Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 36 of 167
Found at i:10987488 original size:16 final size:16
Alignment explanation
Indices: 10987467--10987497 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
10987457 TTGTCACCCT
10987467 ATGTACTCTTAGACAA
1 ATGTACTCTTAGACAA
10987483 ATGTACTCTTAGACA
1 ATGTACTCTTAGACA
10987498 TGGTCTATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (16 bp):
ATGTACTCTTAGACAA
Found at i:10994940 original size:20 final size:20
Alignment explanation
Indices: 10994917--10994962 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
10994907 TTACACTTCG
*
10994917 GTGCCTCTATTTGCAC-TTT
1 GTGCCTCTAATTGCACATTT
10994936 AGTGCCTCTAATTGCACATTT
1 -GTGCCTCTAATTGCACATTT
10994957 GTGCCT
1 GTGCCT
10994963 ATGTTACGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.15, C:0.26, G:0.17, T:0.41
Consensus pattern (20 bp):
GTGCCTCTAATTGCACATTT
Found at i:11000008 original size:40 final size:39
Alignment explanation
Indices: 10999907--11000101 Score: 167
Period size: 40 Copynumber: 4.9 Consensus size: 39
10999897 TGAATGTGTG
* * * * * *
10999907 TTAGGGTATCAAAGTACAAACAAGTGCACGTATGTGCAA
1 TTAGGGTACCGAAGTACAAACAGGGGCACGTATGTGTAT
** * * * *
10999946 TCCGAGGTACCAAAATAAAAACAGGGGTACGTATGTGTAT
1 TTAG-GGTACCGAAGTACAAACAGGGGCACGTATGTGTAT
* * *
10999986 TTAGGGATACCGGAGTACAAACAGGGGCACTTATGTGCAT
1 TTAGGG-TACCGAAGTACAAACAGGGGCACGTATGTGTAT
* * * *
11000026 TTAGGGGCACCGAAGTACATATAGGGGCATGTATGT-TCAT
1 TTA-GGGTACCGAAGTACAAACAGGGGCACGTATGTGT-AT
*
11000066 TTAGGGTACCGAAGTACAAACAGGGGCACATATGTG
1 TTAGGGTACCGAAGTACAAACAGGGGCACGTATGTG
11000102 CATTCAAGGA
Statistics
Matches: 120, Mismatches: 31, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
39 31 0.26
40 86 0.72
41 3 0.03
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (39 bp):
TTAGGGTACCGAAGTACAAACAGGGGCACGTATGTGTAT
Found at i:11000021 original size:80 final size:79
Alignment explanation
Indices: 10999907--11000103 Score: 198
Period size: 80 Copynumber: 2.5 Consensus size: 79
10999897 TGAATGTGTG
* * * * * * *
10999907 TTAGGGTATCAAAGTACAAACAAGTGCACGTATGTGCAATCCGAGGTACCAAAATAAAAACAGGG
1 TTAGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATCAGAGGCACCAAAATAAAAACAGGG
*
10999972 GTACGTATGTGT-AT
66 GCACGTATGT-TCAT
* * * * * * * * * *
10999986 TTAGGGATACCGGAGTACAAACAGGGGCACTTATGTGCATTTAGGGGCACCGAAGTACATATAGG
1 TTAGGG-TACCGAAGTACAAACAGGGGCACATATGTGCAATCAGAGGCACCAAAATAAAAACAGG
*
11000051 GGCATGTATGTTCAT
65 GGCACGTATGTTCAT
11000066 TTAGGGTACCGAAGTACAAACAGGGGCACATATGTGCA
1 TTAGGGTACCGAAGTACAAACAGGGGCACATATGTGCA
11000104 TTCAAGGATA
Statistics
Matches: 96, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
79 37 0.39
80 59 0.61
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (79 bp):
TTAGGGTACCGAAGTACAAACAGGGGCACATATGTGCAATCAGAGGCACCAAAATAAAAACAGGG
GCACGTATGTTCAT
Found at i:11000033 original size:20 final size:20
Alignment explanation
Indices: 11000008--11000071 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
10999998 GAGTACAAAC
*
11000008 AGGGGCACTTATGTGCATTT
1 AGGGGCACTTATGTACATTT
** * *
11000028 AGGGGCACCGAAGTACATAT
1 AGGGGCACTTATGTACATTT
*
11000048 AGGGGCA-TGTATGTTCATTT
1 AGGGGCACT-TATGTACATTT
11000068 AGGG
1 AGGG
11000072 TACCGAAGTA
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.14, G:0.33, T:0.28
Consensus pattern (20 bp):
AGGGGCACTTATGTACATTT
Found at i:11003011 original size:21 final size:22
Alignment explanation
Indices: 11002985--11003038 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
11002975 ATGTATGTAC
*
11002985 ATTAAAGCATATA-ATATATAT
1 ATTAAAGCATATATACATATAT
11003006 ATTAAAG-ATATATACATATAT
1 ATTAAAGCATATATACATATAT
*
11003027 AATAAA-CATATA
1 ATTAAAGCATATA
11003039 CTAATAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 5 0.17
21 24 0.83
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (22 bp):
ATTAAAGCATATATACATATAT
Found at i:11003026 original size:19 final size:21
Alignment explanation
Indices: 11002985--11003026 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
11002975 ATGTATGTAC
*
11002985 ATTAAAGCATATAATATATAT
1 ATTAAAGCATATAATACATAT
11003006 ATTAAAG-ATAT-ATACATAT
1 ATTAAAGCATATAATACATAT
11003025 AT
1 AT
11003027 AATAAACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 4 0.20
21 7 0.35
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
ATTAAAGCATATAATACATAT
Found at i:11003188 original size:18 final size:16
Alignment explanation
Indices: 11003167--11003206 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 16
11003157 AAATATAACG
11003167 ATATATAAAAATAATACT
1 ATATATAAAAA-AATA-T
11003185 ATATAT-AAAAAATAT
1 ATATATAAAAAAATAT
11003200 ATATATA
1 ATATATA
11003207 CCCATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 4 0.19
17 4 0.19
18 6 0.29
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATATAAAAAAATAT
Found at i:11003235 original size:22 final size:23
Alignment explanation
Indices: 11003180--11003249 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
11003170 TATAAAAATA
*
11003180 ATACTATATATAAAAAATATATAT
1 ATACTA-ATATAATAAATATATAT
**
11003204 ATACCCATATAATAAA-ATATAT
1 ATACTAATATAATAAATATATAT
* *
11003226 GTACTAATATTAAT-AATAAATAT
1 ATACTAATA-TAATAAATATATAT
11003249 A
1 A
11003250 ATAGGGATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
22 14 0.39
23 18 0.50
24 4 0.11
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.36
Consensus pattern (23 bp):
ATACTAATATAATAAATATATAT
Found at i:11003249 original size:43 final size:41
Alignment explanation
Indices: 11003150--11003250 Score: 105
Period size: 43 Copynumber: 2.4 Consensus size: 41
11003140 ATAGTAGGTA
*
11003150 TAATAATAAATATAACGATATATAAAAATAATACTATATAT
1 TAATAATAAATATAACCATATATAAAAATAATACTATATAT
* * * *
11003191 AAAAAATATATATATACCCATATAATAAAATATATGTACTA-ATAT
1 TAATAATA-A-ATATAACCATAT-ATAAAA-ATA-ATACTATATAT
11003236 TAATAATAAATATAA
1 TAATAATAAATATAA
11003251 TAGGGATAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
41 6 0.13
42 1 0.02
43 15 0.32
44 7 0.15
45 13 0.28
46 5 0.11
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (41 bp):
TAATAATAAATATAACCATATATAAAAATAATACTATATAT
Found at i:11003319 original size:27 final size:28
Alignment explanation
Indices: 11003273--11003329 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
11003263 AGATATAATA
* *
11003273 ATATATACATAATATGGTATT-AAAAAT
1 ATATATACATAACATAGTATTCAAAAAT
* *
11003300 ATATATACGTAACATAGTATTCAAGAAT
1 ATATATACATAACATAGTATTCAAAAAT
11003328 AT
1 AT
11003330 GTACATGAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (28 bp):
ATATATACATAACATAGTATTCAAAAAT
Found at i:11003409 original size:9 final size:10
Alignment explanation
Indices: 11003396--11003429 Score: 54
Period size: 9 Copynumber: 3.6 Consensus size: 10
11003386 AACATTAAAA
11003396 ATATATATA-
1 ATATATATAC
11003405 ATATATATAC
1 ATATATATAC
11003415 A-ATATATAC
1 ATATATATAC
11003424 ATATAT
1 ATATAT
11003430 TTAGAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATATAC
Found at i:11003524 original size:21 final size:23
Alignment explanation
Indices: 11003475--11003527 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
11003465 CATACGCTAC
11003475 ATAATTAATCTTAATAAAACTAAA
1 ATAATTAATCTTAAT-AAACTAAA
11003499 ATAATTAATCTTAAT-AA-TAAA
1 ATAATTAATCTTAATAAACTAAA
*
11003520 GTAATTAA
1 ATAATTAA
11003528 AAAGGATCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 11 0.39
22 2 0.07
24 15 0.54
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36
Consensus pattern (23 bp):
ATAATTAATCTTAATAAACTAAA
Found at i:11005614 original size:90 final size:90
Alignment explanation
Indices: 11005502--11005707 Score: 412
Period size: 90 Copynumber: 2.3 Consensus size: 90
11005492 CTGAGGCTCG
11005502 ACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTAAAAACAAAAATTGAAAAT
1 ACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTAAAAACAAAAATTGAAAAT
11005567 ATCTCAGCATGTGGCCCGAGGGTTA
66 ATCTCAGCATGTGGCCCGAGGGTTA
11005592 ACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTAAAAACAAAAATTGAAAAT
1 ACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTAAAAACAAAAATTGAAAAT
11005657 ATCTCAGCATGTGGCCCGAGGGTTA
66 ATCTCAGCATGTGGCCCGAGGGTTA
11005682 ACTCACCTCTCGCAATATGAGTTGAT
1 ACTCACCTCTCGCAATATGAGTTGAT
11005708 AGAAACTAAA
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 116 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (90 bp):
ACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTAAAAACAAAAATTGAAAAT
ATCTCAGCATGTGGCCCGAGGGTTA
Found at i:11005897 original size:76 final size:76
Alignment explanation
Indices: 11005739--11005926 Score: 267
Period size: 76 Copynumber: 2.5 Consensus size: 76
11005729 GTATGACCCG
* * *
11005739 AGGCTCAACTCACCTCTCACAATATGAGTTGA-TTTTTTTAATGAACAGAAATTAAAATTACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAGAACAGAAATTAAAATTACATC
* *
11005803 AGCGTGTACTG
66 AACGTGTACTA
11005814 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAA-AGACAGAAATTGAAAA-TACA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAGA-ACAGAAATT-AAAATTACA
11005877 TCAACGTGT-CTTA
64 TCAACGTGTAC-TA
*
11005890 AGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
11005927 GTAACAGAAA
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
75 33 0.32
76 66 0.64
77 4 0.04
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (76 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAGAACAGAAATTAAAATTACATC
AACGTGTACTA
Found at i:11015740 original size:39 final size:39
Alignment explanation
Indices: 11015692--11015898 Score: 315
Period size: 39 Copynumber: 5.3 Consensus size: 39
11015682 CAGGACTTTA
* *
11015692 AGCCCGGATATAATACCAGCACAAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
*
11015731 AGCTCGGATATAACACCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
* * **
11015770 AGCCCAGATATAACACCAACACGAATGCCTTCAAGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
* *
11015809 AGCCTGGATATAACACCAGCATGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
* *
11015848 AGCCCGGATATAACACCAGCACAAATGCCTTCGGGAATT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
11015887 AGCCCGGATATA
1 AGCCCGGATATA
11015899 TATCTCACAC
Statistics
Matches: 150, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 150 1.00
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (39 bp):
AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
Found at i:11018628 original size:44 final size:44
Alignment explanation
Indices: 11018563--11018660 Score: 169
Period size: 44 Copynumber: 2.2 Consensus size: 44
11018553 ATACTCGGCA
11018563 TTCTTCTTTCTTAACTCTATCATAGCACGCGCAGCTTTTTCCTC
1 TTCTTCTTTCTTAACTCTATCATAGCACGCGCAGCTTTTTCCTC
* *
11018607 TTCTTNTTTCTTAACTTTATCATAGCACGCGCAGCTTTTTCCTC
1 TTCTTCTTTCTTAACTCTATCATAGCACGCGCAGCTTTTTCCTC
11018651 TTCTTTCTTT
1 TTC-TTCTTT
11018661 GCTTTCCCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
44 45 0.90
45 5 0.10
ACGTcount: A:0.14, C:0.29, G:0.08, T:0.48
Consensus pattern (44 bp):
TTCTTCTTTCTTAACTCTATCATAGCACGCGCAGCTTTTTCCTC
Found at i:11021814 original size:17 final size:18
Alignment explanation
Indices: 11021787--11021820 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
11021777 ATGCATATGC
11021787 ATGTATTAAAAAATAATA
1 ATGTATTAAAAAATAATA
11021805 ATGT-TTAAAAAATAAT
1 ATGTATTAAAAAATAAT
11021821 TATTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
ATGTATTAAAAAATAATA
Found at i:11032867 original size:25 final size:24
Alignment explanation
Indices: 11032810--11032867 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
11032800 ATCCCTTCAC
* *
11032810 TTCCTCTTCTCTTCCTCTTTACAT
1 TTCCTCTTCTCTCCCACTTTACAT
11032834 TT-CTGCTTCTACTCCCACTTCT-CAT
1 TTCCT-CTTCT-CTCCCACTT-TACAT
11032859 TTCCTCTTC
1 TTCCTCTTC
11032868 CCCTGTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
23 2 0.07
24 7 0.25
25 16 0.57
26 3 0.11
ACGTcount: A:0.09, C:0.40, G:0.02, T:0.50
Consensus pattern (24 bp):
TTCCTCTTCTCTCCCACTTTACAT
Found at i:11035532 original size:23 final size:23
Alignment explanation
Indices: 11035487--11035537 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
11035477 CTACTTTTAC
* **
11035487 ATTATTTATTTTAATTTTTAAAT
1 ATTAATTATTTTAATTTAAAAAT
* *
11035510 TTTAATTATTTTGATTTAAAAAT
1 ATTAATTATTTTAATTTAAAAAT
11035533 ATTAA
1 ATTAA
11035538 AAAATTCCAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
ATTAATTATTTTAATTTAAAAAT
Found at i:11037883 original size:23 final size:24
Alignment explanation
Indices: 11037835--11037896 Score: 83
Period size: 23 Copynumber: 2.6 Consensus size: 24
11037825 TGTAAAACTC
* *
11037835 AATTTAAATATATAAACTATTTTA
1 AATTTAAATATATAAACCATTATA
11037859 AATATTAAA-ATA-AAACCATTATA
1 AAT-TTAAATATATAAACCATTATA
11037882 AATTTAAATATATAA
1 AATTTAAATATATAA
11037897 TTTATTTATC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 5 0.15
23 15 0.45
24 8 0.24
25 5 0.15
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (24 bp):
AATTTAAATATATAAACCATTATA
Found at i:11038421 original size:43 final size:44
Alignment explanation
Indices: 11038374--11038474 Score: 134
Period size: 43 Copynumber: 2.3 Consensus size: 44
11038364 GATAATATAT
* * ** *
11038374 TATTATAGGATATTAAT-TTTTAGTAATTTGATTCCTAATGAGA
1 TATTATAAGATATTAATCTCTTAACAATTTGATTCCTAATAAGA
*
11038417 TATTATAAGATACT-ATCTCTTAACAATTTGATTCCTAATAAGA
1 TATTATAAGATATTAATCTCTTAACAATTTGATTCCTAATAAGA
11038460 TATTATAAGATATTA
1 TATTATAAGATATTA
11038475 TTATAAAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 2 0.04
43 47 0.96
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.44
Consensus pattern (44 bp):
TATTATAAGATATTAATCTCTTAACAATTTGATTCCTAATAAGA
Found at i:11038900 original size:10 final size:10
Alignment explanation
Indices: 11038885--11038909 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
11038875 TGTGGCCTAA
11038885 TTTTTTTCTT
1 TTTTTTTCTT
11038895 TTTTTTTCTT
1 TTTTTTTCTT
11038905 TTTTT
1 TTTTT
11038910 GGGGTTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:11043834 original size:11 final size:11
Alignment explanation
Indices: 11043813--11043868 Score: 60
Period size: 11 Copynumber: 5.1 Consensus size: 11
11043803 AATGACTAAA
11043813 AAATTAT-TTT
1 AAATTATATTT
11043823 AAATTATATTT
1 AAATTATATTT
* *
11043834 AAATTAAATAT
1 AAATTATATTT
*
11043845 AAAATATATTT
1 AAATTATATTT
*
11043856 ATATTTATATTT
1 A-AATTATATTT
11043868 A
1 A
11043869 TGCTAAACTA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
10 7 0.19
11 21 0.57
12 9 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AAATTATATTT
Found at i:11046278 original size:14 final size:14
Alignment explanation
Indices: 11046259--11046286 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11046249 ATCAATCTCA
11046259 TTATCGAAATGACC
1 TTATCGAAATGACC
11046273 TTATCGAAATGACC
1 TTATCGAAATGACC
11046287 GATGTTGCAC
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:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (14 bp):
TTATCGAAATGACC
Found at i:11057063 original size:19 final size:20
Alignment explanation
Indices: 11057019--11057083 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 20
11057009 TTATAATATT
*
11057019 ATTTTAATAATAAAATTTAAC
1 ATTTTAATAAT-AATTTTAAC
11057040 A--TTAATAATAATTTTAA-
1 ATTTTAATAATAATTTTAAC
*
11057057 ATTTTAAATAAT-ATTCTTAAT
1 ATTTT-AATAATAATT-TTAAC
11057078 ATTTTA
1 ATTTTA
11057084 TTGAAAATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
17 1 0.03
18 7 0.18
19 13 0.34
20 11 0.29
21 6 0.16
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTTAATAATAATTTTAAC
Found at i:11057068 original size:20 final size:21
Alignment explanation
Indices: 11057043--11057083 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
11057033 ATTTAACATT
11057043 AATAATAATT-TTAA-ATTTTA
1 AATAAT-ATTCTTAATATTTTA
11057063 AATAATATTCTTAATATTTTA
1 AATAATATTCTTAATATTTTA
11057084 TTGAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 10 0.53
21 6 0.32
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATAATATTCTTAATATTTTA
Found at i:11059250 original size:16 final size:17
Alignment explanation
Indices: 11059206--11059253 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
11059196 TTTAATGCAA
11059206 AGGTACATGCATGGATG
1 AGGTACATGCATGGATG
* *
11059223 -GCTTCAATGCATGG-TG
1 AGGTAC-ATGCATGGATG
11059239 AGGTACATGCATGGA
1 AGGTACATGCATGGA
11059254 CGACTTCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (17 bp):
AGGTACATGCATGGATG
Found at i:11062547 original size:6 final size:6
Alignment explanation
Indices: 11062536--11062665 Score: 70
Period size: 6 Copynumber: 20.2 Consensus size: 6
11062526 AGATCAAATG
*
11062536 AAAGAA AAAGAA AAGAGTGAA AATGAA AAAG-A AAAGAA AAATGAGA AAA-AGA
1 AAAGAA AAAGAA AA-A--GAA AAAGAA AAAGAA AAAGAA AAA-GA-A AAAGA-A
* * * *
11062588 GAGGAA AAATAA CAAA-AA AAAGTGA AAAGAA AACGAGAA AATA-AA AAGATGAA
1 AAAGAA AAAGAA -AAAGAA AAAG-AA AAAGAA AA--AGAA AA-AGAA AA-A-GAA
11062641 AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
11062666 GTGAGAAAGT
Statistics
Matches: 99, Mismatches: 11, Indels: 28
0.72 0.08 0.20
Matches are distributed among these distances:
5 8 0.08
6 58 0.59
7 14 0.14
8 14 0.14
9 5 0.05
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (6 bp):
AAAGAA
Found at i:11062583 original size:20 final size:20
Alignment explanation
Indices: 11062538--11062655 Score: 63
Period size: 21 Copynumber: 5.9 Consensus size: 20
11062528 ATCAAATGAA
11062538 AGAAAAAGAAAAGAGTGAAAAT-
1 AGAAAAAGAAAAGA---AAAATG
11062560 -GAAAAAGAAAAGAAAAATG
1 AGAAAAAGAAAAGAAAAATG
* *
11062579 AGAAAAAGAGAGGAAAAAT-
1 AGAAAAAGAAAAGAAAAATG
*
11062598 A-ACAAAA-AAAAGTGAAAA-G
1 AGA-AAAAGAAAAG-AAAAATG
* *
11062617 A-AAACGAGAAAATAAAAA-G
1 AGAAA-AAGAAAAGAAAAATG
11062636 ATGAAAAAGAAAAAGAAAAA
1 A-GAAAAAG-AAAAGAAAAA
11062656 GAAAAAGAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
18 11 0.14
19 18 0.24
20 22 0.29
21 25 0.33
ACGTcount: A:0.73, C:0.02, G:0.19, T:0.06
Consensus pattern (20 bp):
AGAAAAAGAAAAGAAAAATG
Found at i:11062583 original size:26 final size:25
Alignment explanation
Indices: 11062531--11062584 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
11062521 TCTGTAGATC
* *
11062531 AAATGAAAGAAAAAGAAAAGAGTGA
1 AAATGAAAAAAAAAGAAAAGAGAGA
11062556 AAATGAAAAAGAAAAGAAAA-ATGAGA
1 AAATGAAAAA-AAAAGAAAAGA-GAGA
11062582 AAA
1 AAA
11062585 AGAGAGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.07
Consensus pattern (25 bp):
AAATGAAAAAAAAAGAAAAGAGAGA
Found at i:11062674 original size:18 final size:18
Alignment explanation
Indices: 11062536--11062665 Score: 70
Period size: 20 Copynumber: 6.7 Consensus size: 18
11062526 AGATCAAATG
11062536 AAAGAAAAAGAAAAGAGTGAA
1 AAAGAAAAAGAAAA-A--GAA
*
11062557 AATGAAAAAG-AAAAGAA
1 AAAGAAAAAGAAAAAGAA
* *
11062574 AAATGAGAAAA-AGAGAGGAA
1 AAA-GA-AAAAGA-AAAAGAA
* *
11062594 AAATAACAAA-AAAAAGTGA
1 AAAGAA-AAAGAAAAAG-AA
11062613 AAAGAAAACGAGAAAATA-AA
1 AAAGAAAA--AGAAAA-AGAA
11062633 AAGATGAAAAAGAAAAAGAA
1 AA-A-GAAAAAGAAAAAGAA
11062653 AAAGAAAAAGAAA
1 AAAGAAAAAGAAA
11062666 GTGAGAAAGT
Statistics
Matches: 86, Mismatches: 10, Indels: 29
0.69 0.08 0.23
Matches are distributed among these distances:
17 5 0.06
18 18 0.21
19 18 0.21
20 25 0.29
21 14 0.16
22 6 0.07
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (18 bp):
AAAGAAAAAGAAAAAGAA
Found at i:11067984 original size:34 final size:37
Alignment explanation
Indices: 11067946--11068033 Score: 92
Period size: 40 Copynumber: 2.4 Consensus size: 37
11067936 AAAATAATTA
*
11067946 TTTAAAAATATAAATATAT-ACAAATCA-T-TAAAAT
