Found at i:40901495 original size:22 final size:22
Alignment explanation
Indices: 40901470--40901515 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
40901460 CAAACAGAAA
*
40901470 CAAACTCAAAACAAATCAAATC
1 CAAACACAAAACAAATCAAATC
*
40901492 CAAACACAAAATAAATCAAATC
1 CAAACACAAAACAAATCAAATC
40901514 CA
1 CA
40901516 TTAAGCCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (22 bp):
CAAACACAAAACAAATCAAATC
Found at i:40902226 original size:25 final size:25
Alignment explanation
Indices: 40902178--40902226 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
40902168 ACTGTTATTT
* * * *
40902178 TATTATATATTTCTATTATTTTTAG
1 TATTATAGATTGCTATCATATTTAG
40902203 TATTATAGATTGCTATCATATTTA
1 TATTATAGATTGCTATCATATTTA
40902227 TTTATATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (25 bp):
TATTATAGATTGCTATCATATTTAG
Found at i:40902337 original size:27 final size:27
Alignment explanation
Indices: 40902270--40902337 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 27
40902260 ATTTTACTAC
40902270 ATATTATTTTAAAATTACTTTTATATA
1 ATATTATTTTAAAATTACTTTTATATA
* * ** *
40902297 GTTTTA-TTCCAAATT-GTTTTATATA
1 ATATTATTTTAAAATTACTTTTATATA
40902322 ATAATTATTTTAAAAT
1 AT-ATTATTTTAAAAT
40902338 CATCCTATAC
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
25 10 0.33
26 10 0.33
27 10 0.33
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54
Consensus pattern (27 bp):
ATATTATTTTAAAATTACTTTTATATA
Found at i:40912445 original size:16 final size:16
Alignment explanation
Indices: 40912424--40912462 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
40912414 ACTTGTTCTG
40912424 GTCATTTCAGGTTAAA
1 GTCATTTCAGGTTAAA
** *
40912440 GTCATTTTGGGTTCAA
1 GTCATTTCAGGTTAAA
40912456 GTCATTT
1 GTCATTT
40912463 TAGATTTGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.44
Consensus pattern (16 bp):
GTCATTTCAGGTTAAA
Found at i:40912463 original size:16 final size:16
Alignment explanation
Indices: 40912433--40912463 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40912423 GGTCATTTCA
40912433 GGTTAAAGTCATTTTG
1 GGTTAAAGTCATTTTG
*
40912449 GGTTCAAGTCATTTT
1 GGTTAAAGTCATTTT
40912464 AGATTTGGGT
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:0.23, C:0.10, G:0.23, T:0.45
Consensus pattern (16 bp):
GGTTAAAGTCATTTTG
Found at i:40917802 original size:13 final size:13
Alignment explanation
Indices: 40917784--40917808 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40917774 TAATTTATAT
40917784 GTGTGAAAATTTC
1 GTGTGAAAATTTC
40917797 GTGTGAAAATTT
1 GTGTGAAAATTT
40917809 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:40918997 original size:42 final size:42
Alignment explanation
Indices: 40918895--40919053 Score: 187
Period size: 43 Copynumber: 3.7 Consensus size: 42
40918885 TATGTGATAT
40918895 CGTGTAAGACCACGTCTGGGACATTGGCATCG-ATTTGGGATTAA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTT--GATT-A
* * *
40918939 CGTGTAAGACCATGTCTGAGACATTGGCATCGTATATGATTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGATTA
* *
40918981 CGTGTAAGACC-CTGTCTGGGACAGTGGCATCGTTATTTGATTG
1 CGTGTAAGACCAC-GTCTGGGACATTGGCATCG-TATTTGATTA
* * *
40919024 CATATAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACATTGGCAT
40919054 TTGTATGAGT
Statistics
Matches: 99, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
42 29 0.29
43 36 0.36
44 31 0.31
45 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGATTA
Found at i:40921971 original size:31 final size:32
Alignment explanation
Indices: 40921936--40921998 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 32
40921926 ACAAACTAAC
* **
40921936 CAAAGACTAAAATGTCCAAAA-AAAAAGTCCA
1 CAAAGACCAAAATGAACAAAATAAAAAGTCCA
* *
40921967 CAAAGTCCATAATGAACAAAATAAAAAGTCCA
1 CAAAGACCAAAATGAACAAAATAAAAAGTCCA
40921999 TAGCATATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.57, C:0.19, G:0.10, T:0.14
Consensus pattern (32 bp):
CAAAGACCAAAATGAACAAAATAAAAAGTCCA
Found at i:40922285 original size:25 final size:25
Alignment explanation
Indices: 40922257--40922304 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40922247 ATCAGATCAG
* *
40922257 ATCAGACCATAGCATATCATATCGA
1 ATCAAACCATAGCATAACATATCGA
*
40922282 ATCAAATCATAGCATAACATATC
1 ATCAAACCATAGCATAACATATC
40922305 ATATCCTACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (25 bp):
ATCAAACCATAGCATAACATATCGA
Found at i:40924575 original size:23 final size:23
Alignment explanation
Indices: 40924532--40924575 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
40924522 GATATATTGC
*
40924532 ATTATATAATATTAAGGTAAACT
1 ATTATATAATATTAAGCTAAACT
*
40924555 ATTA-ATACATATTGAGCTAAA
1 ATTATATA-ATATTAAGCTAAA
40924576 AATGCTAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAATATTAAGCTAAACT
Found at i:40930281 original size:66 final size:66
Alignment explanation
Indices: 40930198--40930327 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
40930188 GTAAGAAGAG
* *
40930198 GTTCTGAACTATGTAAGTAATTAGTGTGTTAATTGTTTTATTTTTTTAATTTTAGTTGTAGCTTT
1 GTTCTGAACTATGTAAGTAATTAGTATGCTAATTGTTTTATTTTTTTAATTTTAGTTGTAGCTTT
40930263 A
66 A
*
40930264 GTTCTGAATTATGTAAGTAATTAGTATGCTAATTGTTTTATTTTTTTAATTTTAGTTGTAGCTT
1 GTTCTGAACTATGTAAGTAATTAGTATGCTAATTGTTTTATTTTTTTAATTTTAGTTGTAGCTT
40930328 GCAACTCTCG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.55
Consensus pattern (66 bp):
GTTCTGAACTATGTAAGTAATTAGTATGCTAATTGTTTTATTTTTTTAATTTTAGTTGTAGCTTT
A
Found at i:40930852 original size:27 final size:27
Alignment explanation
Indices: 40930814--40930890 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
40930804 TAGTATTGGC
40930814 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
40930841 GCCTACCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
40930868 GCC-ATTCTGAGAGGCGCCAATGG
1 GCCTA-TCTGGGAGGCGCCAATGG
40930891 GCCGGGCCGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.17, C:0.25, G:0.39, T:0.19
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:40931097 original size:19 final size:19
Alignment explanation
Indices: 40931075--40931112 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40931065 AATTTAATTT
*
40931075 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
40931094 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
