Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 115 of 170
Found at i:35355713 original size:17 final size:17
Alignment explanation
Indices: 35355691--35355726 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
35355681 ACTCAAAGGG
*
35355691 AAATAAACAGCAATAGA
1 AAATAAACAACAATAGA
35355708 AAATAAACAACAATAGA
1 AAATAAACAACAATAGA
35355725 AA
1 AA
35355727 CATGCAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.69, C:0.11, G:0.08, T:0.11
Consensus pattern (17 bp):
AAATAAACAACAATAGA
Found at i:35365983 original size:3 final size:3
Alignment explanation
Indices: 35365975--35365999 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35365965 TGCGTCTTTA
35365975 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
35366000 CGTTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:35369731 original size:14 final size:14
Alignment explanation
Indices: 35369712--35369741 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
35369702 AATCATTTTC
35369712 TGTTAGAGATGTAA
1 TGTTAGAGATGTAA
35369726 TGTTAGAGATGTAA
1 TGTTAGAGATGTAA
35369740 TG
1 TG
35369742 GACGTAGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (14 bp):
TGTTAGAGATGTAA
Found at i:35376229 original size:23 final size:23
Alignment explanation
Indices: 35376199--35376248 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
35376189 ATGTAAAATG
35376199 TTAAACTTCTCTTCTAACCATTT
1 TTAAACTTCTCTTCTAACCATTT
35376222 TTAAACTTCTCTTCTAACCATTT
1 TTAAACTTCTCTTCTAACCATTT
35376245 TTAA
1 TTAA
35376249 TAAACAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAAACTTCTCTTCTAACCATTT
Found at i:35377259 original size:41 final size:41
Alignment explanation
Indices: 35377214--35377364 Score: 257
Period size: 41 Copynumber: 3.7 Consensus size: 41
35377204 GCACTTAGCT
* *
35377214 TGCTAGACATAAAGTCTGAAATGTTTCACCGGCGTCAAGCC
1 TGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCAAGCC
*
35377255 TGCTAGACTTAAAGTCTGAAATGTTTCACTGGCATCAAGCC
1 TGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCAAGCC
*
35377296 TGCTAGACGTAAAGTCTGAAATGTTTCACCGGCATCAAGCC
1 TGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCAAGCC
*
35377337 TGCTAGACTTAAAGTCTAAAATGTTTCA
1 TGCTAGACTTAAAGTCTGAAATGTTTCA
35377365 TTGGCAATAA
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 103 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (41 bp):
TGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCAAGCC
Found at i:35391255 original size:59 final size:59
Alignment explanation
Indices: 35391163--35391274 Score: 188
Period size: 59 Copynumber: 1.9 Consensus size: 59
35391153 TTCTATAATA
*
35391163 AAAATTAGATCCATGGCACTTGATAGTCATGAGAGTAAAATTAGGAGAAAAAATTTGAT
1 AAAATTAGATCCATGGCACTTGATAGTCATGAGAGTAAAATTAGGACAAAAAATTTGAT
** *
35391222 AAAATTAGATCCATGGCACTTGATAGTTGTGAGAGTATAATTAGGACAAAAAA
1 AAAATTAGATCCATGGCACTTGATAGTCATGAGAGTAAAATTAGGACAAAAAA
35391275 AAAAAAAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.27
Consensus pattern (59 bp):
AAAATTAGATCCATGGCACTTGATAGTCATGAGAGTAAAATTAGGACAAAAAATTTGAT
Found at i:35398865 original size:17 final size:17
Alignment explanation
Indices: 35398843--35398876 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
35398833 CCGCAATTCT
35398843 TGGAGGGAATCGACTGC
1 TGGAGGGAATCGACTGC
35398860 TGGAGGGAATCGACTGC
1 TGGAGGGAATCGACTGC
35398877 AAAGAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.41, T:0.18
Consensus pattern (17 bp):
TGGAGGGAATCGACTGC
Found at i:35401736 original size:82 final size:82
Alignment explanation
Indices: 35401599--35401758 Score: 320
Period size: 82 Copynumber: 2.0 Consensus size: 82
35401589 GAAGGGTCCC
35401599 GATAATGATGTTCATTCTCACTACGATGGTGAAGAATATAGTGACCCCAATCAAGATGAAGTCCC
1 GATAATGATGTTCATTCTCACTACGATGGTGAAGAATATAGTGACCCCAATCAAGATGAAGTCCC
35401664 GGATAATATTGACGATA
66 GGATAATATTGACGATA
35401681 GATAATGATGTTCATTCTCACTACGATGGTGAAGAATATAGTGACCCCAATCAAGATGAAGTCCC
1 GATAATGATGTTCATTCTCACTACGATGGTGAAGAATATAGTGACCCCAATCAAGATGAAGTCCC
35401746 GGATAATATTGAC
66 GGATAATATTGAC
35401759 AATAAAGGCA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (82 bp):
GATAATGATGTTCATTCTCACTACGATGGTGAAGAATATAGTGACCCCAATCAAGATGAAGTCCC
GGATAATATTGACGATA
Found at i:35405510 original size:35 final size:35
Alignment explanation
Indices: 35405464--35405534 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
35405454 AATCTGCAAC
35405464 AGATGTTTAAATTAGATTTCAAGAACAAAATTTTA
1 AGATGTTTAAATTAGATTTCAAGAACAAAATTTTA
35405499 AGATGTTTAAATTAGATTTCAAGAACAAAATTTTA
1 AGATGTTTAAATTAGATTTCAAGAACAAAATTTTA
35405534 A
1 A
35405535 CATAGTTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (35 bp):
AGATGTTTAAATTAGATTTCAAGAACAAAATTTTA
Found at i:35409251 original size:18 final size:18
Alignment explanation
Indices: 35409230--35409264 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35409220 CAGAATTCAG
*
35409230 CTCTTTTTCATTCTTTTT
1 CTCTCTTTCATTCTTTTT
*
35409248 CTCTCTTTCCTTCTTTT
1 CTCTCTTTCATTCTTTT
35409265 AGGAAGACAC
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:0.03, C:0.29, G:0.00, T:0.69
Consensus pattern (18 bp):
CTCTCTTTCATTCTTTTT
Found at i:35412907 original size:17 final size:16
Alignment explanation
Indices: 35412881--35412919 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
35412871 ATTTTTTATT
35412881 TTAATTGATATA-ATTA
1 TTAATTGATA-ACATTA
35412897 TTAAGTTGATAACATTA
1 TTAA-TTGATAACATTA
35412914 TTAATT
1 TTAATT
35412920 TTAAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (16 bp):
TTAATTGATAACATTA
Found at i:35414862 original size:6 final size:6
Alignment explanation
Indices: 35414853--35414879 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
35414843 GAATTGGAGG
35414853 TGAAGA TGAAGA TGAAGA TGAAGA TGA
1 TGAAGA TGAAGA TGAAGA TGAAGA TGA
35414880 TGTAGAGCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.19
Consensus pattern (6 bp):
TGAAGA
Found at i:35414868 original size:12 final size:12
Alignment explanation
Indices: 35414808--35414879 Score: 56
Period size: 12 Copynumber: 6.0 Consensus size: 12
35414798 CAAAAGAACG
*
35414808 AGATGAAGATCA
1 AGATGAAGATGA
* *
35414820 AGATCAAGATCA
1 AGATGAAGATGA
* *
35414832 AGATGGAGGTGGA
1 AGATGAAGAT-GA
* * *
35414845 A-TTGGAGGTGA
1 AGATGAAGATGA
35414856 AGATGAAGATGA
1 AGATGAAGATGA
35414868 AGATGAAGATGA
1 AGATGAAGATGA
35414880 TGTAGAGCCA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
11 3 0.06
12 44 0.90
13 2 0.04
ACGTcount: A:0.43, C:0.04, G:0.35, T:0.18
Consensus pattern (12 bp):
AGATGAAGATGA
Found at i:35418757 original size:19 final size:20
Alignment explanation
Indices: 35418711--35418758 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
35418701 CTTATAATAG
35418711 GTATCGATATCTATTTACAA
1 GTATCGATATCTATTTACAA
* *
35418731 GGATCGATA-CT-TTTTCAGA
1 GTATCGATATCTATTTACA-A
35418750 GTATCGATA
1 GTATCGATA
35418759 AAAAGGCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 5 0.21
19 11 0.46
20 8 0.33
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.38
Consensus pattern (20 bp):
GTATCGATATCTATTTACAA
Found at i:35423519 original size:43 final size:43
Alignment explanation
Indices: 35423458--35423546 Score: 160
Period size: 43 Copynumber: 2.1 Consensus size: 43
35423448 TAATTTGGAA
35423458 AATCCAGGATTAAATTGAAAAGACTAGTAAATTGTCAGACTCT
1 AATCCAGGATTAAATTGAAAAGACTAGTAAATTGTCAGACTCT
* *
35423501 AATCCAGGATTAAATTGAAAGGACTAGTAAATTGTTAGACTCT
1 AATCCAGGATTAAATTGAAAAGACTAGTAAATTGTCAGACTCT
35423544 AAT
1 AAT
35423547 GGGAGATTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (43 bp):
AATCCAGGATTAAATTGAAAAGACTAGTAAATTGTCAGACTCT
Found at i:35427350 original size:21 final size:21
Alignment explanation
Indices: 35427326--35427386 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 21
35427316 TACCATATGT
35427326 GAACCCTGTTTTACTACATGC
1 GAACCCTGTTTTACTACATGC
*
35427347 GAACCCTGTTATACTAATACATGC
1 GAACCCTGTT-T--TACTACATGC
*
35427371 GAACCCTGTTATACTA
1 GAACCCTGTTTTACTA
35427387 TGTGCGAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 14 0.41
22 1 0.03
24 19 0.56
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (21 bp):
GAACCCTGTTTTACTACATGC
Found at i:35427372 original size:24 final size:24
Alignment explanation
Indices: 35427340--35427386 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
35427330 CCTGTTTTAC
35427340 TACATGCGAACCCTGTTATACTAA
1 TACATGCGAACCCTGTTATACTAA
35427364 TACATGCGAACCCTGTTATACTA
1 TACATGCGAACCCTGTTATACTA
35427387 TGTGCGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.30
Consensus pattern (24 bp):
TACATGCGAACCCTGTTATACTAA
Found at i:35427394 original size:21 final size:21
Alignment explanation
Indices: 35427313--35427394 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
35427303 AAAAACCATA
* *
35427313 TTATACCATATGTGAACCCTG
1 TTATACTATATGCGAACCCTG
* *
35427334 TTTTACTACATGCGAACCCTG
1 TTATACTATATGCGAACCCTG
35427355 TTATACTAATACATGCGAACCCTG
1 TTATACT-AT--ATGCGAACCCTG
*
35427379 TTATACTATGTGCGAA
1 TTATACTATATGCGAA
35427395 TTTATACCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
21 29 0.57
22 1 0.02
23 2 0.04
24 19 0.37
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (21 bp):
TTATACTATATGCGAACCCTG
Found at i:35427401 original size:17 final size:17
Alignment explanation
Indices: 35427379--35427411 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35427369 GCGAACCCTG
*
35427379 TTATACTATGTGCGAAT
1 TTATACCATGTGCGAAT
35427396 TTATACCATGTGCGAA
1 TTATACCATGTGCGAA
35427412 CCTATGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (17 bp):
TTATACCATGTGCGAAT
Found at i:35429843 original size:49 final size:49
Alignment explanation
Indices: 35429790--35429894 Score: 120
Period size: 49 Copynumber: 2.1 Consensus size: 49
35429780 TACAGTCATA
* *
35429790 GGTTCAACTATAACTAGGGCTCCCAGTTGATAGTGATTATGCAATCACG
1 GGTTCAACTATAACTAGAGCTCCCAGTTGACAGTGATTATGCAATCACG
* * ** * ***
35429839 GGTTCAAGTATAACTTGAGCTCTTAGTTGACAGTGGTTATGTGGTCACG
1 GGTTCAACTATAACTAGAGCTCCCAGTTGACAGTGATTATGCAATCACG
35429888 GGTTCAA
1 GGTTCAA
35429895 GTTTCATGCC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (49 bp):
GGTTCAACTATAACTAGAGCTCCCAGTTGACAGTGATTATGCAATCACG
Found at i:35433859 original size:20 final size:20
Alignment explanation
Indices: 35433828--35433865 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35433818 AATCACTACA
35433828 TTATAAATAAATT-TTTATT
1 TTATAAATAAATTATTTATT
35433847 TTATAATATAAATTATTTA
1 TTATAA-ATAAATTATTTA