1 TTTAAAAATATAAATATATAAAAAATCATTATAAAAT
* *
11067980 TTTAAAAAAATTAAAATATATAAAAAATTATTTATAAAAT
1 TTTAAAAATA-T-AAATATATAAAAAATCA-TTATAAAAT
*
11068020 TATAAAAATATAAA
1 TTTAAAAATATAAA
11068034 AAATTGATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
34 9 0.21
35 1 0.02
36 8 0.19
37 6 0.14
38 3 0.07
39 2 0.05
40 14 0.33
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (37 bp):
TTTAAAAATATAAATATATAAAAAATCATTATAAAAT
Found at i:11067994 original size:17 final size:18
Alignment explanation
Indices: 11067957--11068006 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
11067947 TTAAAAATAT
**
11067957 AAATATATACAAATCATTA
1 AAATATATA-AAAAAATTA
*
11067976 AAAT-TTTAAAAAAATTA
1 AAATATATAAAAAAATTA
11067993 AAATATATAAAAAA
1 AAATATATAAAAAA
11068007 TTATTTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 11 0.42
18 11 0.42
19 4 0.15
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATATATAAAAAAATTA
Found at i:11068033 original size:30 final size:30
Alignment explanation
Indices: 11067986--11068043 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
11067976 AAATTTTAAA
*
11067986 AAAATTAAAATATATAAAAAATT-ATTTAT
1 AAAATTAAAAAATATAAAAAATTGATTTAT
11068015 AAAATTATAAAAATATAAAAAATTGATTT
1 AAAATTA-AAAAATATAAAAAATTGATTT
11068044 TTTAAAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.27
30 15 0.58
31 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAATTAAAAAATATAAAAAATTGATTTAT
Found at i:11073070 original size:86 final size:86
Alignment explanation
Indices: 11072925--11073097 Score: 337
Period size: 86 Copynumber: 2.0 Consensus size: 86
11072915 TATTATGAAA
11072925 AATTAATCTTTTAATCGCATAATAAAGGTGACGTTGCTAAATTGAATACATTACCAAATAGGAGG
1 AATTAATCTTTTAATCGCATAATAAAGGTGACGTTGCTAAATTGAATACATTACCAAATAGGAGG
*
11072990 TTGGATCCCTCGATGTTTTTG
66 TTGGATCCCTCAATGTTTTTG
11073011 AATTAATCTTTTAATCGCATAATAAAGGTGACGTTGCTAAATTGAATACATTACCAAATAGGAGG
1 AATTAATCTTTTAATCGCATAATAAAGGTGACGTTGCTAAATTGAATACATTACCAAATAGGAGG
11073076 TTGGATCCCTCAATGTTTTTG
66 TTGGATCCCTCAATGTTTTTG
11073097 A
1 A
11073098 GAATTTATTA
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (86 bp):
AATTAATCTTTTAATCGCATAATAAAGGTGACGTTGCTAAATTGAATACATTACCAAATAGGAGG
TTGGATCCCTCAATGTTTTTG
Found at i:11085642 original size:31 final size:32
Alignment explanation
Indices: 11085601--11085663 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
11085591 TTATTTATAA
*
11085601 AAGATATTTAT-TAATTAAATA-ATTATATTAT
1 AAGATATTTATGTAA-TAAATATATTAAATTAT
*
11085632 AAGATTTTTATGTAATAAATATATTAAATTAT
1 AAGATATTTATGTAATAAATATATTAAATTAT
11085664 GACAAGTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (32 bp):
AAGATATTTATGTAATAAATATATTAAATTAT
Found at i:11087448 original size:45 final size:45
Alignment explanation
Indices: 11087398--11087483 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
11087388 CGACTACTGT
* * *
11087398 TACTGTTACCATTACTGTTACCGATTCGGCACTTTGTGTGTCGAA
1 TACTGTTACCATTACCGTTACCGATTCAGAACTTTGTGTGTCGAA
* *
11087443 TACTGTTACTATTACCGTTATCGATTCAGAACTTTGTGTGT
1 TACTGTTACCATTACCGTTACCGATTCAGAACTTTGTGTGT
11087484 TTTGTGTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.41
Consensus pattern (45 bp):
TACTGTTACCATTACCGTTACCGATTCAGAACTTTGTGTGTCGAA
Found at i:11087712 original size:18 final size:18
Alignment explanation
Indices: 11087691--11087855 Score: 117
Period size: 18 Copynumber: 9.2 Consensus size: 18
11087681 TAACTGATTA
11087691 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
* * *
11087709 TTACTGGAGAATTGATTG
1 TTACTGAATAATTGACTG
11087727 TTACT-AGAT-ATTAGACTG
1 TTACTGA-ATAATT-GACTG
*
11087745 TTACTGAATAATTGA-TCA
1 TTACTGAATAATTGACT-G
* ** *
11087763 TTACTGGATAGCTGATTG
1 TTACTGAATAATTGACTG
*
11087781 TCACTGAATGAA-TGACTG
1 TTACTGAAT-AATTGACTG
* *
11087799 TTACTGAATAACTTAATTG
1 TTACTGAATAA-TTGACTG
*
11087818 TTACTGAAT-ATCTGA-TT
1 TTACTGAATAAT-TGACTG
*
11087835 TTACTGAATAATTGAATG
1 TTACTGAATAATTGACTG
11087853 TTA
1 TTA
11087856 TTGGATAACT
Statistics
Matches: 114, Mismatches: 21, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
17 20 0.18
18 75 0.66
19 19 0.17
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:11087779 original size:54 final size:54
Alignment explanation
Indices: 11087691--11087809 Score: 136
Period size: 54 Copynumber: 2.2 Consensus size: 54
11087681 TAACTGATTA
* * * *
11087691 TTACTGAATAATTGACTGTTACTGGAGAATTGATTGTTACT-AGAT-ATTAGACTG
1 TTACTGAATAATTGACTATTACTGGAGAACTGATTGTCACTGA-ATGAAT-GACTG
* *
11087745 TTACTGAATAATTGA-TCATTACTGGATAGCTGATTGTCACTGAATGAATGACTG
1 TTACTGAATAATTGACT-ATTACTGGAGAACTGATTGTCACTGAATGAATGACTG
11087799 TTACTGAATAA
1 TTACTGAATAA
11087810 CTTAATTGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
53 1 0.02
54 52 0.93
55 3 0.05
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (54 bp):
TTACTGAATAATTGACTATTACTGGAGAACTGATTGTCACTGAATGAATGACTG
Found at i:11087840 original size:17 final size:19
Alignment explanation
Indices: 11087797--11087845 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
11087787 AATGAATGAC
11087797 TGTTACTGAATAACTTAAT
1 TGTTACTGAATAACTTAAT
* *
11087816 TGTTACTGAATATC-TGAT
1 TGTTACTGAATAACTTAAT
11087834 T-TTACTGAATAA
1 TGTTACTGAATAA
11087846 TTGAATGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 10 0.37
18 4 0.15
19 13 0.48
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (19 bp):
TGTTACTGAATAACTTAAT
Found at i:11087841 original size:54 final size:55
Alignment explanation
Indices: 11087740--11087865 Score: 141
Period size: 54 Copynumber: 2.3 Consensus size: 55
11087730 CTAGATATTA
* *
11087740 GACTGTTACTGAATAA-TTGATCATTACTGGATAGCTGATTGTCACTGAATGAA-T
1 GACTGTTACTGAATAACTTAATCATTACTGAATAGCTGATTGTCACTGAAT-AATT
** * *
11087794 GACTGTTACTGAATAACTTAATTGTTACTGAATATCTGATT-TTACTGAATAATT
1 GACTGTTACTGAATAACTTAATCATTACTGAATAGCTGATTGTCACTGAATAATT
* * *
11087848 GAATGTTATTGGATAACT
1 GACTGTTACTGAATAACT
11087866 GATCAATTGA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
53 2 0.03
54 40 0.66
55 19 0.31
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (55 bp):
GACTGTTACTGAATAACTTAATCATTACTGAATAGCTGATTGTCACTGAATAATT
Found at i:11087941 original size:18 final size:18
Alignment explanation
Indices: 11087679--11087943 Score: 108
Period size: 18 Copynumber: 14.3 Consensus size: 18
11087669 AAAGGTATAA
* *
11087679 AATAACTGATTATTACTG
1 AATAACTGACTGTTACTG
*
11087697 AATAATTGACTGTTACTG
1 AATAACTGACTGTTACTG
* * * *
11087715 GAGAATTGATTGTTACT-
1 AATAACTGACTGTTACTG
*
11087732 AGAT-ATTAGACTGTTACTG
1 A-ATAACT-GACTGTTACTG
* *
11087751 AATAATTGA-TCATTACTG
1 AATAACTGACT-GTTACTG
* * * *
11087769 GATAGCTGATTGTCACTG
1 AATAACTGACTGTTACTG
11087787 AATGAA-TGACTGTTACTG
1 AAT-AACTGACTGTTACTG
* *
11087805 AATAACTTAATTGTTACTG
1 AATAAC-TGACTGTTACTG
* *
11087824 AATATCTGA-TTTTACTG
1 AATAACTGACTGTTACTG
* * *
11087841 AATAATTGAATGTTATTG
1 AATAACTGACTGTTACTG
*
11087859 GATAACTGATCAATTGATCGATACTG
1 AATAACTGA-C---TG-T---TACTG
** * *
11087885 AATAACTGGTTATTATTG
1 AATAACTGACTGTTACTG
* * *
11087903 AATAATTGATTGTTACCG
1 AATAACTGACTGTTACTG
*
11087921 AATAACTGACTGTTGCTG
1 AATAACTGACTGTTACTG
11087939 AATAA
1 AATAA
11087944 ATAATTGTTC
Statistics
Matches: 183, Mismatches: 46, Indels: 36
0.69 0.17 0.14
Matches are distributed among these distances:
17 20 0.11
18 126 0.69
19 21 0.11
21 1 0.01
22 3 0.02
23 1 0.01
26 11 0.06
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (18 bp):
AATAACTGACTGTTACTG
Found at i:11089614 original size:47 final size:47
Alignment explanation
Indices: 11089516--11090522 Score: 1658
Period size: 47 Copynumber: 21.6 Consensus size: 47
11089506 TGATGTCATA
* * * *
11089516 GTATCTTTCAACTATGGTTTTACTCGTTTT-CTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
11089562 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
11089609 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
* * *
11089656 GTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCA-GATTACCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATG-TTGCCATG
* * *
11089702 GTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCA-GATTACCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATG-TTGCCATG
* * *
11089748 GTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCA-GATTACCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATG-TTGCCATG
11089794 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
11089841 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
11089888 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
11089935 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
11089982 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
11090029 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
11090076 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
11090123 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
11090170 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
11090217 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
11090264 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
11090311 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
* * *
11090358 GTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCA-GATTACCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATG-TTGCCATG
* * *
11090404 GTATCTTTCAACCATGGTCTTATTCA-TTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
* ** * * * **
11090450 GTATCTTTTAACCATGGTCTTACACA-TTTCATATCACGTTGCTGTG
1 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
11090496 GTATCTTTCAACCATGGTCTTATTCAT
1 GTATCTTTCAACCATGGTCTTATTCAT
11090523 NNNNNNNNNN
Statistics
Matches: 930, Mismatches: 24, Indels: 13
0.96 0.02 0.01
Matches are distributed among these distances:
45 2 0.00
46 280 0.30
47 647 0.70
48 1 0.00
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.43