40931113 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:40931955 original size:12 final size:12
Alignment explanation
Indices: 40931940--40931971 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40931930 CCGTATTTTT
40931940 TTAAAAAAATTA
1 TTAAAAAAATTA
40931952 TTAAAAAAA-TA
1 TTAAAAAAATTA
40931963 -TAAAAAAAT
1 TTAAAAAAAT
40931972 ATTTTATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.42
11 2 0.11
12 9 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TTAAAAAAATTA
Found at i:40937642 original size:176 final size:177
Alignment explanation
Indices: 40937337--40937689 Score: 699
Period size: 176 Copynumber: 2.0 Consensus size: 177
40937327 TTAAAATAAA
40937337 AAATTAGATTAAATTATGAGTAAAACCAAAGTTAAACACATAAATGCATCAGATAAACAATATTA
1 AAATTAGATTAAATTATGAGTAAAACCAAAGTTAAACACATAAATGCATCAGATAAACAATATTA
40937402 AATGCACTACAATTATTTAGCATGATTTTGTCATTAATTATGAGTTAGTGTCGAGTTTTCTTATG
66 AATGCACTACAATTATTTAGCATGATTTTGTCATTAATTATGAGTTAGTGTCGAGTTTTCTTATG
40937467 ACACCAATTCAATAATATAACTTTTTTTAATTACGAAAATACATTTT
131 ACACCAATTCAATAATATAACTTTTTTTAATTACGAAAATACATTTT
40937514 AAATTAGATT-AATTATGAGTAAAACCAAAGTTAAACACATAAATGCATCAGATAAACAATATTA
1 AAATTAGATTAAATTATGAGTAAAACCAAAGTTAAACACATAAATGCATCAGATAAACAATATTA
40937578 AATGCACTACAATTATTTAGCATGATTTTGTCATTAATTATGAGTTAGTGTCGAGTTTTCTTATG
66 AATGCACTACAATTATTTAGCATGATTTTGTCATTAATTATGAGTTAGTGTCGAGTTTTCTTATG
40937643 ACACCAATTCAATAATATAACTTTTTTTAATTACGAAAATACATTTT
131 ACACCAATTCAATAATATAACTTTTTTTAATTACGAAAATACATTTT
40937690 CATATTTTTC
Statistics
Matches: 176, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
176 166 0.94
177 10 0.06
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (177 bp):
AAATTAGATTAAATTATGAGTAAAACCAAAGTTAAACACATAAATGCATCAGATAAACAATATTA
AATGCACTACAATTATTTAGCATGATTTTGTCATTAATTATGAGTTAGTGTCGAGTTTTCTTATG
ACACCAATTCAATAATATAACTTTTTTTAATTACGAAAATACATTTT
Found at i:40940857 original size:20 final size:20
Alignment explanation
Indices: 40940818--40940855 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
40940808 ACCAAAAATT
40940818 TATTTTAAAAATTAAAAAAG
1 TATTTTAAAAATTAAAAAAG
40940838 TATTTT-AAAATTAAAAAA
1 TATTTTAAAAATTAAAAAA
40940856 AGGCTGGGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
TATTTTAAAAATTAAAAAAG
Found at i:40943052 original size:20 final size:19
Alignment explanation
Indices: 40943023--40943066 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
40943013 AAAATTATAA
*
40943023 AAAAAATCAAAATAATTTTT
1 AAAAAATCAAAAT-ATTTAT
*
40943043 AAAAAGTCAAAATATTTAT
1 AAAAAATCAAAATATTTAT
40943062 AAAAA
1 AAAAA
40943067 CTCCAAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAAATCAAAATATTTAT
Found at i:40943073 original size:20 final size:20
Alignment explanation
Indices: 40943023--40943069 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
40943013 AAAATTATAA
* *
40943023 AAAAAATCAAAATAATTTTT
1 AAAAACTCAAAATAATTTAT
*
40943043 AAAAAGTCAAAAT-ATTTAT
1 AAAAACTCAAAATAATTTAT
40943062 AAAAACTC
1 AAAAACTC
40943070 CAAAGTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAAACTCAAAATAATTTAT
Found at i:40943390 original size:21 final size:21
Alignment explanation
Indices: 40943351--40943390 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40943341 TTCAATTCGC
*
40943351 CTTGACTCGAATTTCATTTCA
1 CTTGACTCGAATTTAATTTCA
40943372 CTTGACTCG-ATTTGAATTT
1 CTTGACTCGAATTT-AATTT
40943391 TTTCAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.20, G:0.12, T:0.45
Consensus pattern (21 bp):
CTTGACTCGAATTTAATTTCA
Found at i:40948285 original size:25 final size:25
Alignment explanation
Indices: 40948255--40948309 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
40948245 TCATCAAATT
40948255 AGAATGACATGTCACTTTCAGAATC
1 AGAATGACATGTCACTTTCAGAATC
* *
40948280 AGAATGACATTTCATTTTCAGAATC
1 AGAATGACATGTCACTTTCAGAATC
40948305 AGAAT
1 AGAAT
40948310 AGCATATCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (25 bp):
AGAATGACATGTCACTTTCAGAATC
Found at i:40954004 original size:113 final size:113
Alignment explanation
Indices: 40953848--40954307 Score: 475
Period size: 113 Copynumber: 4.0 Consensus size: 113
40953838 AAATATCAAG
* *
40953848 ACCAACACGCAGCGTTCTGGTCTTGATGTATATTGGC-ATTAGTGGCGCTTATGAACAAACGCCG
1 ACCAAAACGCAGAGTT-TGGTCTTGATGTATATT-GCAATTAGTGGCGCTTATGAA-AAACGCCG
* * * *
40953912 GTAATGTATAGTATTAGCGGCGCTTAGCG-GAAGCGCCGCAAAAGATGTTA
63 CTAATGTATAGTATTAGCGGCGCTTAGCGTTAAGCGCCGCAAGATATGTTA
* *
40953962 ACCAAAACGCAGAGTTTAGTCTTGATGTATATTGCAATTAGTGGCGCTTATAAAGAAAACGCCGC
1 ACCAAAACGCAGAGTTTGGTCTTGATGTATATTGCAATTAGTGGCGCTTAT-GA-AAAACGCCGC
** * *
40954027 TAATGTATAGTATTAGCGGCGCAGAGCGTTAAACGCCGCAAGATATCTTA
64 TAATGTATAGTATTAGCGGCGCTTAGCGTTAAGCGCCGCAAGATATGTTA
* ** * ** * *
40954077 ATCAAAACGCACTGTTTTGGTCTTGATGTATACTATAATTAGTGGCGTTTATGGTAAAACGCCGC
1 ACCAAAACGCAGAG-TTTGGTCTTGATGTATATTGCAATTAGTGGCGCTTAT-GAAAAACGCCGC
* * * * *
40954142 TACAT-AACAGTATTAGCGGTGCTTAACGTTAAGCGCCGCAAGATATG-CA
64 TA-ATGTATAGTATTAGCGGCGCTTAGCGTTAAGCGCCGCAAGATATGTTA
*
40954191 CACCAAAACGCAGAGTTTGGTATTGATGTATATT--AGATTAGTGGCGCTTATTGAAAAACGCCG
1 -ACCAAAACGCAGAGTTTGGTCTTGATGTATATTGCA-ATTAGTGGCGCTTA-TGAAAAACGCCG
* * * * * *
40954254 CTAAAGTATACTATTAGCGGCGCTT-TCCTAGAAGCGCCGCAAGATATATTA
63 CTAATGTATAGTATTAGCGGCGCTTAGCGT-TAAGCGCCGCAAGATATGTTA
40954305 ACC
1 ACC
40954308 CGANNNNNNN
Statistics
Matches: 285, Mismatches: 49, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
112 6 0.02
113 91 0.32
114 69 0.24
115 85 0.30
116 34 0.12
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (113 bp):
ACCAAAACGCAGAGTTTGGTCTTGATGTATATTGCAATTAGTGGCGCTTATGAAAAACGCCGCTA
ATGTATAGTATTAGCGGCGCTTAGCGTTAAGCGCCGCAAGATATGTTA
Found at i:40955823 original size:147 final size:147
Alignment explanation
Indices: 40955672--40955949 Score: 339
Period size: 147 Copynumber: 1.9 Consensus size: 147
40955662 ATTATGTTTA
* * * *
40955672 TTGAAATGTTGTCGTTTTTGTTTAT-TATATTACTGGCG-TTTGTCGGAAACGCCACAACATTG-
1 TTGAAACGTTGTCG-TTTTGTTAATGT-TATTACTGGCGTTTTATCGAAAACGCCACAACATTGA
* ****
40955734 GGTAAACTGTTGGGGAAACGGGTTCGTTTTGAGTTATAGTTAGTGGCGCTTTA-CTTAAAACGCC
64 GGT-AACTGTTGAGGAAACGACCGCGTTTTGAGTTATAGTTAGTGGCGC-TTAGCTTAAAACGCC
40955798 GCAAAAATGTTCAAACATTTG
127 GCAAAAATGTTCAAACATTTG
* * **