35433866 AACATTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATAAATAAATTATTTATT
Found at i:35438184 original size:6 final size:6
Alignment explanation
Indices: 35438173--35438211 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
35438163 GTCATCGATC
35438173 TGATAT TGATAT TGATAT TGATAT TGATAT TGATAT TGA
1 TGATAT TGATAT TGATAT TGATAT TGATAT TGATAT TGA
35438212 AAGCATGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (6 bp):
TGATAT
Found at i:35468665 original size:25 final size:24
Alignment explanation
Indices: 35468615--35468666 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
35468605 TTTATTTCTC
* *
35468615 AAAAATATTTTTTAATAAAATTTT
1 AAAAATATTTTTTAACAAAATATT
*
35468639 AAAAATATTTTTTGACAATAATATT
1 AAAAATATTTTTTAACAA-AATATT
35468664 AAA
1 AAA
35468667 TACTTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
AAAAATATTTTTTAACAAAATATT
Found at i:35468774 original size:16 final size:16
Alignment explanation
Indices: 35468735--35468783 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
35468725 TGTTTGGTTC
35468735 GCTGTAATGGAATAGAA
1 GCTGTAATGGAATAG-A
*
35468752 G-TATAATGGAATAGA
1 GCTGTAATGGAATAGA
*
35468767 GCTGTAATAGAATAGA
1 GCTGTAATGGAATAGA
35468783 G
1 G
35468784 GCGTAATACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 2 0.07
16 25 0.89
17 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.29, T:0.24
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:35468976 original size:3 final size:3
Alignment explanation
Indices: 35468933--35468957 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35468923 GATGATGATG
35468933 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
35468958 AATTTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:35469088 original size:56 final size:57
Alignment explanation
Indices: 35468974--35469115 Score: 150
Period size: 56 Copynumber: 2.5 Consensus size: 57
35468964 AATAAGATTA
*
35468974 TTAATATAAATAATAAATAATTTAATCATATTTTAACATAATTATTATTAAATATAAT
1 TTAATA-AAATAATAAATAATTTAATAATATTTTAACATAATTATTATTAAATATAAT
* * * *
35469032 TTAATAAAA-AATATATAATTTAATAA-ATTTCTTAATATAATTATTCTTATAT-TAAT
1 TTAATAAAATAATAAATAATTTAATAATA-TT-TTAACATAATTATTATTAAATATAAT
* * *
35469088 TTACTAAAATCAT-AAT-ATATAATAATAT
1 TTAATAAAATAATAAATAATTTAATAATAT
35469116 AAAAATAATA
Statistics
Matches: 71, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
55 10 0.14
56 32 0.45
57 23 0.32
58 6 0.08
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (57 bp):
TTAATAAAATAATAAATAATTTAATAATATTTTAACATAATTATTATTAAATATAAT
Found at i:35472000 original size:13 final size:13
Alignment explanation
Indices: 35471982--35472009 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35471972 AATTGGAGAT
35471982 TCTAAATCCACAA
1 TCTAAATCCACAA
35471995 TCTAAATCCACAA
1 TCTAAATCCACAA
35472008 TC
1 TC
35472010 AGCGAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.25
Consensus pattern (13 bp):
TCTAAATCCACAA
Found at i:35472138 original size:36 final size:36
Alignment explanation
Indices: 35472098--35472168 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
35472088 ACTGGTCAAC
*
35472098 AGGACTGGAATGCTCGCCTATTCATCCTGGTGGAAT
1 AGGACTGGAATGCTCGCCTATTCATCCAGGTGGAAT
35472134 AGGACTGGAATGCTCGCCTATTCATCCAGGTGGAA
1 AGGACTGGAATGCTCGCCTATTCATCCAGGTGGAA
35472169 ATTAAATTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (36 bp):
AGGACTGGAATGCTCGCCTATTCATCCAGGTGGAAT
Found at i:35472608 original size:19 final size:17
Alignment explanation
Indices: 35472572--35472617 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
35472562 AAATGGAGAA
*
35472572 AAGAAAAAAAACGTGAG
1 AAGAAAAGAAACGTGAG
35472589 AAGAAAAGAAACGTACGAG
1 AAGAAAAGAAACGT--GAG
*
35472608 AATAAAAGAA
1 AAGAAAAGAA
35472618 GCAGAAATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 13 0.52
19 12 0.48
ACGTcount: A:0.65, C:0.07, G:0.22, T:0.07
Consensus pattern (17 bp):
AAGAAAAGAAACGTGAG
Found at i:35475564 original size:18 final size:18
Alignment explanation
Indices: 35475541--35475583 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
35475531 TGCCAAGTGC
* *
35475541 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
35475559 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
35475577 GTTTCCT
1 GTATCCT
35475584 TTTTCGAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:35476204 original size:21 final size:21
Alignment explanation
Indices: 35476142--35476725 Score: 690
Period size: 21 Copynumber: 27.4 Consensus size: 21
35476132 CCCTAACTCT
*
35476142 AACCCTAACCTTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
** *
35476163 ATTCCTAAACTCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
* * *
35476185 AAACCTAATCCTTAATTTAAA
1 AACCCTAACCCTTAACTTAAA
*
35476206 AACCCTAAACCCTTAACCTAAA
1 AACCCT-AACCCTTAACTTAAA
* * *
35476228 AAACTTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAA
* * *
35476249 AATCATAAACTCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
** *
35476271 AACCCTAAAACTTAATTTAAA
1 AACCCTAACCCTTAACTTAAA
35476292 AACCCTAACCCTTAACTT-AA
1 AACCCTAACCCTTAACTTAAA
*
35476312 ACCCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
35476334 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
*
35476356 AATCCTAAACCCTTAACTT-AA
1 AACCCT-AACCCTTAACTTAAA
35476377 AACCCTAAACCCTTAACTT-AA
1 AACCCT-AACCCTTAACTTAAA
* *
35476398 AACCCTAAATCTTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
35476420 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
* *
35476441 AACCTTAAACCTTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
*
35476463 AACCTTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
35476484 AACCATAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
**
35476506 AAATCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
35476527 AACCCTAACACTTAACTTAAAA
1 AACCCTAACCCTTAACTT-AAA
* *
35476549 AACCCTAACCTTTAATTTAAAA
1 AACCCTAACCCTTAACTT-AAA
35476571 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
35476592 AACCCTAACCCTTAACTT-AA
1 AACCCTAACCCTTAACTTAAA
**
35476612 AACCCTAACTATTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
35476633 AACCCTAACCCTTAGCTTAAA
1 AACCCTAACCCTTAACTTAAA
*
35476654 AACTCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
* *
35476676 AATCGTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
35476697 AACCCTAACCTTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
35476718 AACCCTAA
1 AACCCTAA
35476726 TCGTAACCCT
Statistics
Matches: 489, Mismatches: 63, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
20 25 0.05
21 272 0.56
22 192 0.39
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.27
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Found at i:35476210 original size:64 final size:64
Alignment explanation
Indices: 35476142--35476725 Score: 675
Period size: 64 Copynumber: 9.1 Consensus size: 64
35476132 CCCTAACTCT
* ** * * *
35476142 AACCCT-AACCTTTAACTTAAAATTCCTAAACTCTTAACTTAAAAAACCTAATCCTTAATTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAAACCTAACCCTTAACTTAAA
* * * * * * *
35476206 AACCCTAAACCCTTAACCTAAAAAACTTAACCCTTAACCTAAAAATCATAAACTCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAAACCT-AACCCTTAACTTAAA
* * **
35476271 AACCCTAAA-ACTTAATTTAAAAACCCTAACCCTTAACTT-AAACCCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAAACCT-AACCCTTAACTTAAA
* *
35476334 AACCCTAAACCCTTAACTTAAAAATCCTAAACCCTTAACTT-AAAACCCTAAACCCTTAACTT-A
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAAACCT-AACCCTTAACTTAA
35476397 A
64 A
* * *
35476398 AACCCTAAATCTTTAACTTAAAAACCCTAACCCTTAACTT-AAAAACCTTAAACCTTTAACTTAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAAACC-T-AACCCTTAACTTAA
35476462 A
64 A
* * *
35476463 AA-CCTTAACCCTTAACTTAAAAACCATAAACCCTTAACTTAAAAAATCTAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAAACCTAACCCTTAACTTAAA
* * *
35476527 AACCCT-AACACTTAACTTAAAAAACCCTAACCTTTAATTTAAAAAACCCTAACCCTTAACTTAA
1 AACCCTAAACCCTTAACTT-AAAAACCCTAACCCTTAACTTAAAAAA-CCTAACCCTTAACTTAA
35476591 A
64 A
** * *
35476592 AACCCT-AACCCTTAACTT-AAAACCCTAACTATTAACTTAAAAACCCTAACCCTTAGCTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAAACCTAACCCTTAACTTAAA
* * * * *
35476654 AACTCTAAACCCTTAACTTAAAAATCGTAACCCTTAACTTAAAAACCCTAACCTTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAAACCTAACCCTTAACTTAAA
35476718 AACCCTAA
1 AACCCTAA
35476726 TCGTAACCCT
Statistics
Matches: 451, Mismatches: 56, Indels: 26
0.85 0.11 0.05
Matches are distributed among these distances:
62 22 0.05
63 81 0.18
64 211 0.47
65 131 0.29
66 6 0.01
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.27
Consensus pattern (64 bp):
AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAAACCTAACCCTTAACTTAAA
Found at i:35476299 original size:107 final size:106
Alignment explanation
Indices: 35476145--35476727 Score: 691
Period size: 107 Copynumber: 5.5 Consensus size: 106
35476135 TAACTCTAAC
* ** * * *
35476145 CCTAACCTTTAACTTAAAATTCCTAAACTCTTAACTTAAAAAACCTAATCCTTAATTTAAAAACC
1 CCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAATCCTTAACTTAAAAACC
* *
35476210 CTAAACCCTTAACCTAAAAAACTTAACCCTTAACCTAAAAAT
66 CT-AACCCTTAACTTAAAAAACTTAACCCTTAACTTAAAAAT
* * * * * *
35476252 CATAAACTCTTAACTTAAAAACCCTAAA-ACTTAATTTAAAAACCCTAACCCTTAACTT-AAACC
1 CCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAATCCTTAACTTAAAAAC
* *
35476315 CCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAAT
65 CCT-AACCCTTAACTTAAAAA-ACTTAACCCTTAACTTAAAAAT
*
35476359 CCTAAACCCTTAACTT-AAAACCCTAAACCCTTAACTT-AAAACCCTAAATCTTTAACTTAAAAA
1 CCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCT-AATCCTTAACTTAAAAA
* *
35476422 CCCTAACCCTTAACTTAAAAACCTTAAACCTTTAACTTAAAAA-
64 CCCTAACCCTTAACTTAAAAAACTT-AACCCTTAACTTAAAAAT
* ** *
35476465 CCTTAACCCTTAACTTAAAAACCATAAACCCTTAACTTAAAAAATCTAACCCTTAACTTAAAAAC
1 CC-TAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAATCCTTAACTTAAAAAC
* * * * *
35476530 CCTAACACTTAACTTAAAAAACCCTAACCTTTAATTTAAAAAAC
65 CCTAACCCTTAACTTAAAAAA-CTTAACCCTTAACTT-AAAAAT
*
35476574 CCTAACCCTTAACTTAAAAACCCT-AACCCTTAACTT-AAAACCCTAA-CTATTAACTTAAAAAC
1 CCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAATC-CTTAACTTAAAAAC
*
35476636 CCTAACCCTTAGCTT-AAAAACTCTAAACCCTTAACTTAAAAAT
65 CCTAACCCTTAACTTAAAAAACT-T-AACCCTTAACTTAAAAAT
* *
35476679 CGTAACCCTTAACTTAAAAACCCT-AACCTTTAACTTAAAAACCCTAATC
1 CCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAATC
35476728 GTAACCCTTA
Statistics