Consensus pattern (47 bp):
GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
Found at i:11107364 original size:25 final size:26
Alignment explanation
Indices: 11107336--11107394 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
11107326 ATCAACAAAT
11107336 AATTCAAAA-TTTATAAAA-A-AATCAA
1 AATTCAAAATTTTA-AAAATATAAT-AA
11107361 AATT-AAAATTTTAAAAATATAATAA
1 AATTCAAAATTTTAAAAATATAATAA
11107386 AATTCAAAA
1 AATTCAAAA
11107395 AATTTAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
24 8 0.27
25 15 0.50
26 7 0.23
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (26 bp):
AATTCAAAATTTTAAAAATATAATAA
Found at i:11108602 original size:102 final size:102
Alignment explanation
Indices: 11108250--11108595 Score: 674
Period size: 102 Copynumber: 3.4 Consensus size: 102
11108240 AGCATTCCAG
11108250 CTCAACAAGCCTACATTTACCTTGCCAATTGCATTATCGACAAAGTTTACTCTAACATGTAGAAA
1 CTCAACAAGCCTACATTTACCTTGCCAATTGCATTATCGACAAAGTTTACTCTAACATGTAGAAA
11108315 TCCTTGAGAGTTTTTGTTTGGGATAGCTTTCATCCCA
66 TCCTTGAGAGTTTTTGTTTGGGATAGCTTTCATCCCA
11108352 CTCAACAAGCCTACATTTACCTTGCCAATTGCATTATCGACAAAGTTTACTCTAACATGTAGAAA
1 CTCAACAAGCCTACATTTACCTTGCCAATTGCATTATCGACAAAGTTTACTCTAACATGTAGAAA
11108417 TCCTTGAGAGTTTTTGTTTGGGATAGCTTTCATCCCA
66 TCCTTGAGAGTTTTTGTTTGGGATAGCTTTCATCCCA
11108454 CTCAACAAGCCTACATTTACCTTGCCAATTGCATTATCGACAAAGTTTACTCTAACATGTAGAAA
1 CTCAACAAGCCTACATTTACCTTGCCAATTGCATTATCGACAAAGTTTACTCTAACATGTAGAAA
11108519 TCCTTGAGAGTTTTTGTTTGGGATAGCTTTCATCCCA
66 TCCTTGAGAGTTTTTGTTTGGGATAGCTTTCATCCCA
* *
11108556 CTCAACAAGCCTACATTTACCTTGCCAATTACTTTATCGA
1 CTCAACAAGCCTACATTTACCTTGCCAATTGCATTATCGA
11108596 GGAAGTTCTT
Statistics
Matches: 242, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 242 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (102 bp):
CTCAACAAGCCTACATTTACCTTGCCAATTGCATTATCGACAAAGTTTACTCTAACATGTAGAAA
TCCTTGAGAGTTTTTGTTTGGGATAGCTTTCATCCCA
Found at i:11111560 original size:13 final size:13
Alignment explanation
Indices: 11111544--11111573 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
11111534 TTTTTACCTT
*
11111544 TTAATTTTCTTAG
1 TTAATTTACTTAG
11111557 TTAATTTACTTAG
1 TTAATTTACTTAG
11111570 TTAA
1 TTAA
11111574 AATCTAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (13 bp):
TTAATTTACTTAG
Found at i:11119378 original size:43 final size:43
Alignment explanation
Indices: 11119295--11119451 Score: 142
Period size: 43 Copynumber: 3.7 Consensus size: 43
11119285 CTGAGACATT
* * * *
11119295 ATGTAAGGCCGTGTCTGGGACA-CAGGCCTCGAT-TGAGATTTAC
1 ATGTAAGACCATGTCTGGGACATC-GGCATCGATAT-TGATTTAC
* *
11119338 GTATAAGACCATGTCTGGGACATCGGCATCG-TATCTGATTT-C
1 ATGTAAGACCATGTCTGGGACATCGGCATCGATAT-TGATTTAC
* * ** *
11119380 ATGTAAGACCTTGTCTGGGATAGAGGCATCGATATTGAGTTAC
1 ATGTAAGACCATGTCTGGGACATCGGCATCGATATTGATTTAC
* *
11119423 ATGTAAGACCACGTCCGGGACATCGGCAT
1 ATGTAAGACCATGTCTGGGACATCGGCAT
11119452 TGTACTTGTT
Statistics
Matches: 90, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
42 32 0.36
43 57 0.63
44 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (43 bp):
ATGTAAGACCATGTCTGGGACATCGGCATCGATATTGATTTAC
Found at i:11129323 original size:15 final size:16
Alignment explanation
Indices: 11129300--11129333 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
11129290 TTTCTCCTAA
*
11129300 ATTTCAATTTT-ATTT
1 ATTTAAATTTTAATTT
11129315 ATTTAAATTTTAATTT
1 ATTTAAATTTTAATTT
11129331 ATT
1 ATT
11129334 GAATTATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTAAATTTTAATTT
Found at i:11133215 original size:42 final size:42
Alignment explanation
Indices: 11133168--11133251 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
11133158 TTTTTTTGAG
11133168 TAAGTAAAACCATGATTATGTTATACTTGCATTACAATTGTA
1 TAAGTAAAACCATGATTATGTTATACTTGCATTACAATTGTA
11133210 TAAGTAAAACCATGATTATGTTATACTTGCATTACAATTGTA
1 TAAGTAAAACCATGATTATGTTATACTTGCATTACAATTGTA
11133252 AGGTAACTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (42 bp):
TAAGTAAAACCATGATTATGTTATACTTGCATTACAATTGTA
Found at i:11135755 original size:13 final size:14
Alignment explanation
Indices: 11135732--11135766 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
11135722 GTTTCAGAGA
11135732 ACAGAATCAGATAT
1 ACAGAATCAGATAT
*
11135746 GCAGAA-CAGATAT
1 ACAGAATCAGATAT
11135759 ACAGAATC
1 ACAGAATC
11135767 CTACCCCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (14 bp):
ACAGAATCAGATAT
Found at i:11140245 original size:26 final size:26
Alignment explanation
Indices: 11140213--11140317 Score: 183
Period size: 26 Copynumber: 4.0 Consensus size: 26
11140203 AATGCCCATT
*
11140213 ATGGAACATTTACCTAAACCATTATC
1 ATGGAACATTTACCTAACCCATTATC
11140239 ATGGAACATTTACCTAACCCATTATC
1 ATGGAACATTTACCTAACCCATTATC
* *
11140265 ATGGAATATTTACCTAATCCATTATC
1 ATGGAACATTTACCTAACCCATTATC
11140291 ATGGAACATTTACCTAACCCATTATC
1 ATGGAACATTTACCTAACCCATTATC
11140317 A
1 A
11140318 ATTTGTACCA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (26 bp):
ATGGAACATTTACCTAACCCATTATC
Found at i:11143059 original size:26 final size:27
Alignment explanation
Indices: 11142984--11143059 Score: 72
Period size: 26 Copynumber: 2.9 Consensus size: 27
11142974 ATTATATATC
*
11142984 TTATTT-TTATTAATTTATATTTAATCA
1 TTATTTATTATTAAATTATATTTAA-CA
*
11143011 TTA-TTA-TATTAAAATATGA-TTAA-A
1 TTATTTATTATTAAATTAT-ATTTAACA
*
11143035 TTATTTATTGTTAAATTATATTTAA
1 TTATTTATTATTAAATTATATTTAA
11143060 TAATAATCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
24 4 0.10
25 4 0.10
26 28 0.70
27 4 0.10
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (27 bp):
TTATTTATTATTAAATTATATTTAACA
Found at i:11144800 original size:22 final size:21
Alignment explanation
Indices: 11144769--11144819 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
11144759 GTCGCGATTC
*
11144769 TAAAAATTTAAAA-AATATAAAT
1 TAAAATTTTAAAATAA-AT-AAT
11144791 TAAAATTTTAAAATAAATAAT
1 TAAAATTTTAAAATAAATAAT
11144812 TCAAAATT
1 T-AAAATT
11144820 ATTTAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 4 0.15
22 20 0.77
23 2 0.08
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATTTTAAAATAAATAAT
Found at i:11146573 original size:55 final size:56
Alignment explanation
Indices: 11146486--11146742 Score: 278
Period size: 55 Copynumber: 4.8 Consensus size: 56
11146476 ATTAGGGTTT
11146486 AAGGATACCATGTAAGACCATGCCAA-AGCATGGCAATTGGTAAGGTTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGA-CATGGCAATTGGTAAGGTTTCATAAGGC
* * *
11146541 AAGGATATCATGTAAGACCATGTCAAGACATGGC-ATTGATAA-GTTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGGTTTC-ATAAGGC
* *
11146596 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGC-ATTGGT--GCG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAG-GTTTCATAAGGC
*
11146649 AAGGATACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAA-GTTTC--AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGGTTTCATAAGGC
* * *
11146698 AAGGATACCACGTAAGACCATGACAAGTCATGGCAA-TGGTAAGGT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGGT
11146743 ACCCATGTAT
Statistics
Matches: 176, Mismatches: 14, Indels: 29
0.80 0.06 0.13
Matches are distributed among these distances:
49 39 0.22
50 2 0.01
52 6 0.03
53 43 0.24
54 14 0.08
55 67 0.38
56 5 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (56 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGGTTTCATAAGGC
Found at i:11146692 original size:108 final size:109
Alignment explanation
Indices: 11146493--11146695 Score: 322
Period size: 108 Copynumber: 1.9 Consensus size: 109
11146483 TTTAAGGATA
*
11146493 CCATGTAAGACCATGCCAAAGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGATATCATGTAAGA
1 CCATGTAAGACCATGCCAAAGCATGGCAATTGGT-AGGTTTCTAAGGCAAGGATACCATGTAAGA
*
11146558 CCATGTCAAGACATGGCATTGATAAGTTTCTATAAGGCAAAGGTC
65 CCATGTCAAGACATGGCAATGATAAGTTTCTATAAGGCAAAGGTC
*
11146603 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGT-GCG-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAAGCATGGCAATTGGTAG-GTTTC-TAAGGCAAGGATACCATGTAAG
*
11146665 ACCATGTCAAGACATGGCAATGGTAAGTTTC
64 ACCATGTCAAGACATGGCAATGATAAGTTTC
11146696 AAAAGGATAC
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
107 4 0.05
108 51 0.59
109 6 0.07
110 26 0.30
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.24
Consensus pattern (109 bp):
CCATGTAAGACCATGCCAAAGCATGGCAATTGGTAGGTTTCTAAGGCAAGGATACCATGTAAGAC
CATGTCAAGACATGGCAATGATAAGTTTCTATAAGGCAAAGGTC
Found at i:11150024 original size:31 final size:32
Alignment explanation
Indices: 11149974--11150077 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 32
11149964 AAACAAGTCT
*
11149974 ACTTAAATATAATAATAAAT-TATATTTAAATA
1 ACTT-AATATAATAATAAATAAATATTTAAATA
* * *
11150006 ATTTATTATAGTAATAAATAAAATATTTAAATA
1 ACTTAATATAATAATAAAT-AAATATTTAAATA
* * *
11150039 ACTTAATATAATGATACATAAA-ATATAAATTA
1 ACTTAATATAATAATAAATAAATATTTAAA-TA
*
11150071 ATTTAAT
1 ACTTAAT
11150078 TTTTATATGC
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
31 19 0.33
32 14 0.24
33 25 0.43
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (32 bp):
ACTTAATATAATAATAAATAAATATTTAAATA
Found at i:11150035 original size:33 final size:33
Alignment explanation
Indices: 11149974--11150064 Score: 105
Period size: 33 Copynumber: 2.8 Consensus size: 33
11149964 AAACAAGTCT
*
11149974 ACTTAAATATAATAATAAAT--TATATTTAAATA
1 ACTT-AATATAATAATAAATAAAATATTTAAATA
* * *
11150006 ATTTATTATAGTAATAAATAAAATATTTAAATA
1 ACTTAATATAATAATAAATAAAATATTTAAATA
* *
11150039 ACTTAATATAATGATACATAAAATAT
1 ACTTAATATAATAATAAATAAAATAT
11150065 AAATTAATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
31 13 0.27
32 3 0.06
33 32 0.67
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (33 bp):
ACTTAATATAATAATAAATAAAATATTTAAATA
Found at i:11150703 original size:15 final size:15