40955819 TTGAAACGTTGTCGTTTTGTTAATGTTATTAGTGGCGTTTTATCGAAAACGCCACGAGTTTGAGG
1 TTGAAACGTTGTCGTTTTGTTAATGTTATTACTGGCGTTTTATCGAAAACGCCACAACATTGAGG
* * * *
40955884 TAAGTGTTGATGAAGCGACCGCGTTTTGAGTTATAGTTAGTGGCGCTTAGTTTAAAACGCCGCAA
66 TAACTGTTGAGGAAACGACCGCGTTTTGAGTTATAGTTAGTGGCGCTTAGCTTAAAACGCCGCAA
40955949 A
131 A
40955950 TTTTTGACCT
Statistics
Matches: 110, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
146 22 0.20
147 85 0.77
148 3 0.03
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (147 bp):
TTGAAACGTTGTCGTTTTGTTAATGTTATTACTGGCGTTTTATCGAAAACGCCACAACATTGAGG
TAACTGTTGAGGAAACGACCGCGTTTTGAGTTATAGTTAGTGGCGCTTAGCTTAAAACGCCGCAA
AAATGTTCAAACATTTG
Found at i:40957190 original size:27 final size:27
Alignment explanation
Indices: 40957152--40957210 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
40957142 ATTTACTCCT
*
40957152 AATTTAAAATTATTTTCCATGCATTCC
1 AATTTAAAATTATTTTCCATACATTCC
*
40957179 AATTTAAAATTATTTTCCATACATTCT
1 AATTTAAAATTATTTTCCATACATTCC
40957206 AATTT
1 AATTT
40957211 TTTTGCTGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.36, C:0.15, G:0.02, T:0.47
Consensus pattern (27 bp):
AATTTAAAATTATTTTCCATACATTCC
Found at i:40971759 original size:30 final size:30
Alignment explanation
Indices: 40971696--40971760 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
40971686 AATAGTTTAT
* *
40971696 ATTTTTATAATTTTTAAAGAATTAAATTAA
1 ATTTTTATAATTTTTAAAGAATCAAAGTAA
* *
40971726 ATTTTTATCATTTTTAAA-AGTCAAAGTATA
1 ATTTTTATAATTTTTAAAGAATCAAAGTA-A
40971756 ATTTT
1 ATTTT
40971761 ACCATTACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (30 bp):
ATTTTTATAATTTTTAAAGAATCAAAGTAA
Found at i:40971761 original size:29 final size:30
Alignment explanation
Indices: 40971693--40971766 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 30
40971683 TTTAATAGTT
* * * *
40971693 TATATTTTTATAATTTTTAAAGAATTAAAT
1 TATAATTTTATCATTTTTAAAGAATCAAAG
*
40971723 TA-AATTTTTATCATTTTTAAA-AGTCAAAG
1 TATAA-TTTTATCATTTTTAAAGAATCAAAG
*
40971752 TATAATTTTACCATT
1 TATAATTTTATCATT
40971767 ACTAAATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (30 bp):
TATAATTTTATCATTTTTAAAGAATCAAAG
Found at i:40973589 original size:131 final size:132
Alignment explanation
Indices: 40973439--40973685 Score: 327
Period size: 131 Copynumber: 1.9 Consensus size: 132
40973429 GGGTTGTGAT
** ** * *
40973439 TTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGGTTTATGGATTCAATGTCAGGTTA
1 TTAGGGGTTAGGAATTAGAGATTAAGAGTTAGGGATTTAAGGTTTAAAGATTCAAGGTCAGATTA
* *
40973504 GGGC-TTAGGGTTTAGATTAATTAGT-GTTTTTAATTTATATATTAAATAAGGTTTAGGTGTTAG
66 -GGCTTTAAGGTTTAGATTAATTAGTACTTTTTAATTTATATATTAAATAAGGTTTAGGTGTTAG
40973567 TAG
130 TAG
* * * * ***
40973570 TTAGGGGTTTGGAATTAGAGGTTAAGAGTTAGTGATTTAGGGTTTAAAGATTTGGGGTCAGATTA
1 TTAGGGGTTAGGAATTAGAGATTAAGAGTTAGGGATTTAAGGTTTAAAGATTCAAGGTCAGATTA
*
40973635 GGCTTTAAGGTTTAGATTAATTAGTACTTTTTAATTTATATATTAATTAAG
66 GGCTTTAAGGTTTAGATTAATTAGTACTTTTTAATTTATATATTAAATAAG
40973686 TTCTTATATA
Statistics
Matches: 98, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
130 3 0.03
131 72 0.73
132 23 0.23
ACGTcount: A:0.29, C:0.02, G:0.27, T:0.41
Consensus pattern (132 bp):
TTAGGGGTTAGGAATTAGAGATTAAGAGTTAGGGATTTAAGGTTTAAAGATTCAAGGTCAGATTA
GGCTTTAAGGTTTAGATTAATTAGTACTTTTTAATTTATATATTAAATAAGGTTTAGGTGTTAGT
AG
Found at i:40974881 original size:83 final size:85
Alignment explanation
Indices: 40974754--40974969 Score: 267
Period size: 83 Copynumber: 2.6 Consensus size: 85
40974744 GAACAGTACT
** * *
40974754 TTTAGGGCGTTTGTGATAAAAGCGCCGCTAAAGATCAT-ATTCTTTAGCGGCGTTTGTGGG-TAA
1 TTTAGGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGA-TCTTTAGCGGCGTTTGTGGGAAAA
* *
40974817 GCGCCGCTAAAGTTCATGTTC
65 GCGCCGCTAAAGGTCATGGTC
* * *
40974838 TTTA-GGCGTTTGTGGGAGAAGCGCCGCTAATGGTCATGATCTTTAACGGCGTTTGTGGGAAAAG
1 TTTAGGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGGGAAAAG
*
40974902 CGCCGCTAAAGGTCTTGGTC
66 CGCCGCTAAAGGTCATGGTC
* * * *
40974922 TTTAGCGGTGTTTGTGGGAAAAGCGCCACTAAAGGTCTTGGTCTTTAG
1 TTTAG-GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTTTAG
40974970 GTCATGGTCT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
83 47 0.42
84 29 0.26
86 35 0.32
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (85 bp):
TTTAGGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGGGAAAAG
CGCCGCTAAAGGTCATGGTC
Found at i:40974969 original size:43 final size:43
Alignment explanation
Indices: 40974754--40974969 Score: 260
Period size: 43 Copynumber: 5.1 Consensus size: 43
40974744 GAACAGTACT
** * **
40974754 TTTAG-GGCGTTTGTGATAAAAGCGCCGCTAAAGATCATATTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
40974796 TTTAGCGGCGTTTGTGGG-TAAGCGCCGCTAAAGTTCATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
40974838 TTTA--GGCGTTTGTGGGAGAAGCGCCGCTAATGGTCATGATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
40974879 TTTAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
40974922 TTTAGCGGTGTTTGTGGGAAAAGCGCCACTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
40974965 TTTAG
1 TTTAG
40974970 GTCATGGTCT
Statistics
Matches: 154, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
40 12 0.08
41 24 0.16
42 30 0.19
43 88 0.57
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:40977525 original size:22 final size:22
Alignment explanation
Indices: 40977460--40977525 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
40977450 CTATCTAAAT
40977460 TTCCTTCCAAAATTCTCTC-AA
1 TTCCTTCCAAAATTCTCTCAAA
40977481 TGTCCTTCCAAAATTCTCTCAAA
1 T-TCCTTCCAAAATTCTCTCAAA
40977504 TTCCTTCCAAAATTCTCTCAAA
1 TTCCTTCCAAAATTCTCTCAAA
40977526 CTCTCAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
21 1 0.02
22 39 0.91
23 3 0.07
ACGTcount: A:0.30, C:0.32, G:0.02, T:0.36
Consensus pattern (22 bp):
TTCCTTCCAAAATTCTCTCAAA
Found at i:40977531 original size:30 final size:30
Alignment explanation
Indices: 40977496--40977554 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
40977486 TTCCAAAATT
*
40977496 CTCTCAAATTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
40977526 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
40977555 TTTCCTTCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:40977531 original size:52 final size:52
Alignment explanation