Matches: 414, Mismatches: 45, Indels: 34
0.84 0.09 0.07
Matches are distributed among these distances:
104 1 0.00
105 46 0.11
106 114 0.28
107 190 0.46
108 61 0.15
109 2 0.00
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.27
Consensus pattern (106 bp):
CCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAATCCTTAACTTAAAAACC
CTAACCCTTAACTTAAAAAACTTAACCCTTAACTTAAAAAT
Found at i:35476733 original size:27 final size:26
Alignment explanation
Indices: 35476676--35476752 Score: 92
Period size: 27 Copynumber: 3.1 Consensus size: 26
35476666 TTAACTTAAA
35476676 AATCGTAACCCTTAACTTAAAAA-CC
1 AATCGTAACCCTTAACTTAAAAACCC
*
35476701 ---C-TAACCTTTAACTTAAAAACCC
1 AATCGTAACCCTTAACTTAAAAACCC
35476723 TAATCGTAACCCTTAACTTAAAAACACC
1 -AATCGTAACCCTTAACTTAAAAAC-CC
35476751 AA
1 AA
35476753 AACCCTAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
21 17 0.40
22 3 0.07
26 1 0.02
27 20 0.47
28 2 0.05
ACGTcount: A:0.44, C:0.29, G:0.03, T:0.25
Consensus pattern (26 bp):
AATCGTAACCCTTAACTTAAAAACCC
Found at i:35476738 original size:43 final size:43
Alignment explanation
Indices: 35476142--35476725 Score: 697
Period size: 43 Copynumber: 13.7 Consensus size: 43
35476132 CCCTAACTCT
* ** *
35476142 AACCCT-AACCTTTAACTTAAAATTCCTAAACTCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
* * * *
35476185 AAACCT-AATCCTTAATTTAAAAACCCTAAACCCTTAACCTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
* * * * * *
35476228 AA-ACTTAACCCTTAACCTAAAAATCATAAACTCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
* *
35476271 AACCCTAAA-ACTTAATTTAAAAACCCTAACCCTTAACTT-AA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
*
35476312 ACCCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
*
35476356 AATCCTAAACCCTTAACTT-AAAACCCTAAACCCTTAACTT-AA
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
* *
35476398 AACCCTAAATCTTTAACTTAAAAACCCTAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * *
35476441 AACCTTAAACCTTTAACTTAAAAACCTTAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* **
35476484 AACCATAAACCCTTAACTTAAAAAATCTAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * *
35476527 AACCCT-AACACTTAACTTAAAAAACCCTAACCTTTAATTTAAAA
1 AACCCTAAACCCTTAACTT-AAAAACCCTAACCCTTAACTT-AAA
35476571 AACCCT-AACCCTTAACTTAAAAACCCTAACCCTTAACTT-AA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
** *
35476612 AACCCT-AACTATTAACTTAAAAACCCTAACCCTTAGCTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * *
35476654 AACTCTAAACCCTTAACTTAAAAATCGTAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
*
35476697 AACCCT-AACCTTTAACTTAAAAACCCTAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAA
35476726 TCGTAACCCT
Statistics
Matches: 468, Mismatches: 62, Indels: 23
0.85 0.11 0.04
Matches are distributed among these distances:
41 48 0.10
42 97 0.21
43 280 0.60
44 43 0.09
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.27
Consensus pattern (43 bp):
AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
Found at i:35476944 original size:112 final size:112
Alignment explanation
Indices: 35476794--35477000 Score: 360
Period size: 112 Copynumber: 1.8 Consensus size: 112
35476784 AACCTAACTC
* *
35476794 TAATATGATATAATTTGATAAATTTACTAACAATTAATACAATTAACAATTAATGATTTGACTAA
1 TAATATGATATAATATGATAAATTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAA
*
35476859 CAAAATGTTAGATTTTACAAAATGTTTTGACTGGTACTAACAATTAA
66 CAAAATGTTAGATTTTACAAAATCTTTTGACTGGTACTAACAATTAA
* * *
35476906 TAATTTGATATAATATGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAA
1 TAATATGATATAATATGATAAATTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAA
35476971 CAAAATGTTAGATTTTACAAAATCTTTTGA
66 CAAAATGTTAGATTTTACAAAATCTTTTGA
35477001 TTGATACAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 89 1.00
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (112 bp):
TAATATGATATAATATGATAAATTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAA
CAAAATGTTAGATTTTACAAAATCTTTTGACTGGTACTAACAATTAA
Found at i:35486053 original size:50 final size:50
Alignment explanation
Indices: 35485928--35486125 Score: 207
Period size: 50 Copynumber: 3.8 Consensus size: 50
35485918 ATTTGGGTAA
* ** *
35485928 AGAGATCCCATGTAAGACCATGTCTGAAACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
* *
35485984 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
35486034 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATAGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
35486084 AGAACTACCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
35486126 GTACAAGAAA
Statistics
Matches: 122, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 81 0.66
53 3 0.02
55 1 0.01
56 37 0.30
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:35489264 original size:25 final size:25
Alignment explanation
Indices: 35489230--35489277 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
35489220 TTTTAATTCG
35489230 AAAACGTGCTATTAGAAGCAGACTC
1 AAAACGTGCTATTAGAAGCAGACTC
*
35489255 AAAACGTGCTATTAGAAGTAGAC
1 AAAACGTGCTATTAGAAGCAGAC
35489278 AATATGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.21
Consensus pattern (25 bp):
AAAACGTGCTATTAGAAGCAGACTC
Found at i:35493004 original size:30 final size:29
Alignment explanation
Indices: 35492956--35493020 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
35492946 TAATTATACC
*
35492956 TAAATTTTAAAATTTAAAAA-ATAAAAGAAT
1 TAAATTTTAAAATATAAAAATAT-AAAG-AT
35492986 TAAATTCTTAAAA-ATAAAAATATAAAGAT
1 TAAATT-TTAAAATATAAAAATATAAAGAT
35493015 TAAATT
1 TAAATT
35493021 AATTTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
29 8 0.25
30 16 0.50
31 8 0.25
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.34
Consensus pattern (29 bp):
TAAATTTTAAAATATAAAAATATAAAGAT
Found at i:35497271 original size:4 final size:4
Alignment explanation
Indices: 35497262--35497307 Score: 74
Period size: 4 Copynumber: 11.0 Consensus size: 4
35497252 CACTAAGTTG
35497262 GTTT GTTT GTTT GTTT GTTT GTTT GTTT GTTT GTTTT GTTTT GTTT
1 GTTT GTTT GTTT GTTT GTTT GTTT GTTT GTTT G-TTT G-TTT GTTT
35497308 TTTTAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 32 0.78
5 9 0.22
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (4 bp):
GTTT
Found at i:35502317 original size:16 final size:15
Alignment explanation
Indices: 35502298--35502342 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
35502288 TTTCAAGTTA
*
35502298 TTTTTGAAAAAATGAT
1 TTTTTAAAAAAAT-AT
35502314 TTTTTAAAAAAAATATT
1 TTTTT-AAAAAAATA-T
35502331 TTTTTAAAAAAA
1 TTTTTAAAAAAA
35502343 AGAAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (15 bp):
TTTTTAAAAAAATAT
Found at i:35502342 original size:17 final size:17
Alignment explanation
Indices: 35502304--35502343 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
35502294 GTTATTTTTG
35502304 AAAAAATGATTTTTTAA
1 AAAAAATGATTTTTTAA
35502321 AAAAAAT-ATTTTTTTAA
1 AAAAAATGA-TTTTTTAA
35502338 AAAAAA
1 AAAAAA
35502344 GAAAAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 1 0.05
17 21 0.95
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AAAAAATGATTTTTTAA
Found at i:35515469 original size:22 final size:24
Alignment explanation
Indices: 35515433--35515478 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
35515423 CAACCAATCA
*
35515433 AATTTCAACACA-TTTCT-TCCTT
1 AATTTCAACAAATTTTCTCTCCTT
*
35515455 AATTTCCACAAATTTTCTCTCCTT
1 AATTTCAACAAATTTTCTCTCCTT
35515479 TACACCCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 5 0.25
24 5 0.25
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTTCAACAAATTTTCTCTCCTT
Found at i:35519888 original size:26 final size:23
Alignment explanation
Indices: 35519859--35519928 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 23
35519849 GACTCACCAT
35519859 AGCTAGTATGAGCTTACCGATATATC
1 AGCTAGTATGAGCTTACCG-T-T-TC
**
35519885 AGCTCTTATGAGCTTACCGTTTC
1 AGCTAGTATGAGCTTACCGTTTC
*
35519908 AACTAG-ATAGAGCTTACCGTT
1 AGCTAGTAT-GAGCTTACCGTT
35519929 CTTCAGCTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
22 2 0.05
23 17 0.45
24 1 0.03
25 1 0.03
26 17 0.45
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (23 bp):
AGCTAGTATGAGCTTACCGTTTC
Found at i:35520439 original size:30 final size:30
Alignment explanation
Indices: 35520398--35520456 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
35520388 TTCTTACTCA
*
35520398 GTTTATTTCTTCGTGTTTTATAGAGGTTCT
1 GTTTATTTCTTCATGTTTTATAGAGGTTCT
*
35520428 GTTTGTTTCTTCATGTTTTATAGAGGTTC
1 GTTTATTTCTTCATGTTTTATAGAGGTTC
35520457 GTTATCTAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.14, C:0.10, G:0.20, T:0.56
Consensus pattern (30 bp):
GTTTATTTCTTCATGTTTTATAGAGGTTCT
Found at i:35526804 original size:15 final size:15
Alignment explanation
Indices: 35526784--35526814 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35526774 GAATCAAACG
35526784 AATCTCATTGAATTA
1 AATCTCATTGAATTA
35526799 AATCTCATTGAATTA
1 AATCTCATTGAATTA
35526814 A
1 A
35526815 TACAATTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (15 bp):
AATCTCATTGAATTA
Found at i:35532901 original size:131 final size:131
Alignment explanation
Indices: 35532659--35532920 Score: 318
Period size: 131 Copynumber: 2.0 Consensus size: 131
35532649 TTTGTCCTCC
* *
35532659 ATAAAACCTTAACTAGAGGAATCATTTTCTTTCTCAAAACTTTTACCTCATGATCCAAAATCTAA
1 ATAAAACCTTAACTAGAGGAATCATTTTCTTTCTCAAAAATTTTACCTCATGATCAAAAATCTAA
* * *
35532724 ACTAACTCCTCCTCAAAAGACAAATTCGAATTTACATCGATCTCCTCAATCAAAACCACATAAGA
66 ACTAACTCCTCCTCAAAAGACAAATTCGAACTCACATCAATCTCCTCAATCAAAACCACATAAGA
35532789 T
131 T
35532790 ATAAAACCTTAACTAGAGGAAT-ATTCTTCTTTCT-AAACAATTTTACCTCAT-ATTCAAAAATC
1 ATAAAACCTTAACTAGAGGAATCATT-TTCTTTCTCAAA-AATTTTACCTCATGA-TCAAAAATC
* *** * * **
35532852 TGAACTGGTTCCTCCTCAAAAGATAAATTC-AACCTCACCA-CAATTTCCTCAATCGGAACCACA
63 TAAACTAACTCCTCCTCAAAAGACAAATTCGAA-CTCA-CATCAATCTCCTCAATCAAAACCACA
*
35532915 TGAGAT
126 TAAGAT
35532921 GGACCAGATC
Statistics
Matches: 112, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
130 9 0.08
131 101 0.90
132 2 0.02
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.29
Consensus pattern (131 bp):
ATAAAACCTTAACTAGAGGAATCATTTTCTTTCTCAAAAATTTTACCTCATGATCAAAAATCTAA
ACTAACTCCTCCTCAAAAGACAAATTCGAACTCACATCAATCTCCTCAATCAAAACCACATAAGA
T
Found at i:35542657 original size:30 final size:30
Alignment explanation
Indices: 35542587--35542668 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
35542577 AGTAACCTCG
* * *
35542587 ATATAATGTTAGA-TTGTGTGAGCAATTATG