Alignment explanation
Indices: 11150685--11150718 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11150675 TCATATTGAA
11150685 TATTTTTATAT-TAAT
1 TATTTTTA-ATCTAAT
11150700 TATTTTTAATCTAAT
1 TATTTTTAATCTAAT
11150715 TATT
1 TATT
11150719 CTTCTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 16 0.89
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTTTAATCTAAT
Found at i:11152552 original size:2 final size:2
Alignment explanation
Indices: 11152545--11152573 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11152535 TGAAAAGAAA
11152545 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
11152574 TATATATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:11153432 original size:19 final size:18
Alignment explanation
Indices: 11153410--11153452 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
11153400 AGGGAGAAGC
* *
11153410 AGAAAAGGATGAAAAATAA
1 AGAAAAGAAAGAAAAA-AA
*
11153429 AGAAAATAAAGAAAAAAA
1 AGAAAAGAAAGAAAAAAA
11153447 AGAAAA
1 AGAAAA
11153453 AAAAAAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (18 bp):
AGAAAAGAAAGAAAAAAA
Found at i:11153453 original size:9 final size:9
Alignment explanation
Indices: 11153420--11153456 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
11153410 AGAAAAGGAT
11153420 GAAAAATAAA
1 GAAAAA-AAA
*
11153430 GAAAATAAA
1 GAAAAAAAA
11153439 GAAAAAAAA
1 GAAAAAAAA
11153448 GAAAAAAAA
1 GAAAAAAAA
11153457 AAGAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 20 0.80
10 5 0.20
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:11158412 original size:22 final size:22
Alignment explanation
Indices: 11158366--11158417 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
11158356 AGTTGCCCTA
**
11158366 TCTTGAGACAATAGGGTGTAGG
1 TCTTGAGACAATAGGGCCTAGG
**
11158388 TCTTGAGACAATAGGGCCTTTG
1 TCTTGAGACAATAGGGCCTAGG
11158410 TCTTGAGA
1 TCTTGAGA
11158418 AAAAATCTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.31, T:0.31
Consensus pattern (22 bp):
TCTTGAGACAATAGGGCCTAGG
Found at i:11173923 original size:43 final size:43
Alignment explanation
Indices: 11173843--11173928 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
11173833 TCATATTTCA
* *
11173843 TTTCTCATCTCATAATCATTTCTCATCTTTTCCATTTCTATAT
1 TTTCTCATCTCATAATCATTTCTCATCTTTGCCATTTCAATAT
* * *
11173886 TTTCTCATCTCATATTCATTTCTTATCTTTGCTATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATCTTTGCCATTTCAATAT
11173929 CGATCATTAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.21, C:0.23, G:0.01, T:0.55
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTCTCATCTTTGCCATTTCAATAT
Found at i:11188988 original size:22 final size:21
Alignment explanation
Indices: 11188955--11188995 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
11188945 AAATGAAATA
*
11188955 AAAGAAATGAAAAAGAGAAAC
1 AAAGAAACGAAAAAGAGAAAC
*
11188976 AAAGCAAACGAAACAGAGAA
1 AAAG-AAACGAAAAAGAGAA
11188996 GAATAGGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.68, C:0.10, G:0.20, T:0.02
Consensus pattern (21 bp):
AAAGAAACGAAAAAGAGAAAC
Found at i:11190091 original size:12 final size:12
Alignment explanation
Indices: 11190074--11190108 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
11190064 TTTGTGTACC
11190074 GCTACTGTTACT
1 GCTACTGTTACT
11190086 GCTACTGTTACT
1 GCTACTGTTACT
* *
11190098 GTTACCGTTAC
1 GCTACTGTTAC
11190109 GGTGTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (12 bp):
GCTACTGTTACT
Found at i:11190266 original size:18 final size:18
Alignment explanation
Indices: 11190245--11190283 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
11190235 ACTGAATATT
*
11190245 TGACTGTTACAGAATAAA
1 TGACTGATACAGAATAAA
*
11190263 TGACTGATACTGAATAAA
1 TGACTGATACAGAATAAA
11190281 TGA
1 TGA
11190284 ATATTACTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (18 bp):
TGACTGATACAGAATAAA
Found at i:11190291 original size:18 final size:19
Alignment explanation
Indices: 11190251--11190293 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
11190241 TATTTGACTG
* *
11190251 TTACAGAATAAATGACTGA
1 TTACTGAATAAATGAATGA
11190270 -TACTGAATAAATGAAT-A
1 TTACTGAATAAATGAATGA
11190287 TTACTGA
1 TTACTGA
11190294 TTAACCGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (19 bp):
TTACTGAATAAATGAATGA
Found at i:11192082 original size:21 final size:22
Alignment explanation
Indices: 11192056--11192096 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
11192046 AGAAAAAAAC
11192056 TGCTATTTT-TTATTATTTTCT
1 TGCTATTTTCTTATTATTTTCT
*
11192077 TGCTATTTTCTTATTGTTTT
1 TGCTATTTTCTTATTATTTT
11192097 TTAACTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.12, C:0.10, G:0.07, T:0.71
Consensus pattern (22 bp):
TGCTATTTTCTTATTATTTTCT
Found at i:11192104 original size:22 final size:21
Alignment explanation
Indices: 11192058--11192107 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
11192048 AAAAAAACTG
*
11192058 CTATTTTTTATTATTTTCTTG
1 CTATTTTTTATTATTTTCTTA
*
11192079 CTATTTTCTTATTGTTTT-TTAA
1 CTATTTT-TTATTATTTTCTT-A
11192101 CTATTTT
1 CTATTTT
11192108 GCTACCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.16, C:0.10, G:0.04, T:0.70
Consensus pattern (21 bp):
CTATTTTTTATTATTTTCTTA
Found at i:11192312 original size:18 final size:20
Alignment explanation
Indices: 11192291--11192331 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
11192281 GAAATATTTA
*
11192291 TTTTAATGT-TTTTA-ATAT
1 TTTTAATGTATTATATATAT
*
11192309 TTTTGATGTATTATATATAT
1 TTTTAATGTATTATATATAT
11192329 TTT
1 TTT
11192332 AAAAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 8 0.42
19 4 0.21
20 7 0.37
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTTAATGTATTATATATAT
Found at i:11194872 original size:37 final size:37
Alignment explanation
Indices: 11194822--11194896 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
11194812 TAAGTATGAC
11194822 TTGGTCCCTGTCTGCCTTACAAAACAAAATTAGGTCA
1 TTGGTCCCTGTCTGCCTTACAAAACAAAATTAGGTCA
*
11194859 TTGGTCCCTGTCTGCCTTGCAAAACAAAATTAGGTCA
1 TTGGTCCCTGTCTGCCTTACAAAACAAAATTAGGTCA
11194896 T
1 T
11194897 CTGTGAAGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (37 bp):
TTGGTCCCTGTCTGCCTTACAAAACAAAATTAGGTCA
Found at i:11201089 original size:12 final size:12
Alignment explanation
Indices: 11201072--11201096 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11201062 ATTCATGTGA
11201072 AATGATGTCTCT
1 AATGATGTCTCT
11201084 AATGATGTCTCT
1 AATGATGTCTCT
11201096 A
1 A
11201097 GGTTGATTTA
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AATGATGTCTCT
Found at i:11208483 original size:20 final size:20
Alignment explanation
Indices: 11208455--11208492 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11208445 AATAGGGTAC
*
11208455 GTCTAGTTCACTGTAATAGA
1 GTCTAGTTCACTATAATAGA
*
11208475 GTCTGGTTCACTATAATA
1 GTCTAGTTCACTATAATA
11208493 CAATAAGACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (20 bp):
GTCTAGTTCACTATAATAGA
Found at i:11208513 original size:16 final size:17
Alignment explanation
Indices: 11208494--11208539 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
11208484 ACTATAATAC
11208494 AATAAG-ACTGTAATGA
1 AATAAGAACTGTAATGA
*
11208510 AAT-AGAATTGTAATGA
1 AATAAGAACTGTAATGA
*
11208526 AAT-AGAATTGTAAT
1 AATAAGAACTGTAAT
11208540 CAGTAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 2 0.07
16 26 0.93
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.30
Consensus pattern (17 bp):
AATAAGAACTGTAATGA
Found at i:11208745 original size:14 final size:14
Alignment explanation
Indices: 11208709--11208749 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
11208699 GTTATTAAAT
*
11208709 TTTAAT-AAAATTA
1 TTTAATAAAAATAA
*
11208722 -TTATTAAAAATAA
1 TTTAATAAAAATAA
11208735 TTTAATAAAAATAA
1 TTTAATAAAAATAA
11208749 T
1 T
11208750 AAATAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 13 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTAATAAAAATAA
Found at i:11208793 original size:58 final size:57
Alignment explanation
Indices: 11208702--11208841 Score: 192
Period size: 58 Copynumber: 2.4 Consensus size: 57
11208692 TGTTATTGTT
*
11208702 ATTAAATTTTAATAAAATTATTATTAAAAATAATTTAATAAAAATAATAA-ATAATTTA
1 ATTAAATTTTAATATAATTATTATTAAAAATAATTTAAT-AAAATAA-AACATAATTTA
* * * *
11208760 ATTATATTTTAACATAATTTTTATTAAATATAATTTAATAAAATAAAACATAATTTA
1 ATTAAATTTTAATATAATTATTATTAAAAATAATTTAATAAAATAAAACATAATTTA
*
11208817 ATAAAATTCTTAATATAATTATTAT
1 ATTAAATT-TTAATATAATTATTAT
11208842 ATGAATTAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
56 2 0.03
57 21 0.30
58 48 0.68
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (57 bp):
ATTAAATTTTAATATAATTATTATTAAAAATAATTTAATAAAATAAAACATAATTTA
Found at i:11213092 original size:24 final size:23
Alignment explanation
Indices: 11213065--11213115 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
11213055 ATTTTTTTAT
*
11213065 TAAAT-AAAAACTTTTAAAATACAA
1 TAAATCAAAAACATTTAAAA-AC-A
*
11213089 TAAATCAAATACATTTAAAAACA
1 TAAATCAAAAACATTTAAAAACA
11213112 TAAA
1 TAAA
11213116 AACAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.21
24 7 0.29
25 12 0.50
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (23 bp):
TAAATCAAAAACATTTAAAAACA
Found at i:11213363 original size:11 final size:11
Alignment explanation
Indices: 11213344--11213423 Score: 85
Period size: 11 Copynumber: 7.4 Consensus size: 11
11213334 AAACATGACA
11213344 AAAAGCAGCAAC
1 AAAA-CAGCAAC
*
11213356 AAACCAGC-AC
1 AAAACAGCAAC
*
11213366 TAAAACAGCAGC
1 -AAAACAGCAAC
*
11213378 AAAACAGCACC
1 AAAACAGCAAC
11213389 AAAACAGC-AC
1 AAAACAGCAAC
*
11213399 CAAACAGCAAC
1 AAAACAGCAAC
11213410 AAAACAGC-AC
1 AAAACAGCAAC
11213420 AAAA
1 AAAA
11213424 AACAACATCA
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
10 16 0.28
11 38 0.66
12 4 0.07