Indices: 40977474--40977573 Score: 150
Period size: 52 Copynumber: 1.9 Consensus size: 52
40977464 TTCCAAAATT
*
40977474 CTCTC-AATGTCCTTCCAAAATTCTCTCAAATTCCTT-CCAAAATTCTCTCAAA
1 CTCTCAAAT-TCCTTCCAAAATCCTCTCAAATTCCTTCCCAAAA-TCTCTCAAA
*
40977526 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCCCAAAATCTCT
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAATTCCTTCCCAAAATCTCT
40977574 AAAATCCATA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
52 35 0.80
53 9 0.20
ACGTcount: A:0.29, C:0.35, G:0.01, T:0.35
Consensus pattern (52 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAATTCCTTCCCAAAATCTCTCAAA
Found at i:40977553 original size:22 final size:22
Alignment explanation
Indices: 40977526--40977578 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
40977516 TTCTCTCAAA
40977526 CTCTCAAATTCCTT-CCAAAAT
1 CTCTCAAATTCCTTCCCAAAAT
*
40977547 CCTCTCAATTTCCTTCCCAAAAT
1 -CTCTCAAATTCCTTCCCAAAAT
*
40977570 CTCTAAAAT
1 CTCTCAAAT
40977579 CCATATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCCAAAAT
Found at i:40977607 original size:17 final size:18
Alignment explanation
Indices: 40977582--40977615 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40977572 CTAAAATCCA
40977582 TATTAAATTTC-TTTTTC
1 TATTAAATTTCATTTTTC
*
40977599 TATTCAATTTCATTTTT
1 TATTAAATTTCATTTTT
40977616 TAAAGATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTAAATTTCATTTTTC
Found at i:40977630 original size:12 final size:11
Alignment explanation
Indices: 40977613--40977662 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
40977603 CAATTTCATT
40977613 TTTTAAAGATAA
1 TTTTAAA-ATAA
40977625 TTTT-AAATAA
1 TTTTAAAATAA
* **
40977635 TTTT-ATATTT
1 TTTTAAAATAA
40977645 TTTTAAAATAA
1 TTTTAAAATAA
40977656 TTTTAAA
1 TTTTAAA
40977663 TTTTTTAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
10 15 0.48
11 12 0.39
12 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAA
Found at i:40977645 original size:31 final size:30
Alignment explanation
Indices: 40977610--40977676 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
40977600 ATTCAATTTC
40977610 ATTTTTTAAAGATAATTTTAAATAATTTT-AT
1 ATTTTTTAAA-ATAATTTTAAAT-ATTTTAAT
*
40977641 ATTTTTTTAAAATAATTTTAAATTTTTTAAT
1 A-TTTTTTAAAATAATTTTAAATATTTTAAT
40977672 ATTTT
1 ATTTT
40977677 CAACAATGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
30 8 0.24
31 16 0.48
32 9 0.27
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (30 bp):
ATTTTTTAAAATAATTTTAAATATTTTAAT
Found at i:40977655 original size:21 final size:20
Alignment explanation
Indices: 40977625--40977668 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
40977615 TTAAAGATAA
*
40977625 TTTTAAATAATTTTATATTT
1 TTTTAAATAATTTTAAATTT
40977645 TTTTAAAATAATTTTAAATTT
1 TTTT-AAATAATTTTAAATTT
40977666 TTT
1 TTT
40977669 AATATTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAAATAATTTTAAATTT
Found at i:40977669 original size:20 final size:21
Alignment explanation
Indices: 40977625--40977670 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
40977615 TTAAAGATAA
*
40977625 TTTT-AAATAATTTTATATTT
1 TTTTAAAATAATTTTATAATT
40977645 TTTTAAAATAATTTTA-AATT
1 TTTTAAAATAATTTTATAATT
40977665 TTTTAA
1 TTTTAA
40977671 TATTTTCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTAAAATAATTTTATAATT
Found at i:40978671 original size:7 final size:7
Alignment explanation
Indices: 40978659--40978683 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40978649 AGTGGATTGA
40978659 TATTTAG
1 TATTTAG
40978666 TATTTAG
1 TATTTAG
40978673 TATTTAG
1 TATTTAG
40978680 TATT
1 TATT
40978684 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:40978979 original size:30 final size:30
Alignment explanation
Indices: 40978945--40979037 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 30
40978935 GCTATTAGGT
40978945 ACGGATTGGCCTAGATACTGGTCAGAGTAC
1 ACGGATTGGCCTAGATACTGGTCAGAGTAC
** * *
40978975 ACGGAAATGTGG-GAAAAT-C-GG-CATGAG--G
1 ACGG--AT-TGGCCTAGATACTGGTCA-GAGTAC
40979003 ACGGATTGGCCTAGATACTGGTCAGAGTAC
1 ACGGATTGGCCTAGATACTGGTCAGAGTAC
40979033 ACGGA
1 ACGGA
40979038 AATGTGGGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 20
0.62 0.11 0.27
Matches are distributed among these distances:
25 3 0.07
26 5 0.11
27 1 0.02
28 9 0.20
29 4 0.09
30 14 0.31
31 1 0.02
32 5 0.11
33 3 0.07
ACGTcount: A:0.30, C:0.17, G:0.33, T:0.19
Consensus pattern (30 bp):
ACGGATTGGCCTAGATACTGGTCAGAGTAC
Found at i:40979035 original size:58 final size:58
Alignment explanation
Indices: 40978945--40979058 Score: 228
Period size: 58 Copynumber: 2.0 Consensus size: 58
40978935 GCTATTAGGT
40978945 ACGGATTGGCCTAGATACTGGTCAGAGTACACGGAAATGTGGGAAAATCGGCATGAGG
1 ACGGATTGGCCTAGATACTGGTCAGAGTACACGGAAATGTGGGAAAATCGGCATGAGG
40979003 ACGGATTGGCCTAGATACTGGTCAGAGTACACGGAAATGTGGGAAAATCGGCATGA
1 ACGGATTGGCCTAGATACTGGTCAGAGTACACGGAAATGTGGGAAAATCGGCATGA
40979059 ATATCTACCT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.32, C:0.16, G:0.33, T:0.19
Consensus pattern (58 bp):
ACGGATTGGCCTAGATACTGGTCAGAGTACACGGAAATGTGGGAAAATCGGCATGAGG
Found at i:40979123 original size:21 final size:21
Alignment explanation
Indices: 40979097--40979139 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40979087 GTTCCAGAGT
40979097 TAGCGTGCGTTCCAGAATACA
1 TAGCGTGCGTTCCAGAATACA
40979118 TAGCGTGCGTTCCAGAATACA
1 TAGCGTGCGTTCCAGAATACA
40979139 T
1 T
40979140 GCCATGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (21 bp):
TAGCGTGCGTTCCAGAATACA
Found at i:40980016 original size:57 final size:57
Alignment explanation
Indices: 40979942--40980864 Score: 1810
Period size: 57 Copynumber: 16.2 Consensus size: 57
40979932 TACCCTAACC
*
40979942 TAATTTATTTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
40979999 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
40980056 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
40980113 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
40980170 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
40980227 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
40980284 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
40980341 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
40980398 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