1 ATATAATGTCA-ACTTGTGTGAGCAATCATA
* *
35542617 TTATAATGTCAACTTGTGTGAGCAATCCTA
1 ATATAATGTCAACTTGTGTGAGCAATCATA
* *
35542647 ATATATTGTCATCTTGTGTGAG
1 ATATAATGTCAACTTGTGTGAG
35542669 AAACTTATTC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 1 0.02
30 42 0.98
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (30 bp):
ATATAATGTCAACTTGTGTGAGCAATCATA
Found at i:35555205 original size:15 final size:15
Alignment explanation
Indices: 35555185--35555227 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
35555175 TTTAATTGTT
35555185 TTATAAAATTATAAA
1 TTATAAAATTATAAA
35555200 TTATAAAA-TATATAA
1 TTATAAAATTATA-AA
35555215 TT-TAAAATT-TAAA
1 TTATAAAATTATAAA
35555228 ATTTCAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.08
14 11 0.42
15 13 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTATAAAATTATAAA
Found at i:35555216 original size:22 final size:21
Alignment explanation
Indices: 35555186--35555229 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
35555176 TTAATTGTTT
35555186 TATAAAA-TTATAAATTATAAAA
1 TATAAAATTTA-AAATT-TAAAA
*
35555208 TATATAATTTAAAATTTAAAA
1 TATAAAATTTAAAATTTAAAA
35555229 T
1 T
35555230 TTCAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 11 0.55
23 3 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TATAAAATTTAAAATTTAAAA
Found at i:35555220 original size:14 final size:14
Alignment explanation
Indices: 35555188--35555238 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
35555178 AATTGTTTTA
35555188 TAAAAT-TATAAATT
1 TAAAATATAT-AATT
35555202 ATAAAATATATAATT
1 -TAAAATATATAATT
* *
35555217 TAAAATTTAAAATT
1 TAAAATATATAATT
35555231 TCAAAATA
1 T-AAAATA
35555239 ATACATAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 13 0.42
15 15 0.48
16 3 0.10
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAAATATATAATT
Found at i:35562071 original size:235 final size:233
Alignment explanation
Indices: 35561660--35562129 Score: 796
Period size: 235 Copynumber: 2.0 Consensus size: 233
35561650 CGGTCGAACA
* * *
35561660 TCTGATAATTTGTAAAGTCAAGGAAAATAACTACGTAAGCAATGAATGCTTAGTGAGCTCGTATA
1 TCTGATAATCTGTAAAGTAAAGGAAAATAACTACATAAGCAATGAATGCTTAGTGAGCTCGTATA
* *
35561725 AACTATAAACATAACATTTCATTTTAATAATGAAACTTTATGGCGTAATTATAAACTTATACTAA
66 AACTATAAACATAACATTTCATTTTAATAATGAAACTTTATGGCGTAATTATAAACCTATACCAA
** * *
35561790 TGCCATGGGATTAATATATAGGAATGCATCTAAAACACACATATACCTAAACTTATACATATTTG
131 TGCCATAAGATTAATATATAAGAATGCATCTAAAACACACATATACCTAAACTTAAACATATTTG
35561855 ACCATAAGTCATCCATATATATATAAACATAACATTTAAT
196 ACCATAAGTCATCC--ATATATATAAACATAACATTTAAT
*
35561895 TCTGATAATCTGTTAAGTAAAGGAAAATAACTACATAAGCAATGAATGCTTAGTGAGCTCGTATA
1 TCTGATAATCTGTAAAGTAAAGGAAAATAACTACATAAGCAATGAATGCTTAGTGAGCTCGTATA
* *
35561960 AACTTTAAACATAACATTTCATTTTAATAATGAAACTTTATGGGGTAATTATAAACCTATACCAA
66 AACTATAAACATAACATTTCATTTTAATAATGAAACTTTATGGCGTAATTATAAACCTATACCAA
* *
35562025 TGCCATAAGATTAATATATAAGAGTGCATCTAAAACACATATATACCTAAACTTAAACATATTTG
131 TGCCATAAGATTAATATATAAGAATGCATCTAAAACACACATATACCTAAACTTAAACATATTTG
35562090 ACCATAAGTCATCCATATATATAAACATAACATTTAAT
196 ACCATAAGTCATCCATATATATAAACATAACATTTAAT
35562128 TC
1 TC
35562130 ATCATTGTTA
Statistics
Matches: 221, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
233 26 0.12
235 195 0.88
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.32
Consensus pattern (233 bp):
TCTGATAATCTGTAAAGTAAAGGAAAATAACTACATAAGCAATGAATGCTTAGTGAGCTCGTATA
AACTATAAACATAACATTTCATTTTAATAATGAAACTTTATGGCGTAATTATAAACCTATACCAA
TGCCATAAGATTAATATATAAGAATGCATCTAAAACACACATATACCTAAACTTAAACATATTTG
ACCATAAGTCATCCATATATATAAACATAACATTTAAT
Found at i:35565785 original size:35 final size:35
Alignment explanation
Indices: 35565729--35565839 Score: 150
Period size: 35 Copynumber: 3.1 Consensus size: 35
35565719 AAACCACCCA
* *
35565729 AACACACCAGATGCTCATAAGAGCCAATCCAACTGT
1 AACACACCA-ATGCTCATAAGAGCTAATCCAACCGT
** *
35565765 AACATGCCAATGCTCATAAGAGTTAATCCAACCGT
1 AACACACCAATGCTCATAAGAGCTAATCCAACCGT
* *
35565800 AACACATCAATGCTCATAAGAGCTAATCCAACCGA
1 AACACACCAATGCTCATAAGAGCTAATCCAACCGT
35565835 AACAC
1 AACAC
35565840 GTCAAACATA
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 58 0.89
36 7 0.11
ACGTcount: A:0.41, C:0.29, G:0.13, T:0.18
Consensus pattern (35 bp):
AACACACCAATGCTCATAAGAGCTAATCCAACCGT
Found at i:35569333 original size:11 final size:11
Alignment explanation
Indices: 35569319--35569472 Score: 100
Period size: 11 Copynumber: 14.9 Consensus size: 11
35569309 TTTTTTTAAA
35569319 TTTTAAAATAT
1 TTTTAAAATAT
35569330 TTTTAAAATAT
1 TTTTAAAATAT
**
35569341 TTTTTTAAT-T
1 TTTTAAAATAT
*
35569351 TTTT----TAA
1 TTTTAAAATAT
35569358 TTTTAAAATAT
1 TTTTAAAATAT
35569369 TTTTAAAATACT
1 TTTTAAAATA-T
* *
35569381 TTTT---TTAA
1 TTTTAAAATAT
35569389 TTTTAAAATAT
1 TTTTAAAATAT
35569400 TTTTAAAATACT
1 TTTTAAAATA-T
**
35569412 TTTT-TTA-AT
1 TTTTAAAATAT
*
35569421 TTTAAAAATAT
1 TTTTAAAATAT
35569432 TTTTAAAATACT
1 TTTTAAAATA-T
**
35569444 TTTTTTAAT-T
1 TTTTAAAATAT
35569454 TTTT-AAA-AT
1 TTTTAAAATAT
35569463 TTTTAAAATA
1 TTTTAAAATA
35569473 AAAATGGGCT
Statistics
Matches: 110, Mismatches: 17, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
6 1 0.01
7 4 0.04
8 4 0.04
9 13 0.12
10 15 0.14
11 55 0.50
12 18 0.16
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:35569333 original size:39 final size:39
Alignment explanation
Indices: 35569265--35569472 Score: 214
Period size: 31 Copynumber: 5.6 Consensus size: 39
35569255 AATAAATATA
* * *
35569265 TTTATTTTTTTTAATTTTAAAATATTTTTTACATACTTT
1 TTTAATTTTTTTAATTTTAAAATATTTTTAAAATACTTT
*
35569304 TTTAATTTTTTTAAATTTTAAAATATTTTTAAAATATTTT
1 TTTAATTTTTTT-AATTTTAAAATATTTTTAAAATACTTT
35569344 TTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC---
1 TTTAATTTTTTTAATTTTAAAATATTTTTAAAATACTTT
35569380 -----TTTTTTTAATTTTAAAATATTTTTAAAATAC-TT
1 TTTAATTTTTTTAATTTTAAAATATTTTTAAAATACTTT
35569413 TT-------TTTAATTTTAAAAATATTTTTAAAATACTTTT
1 TTTAATTTTTTTAATTTT-AAAATATTTTTAAAATAC-TTT
*
35569447 TTTAATTTTTTAAAATTTTTAAAATA
1 TTTAATTTTTT-TAA-TTTTAAAATA
35569473 AAAATGGGCT
Statistics
Matches: 146, Mismatches: 6, Indels: 31
0.80 0.03 0.17
Matches are distributed among these distances:
31 40 0.27
32 18 0.12
34 4 0.03
39 34 0.23
40 36 0.25
41 2 0.01
42 8 0.05
43 4 0.03
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (39 bp):
TTTAATTTTTTTAATTTTAAAATATTTTTAAAATACTTT
Found at i:35569354 original size:8 final size:9
Alignment explanation
Indices: 35569265--35569361 Score: 52
Period size: 9 Copynumber: 10.0 Consensus size: 9
35569255 AATAAATATA
*
35569265 TTTATTTTT
1 TTTAATTTT
35569274 TTTAA-TTT
1 TTTAATTTT
**
35569282 TAAAATATTT
1 TTTAAT-TTT
35569292 TTTACATACTTT
1 TTTA-AT--TTT
35569304 TTTAATTTT
1 TTTAATTTT
*
35569313 TTTAAATTT
1 TTTAATTTT
**
35569322 TAAAATATTT
1 TTTAAT-TTT
*
35569332 TTAAAATATTTT
1 TT--TA-ATTTT
35569344 TTTAATTTT
1 TTTAATTTT
35569353 TTTAATTTT
1 TTTAATTTT
35569362 AAAATATTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
8 6 0.09
9 32 0.47
10 10 0.15
11 4 0.06
12 14 0.21
13 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTAATTTT
Found at i:35569435 original size:63 final size:62
Alignment explanation
Indices: 35569349--35569472 Score: 214
Period size: 63 Copynumber: 2.0 Consensus size: 62
35569339 ATTTTTTTAA
35569349 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA-TTTTAAAATATTTTTAAAATAC
1 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTAAAA-ATTTTTAAAATAC
*
35569411 TTTTTTTAATTTTAAAAATATTTTTAAAATACTTTTTTTAATTTTTTAAAATTTTTAAAATA
1 TTTTTTTAATTTT-AAAATATTTTTAAAATACTTTTTTTAATTTTTAAAAATTTTTAAAATA
35569473 AAAATGGGCT
Statistics
Matches: 59, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
62 13 0.22
63 39 0.66
64 7 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (62 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTAAAAATTTTTAAAATAC
Found at i:35576915 original size:23 final size:23
Alignment explanation
Indices: 35576871--35576915 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
35576861 TCTTATTTTG
* *
35576871 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
35576894 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
35576916 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:35577151 original size:3 final size:3
Alignment explanation
Indices: 35577143--35577177 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
35577133 ATCTTGTATC
*
35577143 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
35577178 ATTCATGCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:35577241 original size:21 final size:21
Alignment explanation
Indices: 35577217--35577261 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
35577207 TATATATTGT
*
35577217 TTTATATATAGTATACGTATG
1 TTTATATATAGTATACATATG
*
35577238 TTTATATATATTATACATATG
1 TTTATATATAGTATACATATG
35577259 TTT
1 TTT
35577262 TTGTGTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.53
Consensus pattern (21 bp):
TTTATATATAGTATACATATG
Found at i:35581909 original size:14 final size:15
Alignment explanation
Indices: 35581883--35581915 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
35581873 TCCCAAGCTG
35581883 GGAAGGACCTTATGT
1 GGAAGGACCTTATGT
*
35581898 GGAAGG-CCTTATTT
1 GGAAGGACCTTATGT
35581912 GGAA
1 GGAA
35581916 AAGTGTCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (15 bp):
GGAAGGACCTTATGT
Found at i:35583362 original size:45 final size:45
Alignment explanation
Indices: 35583234--35583450 Score: 129
Period size: 44 Copynumber: 4.9 Consensus size: 45
35583224 CAGATCAGTG
* * **
35583234 AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGTAGATCG
1 AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGGTTA
* * * * * *** *
35583279 AAGACACCAG-CCTTGCCTCCCTAG-GTTG-CAGCGGAGCAGGTTA
1 AAAATAGCAGATCTTGCCTTCCT-GCACCGACAGCGAAGCAGGTTA
* * * **
35583322 AAAATTGCAGATCTTGCCTTCTTGCACCGACAGCGAAGCAGATCG
1 AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGGTTA
* * * * * **** *
35583367 AAGACACCAG-CCTTGCCTCCCTGGGTTG-CAGCGGAGCAGGTTA
1 AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGGTTA
*
35583410 AAAATAGCAGATCTTGCCTTCCTGCACCGATAGCGAAGCAG
1 AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAG
35583451 ATCGATGACC
Statistics
Matches: 113, Mismatches: 53, Indels: 12
0.63 0.30 0.07
Matches are distributed among these distances:
43 35 0.31
44 44 0.39
45 34 0.30
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.20