ACGTcount: A:0.57, C:0.30, G:0.11, T:0.01
Consensus pattern (11 bp):
AAAACAGCAAC
Found at i:11213413 original size:32 final size:33
Alignment explanation
Indices: 11213344--11213424 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 33
11213334 AAACATGACA
* * *
11213344 AAAAGCAGCAACAAACCAGCACTAAAACAGCAGC
1 AAAA-CAGCACCAAAACAGCACTAAAACAGCAAC
*
11213378 AAAACAGCACCAAAACAGCAC-CAAACAGCAAC
1 AAAACAGCACCAAAACAGCACTAAAACAGCAAC
*
11213410 AAAACAGCACAAAAA
1 AAAACAGCACCAAAA
11213425 ACAACATCAC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 23 0.55
33 15 0.36
34 4 0.10
ACGTcount: A:0.58, C:0.30, G:0.11, T:0.01
Consensus pattern (33 bp):
AAAACAGCACCAAAACAGCACTAAAACAGCAAC
Found at i:11215357 original size:55 final size:55
Alignment explanation
Indices: 11215296--11215404 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
11215286 TAGCATTTAT
11215296 TAGTATAGTTTATTTGACTTACTAATTTAGCCTATAAATAAGCTCCTTTACAATC
1 TAGTATAGTTTATTTGACTTACTAATTTAGCCTATAAATAAGCTCCTTTACAATC
*
11215351 TAGTATAGTTTATTTGACTTACTAATTTAGCCTATAAATAGGCTCCTTTACAAT
1 TAGTATAGTTTATTTGACTTACTAATTTAGCCTATAAATAAGCTCCTTTACAAT
11215405 TTTAGAATTA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (55 bp):
TAGTATAGTTTATTTGACTTACTAATTTAGCCTATAAATAAGCTCCTTTACAATC
Found at i:11227721 original size:120 final size:122
Alignment explanation
Indices: 11227551--11227781 Score: 317
Period size: 122 Copynumber: 1.9 Consensus size: 122
11227541 ACTCAACCAC
* * *
11227551 AATAACAATGAGAATAAGAATAAAAATGTAATGGGTTTGAGGTTTTCCTAAT-CTCAATTTAACA
1 AATAACAATGAGAATAAGAATAAAAATGTAATAGGTATGAGGTGTTCCTAATACTCAATTTAACA
*
11227615 C-AGAATGTATGATAACTAACCTAGGAATGCAAATTAAATGATAGACATTGGCATGGT
66 CGA-AATGTATGATAACTAACCTAAGAATGCAAATTAAATGATAGACATTGGCATGGT
* ** * **
11227672 AATAAC-ATGAGAATAAGCATAGTAATGTCATAGGTATG-GGCTGTTCCTAATAACTTGATTTAA
1 AATAACAATGAGAATAAGAATAAAAATGTAATAGGTATGAGG-TGTTCCTAAT-ACTCAATTTAA
11227735 CACGAAATGTATGATAACTAACCTAAGAATGCAAATTAAATGATAGA
64 CACGAAATGTATGATAACTAACCTAAGAATGCAAATTAAATGATAGA
11227782 AAAATGAAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
119 2 0.02
120 35 0.36
121 6 0.06
122 52 0.54
123 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (122 bp):
AATAACAATGAGAATAAGAATAAAAATGTAATAGGTATGAGGTGTTCCTAATACTCAATTTAACA
CGAAATGTATGATAACTAACCTAAGAATGCAAATTAAATGATAGACATTGGCATGGT
Found at i:11227954 original size:61 final size:61
Alignment explanation
Indices: 11227879--11227997 Score: 175
Period size: 61 Copynumber: 2.0 Consensus size: 61
11227869 ACGCTAAGGT
* * *
11227879 AAAGAGATTAAGCGTAAAAAATGAAGTGGGAAGTGGTGCATGGGCATGCCAGAGAGGCCGG
1 AAAGAGATTAAGCGTAAAAAATAAAGTGGAAAGTGGTGCACGGGCATGCCAGAGAGGCCGG
* * * *
11227940 AAAGAGATTGAGCGTCAAAAATAAAGTGGAAAGTGGTGCACGGGCATGGCAGGGAGGC
1 AAAGAGATTAAGCGTAAAAAATAAAGTGGAAAGTGGTGCACGGGCATGCCAGAGAGGC
11227998 AGTGTGGAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.36, C:0.12, G:0.38, T:0.14
Consensus pattern (61 bp):
AAAGAGATTAAGCGTAAAAAATAAAGTGGAAAGTGGTGCACGGGCATGCCAGAGAGGCCGG
Found at i:11229214 original size:45 final size:45
Alignment explanation
Indices: 11229143--11229232 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
11229133 GTTTGAGTTC
* * * *
11229143 ACCTGTGCCAACATCAATAATTGTTTTGGCAGTTGCTAAAAAGGG
1 ACCTATGCCAACATCAATAATCGTTTTAGCAGTTGCCAAAAAGGG
11229188 ACCTATGCCAACATCAATAATCGTTTTAGCAGTTGCCAAAAAGGG
1 ACCTATGCCAACATCAATAATCGTTTTAGCAGTTGCCAAAAAGGG
11229233 TTTTCCCAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (45 bp):
ACCTATGCCAACATCAATAATCGTTTTAGCAGTTGCCAAAAAGGG
Found at i:11234377 original size:17 final size:16
Alignment explanation
Indices: 11234355--11234386 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
11234345 ATATTTTTGC
11234355 ATGAAAATTGATATGAT
1 ATGAAAATTG-TATGAT
11234372 ATGAAAATTGTATGA
1 ATGAAAATTGTATGA
11234387 AAATATTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (16 bp):
ATGAAAATTGTATGAT
Found at i:11237070 original size:22 final size:22
Alignment explanation
Indices: 11237044--11237088 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
11237034 TGTGATGACG
11237044 TTATCTT-ATAAATATGCTGAAT
1 TTATCTTGA-AAATATGCTGAAT
*
11237066 TTATCTTGAAAATATGTTGAAT
1 TTATCTTGAAAATATGCTGAAT
11237088 T
1 T
11237089 GATTTGGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.47
Consensus pattern (22 bp):
TTATCTTGAAAATATGCTGAAT
Found at i:11237512 original size:14 final size:16
Alignment explanation
Indices: 11237474--11237505 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
11237464 ATAAATAATA
11237474 ATAT-AAAATTACATT
1 ATATAAAAATTACATT
11237489 ATATAAAAATTACATT
1 ATATAAAAATTACATT
11237505 A
1 A
11237506 AAAAAATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAAAATTACATT
Found at i:11237740 original size:109 final size:109
Alignment explanation
Indices: 11237607--11238122 Score: 701
Period size: 109 Copynumber: 4.7 Consensus size: 109
11237597 ACATTACTAA
11237607 AAAATCATAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAT
1 AAAATCATAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAT
11237672 AAAATAGCTATAATTTTTTTTAAATATATTACTAAAAAAATCAC
66 AAAATAGCTATAATTTTTTTTAAATATATTACTAAAAAAATCAC
11237716 AAAATCATAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAT
1 AAAATCATAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAT
*
11237781 AAAATAGTTATAAAATTATTTTTTTAAATATATTACT-AAAAAATCAC
66 AAAATAGCTAT--AA-T-TTTTTTTAAATATATTACTAAAAAAATCAC
* * * *
11237828 AATA-CACTAATACACTGAACCACTAAACAGTAACAATTTATGTAACCTAATCATAAATTACTAA
1 AAAATCA-TAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAA
* * * *
11237892 CAAAATAACTATAAATTTATTTTT---T-T-TTA--AAAATACATTACTAA
65 TAAAATAGCTAT-AATTT-TTTTTAAATATATTACTAAAA-A-AAT-C-AC
* * *
11237936 AAAATCATAATACACTAAACCACTAAACACTAGCACTTTATGTAACCTAATCATAAATTACTAAT
1 AAAATCATAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAT
11238001 AAAATAGCTATAATTTTTTTTAAATATATTACTAAAAAAATCAC
66 AAAATAGCTATAATTTTTTTTAAATATATTACTAAAAAAATCAC
* * *
11238045 AATA-CACTAATACACTAAACCACTAAACACTAACAATTTTTATAACTTAATCATAAATTACTAA
1 AAAATCA-TAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAA
* *
11238109 CAAAATAACTATAA
65 TAAAATAGCTATAA
11238123 AATTATTTTT
Statistics
Matches: 360, Mismatches: 27, Indels: 40
0.84 0.06 0.09
Matches are distributed among these distances:
104 3 0.01
105 4 0.01
106 8 0.02
107 7 0.02
108 69 0.19
109 148 0.41
110 8 0.02
111 12 0.03
112 78 0.22
113 23 0.06
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.32
Consensus pattern (109 bp):
AAAATCATAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAT
AAAATAGCTATAATTTTTTTTAAATATATTACTAAAAAAATCAC
Found at i:11238106 original size:217 final size:218
Alignment explanation
Indices: 11237492--11238212 Score: 832
Period size: 217 Copynumber: 3.3 Consensus size: 218
11237482 TTACATTATA
* * *
11237492 TAAAAATTACATTA--AAAAAATCACAAAACACTAAACCA-TAAACACTAACA---AT-TTA--T
1 TAAAAA-TACATTACTAAAAAATCATAATACACTAAACCACTAAACACTAACATTTATGTAACCT
* * * *
11237548 AATCATAAATTACTAACACAAAATAACTAAAAAATTATTTTTTTTAAATACATTACT---AAA--
65 AATCATAAATTACT-A-ATAAAATAGCT-ATAAATTA-TTTTTTTAAATATATTACTAAAAAATC
11237608 A-AAT-CA-TAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCATAAATTACTA
126 ACAATACACTAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCATAAATTACTA
* *
11237670 ATAAAATAGCTAT-AATTT-TTTTTAAATATAT
191 ACAAAATAACTATAAATTTATTTTT---T-T-T
* * *
11237701 TACTAAAA-A-AAT-C-ACAAAATCATAATACACTAAACCACTAAACACTAACAATTTATATAAC
1 TA--AAAATACATTACTAAAAAATCATAATACACTAAACCACTAAACACTAAC-ATTTATGTAAC
*
11237762 CTAATCATAAATTACTAATAAAATAGTTATAAAATTATTTTTTTAAATATATTACTAAAAAATCA
63 CTAATCATAAATTACTAATAAAATAGCTAT-AAATTATTTTTTTAAATATATTACTAAAAAATCA
* * *
11237827 CAATACACTAATACACTGAACCACTAAACAGTAACAATTTATGTAACCTAATCATAAATTACTAA
127 CAATACACTAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAA
11237892 CAAAATAACTATAAATTTATTTTTTTT
192 CAAAATAACTATAAATTTATTTTTTTT
*
11237919 TAAAAATACATTACTAAAAAATCATAATACACTAAACCACTAAACACTAGCACTTTATGTAACCT
1 TAAAAATACATTACTAAAAAATCATAATACACTAAACCACTAAACACTAACA-TTTATGTAACCT
11237984 AATCATAAATTACTAATAAAATAGCTAT-AA-T-TTTTTTTAAATATATTACTAAAAAAATCACA
65 AATCATAAATTACTAATAAAATAGCTATAAATTATTTTTTTAAATATATTACT-AAAAAATCACA
* *
11238046 ATACACTAATACACTAAACCACTAAACACTAACAATTTTTATAACTTAATCATAAATTACTAACA
129 ATACACTAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACA
* **
11238111 AAATAACTATAAAATTA-TTTTTAA
194 AAATAACTATAAATTTATTTTTTTT
* ** * *
11238135 AAAAAATTACATTACTAAAAAATCGCAATACCCTAAACCACTAAACACTAACAATT-TGTAACCT
1 TAAAAA-TACATTACTAAAAAATCATAATACACTAAACCACTAAACACTAACATTTATGTAACCT
11238199 AATCTCATAAATTA
65 AA--TCATAAATTA
11238213 TTAACCAAAT
Statistics
Matches: 447, Mismatches: 34, Indels: 54
0.84 0.06 0.10
Matches are distributed among these distances:
208 23 0.05
209 14 0.03
210 1 0.00
211 4 0.01
213 21 0.05
214 16 0.04
215 11 0.02
216 53 0.12
217 141 0.32
218 8 0.02
219 6 0.01
220 75 0.17
221 64 0.14
222 5 0.01
223 5 0.01
ACGTcount: A:0.51, C:0.16, G:0.01, T:0.31
Consensus pattern (218 bp):
TAAAAATACATTACTAAAAAATCATAATACACTAAACCACTAAACACTAACATTTATGTAACCTA
ATCATAAATTACTAATAAAATAGCTATAAATTATTTTTTTAAATATATTACTAAAAAATCACAAT
ACACTAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACAAA
ATAACTATAAATTTATTTTTTTT
Found at i:11238229 original size:329 final size:320
Alignment explanation
Indices: 11237493--11238234 Score: 1045
Period size: 329 Copynumber: 2.3 Consensus size: 320
11237483 TACATTATAT
*
11237493 AAAAATTACATTAAAAAAATCACAAAACACTAAACCA-TAAACACTAACAA-TT-T-A--TAATC
1 AAAAATTACATTAAAAAAATCACAATACACTAAACCACTAAACACTAACAATTTGTAACCTAATC
*
11237552 ATAAATTACTAACACAAAATAACTAAAAAATTATTTTTTTTAAATACATTACTAAAAAATCATAA
66 ATAAATTACTAACA-AAAATAACTATAAAATTATTTTTTTTAAATACATTACTAAAAAATCATAA