40980455 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
40980512 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
40980569 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
40980626 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
40980683 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
40980740 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
**
40980797 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA-CCTAATT
40980855 TAATTTAATT
1 TAATTTAATT
40980865 NNNNNNNNNN
Statistics
Matches: 862, Mismatches: 3, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
57 847 0.98
58 15 0.02
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (57 bp):
TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATT
Found at i:40994507 original size:25 final size:24
Alignment explanation
Indices: 40994479--40994528 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
40994469 ATATATGCGT
40994479 ATAAAT-ATAGAAATAATAAGTGATA
1 ATAAATAATA-AAATAATAA-TGATA
*
40994504 ATAAATAATATAATAATAATGATA
1 ATAAATAATAAAATAATAATGATA
40994528 A
1 A
40994529 AAGTAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 14 0.61
26 3 0.13
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (24 bp):
ATAAATAATAAAATAATAATGATA
Found at i:40994518 original size:12 final size:12
Alignment explanation
Indices: 40994490--40994528 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
40994480 TAAATATAGA
40994490 AATAATAAGTGAT
1 AATAATAA-TGAT
40994503 AATAAATAAT-AT
1 AAT-AATAATGAT
40994515 AATAATAATGAT
1 AATAATAATGAT
40994527 AA
1 AA
40994529 AAGTAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.25
12 9 0.38
13 4 0.17
14 5 0.21
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (12 bp):
AATAATAATGAT
Found at i:40995269 original size:21 final size:21
Alignment explanation
Indices: 40995235--40995274 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40995225 TATAGGCCGC
40995235 AAAAGAGAAAGAAAATAAATCG
1 AAAAGAGAAAGAAAA-AAATCG
*
40995257 AAAA-AGAAGGAAAAAAAT
1 AAAAGAGAAAGAAAAAAAT
40995275 ATTGCTTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.07
Consensus pattern (21 bp):
AAAAGAGAAAGAAAAAAATCG
Found at i:40999813 original size:85 final size:81
Alignment explanation
Indices: 40999704--41000367 Score: 367
Period size: 85 Copynumber: 8.0 Consensus size: 81
40999694 GTTTCTTCTG
* * *
40999704 TCTGCTCCACTGCAACTTCGGGGAGATAAGACTGGATGCGATCTGCTCTACTGTAACTTTAGCA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAG-AT
* * *
40999768 AGATAATATATGTGGTTTTAA
65 AGAT-A-AGATCT--TTTCAA
* *
40999789 TTTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGATA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGATA
40999854 GATAAGATCTTTTCAA
66 GATAAGATCTTTTCAA
* * * * * * *
40999870 TCTGCTCCACTGTAACTTCAGGGAGATAGGATTGGTTTCTTCTG-TCTGCGCCACTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGG---ATGC-GATCTGCTCTACTGCAACTTCA
** **
40999934 GGGAGATAAGA-CTGGAT-AGGA
62 GATAGATAAGATCT-TTTCA--A
* * * *** ** **
40999955 TCTGCTCTACTGCAACTTTAGAGAGATAAGATCT-G-TTTAATCCACTCTACTGCAACTTCAGGG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTGGATGCGATCTGCTCTACTGCAACTTCAGAT
* * **
41000018 AGATAGGATTGGTTTCTTCTG
65 AGATAAGA-T--CTT-TTCAA
* * * *
41000039 TCTGCTCCACTACCACTTCAGGGAGATAAGACTGGATACGATCTGCTCTACTGCAACTTCAGAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGATA
41000104 GATAAGATCTGTTT-AA
66 GATAAGATCT-TTTCAA
* * * * * * * *
41000120 TCTGCTCCACTGCAACTTCAGGAAGATAGGATTGGTTTCTTCTATCTGCTCCACTGTAACTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGG---ATGCGATCTGCTCTACTGCAACTTCAG
** * * *
41000185 GGAGATAAGA-CTGGATACGA
63 ATAGATAAGATCT--TTTCAA
* * * *** ** * *
41000205 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCACTCCACTGCAACTTTAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-C--TGGATGCGATCTGCTCTACTGCAACTTCAG
** * **
41000270 GGAGATAGGAT-TGTTTCTTTTG
63 ATAGATAAGATCT-TTTC---AA
* * * *
41000292 TCTGCTCCACTGCAACTTCAGGGAGACAAGACTGTATGCAATCTGCTCT-CTGCAACTTCAGAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGATA
41000356 GATAAGATCTTT
66 GATAAGATCTTT
41000368 GGTTTTAATC
Statistics
Matches: 449, Mismatches: 98, Indels: 66
0.73 0.16 0.11
Matches are distributed among these distances:
81 94 0.21
82 3 0.01
83 34 0.08
84 106 0.24
85 179 0.40
86 2 0.00
87 28 0.06
88 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (81 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGATA
GATAAGATCTTTTCAA
Found at i:40999899 original size:210 final size:210
Alignment explanation
Indices: 40999600--40999983 Score: 587
Period size: 210 Copynumber: 1.8 Consensus size: 210
40999590 ACAATTTTAA
* *
40999600 AGATAAGTCTGATGCGATCTACTCTCTGCAACTTCAGAGAGATAAGATCTATGGCTTTAATCCGC
1 AGATAAGACTGATGCGATCTACTCTCTGCAACTTCAGAGAGATAAGATCTAT-G-TTCAATCCGC
* * *
40999665 TCCACTGCAGCTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCAACTTCGGGGAGA
64 TCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCGCCACTGCAACTTCAGGGAGA
*
40999730 TAAGACTGGAT-GCGATCTGCTCTACTGTAACTTTAGCA-AGATAATATATGTGGTTTTAATTTG
129 TAAGACTGGATAG-GATCTGCTCTACTGCAACTTTAG-AGAGATAATATATGTGGTTTTAATTTG
40999793 CTCCACTGCAACTTCAGGG
192 CTCCACTGCAACTTCAGGG
* * * *
40999812 AGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGATAGATAAGATCT-T-TTCAATCTGC
1 AGATAAGACT-GATGCGATCTACTCT-CTGCAACTTCAGAGAGATAAGATCTATGTTCAATCCGC
*
40999875 TCCACTGTAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCGCCACTGCAACTTCAGGGAGA
64 TCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCGCCACTGCAACTTCAGGGAGA
40999940 TAAGACTGGATAGGATCTGCTCTACTGCAACTTTAGAGAGATAA
129 TAAGACTGGATAGGATCTGCTCTACTGCAACTTTAGAGAGATAA
40999984 GATCTGTTTA
Statistics
Matches: 157, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
209 1 0.01
210 108 0.69
211 1 0.01
212 9 0.06
213 14 0.09
214 24 0.15
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (210 bp):
AGATAAGACTGATGCGATCTACTCTCTGCAACTTCAGAGAGATAAGATCTATGTTCAATCCGCTC
CACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCGCCACTGCAACTTCAGGGAGATA
AGACTGGATAGGATCTGCTCTACTGCAACTTTAGAGAGATAATATATGTGGTTTTAATTTGCTCC
ACTGCAACTTCAGGG
Found at i:40999924 original size:125 final size:125
Alignment explanation
Indices: 40999791--41000417 Score: 904