Consensus pattern (45 bp):
AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGGTTA
Found at i:35583405 original size:43 final size:43
Alignment explanation
Indices: 35583264--35583405 Score: 104
Period size: 43 Copynumber: 3.3 Consensus size: 43
35583254 CCTGCACCGA
* *
35583264 CAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTAGGTTG
1 CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
* * ** * *** * * * ****
35583307 CAGCGGAGCAGGTTAAAAATTGCAGATCTTGCCTTCTTGCACCG
1 CAGCGAAGCAGATCGAAGACACCAG-CCTTGCCTCCCTGGGTTG
35583351 ACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
1 -CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
*
35583395 CAGCGGAGCAG
1 CAGCGAAGCAG
35583406 GTTAAAAATA
Statistics
Matches: 64, Mismatches: 33, Indels: 4
0.63 0.33 0.04
Matches are distributed among these distances:
43 26 0.41
44 21 0.33
45 17 0.27
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.18
Consensus pattern (43 bp):
CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
Found at i:35583478 original size:88 final size:88
Alignment explanation
Indices: 35583234--35583455 Score: 399
Period size: 88 Copynumber: 2.5 Consensus size: 88
35583224 CAGATCAGTG
*
35583234 AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCC
1 AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
*
35583299 CTAGGTTGCAGCGGAGCAGGTTA
66 CTGGGTTGCAGCGGAGCAGGTTA
* *
35583322 AAAATTGCAGATCTTGCCTTCTTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
1 AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
35583387 CTGGGTTGCAGCGGAGCAGGTTA
66 CTGGGTTGCAGCGGAGCAGGTTA
*
35583410 AAAATAGCAGATCTTGCCTTCCTGCACCGATAGCGAAGCAGATCGA
1 AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
35583456 TGACCCTGGC
Statistics
Matches: 127, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 127 1.00
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.20
Consensus pattern (88 bp):
AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
CTGGGTTGCAGCGGAGCAGGTTA
Found at i:35583534 original size:44 final size:43
Alignment explanation
Indices: 35583467--35583587 Score: 154
Period size: 44 Copynumber: 2.7 Consensus size: 43
35583457 GACCCTGGCT
* *
35583467 CTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGT-AAGTC
1 CTATCTCCCTAG-CAGCAGTGGAATAGGTTGAAGATTGTGAA-TC
*
35583511 CTATCTCCCTAGTCAGCAATGGAATAGGTTGAAGATTGTGAATC
1 CTATCTCCCTAG-CAGCAGTGGAATAGGTTGAAGATTGTGAATC
* *
35583555 CTATCTCCCTGAGCAACAGTGGAGTAGGTTGAA
1 CTATCTCCCT-AGCAGCAGTGGAATAGGTTGAA
35583588 AATAGTTGAT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
44 64 0.94
45 4 0.06
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (43 bp):
CTATCTCCCTAGCAGCAGTGGAATAGGTTGAAGATTGTGAATC
Found at i:35584200 original size:45 final size:44
Alignment explanation
Indices: 35584081--35584378 Score: 168
Period size: 44 Copynumber: 6.8 Consensus size: 44
35584071 TCGCATCTAG
* * *
35584081 TCTTATCTCCCTAAAGTTCCAGTGGAGCAGACTAAG-TAATCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGATAGTCAA
* * *
35584124 GTCTTATC-CTCCTAAAGTTGTC-GT-GAGGCAGACTGAAGATGGTGAA
1 -TCTTATCTC-CCTGAAGTTG-CAGTGGA-GCAGACT-AAGATAGTCAA
* ** *
35584170 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT-AA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGATAGTCAA
* * * **
35584214 TCCTATCTCCCTGAAGTTGCAGTAGAGCAGATTAA-A-ACCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGATA-GTCA-A
* * * * * * * **
35584258 TCTTATCTCTCTGAAATTGCAGTAGAGTAGA-TCACATCG--GG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGATAGTCAA
* *
35584299 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTCAAGAAAG-CAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGATAGTCAA
* * *
35584343 GTCTTATCCCCCTGAAATTACAGTGGAGCAGACTAA
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
35584379 ATAAACAAAT
Statistics
Matches: 199, Mismatches: 38, Indels: 34
0.73 0.14 0.13
Matches are distributed among these distances:
41 29 0.15
42 1 0.01
43 11 0.06
44 90 0.45
45 61 0.31
46 7 0.04
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGATAGTCAA
Found at i:35584281 original size:44 final size:44
Alignment explanation
Indices: 35583951--35584289 Score: 182
Period size: 44 Copynumber: 7.8 Consensus size: 44
35583941 GAAGATGACG
* * *
35583951 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCAAT
* * * * *
35583995 AATCCTATCTCTCTGAAGTTGTAGT-GAAGTAGATTAAAATCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTAG-AGCAGATTAAAACCA-AT
* * * *** *
35584039 GATCTTATCTCTCTGAAGTTACAG-AGAGCAGA-TCGCATC--T
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCAAT
* * * * * *
35584079 AGTCTTATCTCCCTAAAGTTCCAGTGGAGCAGACTAAGTAATC-A-
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAA--AACCAAT
* * * * ***
35584123 AGTCTTATC-CTCCTAAAGTTGTC-GT-GAGGCAGACTGAAGA-TGGT
1 AATCTTATCTC-CCTGAAGTTG-CAGTAGA-GCAGA-TTAAAACCAAT
* *
35584167 GAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 -AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCAAT
*
35584212 AATCCTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCA-AT
* * * *
35584256 GATCTTATCTCTCTGAAATTGCAGTAGAGTAGAT
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGAT
35584290 CACATCGGGT
Statistics
Matches: 228, Mismatches: 46, Indels: 42
0.72 0.15 0.13
Matches are distributed among these distances:
40 19 0.08
41 7 0.03
42 5 0.02
43 10 0.04
44 154 0.68
45 30 0.13
46 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCAAT
Found at i:35584413 original size:217 final size:217
Alignment explanation
Indices: 35583936--35584413 Score: 594
Period size: 217 Copynumber: 2.2 Consensus size: 217
35583926 ACAATTTAAA
* *
35583936 AGACTGAAGATGACGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
1 AGACTGAAGATAACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
* * * * *
35584001 ATCTCTCTGAAGTTGTAGTGAAGTAGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAGA
66 ATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAATTACAGAGA
* * * *
35584066 GCAGATCGCATCTAGTCTTATCTCCCTAAAGTTCCAGTGGAGCAGACTAAGTAATCAAGTCTTAT
131 GCAGATCACATCGAGTCTTATCTCCCTAAAGTTCCAGTGGAGCAGACTAAGAAAGCAAGTCTTAT
* *
35584131 CCTCCTAAAGTTGTCGTGAGGC
196 CCCCCTAAAGTTGACGTGAGGC
**** *
35584153 AGACTGAAGATGGTGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
1 AGACTGAAGATAACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
*
35584218 ATCTCCCTGAAGTTGCAGT-AGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAATTGCAGTA
66 ATCTCCCTGAAGTTGCAGTGA-AGCAGATTAAAACCACAGATCTTATCTCTCTGAAATTACAG-A
* * * * *
35584282 GAGTAGATCACATCGGGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTCAAGAAAGCAAGTCT
129 GAGCAGATCACATCGAGTCTTATCTCCCTAAAGTTCCAGTGGAGCAGACT-AAGAAAGCAAGTCT
35584347 TATCCCCCTGAAA-TT-ACAGTG-GAGC
193 TATCCCCCT-AAAGTTGAC-GTGAG-GC
* *
35584372 AGACT-AA-ATAAACAAAT-TCTGTCTCCCT-AAGTTGTAGTGGAG
1 AGACTGAAGAT-AACAAATCT-TATCTCCCTAAAGTTGCAGTGGAG
35584414 TGGATTAGAG
Statistics
Matches: 227, Mismatches: 26, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
216 1 0.00
217 132 0.58
218 59 0.26
219 32 0.14
220 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (217 bp):
AGACTGAAGATAACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
ATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAATTACAGAGA
GCAGATCACATCGAGTCTTATCTCCCTAAAGTTCCAGTGGAGCAGACTAAGAAAGCAAGTCTTAT
CCCCCTAAAGTTGACGTGAGGC
Found at i:35584462 original size:217 final size:217
Alignment explanation
Indices: 35583936--35584467 Score: 587
Period size: 217 Copynumber: 2.5 Consensus size: 217
35583926 ACAATTTAAA
* * *
35583936 AGACTGAAGATGACGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
1 AGACTGAAGATAACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
* * * * *
35584001 ATCTCTCTGAAGTTGTAGTGAAGTAGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAGA
66 ATCTCTCTGAAGTTGCAGTTAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAATTACAGAGA
* * * *
35584066 GCAGATCGCATCTAGTCTTATCTCCCTAAAGTTCCAGTGGAGCAGACTAAGTAATCAAGTCTTAT
131 GCAGATCACATCGAGTCTTATCTCCCTAAAGTTCCAGTGGAGCAGACTAAGAAAGCAAGTCTTAT
* *
35584131 CCTCCTAAAGTTGTCGTGAGGC
196 CCCCCTAAAGTTGACGTGAGGC
****
35584153 AGACTGAAGATGGTGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
1 AGACTGAAGATAACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
* *
35584218 ATCTCCCTGAAGTTGCAG-TAGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAATTGCAGTA
66 ATCTCTCTGAAGTTGCAGTTA-AGCAGATTAAAACCACAGATCTTATCTCTCTGAAATTACAG-A
* * * * *
35584282 GAGTAGATCACATCGGGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTCAAGAAAGCAAGTCT
129 GAGCAGATCACATCGAGTCTTATCTCCCTAAAGTTCCAGTGGAGCAGACT-AAGAAAGCAAGTCT
35584347 TATCCCCCTGAAA-TT-ACAGTG-GAGC
193 TATCCCCCT-AAAGTTGAC-GTGAG-GC
* * ** * ** *
35584372 AGACT-AA-ATAAACAAAT-TCTGTCTCCCT-AAGTTGTAGTGGAGTGGATTAGAG-TGATGGAT
1 AGACTGAAGAT-AACAAATCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT-AAT
** * *
35584432 TTTATCTCTCTGAAATTACAGTTAAGCAGATTAAAA
63 CCTATCTCTCTGAAGTTGCAGTTAAGCAGATTAAAA
35584468 GTTACGAGTC
Statistics
Matches: 267, Mismatches: 38, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
216 3 0.01
217 168 0.63
218 61 0.23
219 32 0.12
220 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (217 bp):
AGACTGAAGATAACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
ATCTCTCTGAAGTTGCAGTTAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAATTACAGAGA
GCAGATCACATCGAGTCTTATCTCCCTAAAGTTCCAGTGGAGCAGACTAAGAAAGCAAGTCTTAT
CCCCCTAAAGTTGACGTGAGGC
Found at i:35584769 original size:21 final size:21
Alignment explanation
Indices: 35584724--35584799 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
35584714 ATCTTCAAGG
*
35584724 ATATGTAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
35584743 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
35584764 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
35584785 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
35584800 AGACATAATT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
19 18 0.33
21 36 0.67
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:35585218 original size:16 final size:15
Alignment explanation
Indices: 35585193--35585227 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
35585183 TTTAATCATC
35585193 TATTTGTTATTTTTGT
1 TATTTGTTATTTTT-T
*
35585209 TATTTTTTATTTTTT
1 TATTTGTTATTTTTT
35585224 TATT
1 TATT
35585228 CTTAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (15 bp):