11237617 TACACTAAACCACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAATAAAATAGCTA
130 TACACTAAACCACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAATAAAATAGCTA
11237682 TAATTTTTTTTAAATATATTACTAAAAAAATCACAAAATCATAATACACTAAACCACTAAACACT
195 TAATTTTTTTTAAATATATTACTAAAAAAATCACAAAATCATAATACACTAAACCACTAAACACT
* ** *
11237747 AACAATTTATATAACCTAATCATAAATTACTAATAAAATAGTTATAAAATTATTTTTTTAA
260 AACAATTTATATAACCTAATCATAAATTACTAACAAAATAACTATAAAATTATTTTTTAAA
* * * * *
11237808 ATATATTAC-TAAAAAATCACAATACACTAATACACTGAACCACTAAACAGTAACAATTTATGTA
1 AAAAATTACAT-TAAAA--A-AAT-CAC-AATACACTAAACCACTAAACACTAACAA-TT-TGTA
*
11237872 ACCTAATCATAAATTACTAAC-AAAATAACTATAAATTTATTTTTTTTTAAAAATACATTACTAA
58 ACCTAATCATAAATTACTAACAAAAATAACTATAAAATTA-TTTTTTTT--AAATACATTACTAA
* * *
11237936 AAAATCATAATACACTAAACCACTAAACACTAGCACTTTATGTAACCTAATCATAAATTACTAAT
120 AAAATCATAATACACTAAACCACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAT
*
11238001 AAAATAGCTATAATTTTTTTTAAATATATTACTAAAAAAATCACAATA-CACTAATACACTAAAC
185 AAAATAGCTATAATTTTTTTTAAATATATTACTAAAAAAATCACAAAATCA-TAATACACTAAAC
* *
11238065 CACTAAACACTAACAATTTTTATAACTTAATCATAAATTACTAACAAAATAACTATAAAATTA-T
249 CACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACAAAATAACTATAAAATTATT
11238129 TTTTAAA
314 TTTTAAA
* *
11238136 AAAAATTACATTACTAAAAAATCGCAATACCCTAAACCACTAAACACTAACAATTTGTAACCTAA
1 AAAAATTACATTA--AAAAAATCACAATACACTAAACCACTAAACACTAACAATTTGTAACCTAA
*
11238201 TCTCATAAATTATTAACCAAATAAATAACTATAA
64 --TCATAAATTACTAA-C-AA-AAATAACTATAA
11238235 CAAAATACAA
Statistics
Matches: 374, Mismatches: 26, Indels: 40
0.85 0.06 0.09
Matches are distributed among these distances:
314 1 0.00
315 11 0.03
317 1 0.00
318 3 0.01
319 3 0.01
320 12 0.03
321 12 0.03
323 11 0.03
324 3 0.01
325 39 0.10
326 20 0.05
327 11 0.03
328 37 0.10
329 207 0.55
330 3 0.01
ACGTcount: A:0.51, C:0.16, G:0.01, T:0.31
Consensus pattern (320 bp):
AAAAATTACATTAAAAAAATCACAATACACTAAACCACTAAACACTAACAATTTGTAACCTAATC
ATAAATTACTAACAAAAATAACTATAAAATTATTTTTTTTAAATACATTACTAAAAAATCATAAT
ACACTAAACCACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAATAAAATAGCTAT
AATTTTTTTTAAATATATTACTAAAAAAATCACAAAATCATAATACACTAAACCACTAAACACTA
ACAATTTATATAACCTAATCATAAATTACTAACAAAATAACTATAAAATTATTTTTTAAA
Found at i:11238384 original size:3 final size:3
Alignment explanation
Indices: 11238378--11238439 Score: 106
Period size: 3 Copynumber: 20.3 Consensus size: 3
11238368 TACATTACCT
11238378 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTCC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C
*
11238424 TTC TTC TTC TCC TTC T
1 TTC TTC TTC TTC TTC T
11238440 CCTTTCTCTC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:11238738 original size:23 final size:23
Alignment explanation
Indices: 11238703--11238746 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
11238693 AATATAAATA
11238703 TTAAAAAATAAAAATAATATTTT
1 TTAAAAAATAAAAATAATATTTT
*
11238726 TTAAACAAA-AAAATTAATATT
1 TTAAA-AAATAAAAATAATATT
11238747 AAAAAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
TTAAAAAATAAAAATAATATTTT
Found at i:11239367 original size:29 final size:30
Alignment explanation
Indices: 11239329--11239385 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
11239319 AAAAAATGTC
11239329 ATTTTTTAAATATTATA-AA-AATAAACCAA
1 ATTTTTTAAA-ATTATACAAGAATAAACCAA
*
11239358 ATTTTTTAAAATTTTACAAGAATAAACC
1 ATTTTTTAAAATTATACAAGAATAAACC
11239386 TTAAAAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 5 0.20
29 12 0.48
30 8 0.32
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.39
Consensus pattern (30 bp):
ATTTTTTAAAATTATACAAGAATAAACCAA
Found at i:11245348 original size:5 final size:5
Alignment explanation
Indices: 11245300--11245331 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
11245290 TGCTATATGG
11245300 ATTTT ACTTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT A-TTTT ATTTT ATTTT ATTTT ATTTT A
11245332 CCATTGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:11246269 original size:25 final size:24
Alignment explanation
Indices: 11246233--11246279 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
11246223 AGTTAATAAT
11246233 AATTCTCTTTGAGATTTTCTTCAAG
1 AATTCTCTTTGAG-TTTTCTTCAAG
*
11246258 AATTGCTC-TTGAGTTTTTTTCA
1 AATT-CTCTTTGAGTTTTCTTCA
11246280 GAAGCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 8 0.40
25 9 0.45
26 3 0.15
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (24 bp):
AATTCTCTTTGAGTTTTCTTCAAG
Found at i:11248359 original size:19 final size:19
Alignment explanation
Indices: 11248335--11248385 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
11248325 AGTGAATTTT
11248335 GATGAAATTGTAATTTAGG
1 GATGAAATTGTAATTTAGG
11248354 GATGAAATTGTAATTTAGG
1 GATGAAATTGTAATTTAGG
11248373 GACT-AAATTGTAA
1 GA-TGAAATTGTAA
11248386 AGATGCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 30 0.97
20 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (19 bp):
GATGAAATTGTAATTTAGG
Found at i:11249115 original size:26 final size:26
Alignment explanation
Indices: 11249055--11249116 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
11249045 GTCCTGATAT
11249055 ATGGCTCTTCGTGAGCTTCCCAATTA
1 ATGGCTCTTCGTGAGCTTCCCAATTA
* * * ***
11249081 AAGGATCTTTGTGAGCTTCTTGATTA
1 ATGGCTCTTCGTGAGCTTCCCAATTA
11249107 ATGGCTCTTC
1 ATGGCTCTTC
11249117 AGAACTTCCC
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (26 bp):
ATGGCTCTTCGTGAGCTTCCCAATTA
Found at i:11249232 original size:24 final size:23
Alignment explanation
Indices: 11249205--11249252 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
11249195 TACCTGTTAT
*
11249205 TGGCTCGCATGAGCTTCTCGATTA
1 TGGCTCGCATGAGCTT-TCCATTA
**
11249229 TGGCTCTTATGAGCTTTCCATTA
1 TGGCTCGCATGAGCTTTCCATTA
11249252 T
1 T
11249253 ATAGCTCGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.40
Consensus pattern (23 bp):
TGGCTCGCATGAGCTTTCCATTA
Found at i:11249284 original size:25 final size:25
Alignment explanation
Indices: 11249262--11249309 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
11249252 TATAGCTCGG
11249262 ATAAGCTTCCCGTTACATGGCTCAC
1 ATAAGCTTCCCGTTACATGGCTCAC
* * *
11249287 ATGAGCTTCCTGTTATATGGCTC
1 ATAAGCTTCCCGTTACATGGCTC
11249310 TAGAAAGGGC
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:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (25 bp):
ATAAGCTTCCCGTTACATGGCTCAC
Found at i:11259937 original size:13 final size:13
Alignment explanation
Indices: 11259919--11259943 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11259909 ATATCACCTT
11259919 GCAAAGACAAGGC
1 GCAAAGACAAGGC
11259932 GCAAAGACAAGG
1 GCAAAGACAAGG
11259944 AGCATACTTT
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:0.48, C:0.20, G:0.32, T:0.00
Consensus pattern (13 bp):
GCAAAGACAAGGC
Found at i:11269470 original size:405 final size:403
Alignment explanation
Indices: 11268718--11269527 Score: 1386
Period size: 405 Copynumber: 2.0 Consensus size: 403
11268708 CAAAAAGAAA
11268718 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
1 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
* *
11268783 TTGAAAACAATTCAGCAGTTAAGAGTAGGTAACAACACATGCTGCTTGGATGCAAATAAAGACCT
66 TCGAAAACAATTCAACAGTTAAGAGTAGGTAACAACACATGCTGCTTGGATGCAAATAAAGACCT
* * * *
11268848 TTGCGTTTATTAGCAACACATTACATTTAAGAGATAAAGCTTGACACGCCTTGCATCAAGCAACT
131 CTGCCTTTATTAGAAACACATTACATTTAAGAGATAAAGCTTGACACGCCTGGCATCAAGCAACT
** *
11268913 AACCAGAATTGACAATAAGAATGATAACAGCATGATTTTATCAAAATGCCTTCAGCATGTAATAC
196 AACCAGAATCAACAATAAGAATGATAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAATAC
* *
11268978 TTTCCAACTTATAACCAGAATTCATCATACAAAGAAAGAAATACAGGAAATGTACTTTAAATGGA
261 TTTCCAACTTAAAACCAGAATTCATCATACAAAGAAAGAAATACAGGAAATGTACTTTAAAGGGA
* * *
11269043 TGGAAAGGATGTACGATAATTTGATTGGATAAGGTAAGAAGAGTAAGGTAAAGATAAGGAAAATT
326 TGGAAAGGATGTACGATAATTTGATTGGACAAGGTAAGAAGAGTAAGGTAAAGAGAAGGAAAATG
11269108 ATGCTTTATTGTC
391 ATGCTTTATTGTC
*
11269121 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCGGGAATTGGAGAAAGAGT
1 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
11269186 TCGAAAACAATTCAACAGTTAAGAGTAGGTAACAACACATATGCTGCTTGGATGCAAATAAAGAC
66 TCGAAAACAATTCAACAGTTAAGAGTAGGTAACAACAC--ATGCTGCTTGGATGCAAATAAAGAC
* * *
11269251 CTCTGCCTTTATTAGAAACACATTATATTTAAGAGATAAAGGTTGACACGCCTGGCGTCAAGCAA
129 CTCTGCCTTTATTAGAAACACATTACATTTAAGAGATAAAGCTTGACACGCCTGGCATCAAGCAA
* *
11269316 CTAACCAGAATCAACAATAAGAATGTTAACAGCATGATTTCATTAAAATGCCTTCAGCATGTAAT
194 CTAACCAGAATCAACAATAAGAATGATAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAAT
*
11269381 ACTTTCCAACTTAAAACCAGAATTCATCATACATAGAAAGAAATACAGGAAATGTACTTTAAAGG
259 ACTTTCCAACTTAAAACCAGAATTCATCATACAAAGAAAGAAATACAGGAAATGTACTTTAAAGG
* * *
11269446 GATGGAAAGGATGTACGTTAATTTGATTGGACAAGGTAAGAAGATTAAGGTAAAGGGAAGGAAAA
324 GATGGAAAGGATGTACGATAATTTGATTGGACAAGGTAAGAAGAGTAAGGTAAAGAGAAGGAAAA
11269511 TGATGCTTTATTGTC
389 TGATGCTTTATTGTC
11269526 TG
1 TG
11269528 TTGGAGGAGA
Statistics
Matches: 381, Mismatches: 24, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
403 100 0.26
405 281 0.74
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (403 bp):
TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
TCGAAAACAATTCAACAGTTAAGAGTAGGTAACAACACATGCTGCTTGGATGCAAATAAAGACCT
CTGCCTTTATTAGAAACACATTACATTTAAGAGATAAAGCTTGACACGCCTGGCATCAAGCAACT
AACCAGAATCAACAATAAGAATGATAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAATAC
TTTCCAACTTAAAACCAGAATTCATCATACAAAGAAAGAAATACAGGAAATGTACTTTAAAGGGA
TGGAAAGGATGTACGATAATTTGATTGGACAAGGTAAGAAGAGTAAGGTAAAGAGAAGGAAAATG
ATGCTTTATTGTC
Found at i:11270227 original size:31 final size:31
Alignment explanation
Indices: 11270189--11270250 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
11270179 GATAACCATC
11270189 ACATAGTACCGAAAATTCAAAAGGTAACACT