Period size: 125 Copynumber: 5.0 Consensus size: 125
40999781 GGTTTTAATT
* *
40999791 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGATAGA
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGA
** *
40999856 TAAGATCT-TTTCAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTGGTTTCTTCTGTC
66 TAAGATCTGTTT-AATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTC
* *
40999916 TGCGCCACTGCAACTTCAGGGAGATAAGACTGGATAG-GATCTGCTCTACTGCAACTTTAGAGAG
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGAT-GCGATCTGCTCTACTGCAACTTCAGAGAG
*
40999980 ATAAGATCTGTTTAATCCACTCTACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTC
65 ATAAGATCTGTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTC
* * *
41000041 TGCTCCACTACCACTTCAGGGAGATAAGACTGGATACGATCTGCTCTACTGCAACTTCAGAGAGA
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGA
** * *
41000106 TAAGATCTGTTTAATCTGCTCCACTGCAACTTCAGGAAGATAGGATTGGTTTCTTCTATC
66 TAAGATCTGTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTC
* *
41000166 TGCTCCACTGTAACTTCAGGGAGATAAGACTGGATACGATCTGCTCTACTGCAACTTCAGAGAGA
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGA
* *
41000231 TAAGATCTGTGGTTTTAATCCACTCCACTGCAACTTTAGGGAGATAGGATT-GTTTCTTTTGTC
66 TAAGATC--T-G-TTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTC
* * *
41000294 TGCTCCACTGCAACTTCAGGGAGACAAGACTGTATGCAATCTGCTCT-CTGCAACTTCAGAGAGA
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGA
**
41000358 TAAGATCTTTGGTTTTAATCCACTCCACTGCAACCTT-AGGGAGATAGGATTATTTTCTTC
66 TAAGATC--T-G-TTTAATCCACTCCACTGCAA-CTTCAGGGAGATAGGATTGGTTTCTTC
41000418 AATTTTTTTA
Statistics
Matches: 459, Mismatches: 34, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
125 295 0.64
126 4 0.01
127 64 0.14
128 62 0.14
129 34 0.07
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (125 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGA
TAAGATCTGTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTC
Found at i:41000085 original size:210 final size:209
Alignment explanation
Indices: 40999628--41000147 Score: 551
Period size: 210 Copynumber: 2.5 Consensus size: 209
40999618 CTACTCTCTG
* * *
40999628 CAACTTCAGAGAGATAAGATCTATGGCTTTAATCCGCTCCACTGCAGCTTCAGGGAGATAGGATT
1 CAACTTCAGAGAGATAAGATCTAT-AC---AATCTGCTCCACTGCAACTTCAGGGAGATAGGATT
* *
40999693 GGTTTCTTCTGTCTGCTCCACTGCAACTTCGGGGAGATAAGACTGGATGCGATCTGCTCTACTGT
62 GGTTTCTTCTGTCTGC-CCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGC
* * ***
40999758 AACTTTAGCAAGATAATATATGTGGTTTTAATTTGCTCCACTGCAACTTCAGGGAGATAAGACTG
126 AACTTTAGCAAGATAATAGATCTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAAGACTG
* * *
40999823 GATGTGATCTGCTCTACTG
191 GATCTGATCTGCTCCACTA
* * * *
40999842 CAACTTCAGATAGATAAGATCTTTTCAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTGGTT
1 CAACTTCAGAGAGATAAGATCTATACAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGGTT
40999907 TCTTCTGTCTGCGCCACTGCAACTTCAGGGAGATAAGACTGGATAG-GATCTGCTCTACTGCAAC
66 TCTTCTGTCTGC-CCACTGCAACTTCAGGGAGATAAGACTGGAT-GCGATCTGCTCTACTGCAAC
* * *
40999971 TTTAG-AGAGAT-A-AGATCT-G-TTTAATCCACTCTACTGCAACTTCAGGGAGATAGGATTGGT
129 TTTAGCA-AGATAATAGATCTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAAGACTGG-
*
41000031 TTCTTCTG-TCTGCTCCACTA
192 ---ATCTGATCTGCTCCACTA
* * * * * *
41000051 CCACTTCAGGGAGATAAGA-CTGGATACGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCT-
1 CAACTTCAGAGAGATAAGATCT--ATACAATCTGCTCCACTGCAACTTCAGGGAGATAGGAT-TG
** *
41000114 GTTTAATCTG-CT--CCACTGCAACTTCAGGAAGATA
63 GTTTCTTCTGTCTGCCCACTGCAACTTCAGGGAGATA
41000148 GGATTGGTTT
Statistics
Matches: 263, Mismatches: 34, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
206 55 0.21
207 1 0.00
208 6 0.02
209 30 0.11
210 146 0.56
211 2 0.01
213 1 0.00
214 22 0.08
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (209 bp):
CAACTTCAGAGAGATAAGATCTATACAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGGTT
TCTTCTGTCTGCCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTT
TAGCAAGATAATAGATCTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAAGACTGGATCT
GATCTGCTCCACTA
Found at i:41000514 original size:50 final size:50
Alignment explanation
Indices: 41000450--41000622 Score: 190
Period size: 50 Copynumber: 3.5 Consensus size: 50
41000440 GGGAAACAAT
* * *
41000450 ATTCACTGTCGTAGCTTCAATCTATTCCATTGCACAGCCAGGGAAGTAAG
1 ATTCGCTGTTGTAGCTTCAATCTATTCCACTGCACAGCCAGGGAAGTAAG
* ** * * *
41000500 ATTCGCTGTTGTAGCTTCAATCTTTTTAACTGCA-ATGTCGGGGAAGCAAG
1 ATTCGCTGTTGTAGCTTCAATCTATTCCACTGCACA-GCCAGGGAAGTAAG
* * *
41000550 ATTCGCCT-TTGTGGCTTCAATCTGTTCCACTGCACCA-CCTGGGAAGTAAG
1 ATTCG-CTGTTGTAGCTTCAATCTATTCCACTGCA-CAGCCAGGGAAGTAAG
41000600 ATTCGCTGTTGTAGCTTCAATCT
1 ATTCGCTGTTGTAGCTTCAATCT
41000623 TTTCATCTGT
Statistics
Matches: 101, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
49 3 0.03
50 95 0.94
51 2 0.02
52 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (50 bp):
ATTCGCTGTTGTAGCTTCAATCTATTCCACTGCACAGCCAGGGAAGTAAG
Found at i:41000594 original size:100 final size:100
Alignment explanation
Indices: 41000414--41000625 Score: 284
Period size: 100 Copynumber: 2.1 Consensus size: 100
41000404 GGATTATTTT
* * * *
41000414 CTTCAATTTTTTTAACTGTAATATTGGGGAAACAATATTCACTGTCGTAGCTTCAATCTATTCCA
1 CTTCAATCTTTTTAACTGCAATATCGGGGAAACAAGATTCACTGTCGTAGCTTCAATCTATTCCA
*
41000479 TTGCACAGCCAGGGAAGTAAGATTCGCTGTTGTAG
66 CTGCACAGCCAGGGAAGTAAGATTCGCTGTTGTAG
* * * * * *
41000514 CTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCT-TTGTGGCTTCAATCTGTTCC
1 CTTCAATCTTTTTAACTGCAATATCGGGGAAACAAGATTC-ACTGTCGTAGCTTCAATCTATTCC
*
41000578 ACTGCACCA-CCTGGGAAGTAAGATTCGCTGTTGTAG
65 ACTGCA-CAGCCAGGGAAGTAAGATTCGCTGTTGTAG
41000614 CTTCAATCTTTT
1 CTTCAATCTTTT
41000626 CATCTGTATT
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
100 94 0.96
101 4 0.04
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (100 bp):
CTTCAATCTTTTTAACTGCAATATCGGGGAAACAAGATTCACTGTCGTAGCTTCAATCTATTCCA
CTGCACAGCCAGGGAAGTAAGATTCGCTGTTGTAG
Found at i:41000903 original size:44 final size:44
Alignment explanation
Indices: 41000855--41001000 Score: 222
Period size: 44 Copynumber: 3.3 Consensus size: 44
41000845 AGGGAGGCAA
* *
41000855 GGCTTACAATCTTCAACTTATTCCACTGCTGTCCAGGGAGATAG