TATTTGTTATTTTTT
Found at i:35585306 original size:7 final size:7
Alignment explanation
Indices: 35585294--35585326 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
35585284 ATCATTATTA
35585294 TTATTTT
1 TTATTTT
35585301 TTATTTT
1 TTATTTT
35585308 TTA-TTT
1 TTATTTT
35585314 TTATTTT
1 TTATTTT
35585321 TATATT
1 T-TATT
35585327 CATGTGCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.25
7 14 0.58
8 4 0.17
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TTATTTT
Found at i:35585314 original size:13 final size:14
Alignment explanation
Indices: 35585288--35585326 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
35585278 TCTTGTATCA
*
35585288 TTATTATTAT-TTT
1 TTATTTTTATATTT
35585301 TTATTTTT-TATTT
1 TTATTTTTATATTT
35585314 TTATTTTTATATT
1 TTATTTTTATATT
35585327 CATGTGCATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 1 0.04
13 18 0.78
14 4 0.17
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTATTTTTATATTT
Found at i:35587006 original size:19 final size:19
Alignment explanation
Indices: 35586930--35587014 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 19
35586920 TATGTGGCAA
35586930 AAAATT-TATAAAAA-TA-
1 AAAATTATATAAAAATTAT
*
35586946 AAAATCA-ATAAAAATTATT
1 AAAATTATATAAAAATTA-T
* *
35586965 AAAAATATA-AAAAATTGT
1 AAAATTATATAAAAATTAT
* *
35586983 CAAATTTTATAAAAATTAT
1 AAAATTATATAAAAATTAT
35587002 AAAA-TATATAAAA
1 AAAATTATATAAAA
35587015 TGCACCAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
16 12 0.23
17 2 0.04
18 15 0.28
19 23 0.43
20 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (19 bp):
AAAATTATATAAAAATTAT
Found at i:35587219 original size:10 final size:10
Alignment explanation
Indices: 35587206--35587314 Score: 50
Period size: 10 Copynumber: 11.1 Consensus size: 10
35587196 ATTTCTTCAC
35587206 ATTTTTTATA
1 ATTTTTTATA
*
35587216 ATTTTCTTATG
1 ATTTT-TTATA
* **
35587227 ACTTCATA-A
1 ATTTTTTATA
*
35587236 AATTT-TATA
1 ATTTTTTATA
*
35587245 ATTTTTTCT-
1 ATTTTTTATA
*
35587254 ATATTTCTAT-
1 AT-TTTTTATA
*
35587264 ATATTTTATA
1 ATTTTTTATA
35587274 ATTTTTT-TA
1 ATTTTTTATA
*
35587283 CTATTTTTATA
1 AT-TTTTTATA
*
35587294 ATTTTTTTTCA
1 ATTTTTTAT-A
35587305 A-TTTTTATA
1 ATTTTTTATA
35587314 A
1 A
35587315 AAAAAATTCT
Statistics
Matches: 73, Mismatches: 18, Indels: 17
0.68 0.17 0.16
Matches are distributed among these distances:
8 2 0.03
9 20 0.27
10 39 0.53
11 12 0.16
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.63
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:35587269 original size:29 final size:28
Alignment explanation
Indices: 35587209--35587298 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 28
35587199 TCTTCACATT
* * *
35587209 TTTTATAATTTTCTTA-TGACTTCATAAAA
1 TTTTATAATTTTTTTACT-ATTTC-TATAA
35587238 TTTTATAATTTTTTCTA-TATTTCTATATA
1 TTTTATAATTTTTT-TACTATTTCTATA-A
*
35587267 TTTTATAATTTTTTTACTATTTTTATAA
1 TTTTATAATTTTTTTACTATTTCTATAA
35587295 TTTT
1 TTTT
35587299 TTTTCAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
28 10 0.19
29 41 0.76
30 3 0.06
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (28 bp):
TTTTATAATTTTTTTACTATTTCTATAA
Found at i:35587292 original size:20 final size:20
Alignment explanation
Indices: 35587267--35587314 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
35587257 TTTCTATATA
*
35587267 TTTTATAATTTTTTTACTAT
1 TTTTATAATTTTTTTACAAT
*
35587287 TTTTATAATTTTTTTTCAAT
1 TTTTATAATTTTTTTACAAT
35587307 TTTTATAA
1 TTTTATAA
35587315 AAAAAATTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTATAATTTTTTTACAAT
Found at i:35587370 original size:19 final size:19
Alignment explanation
Indices: 35587328--35587382 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
35587318 AAATTCTAAT
35587328 TTTTAATATTTTTATTAAA
1 TTTTAATATTTTTATTAAA
* *
35587347 ATTTAATAGTTTTTA-TAAG
1 TTTTAATA-TTTTTATTAAA
*
35587366 TTTTATTGATTTTTATT
1 TTTTAAT-ATTTTTATT
35587383 TTTTATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 21 0.72
20 8 0.28
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTAATATTTTTATTAAA
Found at i:35594234 original size:37 final size:37
Alignment explanation
Indices: 35594193--35594265 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
35594183 ATAATGATAA
35594193 GATTTGCTCAATTAAG-TTCCATTCAATATAACAGTAT
1 GATTTGCTCAATTAAGCTT-CATTCAATATAACAGTAT
*
35594230 GATTTGCTCAATTGAGCTTCATTCAATATAACAGTA
1 GATTTGCTCAATTAAGCTTCATTCAATATAACAGTA
35594266 AAATTTGGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 32 0.94
38 2 0.06
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.37
Consensus pattern (37 bp):
GATTTGCTCAATTAAGCTTCATTCAATATAACAGTAT
Found at i:35597074 original size:15 final size:15
Alignment explanation
Indices: 35597054--35597105 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
35597044 ACTATAAAAC
35597054 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
35597069 ATTTATAATTCTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
35597088 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
35597103 ATT
1 ATT
35597106 AAATAAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:35597124 original size:13 final size:12
Alignment explanation
Indices: 35597097--35597144 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
35597087 TATTTATTAT
*
35597097 TAAAATATTAAA
1 TAAATTATTAAA
35597109 TAAATTATTAAAA
1 TAAATTATT-AAA
*
35597122 TAAATTATATTAA
1 TAAATTAT-TAAA
*
35597135 TAATTTATTA
1 TAAATTATTA
35597145 TATGACTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 9 0.30
13 20 0.67
14 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAATTATTAAA
Found at i:35602143 original size:47 final size:46
Alignment explanation
Indices: 35602028--35602152 Score: 144
Period size: 46 Copynumber: 2.7 Consensus size: 46
35602018 GGCAATTTAC
* * *
35602028 CTGCTCGACCAGTGGTTTATGCACAACGTATTTTACAGTAGTTTAT
1 CTGCTCGACCAGTGGTTTATCCACAACGTATTTTACAGGAGTTCAT
* * * *
35602074 CTGCTCAACCAGCGATTTATCCACAACGTATTTTAGTCGGGAG-TCAT
1 CTGCTCGACCAGTGGTTTATCCACAACGTATTTTA--CAGGAGTTCAT
* *
35602121 CTGCTCGACCAGTGGTTCATCCACAACATATT
1 CTGCTCGACCAGTGGTTTATCCACAACGTATT
35602153 AAACAACATT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
46 31 0.48
47 30 0.46
48 4 0.06
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (46 bp):
CTGCTCGACCAGTGGTTTATCCACAACGTATTTTACAGGAGTTCAT
Found at i:35602232 original size:94 final size:94
Alignment explanation
Indices: 35602117--35602335 Score: 239
Period size: 94 Copynumber: 2.3 Consensus size: 94
35602107 TAGTCGGGAG
* * * ** *
35602117 TCATCTGCTCGACCAGTGGTTCATCCACAACATATTAAACAACATTT-ATTTGCACCTATGGATG
1 TCATCTGCACGACCAGTGGTTCATCCACAACATATT-AAC-ACATTTGATATACACAAAAGGATG
*
35602181 GTTAATCCACCAATACTT-TTA-GTTGGCAGT
64 GTTAATCCACCAATA-TTCTTATGTTAGCAGT
* ** * *
35602211 TTATCTGCACGACCAGTGGTTCATCCACAATGTATTAGCATATTTGATATACACAAAAGGATGGT
1 TCATCTGCACGACCAGTGGTTCATCCACAACATATTAACACATTTGATATACACAAAAGGATGGT
*
35602276 TCATCCACCAATATTCTTATTGTTAGCAGT
66 TAATCCACCAATATTCTTA-TGTTAGCAGT
*
35602306 TCATCTGCAACGATCAGTGGTT-ATCCACAA
1 TCATCTGC-ACGACCAGTGGTTCATCCACAA
35602336 TGTGGTGTGA
Statistics
Matches: 105, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
92 7 0.07
93 31 0.30
94 32 0.30
95 23 0.22
96 12 0.11
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (94 bp):
TCATCTGCACGACCAGTGGTTCATCCACAACATATTAACACATTTGATATACACAAAAGGATGGT
TAATCCACCAATATTCTTATGTTAGCAGT
Found at i:35610322 original size:22 final size:22
Alignment explanation
Indices: 35610297--35610339 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
35610287 TAATAAAAAG
35610297 AATATCTACAAAATATTCCTAA
1 AATATCTACAAAATATTCCTAA
* *
35610319 AATATTTACAGAATATTCCTA
1 AATATCTACAAAATATTCCTA
35610340 CACTCCCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (22 bp):
AATATCTACAAAATATTCCTAA
Found at i:35614056 original size:22 final size:22
Alignment explanation
Indices: 35614031--35614073 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
35614021 TAATAAAAAG
35614031 AATATCTACAAAATATTCCTAA
1 AATATCTACAAAATATTCCTAA
* * *
35614053 AATATTTACAGAGTATTCCTA
1 AATATCTACAAAATATTCCTA
35614074 CAATTATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (22 bp):
AATATCTACAAAATATTCCTAA
Found at i:35627608 original size:84 final size:84
Alignment explanation
Indices: 35627520--35627749 Score: 218
Period size: 84 Copynumber: 2.7 Consensus size: 84
35627510 GTACTCCAAG
** *
35627520 GAGACTCAAGTTCA-AGCAAAG-GGTATATGTTAATAA-CATAAATGATGATAACCAAAACAGTA
1 GAGACTCAAGTTCAGA-CAAAGAGAAAT-TGTTAACAACCA-AAATGATGATAACCAAAACAGTA
*
35627582 GAGTCAAGGAGTTTACCCCGAA
63 AAGTCAAGGAGTTTACCCCGAA
* * * *
35627604 GAGACTCAAGTTCAGACGAAGAGAAATTGTTGACAACCAAAATGGTGATAACCAAAACGGTAAAG
1 GAGACTCAAGTTCAGACAAAGAGAAATTGTTAACAACCAAAATGATGATAACCAAAACAGTAAAG
* *
35627669 TCAAGGAGTGTACTCC-AA
66 TCAAGGAGTTTACCCCGAA
* * * * * * * *
35627687 TGAGACTGAAATTTC-GGCGAAGAGTAATTGTTGACAACCAAAATGGTGATAACAAAAACAGTA
1 -GAGACT-CAAGTTCAGACAAAGAGAAATTGTTAACAACCAAAATGATGATAACCAAAACAGTA
35627750 GAATCGAGGA
Statistics
Matches: 125, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
83 2 0.02
84 112 0.90
85 11 0.09
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (84 bp):
GAGACTCAAGTTCAGACAAAGAGAAATTGTTAACAACCAAAATGATGATAACCAAAACAGTAAAG
TCAAGGAGTTTACCCCGAA
Found at i:35627960 original size:81 final size:81
Alignment explanation
Indices: 35627851--35628177 Score: 573
Period size: 81 Copynumber: 4.0 Consensus size: 81
35627841 GGAGTTTAGT
* *
35627851 CTTGAGTCCTGCCAAAGAAATCTCGACAACAGAAATTCTGATGATCAAAATAGTAGAGGTGAGGA
1 CTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTAGAGGTGAGGA
35627916 CTCTGCTCCAACGAAA
66 CTCTGCTCCAACGAAA
35627932 CTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTAGAGGTGAGGA
1 CTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTAGAGGTGAGGA
*
35627997 CTCTGCTCCAACGACA
66 CTCTGCTCCAACGAAA
35628013 CTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTAGAGGTGAGGA
1 CTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTAGAGGTGAGGA
* *
35628078 CACTGCTCCAACAAAA
66 CTCTGCTCCAACGAAA
* *
35628094 CTTGAGTCCTGCCGAAGAGCTCTTGACAACAGAAATTCTGATGATCAAAATAGTAGAGGTGAGGA
1 CTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTAGAGGTGAGGA
* *
35628159 CTCAGCTCCAAGGAAA
66 CTCTGCTCCAACGAAA
35628175 CTT
1 CTT
35628178 ATCTTCAGGC
Statistics
Matches: 234, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 234 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (81 bp):
CTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTAGAGGTGAGGA
CTCTGCTCCAACGAAA
Found at i:35632135 original size:7 final size:7
Alignment explanation
Indices: 35632123--35632158 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
35632113 TATAGCAGTC
*
35632123 TTTGAGG
1 TTTGAGT
35632130 TTTGAGT
1 TTTGAGT
35632137 TTTGAGT
1 TTTGAGT
35632144 TTTGAGT
1 TTTGAGT
35632151 TTTGAGT
1 TTTGAGT
35632158 T
1 T
35632159 AAGATTCTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.00, G:0.31, T:0.56
Consensus pattern (7 bp):
TTTGAGT
Found at i:35640325 original size:24 final size:23
Alignment explanation
Indices: 35640266--35640337 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
35640256 GCGCATTCGT
*
35640266 ATATGAGAGTCCCTTGTGTGGGATG
1 ATATGAGAG-CCCTT-TATGGGATG
* *
35640291 -TATAAGAGCCCTTTTTGGGATG
1 ATATGAGAGCCCTTTATGGGATG
*
35640313 CATATGAGAGCCCATTATGGGATG
1 -ATATGAGAGCCCTTTATGGGATG
35640337 A
1 A
35640338 ATGGAAGTCC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 8 0.20
23 6 0.15
24 26 0.65
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.31
Consensus pattern (23 bp):
ATATGAGAGCCCTTTATGGGATG
Found at i:35640424 original size:28 final size:28
Alignment explanation
Indices: 35640393--35640561 Score: 137
Period size: 28 Copynumber: 6.0 Consensus size: 28
35640383 TAGGATGATT
35640393 TTAAACGTGGAAGTCCGTCAGAACGATC
1 TTAAACGTGGAAGTCCGTCAGAACGATC
* ** * *
35640421 TTAAATGTGGAAGTTTG-CTAGGACAATC
1 TTAAACGTGGAAGTCCGTC-AGAACGATC
* * **
35640449 TTAAACGTGGAAGTCTGCCAGAATAATC
1 TTAAACGTGGAAGTCCGTCAGAACGATC
* * *
35640477 CTAAGCGTGGAAGTCC-TCCAGGACGATC
1 TTAAACGTGGAAGTCCGT-CAGAACGATC
* * * *
35640505 TTAAACATGGAAATTCATCAGAACGATC
1 TTAAACGTGGAAGTCCGTCAGAACGATC
*
35640533 TTAAATGTGGAAGTCCGTCATG-ACGATC
1 TTAAACGTGGAAGTCCGTCA-GAACGATC
35640561 T
1 T
35640562 AATGTGAAAG
Statistics
Matches: 109, Mismatches: 27, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
27 1 0.01
28 105 0.96
29 3 0.03
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (28 bp):
TTAAACGTGGAAGTCCGTCAGAACGATC
Found at i:35640436 original size:56 final size:56
Alignment explanation
Indices: 35640372--35640546 Score: 190
Period size: 56 Copynumber: 3.1 Consensus size: 56
35640362 ACCATACACA
* *
35640372 TGGAAGTTTGCTAGGATGATTTTAAACGTGGAAGTCCGTCAGAACGATCTTAAATG
1 TGGAAGTTTGCTAGGACGATCTTAAACGTGGAAGTCCGTCAGAACGATCTTAAATG
* * * ** * **
35640428 TGGAAGTTTGCTAGGACAATCTTAAACGTGGAAGTCTGCCAGAATAATCCTAAGCG
1 TGGAAGTTTGCTAGGACGATCTTAAACGTGGAAGTCCGTCAGAACGATCTTAAATG
* * * * * *
35640484 TGGAAGTCCT-CCAGGACGATCTTAAACATGGAAATTCATCAGAACGATCTTAAATG
1 TGGAAGT-TTGCTAGGACGATCTTAAACGTGGAAGTCCGTCAGAACGATCTTAAATG
35640540 TGGAAGT
1 TGGAAGT
35640547 CCGTCATGAC
Statistics
Matches: 94, Mismatches: 24, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
56 93 0.99
57 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (56 bp):
TGGAAGTTTGCTAGGACGATCTTAAACGTGGAAGTCCGTCAGAACGATCTTAAATG
Found at i:35643554 original size:23 final size:24
Alignment explanation
Indices: 35643528--35643588 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
35643518 ATAAAAAATT
* *
35643528 TAAAGAAAAATAATTGAAATA-AA
1 TAAAGAAAAATAAGTAAAATAGAA
**
35643551 TAAACTAAAATAAGTAAAATAGAA
1 TAAAGAAAAATAAGTAAAATAGAA
*
35643575 TAACAGAACAATAA
1 TAA-AGAAAAATAA
35643589 ATAAGAAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
23 17 0.59
24 5 0.17
25 7 0.24
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.20
Consensus pattern (24 bp):
TAAAGAAAAATAAGTAAAATAGAA
Found at i:35657003 original size:15 final size:15
Alignment explanation
Indices: 35656983--35657034 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
35656973 ACTCTCATCA
*
35656983 TTCTTTTCTTTTTTT
1 TTCTTTTCTCTTTTT
* *
35656998 TTCTTTTCACTCTTT
1 TTCTTTTCTCTTTTT
35657013 TTCTTTTTCTCTTTTT
1 TTC-TTTTCTCTTTTT
*
35657029 CTCTTT
1 TTCTTT
35657035 CTCGCTCAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (15 bp):
TTCTTTTCTCTTTTT
Found at i:35657024 original size:14 final size:14
Alignment explanation
Indices: 35656995--35657037 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
35656985 CTTTTCTTTT
*
35656995 TTTTTCTTTTCACTC
1 TTTTTCTTTT-TCTC
35657010 TTTTTCTTTTTCTC
1 TTTTTCTTTTTCTC
*
35657024 TTTTTCTCTTTCTC
1 TTTTTCTTTTTCTC
35657038 GCTCAATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTCTTTTTCTC
Found at i:35661889 original size:19 final size:19
Alignment explanation
Indices: 35661865--35661901 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
35661855 CTTGAAGACA
*
35661865 AGGCCCAATAAGATGTTCC
1 AGGCCCAATAAGAAGTTCC
35661884 AGGCCCAATAAGAAGTTC
1 AGGCCCAATAAGAAGTTC
35661902 AAACTAGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (19 bp):
AGGCCCAATAAGAAGTTCC
Found at i:35664045 original size:18 final size:18
Alignment explanation
Indices: 35664024--35664067 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
35664014 AAAGGAAGAC
35664024 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
35664042 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
35664060 AGAGAAAA
1 AGA-AAAA
35664068 AAGAGATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:35665906 original size:34 final size:33
Alignment explanation
Indices: 35665831--35665906 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
35665821 GAGTTAGTTT
*
35665831 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGA
1 ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGA
* *
35665864 ATTAATTTTAGTTTAGCTTAAATAAGTGTTAGTA
1 ATTAATTTTAGTTCAGCTCAAATAAGTGTTAG-A
35665898 ATTAATTTT
1 ATTAATTTT
35665907 TTTAAATTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 29 0.74
34 10 0.26
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (33 bp):
ATTAATTTTAGTTCAGCTCAAATAAGTGTTAGA
Found at i:35682364 original size:15 final size:15
Alignment explanation
Indices: 35682344--35682382 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 15
35682334 CATAATTGTT
35682344 ATAAAATATAATTTA
1 ATAAAATATAATTTA
35682359 ATAAAATATATAATTTA
1 AT-AAA-ATATAATTTA
35682376 ATAAAAT
1 ATAAAAT
35682383 TGTTAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.18
16 6 0.27
17 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAATATAATTTA
Found at i:35682389 original size:17 final size:17
Alignment explanation
Indices: 35682349--35682382 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
35682339 TTGTTATAAA
35682349 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35682366 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35682383 TGTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:35682469 original size:26 final size:28
Alignment explanation
Indices: 35682422--35682501 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 28
35682412 TAATAAAATC
35682422 ATAATATATAATACTACAATATAATTTAA-A
1 ATAATATATAAT--TA-AATATAATTTAATA
*
35682452 ATAAT-TATTATTAAATATAATTTAATA
1 ATAATATATAATTAAATATAATTTAATA
* *
35682479 ATAATATATAATTTAATAAAATT
1 ATAATATATAATTAAATATAATT
35682502 CTTATTCTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
26 12 0.27
27 8 0.18
28 14 0.32
29 5 0.11
30 5 0.11
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (28 bp):
ATAATATATAATTAAATATAATTTAATA
Found at i:35682544 original size:108 final size:113
Alignment explanation
Indices: 35682329--35682588 Score: 356
Period size: 117 Copynumber: 2.3 Consensus size: 113
35682319 TTAATCATAT
* * *
35682329 TTTAACATAATTGTTATAAAATATAATTTAATAA-AATATATAATTTAATAAAATTGTTAATAAA
1 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAA-T-TTAAT--A
*
35682393 TATTCTTATATGAATTTACTAATAAAATCATAATATATAATAC-TACAATATAA
62 TATTCTTATATGAATTTAC--ATAAAATCATAATATATAATACATAAAATATAA
*
35682446 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAA-TT-CT-TATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAATTTAATATATT
35682508 CTTATATGAATTTAC-TAAAATCATAATATATAATACTATAAAATATAA
66 CTTATATGAATTTACATAAAATCATAATATATAATAC-ATAAAATATAA
35682556 TTT-AAATAATTATTATTAAATATAATTT-ATAAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAT
35682589 CTACTTTATT
Statistics
Matches: 135, Mismatches: 5, Indels: 15
0.87 0.03 0.10
Matches are distributed among these distances:
108 26 0.19
109 25 0.19
110 12 0.09
111 19 0.14
114 1 0.01
115 2 0.01
117 31 0.23
118 19 0.14
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (113 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAATTTAATATATT
CTTATATGAATTTACATAAAATCATAATATATAATACATAAAATATAA
Found at i:35682580 original size:32 final size:32
Alignment explanation
Indices: 35682544--35682607 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
35682534 TATATAATAC
*
35682544 TATAAAATATAATTTAAATAATTATTATTAAA
1 TATAAAATATAATCTAAATAATTATTATTAAA
** ** *
35682576 TATAATTTATAATCTACTTTATTATTATTAAA
1 TATAAAATATAATCTAAATAATTATTATTAAA
35682608 CTGCAATACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (32 bp):
TATAAAATATAATCTAAATAATTATTATTAAA
Found at i:35684286 original size:54 final size:54
Alignment explanation
Indices: 35684226--35684351 Score: 171
Period size: 62 Copynumber: 2.2 Consensus size: 54
35684216 CGTAGTTTAG
35684226 AATCAAGTTGATTATATCTAATGATCAAATTAATATATTATCCATATGTTTTTT
1 AATCAAGTTGATTATATCTAATGATCAAATTAATATATTATCCATATGTTTTTT
*
35684280 AATCAAGTTGTTTACTTGATTATATCTAATGATCCAATTAATATATTATCCATATGTTTTTT
1 AATCAA---G-----TTGATTATATCTAATGATCAAATTAATATATTATCCATATGTTTTTT
35684342 AATCAAGTTG
1 AATCAAGTTG
35684352 TTTACTTGAT
Statistics
Matches: 63, Mismatches: 1, Indels: 16
0.79 0.01 0.20
Matches are distributed among these distances:
54 9 0.14
57 1 0.02
59 1 0.02
62 52 0.83
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.46
Consensus pattern (54 bp):
AATCAAGTTGATTATATCTAATGATCAAATTAATATATTATCCATATGTTTTTT
Found at i:35684418 original size:64 final size:64
Alignment explanation
Indices: 35684233--35684510 Score: 465
Period size: 64 Copynumber: 4.4 Consensus size: 64
35684223 TAGAATCAAG
*
35684233 TTGATTATATCTAATGAT-CAA-ATTAATATATTATCCATATGTTTTTTAATCAAGTTGTTTAC
1 TTGATTATATCTAATGATCCAATTTTAATATATTATCCATATGTTTTTTAATCAAGTTGTTTAC
35684295 TTGATTATATCTAATGATCCAA--TTAATATATTATCCATATGTTTTTTAATCAAGTTGTTTAC
1 TTGATTATATCTAATGATCCAATTTTAATATATTATCCATATGTTTTTTAATCAAGTTGTTTAC
* *
35684357 TTGATTATATCTAATGATTCAATTTTAATATATTATCCATATGTTTTTTAATCAATTTGTTTAC
1 TTGATTATATCTAATGATCCAATTTTAATATATTATCCATATGTTTTTTAATCAAGTTGTTTAC
** *
35684421 TTGATTATAAGTAATGATCCAATTTTAATATATTATCCATATGTTTTTTAATCAATTTGTTTAC