1 ACATAGTACCGAAAATTCAAAAGGTAACACT
*
11270220 ACATAGTACCGGAAATTCAAAAGGTAACACT
1 ACATAGTACCGAAAATTCAAAAGGTAACACT
11270251 CAATTAACCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (31 bp):
ACATAGTACCGAAAATTCAAAAGGTAACACT
Found at i:11288517 original size:24 final size:23
Alignment explanation
Indices: 11288490--11288535 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
11288480 ATTGTTCTAC
11288490 AAAATTAATCAAACA-AAAAAATAG
1 AAAATT-ATCAAA-AGAAAAAATAG
*
11288514 AAAATTGTCAAAAGAAAAAATA
1 AAAATTATCAAAAGAAAAAATA
11288536 AAATCGGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 13 0.65
24 6 0.30
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.17
Consensus pattern (23 bp):
AAAATTATCAAAAGAAAAAATAG
Found at i:11296293 original size:18 final size:18
Alignment explanation
Indices: 11296252--11296307 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
11296242 TTTTTGTTTT
11296252 TTTATAAATTTATAAAA-A
1 TTTATAAATTT-TAAAATA
* *
11296270 --TATAAATTTTGAAATT
1 TTTATAAATTTTAAAATA
11296286 TTTATAAATTTTAAAATA
1 TTTATAAATTTTAAAATA
11296304 TTTA
1 TTTA
11296308 AATTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 4 0.13
16 9 0.29
18 18 0.58
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTTATAAATTTTAAAATA
Found at i:11299670 original size:14 final size:14
Alignment explanation
Indices: 11299651--11299678 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11299641 ACGGTGAAAG
11299651 TATGATTTCAAGTT
1 TATGATTTCAAGTT
11299665 TATGATTTCAAGTT
1 TATGATTTCAAGTT
11299679 AACAAGGAAA
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:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (14 bp):
TATGATTTCAAGTT
Found at i:11309362 original size:22 final size:22
Alignment explanation
Indices: 11309326--11309391 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
11309316 TTGCATATTT
*
11309326 ATTCATTACTAACATTCATTCGTC
1 ATTCATT-C-AACATTCATTCGAC
* *
11309350 ATTTATTCAACATTCATTTGAC
1 ATTCATTCAACATTCATTCGAC
*
11309372 ATTCATTCATTCATTCATTC
1 ATTCATTCA-ACATTCATTC
11309392 ATTGCATGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
22 20 0.57
23 9 0.26
24 6 0.17
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.45
Consensus pattern (22 bp):
ATTCATTCAACATTCATTCGAC
Found at i:11321124 original size:47 final size:47
Alignment explanation
Indices: 11321028--11321127 Score: 128
Period size: 47 Copynumber: 2.1 Consensus size: 47
11321018 TTACACAGAT
* * * * *
11321028 CACATATCACACTGATGCCATATCCCAGATATGATCATATATAGTAG
1 CACATATCACACGGATGCCAAATCCCAAATATGATCATATACAGAAG
* * *
11321075 CACATATCACACGGATGCCAAATCCCAAATATGGTCTTATACGGAAG
1 CACATATCACACGGATGCCAAATCCCAAATATGATCATATACAGAAG
11321122 CACATA
1 CACATA
11321128 ATCGCATCTC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (47 bp):
CACATATCACACGGATGCCAAATCCCAAATATGATCATATACAGAAG
Found at i:11331934 original size:16 final size:17
Alignment explanation
Indices: 11331903--11331935 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11331893 TTCATAAGTA
11331903 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
11331920 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
11331936 GCTCCATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:11332291 original size:46 final size:46
Alignment explanation
Indices: 11332216--11332442 Score: 276
Period size: 46 Copynumber: 5.0 Consensus size: 46
11332206 TTATCTTTGA
* * * * * ** *
11332216 CATGATGCCATGGTGTCTTTCAACTATGGTCTTTCTCATTTTTTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* ** ***
11332262 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* * *
11332307 CATGTTACCATAGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
11332353 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
11332399 CATGTTGCCATGGTATCCTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
11332443 GTCAGAAAGT
Statistics
Matches: 156, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
45 37 0.24
46 119 0.76
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:11332360 original size:91 final size:92
Alignment explanation
Indices: 11332231--11332439 Score: 276
Period size: 91 Copynumber: 2.3 Consensus size: 92
11332221 TGCCATGGTG
* * * * *
11332231 TCTTTCAACTATGGTCTTTCTCATTTTTTGTCAGGTTGCCATGGTATCTTTCAACCATGGTCTTA
1 TCTTTCAACCATGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTA
** * *
11332296 TTCA-TTCCCGTCATGTTACCATAGTA
66 CACATTTCACATCATGTTACCATAGTA
**
11332322 TCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGGTATCTTTCAACCATGGTCTTA
1 TCTTTCAACCATGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTA
* * *
11332387 CACATTTCATATCATGTTGCCATGGTA
66 CACATTTCACATCATGTTACCATAGTA
*
11332414 TCCTTCAACCATGGTCTTACACATTT
1 TCTTTCAACCATGGTCTTACACATTT
11332440 CATGTCAGAA
Statistics
Matches: 102, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
91 60 0.59
92 42 0.41
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (92 bp):
TCTTTCAACCATGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTA
CACATTTCACATCATGTTACCATAGTA
Found at i:11343313 original size:30 final size:30
Alignment explanation
Indices: 11343277--11343339 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
11343267 AAAAACTATA
11343277 ATAAAGAAATCCAA-G-ACAGAGGAATCCAAG
1 ATAAAGAAATCCAAGGTACAGA--AATCCAAG
*
11343307 ATAAAGATATCCAAGGTACAGAAATCCAAG
1 ATAAAGAAATCCAAGGTACAGAAATCCAAG
11343337 ATA
1 ATA
11343340 CCACATCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 24 0.80
31 1 0.03
32 5 0.17
ACGTcount: A:0.52, C:0.16, G:0.17, T:0.14
Consensus pattern (30 bp):
ATAAAGAAATCCAAGGTACAGAAATCCAAG
Found at i:11343318 original size:15 final size:15
Alignment explanation
Indices: 11343277--11343339 Score: 72
Period size: 15 Copynumber: 4.2 Consensus size: 15
11343267 AAAAACTATA
11343277 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
11343292 ACAGAGGAATCCAAG
1 ATAAAGAAATCCAAG
*
11343307 ATAAAGATATCCAAG
1 ATAAAGAAATCCAAG
* *
11343322 GTACAGAAATCCAAG
1 ATAAAGAAATCCAAG
11343337 ATA
1 ATA
11343340 CCACATCATA
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.52, C:0.16, G:0.17, T:0.14
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:11352938 original size:15 final size:13
Alignment explanation
Indices: 11352909--11352935 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11352899 GCTCGACAGG
11352909 GACACACCCGTGT
1 GACACACCCGTGT
11352922 GACACACCCGTGT
1 GACACACCCGTGT
11352935 G
1 G
11352936 TGATTACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.37, G:0.26, T:0.15
Consensus pattern (13 bp):
GACACACCCGTGT
Found at i:11360232 original size:12 final size:12
Alignment explanation
Indices: 11360215--11360242 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
11360205 CCTAGCTAAG
11360215 TATAAATATATA
1 TATAAATATATA
11360227 TATAAATATATA
1 TATAAATATATA
11360239 TATA
1 TATA
11360243 TATCAGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TATAAATATATA
Found at i:11364202 original size:19 final size:18
Alignment explanation
Indices: 11364165--11364203 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
11364155 AGAAGGATGT
**
11364165 AATTGAGGCTAGTTTTGA
1 AATTGAGGCTAAATTTGA
11364183 AATTGAGGCTCAAATTTGA
1 AATTGAGGCT-AAATTTGA
11364202 AA
1 AA
11364204 GTTATGGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.33
Consensus pattern (18 bp):
AATTGAGGCTAAATTTGA
Found at i:11365137 original size:23 final size:22
Alignment explanation
Indices: 11365097--11365139 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
11365087 AATTCTTTCC
*
11365097 TTGGTATTGTTTCGTTTCTTAG
1 TTGGTATTGTTTAGTTTCTTAG
*
11365119 TTGGTAATTGTTTATTTTCTT
1 TTGGT-ATTGTTTAGTTTCTT
11365140 GAATTGTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.12, C:0.07, G:0.19, T:0.63
Consensus pattern (22 bp):
TTGGTATTGTTTAGTTTCTTAG
Found at i:11365180 original size:13 final size:13
Alignment explanation
Indices: 11365162--11365196 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
11365152 ATCATGTTCA
11365162 TAGTTAATTAATT
1 TAGTTAATTAATT
11365175 TAGTTAATTAATT
1 TAGTTAATTAATT
11365188 TAGTTAATT
1 TAGTTAATT
11365197 TTTAGTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (13 bp):
TAGTTAATTAATT
Found at i:11366418 original size:23 final size:23
Alignment explanation
Indices: 11366392--11366438 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
11366382 AAGTTTAATT
11366392 TATTAAACTTAACTTCAAAACTA
1 TATTAAACTTAACTTCAAAACTA
*
11366415 TATTAAACTTAGCTTCAAAACTA
1 TATTAAACTTAACTTCAAAACTA
11366438 T
1 T
11366439 CTAATTCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (23 bp):
TATTAAACTTAACTTCAAAACTA
Found at i:11369670 original size:24 final size:24
Alignment explanation
Indices: 11369614--11369732 Score: 179
Period size: 24 Copynumber: 5.0 Consensus size: 24
11369604 GAGAAAGTGA
11369614 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
11369638 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
11369661 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
11369685 AAAAGGACTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
11369709 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
11369733 ATGATAAAGC
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
23 23 0.26
24 54 0.62
25 10 0.11
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:11369961 original size:31 final size:31
Alignment explanation
Indices: 11369926--11369990 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
11369916 CATTTACAGT
*
11369926 AAAAGGCTTCGGCCCAGTAATATGAAATATG
1 AAAAGGCTTCGACCCAGTAATATGAAATATG
**
11369957 AAAAGGCTTCGACCCAGTGTTATGAAATATG
1 AAAAGGCTTCGACCCAGTAATATGAAATATG
11369988 AAA
1 AAA
11369991 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAAGGCTTCGACCCAGTAATATGAAATATG
Done.