1 GGCTTACAATCTTCAACCTATTCCACTGCTGTCCAAGGAGATAG
41000899 GGCTTACAATCTTCAACCTATTCCACTGCTGTCCAAGGAGATAG
1 GGCTTACAATCTTCAACCTATTCCACTGCTGTCCAAGGAGATAG
* * *
41000943 GACTTGCAATCTTCAACCTATTCCACTGCTGTCCATGGAGATA-
1 GGCTTACAATCTTCAACCTATTCCACTGCTGTCCAAGGAGATAG
*
41000986 GGATTCACAATCTTC
1 GGCTT-ACAATCTTC
41001001 GATCTACTTC
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
43 3 0.03
44 90 0.97
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (44 bp):
GGCTTACAATCTTCAACCTATTCCACTGCTGTCCAAGGAGATAG
Found at i:41002293 original size:6 final size:6
Alignment explanation
Indices: 41002284--41002311 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
41002274 TCCATTTTTA
41002284 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
41002312 TATCACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:41003107 original size:25 final size:25
Alignment explanation
Indices: 41003079--41003144 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
41003069 AAGAGAGTTC
*
41003079 AAAAGAATGAAAGAATAATTATTCA
1 AAAAGAATGAAAGAATAATTACTCA
* *
41003104 AAAAGAATGAAAGAATATTTGCTCA
1 AAAAGAATGAAAGAATAATTACTCA
41003129 AAAATGAATGTAAAGA
1 AAAA-GAATG-AAAGA
41003145 TGTATTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 26 0.72
26 5 0.14
27 5 0.14
ACGTcount: A:0.58, C:0.05, G:0.15, T:0.23
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:41007043 original size:3 final size:3
Alignment explanation
Indices: 41007035--41007080 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
41007025 GTACATGGTT
41007035 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
41007081 GAGTACTAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:41010156 original size:30 final size:30
Alignment explanation
Indices: 41010122--41010178 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
41010112 CCATCTCGTT
*
41010122 GAGCTCCATTTAGCTC-ATTTCCAGCTCCAA
1 GAGCTCCAATTAGCTCAATTT-CAGCTCCAA
*
41010152 GAGCTCGAATTAGCTCAATTTCAGCTC
1 GAGCTCCAATTAGCTCAATTTCAGCTC
41010179 GATAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.30
Consensus pattern (30 bp):
GAGCTCCAATTAGCTCAATTTCAGCTCCAA
Found at i:41013341 original size:24 final size:24
Alignment explanation
Indices: 41013307--41013393 Score: 104
Period size: 24 Copynumber: 3.6 Consensus size: 24
41013297 GTGGATGTTC
*
41013307 AACCTTTCACCTTTCATCTCCCTT
1 AACCTTTCACCTTTCATCTTCCTT
* *
41013331 AACCTTCCACCTTTCATCTTCTTT
1 AACCTTTCACCTTTCATCTTCCTT
*
41013355 AA-CTTTTAGCCTTTCATCTTCCTT
1 AACCTTTCA-CCTTTCATCTTCCTT
*
41013379 AAACCTTTCATCTTT
1 -AACCTTTCACCTTT
41013394 TTGTAACCCC
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
23 4 0.08
24 37 0.71
25 6 0.12
26 5 0.10
ACGTcount: A:0.18, C:0.34, G:0.01, T:0.46
Consensus pattern (24 bp):
AACCTTTCACCTTTCATCTTCCTT
Found at i:41016572 original size:19 final size:19
Alignment explanation
Indices: 41016545--41016637 Score: 68
Period size: 19 Copynumber: 5.1 Consensus size: 19
41016535 AATAAATTAC
*
41016545 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTAAGT
*
41016564 TCATTTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
** *** *
41016583 TGC-T-GGAACAAATT-ACT
1 T-CATCTTAGTTAATTAAGT
41016600 -CATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
*
41016618 TCATCTTAGTTAATTTAGT
1 TCATCTTAGTTAATTAAGT
41016637 T
1 T
41016638 GCTGGAATAA
Statistics
Matches: 54, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
15 1 0.02
16 1 0.02
17 7 0.13
18 7 0.13
19 37 0.69
20 1 0.02
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:41016589 original size:54 final size:54
Alignment explanation
Indices: 41016526--41016647 Score: 208
Period size: 54 Copynumber: 2.3 Consensus size: 54
41016516 ATAAGTATTT
* *
41016526 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATTTTAGTTAATTA
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGTTAATTA
* *
41016580 AGTTGCTGGAACAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGTTAATTT
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGTTAATTA
41016634 AGTTGCTGGAATAA
1 AGTTGCTGGAATAA
41016648 TTTATTGTTG
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (54 bp):
AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGTTAATTA
Found at i:41016755 original size:10 final size:10
Alignment explanation
Indices: 41016740--41016767 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
41016730 TAAGTCTAAT
41016740 ATGTGTTTTA
1 ATGTGTTTTA
41016750 ATGTGTTTTA
1 ATGTGTTTTA
41016760 ATGTGTTT
1 ATGTGTTT
41016768 GTTAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.21, T:0.61
Consensus pattern (10 bp):
ATGTGTTTTA
Found at i:41018288 original size:20 final size:20
Alignment explanation
Indices: 41018263--41018308 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
41018253 AGGTGGTTTG
41018263 TATTTAGGGTGGAGGCAGCA
1 TATTTAGGGTGGAGGCAGCA
41018283 TATTTAGGGTGGAGGCAGCA
1 TATTTAGGGTGGAGGCAGCA
41018303 TATTTA
1 TATTTA
41018309 TGGCCATCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.09, G:0.35, T:0.30
Consensus pattern (20 bp):
TATTTAGGGTGGAGGCAGCA
Found at i:41021315 original size:57 final size:57
Alignment explanation
Indices: 41021252--41021368 Score: 216
Period size: 57 Copynumber: 2.1 Consensus size: 57
41021242 TATCAAACAA
* *
41021252 TCAATTCAAGATATATTAGGGTTTATTGCAGGGTGTATTAAAGAATTGGAATCCATT
1 TCAATTCAAGATATATCAGGGTTTATTGCAGGGTATATTAAAGAATTGGAATCCATT
41021309 TCAATTCAAGATATATCAGGGTTTATTGCAGGGTATATTAAAGAATTGGAATCCATT
1 TCAATTCAAGATATATCAGGGTTTATTGCAGGGTATATTAAAGAATTGGAATCCATT
41021366 TCA
1 TCA
41021369 GATGAGAGCC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (57 bp):
TCAATTCAAGATATATCAGGGTTTATTGCAGGGTATATTAAAGAATTGGAATCCATT
Found at i:41023358 original size:44 final size:43
Alignment explanation
Indices: 41023295--41023624 Score: 235
Period size: 44 Copynumber: 7.5 Consensus size: 43
41023285 GAAATAGATC
* *
41023295 GAAGATTGTGAATCCTATCTCCTTGGACAATAGCGACATAGGTT
1 GAAGATTGTGAATCCTATCTCCCTGGACAGTAGCGA-ATAGGTT
* *
41023339 GAAGATTGTGAATCCTATCTCCCTGGATAGCAGCGAAATAGGTT
1 GAAGATTGTGAATCCTATCTCCCTGGACAGTAGCG-AATAGGTT
* * *
41023383 GAAGATTGTGAGTCCTATCTCCCTAGACAGTAGTGGAATAGGTT
1 GAAGATTGTGAATCCTATCTCCCTGGACAGTAG-CGAATAGGTT
** * *
41023427 GAAGATT-ACAAGACTTATCTCCCTGAGCAGCAGTA--GAATAGGTT
1 GAAGATTGTGAA-TCCTATCTCCCTG-G-A-CAGTAGCGAATAGGTT
*
41023471 GAAGATTG-CAAGTCCTATCTCCCTGGGTAGCAGT-G-GAATAGGTT
1 GAAGATTGTGAA-TCCTATCTCCCT-GG-A-CAGTAGCGAATAGGTT
** * * * * *
41023515 GAAGATTACGAATCTTATCTCCCTGGTCAATAGTGGAATAAGTT
1 GAAGATTGTGAATCCTATCTCCCTGGACAGTAG-CGAATAGGTT
** ** * *
41023559 GAAGATTACGAATGTTATCTCCCTGGTCAACAGT-G-GAATAAGTG
1 GAAGATTGTGAATCCTATCTCCCTGG---ACAGTAGCGAATAGGTT
*
41023603 GAAGATCGTGAATCCTATCTCC
1 GAAGATTGTGAATCCTATCTCC
41023625 TTGAGTAGTA
Statistics
Matches: 237, Mismatches: 33, Indels: 32
0.78 0.11 0.11
Matches are distributed among these distances:
41 3 0.01
42 1 0.00
43 3 0.01
44 214 0.90
45 6 0.03
46 2 0.01
47 8 0.03
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (43 bp):
GAAGATTGTGAATCCTATCTCCCTGGACAGTAGCGAATAGGTT
Found at i:41023473 original size:132 final size:132
Alignment explanation
Indices: 41023332--41023624 Score: 369
Period size: 132 Copynumber: 2.2 Consensus size: 132
41023322 CAATAGCGAC
** *
41023332 ATAGGTTGAAGATTGTGAATCCTATCTCCCTGGATAGCAGCGAAATAGGTTGAAGATTGTGAGTC
1 ATAGGTTGAAGATTGTGAATCCTATCTCCCTGGATAGCAGCGAAATAGGTTGAAGATTACGAATC
* * *
41023397 CTATCTCCCTAGACAGTAGTGGAATAGGTTGAAGATTAC-AA-GACTTATCTCCCTGAG-CAGCA
66 CTATCTCCCTAGACAATAGTGGAATAAGTTGAAGATTACGAATG--TTATCTCCCTG-GTCAACA
41023459 GTAGA
128 GTAGA
* * * *
41023464 ATAGGTTGAAGATTG-CAAGTCCTATCTCCCTGGGTAGCAGTGGAATAGGTTGAAGATTACGAAT
1 ATAGGTTGAAGATTGTGAA-TCCTATCTCCCTGGATAGCAGCGAAATAGGTTGAAGATTACGAAT
* * *
41023528 CTTATCTCCCTGGTCAATAGTGGAATAAGTTGAAGATTACGAATGTTATCTCCCTGGTCAACAGT
65 CCTATCTCCCTAGACAATAGTGGAATAAGTTGAAGATTACGAATGTTATCTCCCTGGTCAACAGT
*
41023593 GGA
130 AGA
* * *
41023596 ATAAGTGGAAGATCGTGAATCCTATCTCC
1 ATAGGTTGAAGATTGTGAATCCTATCTCC
41023625 TTGAGTAGTA
Statistics
Matches: 138, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
131 3 0.02
132 130 0.94
133 4 0.03
134 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (132 bp):
ATAGGTTGAAGATTGTGAATCCTATCTCCCTGGATAGCAGCGAAATAGGTTGAAGATTACGAATC
CTATCTCCCTAGACAATAGTGGAATAAGTTGAAGATTACGAATGTTATCTCCCTGGTCAACAGTA
GA
Found at i:41023554 original size:88 final size:87
Alignment explanation
Indices: 41023332--41023608 Score: 276
Period size: 88 Copynumber: 3.1 Consensus size: 87
41023322 CAATAGCGAC
** * * * **
41023332 ATAGGTTGAAGATTGTGAATCCTATCTCCCTGGAT-AGCAGCGAAATAGGTTGAAGATTGTGAGT
1 ATAGGTTGAAGATTACGAATCTTATCTCCCTGG-TCAGCAGTGGAATAGGTTGAAGATTGCAAGT
** *
41023396 CCTATCTCCCTAGACAGTAGTGGA
65 CCTATCTCCCT-GGTAGCAGTGGA
* *
41023420 ATAGGTTGAAGATTAC-AAGACTTATCTCCCTGAG-CAGCAGTAGAATAGGTTGAAGATTGCAAG
1 ATAGGTTGAAGATTACGAA-TCTTATCTCCCTG-GTCAGCAGTGGAATAGGTTGAAGATTGCAAG
41023483 TCCTATCTCCCTGGGTAGCAGTGGA
64 TCCTATCTCCCT-GGTAGCAGTGGA
** * *
41023508 ATAGGTTGAAGATTACGAATCTTATCTCCCTGGTCAATAGTGGAATAAGTTGAAGATTACGAATG
1 ATAGGTTGAAGATTACGAATCTTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGC-AA-G
*
41023573 T--TATCTCCCTGGTCAACAGTGGA
64 TCCTATCTCCCTGGT-AGCAGTGGA
* *
41023596 ATAAGTGGAAGAT
1 ATAGGTTGAAGAT
41023609 CGTGAATCCT
Statistics
Matches: 159, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
87 6 0.04
88 146 0.92
89 5 0.03
90 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.28
Consensus pattern (87 bp):
ATAGGTTGAAGATTACGAATCTTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGCAAGTC
CTATCTCCCTGGTAGCAGTGGA
Found at i:41023638 original size:132 final size:129
Alignment explanation
Indices: 41023339--41023671 Score: 352
Period size: 132 Copynumber: 2.5 Consensus size: 129
41023329 GACATAGGTT
* * ** * *
41023339 GAAGATTGTGAATCCTATCTCCCTGGATAGCAGCGAAATAGGTTGAAGATTGTGAGTCCTATCTC
1 GAAGA-TGTGAATCCTATCTCCCTGG-TAGCAGTGGAATAGGTTGAAGATTACGAATCTTATCTC
* * * *
41023404 CCTAGACAGTAGTGGAATAGGTTGAAGATTACAAGACTTATCTCCCTGAGCAGCAGTAGAATAGG
64 CCTAGACAATAGTGGAATAAGTTGAAGATTACAAGA-TTATCTCCCTGAGCAACAGTAGAATAAG
*
41023469 TT
128 TG
41023471 GAAGAT-TGCAAGTCCTATCTCCCTGGGTAGCAGTGGAATAGGTTGAAGATTACGAATCTTATCT
1 GAAGATGTG-AA-TCCTATCTCCCT-GGTAGCAGTGGAATAGGTTGAAGATTACGAATCTTATCT
* * *
41023535 CCCTGGTCAATAGTGGAATAAGTTGAAGATTACGAATG-TTATCTCCCTG-GTCAACAGTGGAAT
63 CCCTAGACAATAGTGGAATAAGTTGAAGATTAC-AA-GATTATCTCCCTGAG-CAACAGTAGAAT
41023598 AAGTG
125 AAGTG
* * * *
41023603 GAAGATCGTGAATCCTATCTCCTTGAGTAGTAGTGGAGTAGGCTG-AGAATTAC-AGATCTTATC
1 GAAGAT-GTGAATCCTATCTCCCTG-GTAGCAGTGGAATAGGTTGAAG-ATTACGA-ATCTTATC
41023666 TCCCTA
62 TCCCTA
41023672 AGCAGTAGTG
Statistics
Matches: 171, Mismatches: 19, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
130 2 0.01
131 8 0.05
132 152 0.89
133 6 0.04
134 3 0.02
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (129 bp):
GAAGATGTGAATCCTATCTCCCTGGTAGCAGTGGAATAGGTTGAAGATTACGAATCTTATCTCCC
TAGACAATAGTGGAATAAGTTGAAGATTACAAGATTATCTCCCTGAGCAACAGTAGAATAAGTG
Found at i:41023774 original size:44 final size:44
Alignment explanation
Indices: 41023375--41023770 Score: 242
Period size: 44 Copynumber: 9.0 Consensus size: 44
41023365 ATAGCAGCGA
** *
41023375 AATAGGTTGAAGATT-GTGAGTCCTATCTCCCT-AGACAGTAGTGG
1 AATAGGTTGAAGATTACAGA-TCTTATCTCCCTGAG-CAGTAGTGG
* *
41023419 AATAGGTTGAAGATTACAAGA-CTTATCTCCCTGAGCAGCAGTAG
1 AATAGGTTGAAGATTAC-AGATCTTATCTCCCTGAGCAGTAGTGG
* * * * *
41023463 AATAGGTTGAAGATTGCA-AGTCCTATCTCCCTGGGTAGCAGTGG
1 AATAGGTTGAAGATTACAGA-TCTTATCTCCCTGAGCAGTAGTGG
*
41023507 AATAGGTTGAAGATTAC-GAATCTTATCTCCCTG-GTCAATAGTGG
1 AATAGGTTGAAGATTACAG-ATCTTATCTCCCTGAG-CAGTAGTGG
* * **
41023551 AATAAGTTGAAGATTAC-GAATGTTATCTCCCTG-GTCAACAGTGG
1 AATAGGTTGAAGATTACAG-ATCTTATCTCCCTGAG-CAGTAGTGG
* * * * * *
41023595 AATAAGTGGAAGA-T-CGTGAATCCTATCTCCTTGAGTAGTAGTGG
1 AATAGGTTGAAGATTAC-AG-ATCTTATCTCCCTGAGCAGTAGTGG
* * *
41023639 AGTAGGCTG-AGAATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 AATAGGTTGAAG-ATTACAGATCTTATCTCCCTGAGCAGTAGTGG
** * * ** * * * * *
41023683 AGCAGATCGAAG-TCCCCAG-CCTTATTTCCCTGAGTAGCAGCGG
1 AATAGGTTGAAGAT-TACAGATCTTATCTCCCTGAGCAGTAGTGG
* * * *
41023726 AGTAGGTTGAAAATTACAGATGTTATCTCCCTAAGCAGTAGTGG
1 AATAGGTTGAAGATTACAGATCTTATCTCCCTGAGCAGTAGTGG
41023770 A
1 A
41023771 GTAGATCGAA
Statistics
Matches: 275, Mismatches: 59, Indels: 36
0.74 0.16 0.10
Matches are distributed among these distances:
42 2 0.01
43 35 0.13
44 227 0.83
45 8 0.03
46 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
AATAGGTTGAAGATTACAGATCTTATCTCCCTGAGCAGTAGTGG
Done.