1 TTGATTATATCTAATGATCCAATTTTAATATATTATCCATATGTTTTTTAATCAAGTTGTTTAC
*
35684485 TTGATTATATGTAATGATCCAATTTT
1 TTGATTATATCTAATGATCCAATTTT
35684511 TATTTTATTT
Statistics
Matches: 207, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
62 79 0.38
63 3 0.01
64 125 0.60
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.50
Consensus pattern (64 bp):
TTGATTATATCTAATGATCCAATTTTAATATATTATCCATATGTTTTTTAATCAAGTTGTTTAC
Found at i:35684711 original size:36 final size:32
Alignment explanation
Indices: 35684626--35684700 Score: 141
Period size: 32 Copynumber: 2.3 Consensus size: 32
35684616 TAGAAATATT
*
35684626 TTTAATTAATGAGTAGTATATGAATATACACA
1 TTTAATTAATGAGTTGTATATGAATATACACA
35684658 TTTAATTAATGAGTTGTATATGAATATACACA
1 TTTAATTAATGAGTTGTATATGAATATACACA
35684690 TTTAATTAATG
1 TTTAATTAATG
35684701 CGTGCGTTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (32 bp):
TTTAATTAATGAGTTGTATATGAATATACACA
Found at i:35685180 original size:12 final size:12
Alignment explanation
Indices: 35685163--35685209 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
35685153 GCCGCATTTT
35685163 AAGCAAAAGAAC
1 AAGCAAAAGAAC
35685175 AAGCAAAAGAAC
1 AAGCAAAAGAAC
*
35685187 GAGCAAAAGAA-
1 AAGCAAAAGAAC
35685198 AAG--AAAGAAC
1 AAGCAAAAGAAC
35685208 AA
1 AA
35685210 ATAACAAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 2 0.06
12 22 0.69
ACGTcount: A:0.68, C:0.13, G:0.19, T:0.00
Consensus pattern (12 bp):
AAGCAAAAGAAC
Found at i:35687251 original size:16 final size:16
Alignment explanation
Indices: 35687230--35687278 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
35687220 TTCGCTGTAT
35687230 TGGAATAGAGGCATAA
1 TGGAATAGAGGCATAA
35687246 TGGAATAGAGG-AGTAA
1 TGGAATAGAGGCA-TAA
* *
35687262 TGAAATAGAGGCGTAA
1 TGGAATAGAGGCATAA
35687278 T
1 T
35687279 AGCAAATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 1 0.03
16 28 0.97
ACGTcount: A:0.43, C:0.04, G:0.33, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGGCATAA
Found at i:35687657 original size:120 final size:120
Alignment explanation
Indices: 35687498--35687833 Score: 627
Period size: 120 Copynumber: 2.8 Consensus size: 120
35687488 TTAATCATAT
*
35687498 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATACAATTCTTAATATT
1 TTTAACATAATTATTATTAATTATAATTTAATAAAAATATATAATTTAATACAATTCTTAATATT
35687563 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
* *
35687618 TTTAACATAATTATTATTAATTATAATTTAATAATAATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAATTATAATTTAATAAAAATATATAATTTAATACAATTCTTAATATT
35687683 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
35687738 TTTAACATAATTATTATTAATTATAATTTAATAAAAATATATAATTTAATACAATTCTTAATATT
1 TTTAACATAATTATTATTAATTATAATTTAATAAAAATATATAATTTAATACAATTCTTAATATT
**
35687803 AAATATTCTTATATGAATTTAATAAAATCAT
66 AAATATTCTTATATGAATTTTCTAAAATCAT
35687834 GTAAAAAGAA
Statistics
Matches: 209, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 209 1.00
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (120 bp):
TTTAACATAATTATTATTAATTATAATTTAATAAAAATATATAATTTAATACAATTCTTAATATT
AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
Found at i:35687662 original size:18 final size:17
Alignment explanation
Indices: 35687635--35687673 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
35687625 TAATTATTAT
35687635 TAATTATAATTTAATAA
1 TAATTATAATTTAATAA
35687652 TAATATATAATTTAATAA
1 TAAT-TATAATTTAATAA
35687670 -AATT
1 TAATT
35687674 CTTAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.05
17 7 0.33
18 13 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATTATAATTTAATAA
Found at i:35691483 original size:22 final size:24
Alignment explanation
Indices: 35691435--35691487 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
35691425 AATTTTGTGT
35691435 TATTTTTAAAATTATTAAATAATA
1 TATTTTTAAAATTATTAAATAATA
35691459 TATTTTTATAAATT-TTAAA-ATATA
1 TATTTTTA-AAATTATTAAATA-ATA
35691483 TATTT
1 TATTT
35691488 GCTAATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 1 0.04
24 21 0.78
25 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTTTTAAAATTATTAAATAATA
Found at i:35697173 original size:19 final size:19
Alignment explanation
Indices: 35697149--35697192 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
35697139 AAAATTAGAA
35697149 AAAAATTGTTAAAAA-ATAT
1 AAAAATTG-TAAAAATATAT
*
35697168 AAAAATTGTAAAAATTTAT
1 AAAAATTGTAAAAATATAT
35697187 AAAAAT
1 AAAAAT
35697193 CATAAAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
AAAAATTGTAAAAATATAT
Found at i:35697189 original size:28 final size:30
Alignment explanation
Indices: 35697149--35697220 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 30
35697139 AAAATTAGAA
*
35697149 AAAAATTGT-TAAAAAAT-ATAAAA-ATTGT
1 AAAAATT-TATAAAAAATCATAAAAGATTAT
35697177 AAAAATTTAT-AAAAATCATAAAAGATTAT
1 AAAAATTTATAAAAAATCATAAAAGATTAT
*
35697206 -AAAATGTATAAAAAA
1 AAAAATTTATAAAAAA
35697221 GCCCTTTAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 7 0.18
28 22 0.58
29 9 0.24
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (30 bp):
AAAAATTTATAAAAAATCATAAAAGATTAT
Found at i:35697198 original size:19 final size:19
Alignment explanation
Indices: 35697165--35697209 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
35697155 TGTTAAAAAA
**
35697165 TATAAAAATTGTAAAA-ATT
1 TATAAAAATCATAAAAGA-T
35697184 TATAAAAATCATAAAAGAT
1 TATAAAAATCATAAAAGAT
35697203 TATAAAA
1 TATAAAA
35697210 TGTATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (19 bp):
TATAAAAATCATAAAAGAT
Found at i:35697207 original size:10 final size:9
Alignment explanation
Indices: 35697083--35697219 Score: 64
Period size: 10 Copynumber: 14.6 Consensus size: 9
35697073 ACATGTGACA
35697083 AAAAATTAT
1 AAAAATTAT
35697092 AAAAA--AT
1 AAAAATTAT
* *
35697099 AGAAATCAAT
1 AAAAAT-TAT
*
35697109 AAAAAATAT
1 AAAAATTAT
*
35697118 AAAAGTTATT
1 AAAAATTA-T
**
35697128 AAATTTTATT
1 AAAAATTA-T
* *
35697138 CAAAATTAGAA
1 AAAAATT--AT
*
35697149 AAAAATTGTT
1 AAAAATT-AT
*
35697159 AAAAAATAT
1 AAAAATTAT
*
35697168 AAAAATTGT
1 AAAAATTAT
35697177 AAAAATTTAT
1 AAAAA-TTAT
*
35697187 AAAAATCAT
1 AAAAATTAT
35697196 AAAAGATTAT
1 AAAA-ATTAT
35697206 -AAAATGTAT
1 AAAAAT-TAT
35697215 AAAAA
1 AAAAA
35697220 AGCCCTTTAA
Statistics
Matches: 96, Mismatches: 22, Indels: 19
0.70 0.16 0.14
Matches are distributed among these distances:
7 6 0.06
8 2 0.02
9 39 0.41
10 42 0.44
11 6 0.06
12 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:35697404 original size:9 final size:9
Alignment explanation
Indices: 35697390--35697574 Score: 103
Period size: 9 Copynumber: 20.0 Consensus size: 9
35697380 TTTTGGAATG
35697390 ATAATTTTT
1 ATAATTTTT
35697399 ATAATTTTT
1 ATAATTTTT
* *
35697408 TTACGAATTTT
1 ATA--ATTTTT
*
35697419 ATATTTCTTT
1 ATAATT-TTT
*
35697429 AAAATTTTT
1 ATAATTTTT
35697438 ATAATTTTCTT
1 ATAA-TTT-TT
*
35697449 ATGA-TTTT
1 ATAATTTTT
*
35697457 ATAAAATTTT
1 AT-AATTTTT
*
35697467 AAAATTTTT
1 ATAATTTTT
35697476 AT-ATTTTT
1 ATAATTTTT
**
35697484 ACGATTTTT
1 ATAATTTTT
*
35697493 ATATTTTTTT
1 ATA-ATTTTT
35697503 ATAA--TTT
1 ATAATTTTT
35697510 ATAATTATTT
1 ATAATT-TTT
* *
35697520 ATTAAAATTTA
1 A-T-AATTTTT
*
35697531 ATATTTTTT
1 ATAATTTTT
*
35697540 ATAAATTTT
1 ATAATTTTT
35697549 ATAAATTTTT
1 AT-AATTTTT
35697559 AT--TTTTT
1 ATAATTTTT
35697566 ATAATTTTT
1 ATAATTTTT
35697575 TCCACACGTC
Statistics
Matches: 133, Mismatches: 26, Indels: 34
0.69 0.13 0.18
Matches are distributed among these distances:
7 14 0.11
8 11 0.08
9 53 0.40
10 36 0.27
11 16 0.12
12 3 0.02
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:35697468 original size:38 final size:39
Alignment explanation
Indices: 35697392--35697495 Score: 119
Period size: 38 Copynumber: 2.8 Consensus size: 39
35697382 TTGGAATGAT
* **
35697392 AATTTTTATAATTTTTTTACGAATTTTATATTTCTTTAA
1 AATTTTTATAATTTTCTTACGAATTTTATAAATCTTTAA
*
35697431 AATTTTTATAATTTTCTTATG-ATTTTATAAAAT-TTTAA
1 AATTTTTATAATTTTCTTACGAATTTTAT-AAATCTTTAA
*
35697469 AATTTTTAT-A-TTT-TTACGATTTTTATA
1 AATTTTTATAATTTTCTTACGAATTTTATA
35697496 TTTTTTTATA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
35 5 0.09
36 9 0.16
37 1 0.02
38 21 0.37
39 21 0.37
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.61
Consensus pattern (39 bp):
AATTTTTATAATTTTCTTACGAATTTTATAAATCTTTAA
Found at i:35697549 original size:19 final size:18
Alignment explanation
Indices: 35697400--35697549 Score: 76
Period size: 19 Copynumber: 8.1 Consensus size: 18
35697390 ATAATTTTTA
*
35697400 TAAT-TTTTTTACGAATTT
1 TAATATTTTTTA-AAATTT
35697418 T-ATATTTCTTTAAAATTT
1 TAATATTT-TTTAAAATTT
* **
35697436 TTATAATTTTCTTATGATTT
1 TAAT-ATTTT-TTAAAATTT
**
35697456 T-ATAAAATTTTAAAATTT
1 TAAT-ATTTTTTAAAATTT
* **
35697474 TTATA-TTTTTACGATTT
1 TAATATTTTTTAAAATTT
* *
35697491 TTATATTTTTTTATAATTT
1 TAATA-TTTTTTAAAATTT
*
35697510 ATAATTATTTATTAAAA-TT
1 -TAA-TATTTTTTAAAATTT
35697529 TAATATTTTTTATAAATTT
1 TAATATTTTTTA-AAATTT
35697548 TA
1 TA
35697550 TAAATTTTTA
Statistics
Matches: 104, Mismatches: 16, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
17 24 0.23
18 25 0.24
19 31 0.30
20 22 0.21
21 2 0.02
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (18 bp):
TAATATTTTTTAAAATTT
Found at i:35697557 original size:19 final size:19
Alignment explanation
Indices: 35697390--35697560 Score: 74
Period size: 19 Copynumber: 9.1 Consensus size: 19
35697380 TTTTGGAATG
*
35697390 ATAATTTTTAT-AATTTTT
1 ATAAATTTTATAAATTTTT
* *
35697408 TTACGAATTTTAT-ATTTCTTT
1 ATA--AATTTTATAAATT-TTT
*
35697429 A-AAATTTTTATAATTTTCTT
1 ATAAA-TTTTATAAATTT-TT
* *
35697449 AT-GATTTTATAAAATTTT
1 ATAAATTTTATAAATTTTT
*
35697467 A-AAATTTT-TATATTTTT
1 ATAAATTTTATAAATTTTT
** * **
35697484 ACGATTTTTATATTTTTTT
1 ATAAATTTTATAAATTTTT
35697503 AT-AA-TTTAT-AATTATTT
1 ATAAATTTTATAAATT-TTT
* *
35697520 ATTAAAATTTA-ATATTTTTT
1 A-TAAATTTTATA-AATTTTT
35697540 ATAAATTTTATAAATTTTT
1 ATAAATTTTATAAATTTTT
35697559 AT
1 AT
35697561 TTTTTATAAT
Statistics
Matches: 116, Mismatches: 20, Indels: 33
0.69 0.12 0.20
Matches are distributed among these distances:
16 2 0.02
17 17 0.15
18 19 0.16
19 44 0.38
20 28 0.24
21 6 0.05
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
ATAAATTTTATAAATTTTT
Found at i:35698311 original size:20 final size:19
Alignment explanation
Indices: 35698269--35698312 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
35698259 CTAGTTATAG
* *
35698269 TTTTAGATTATTTTAGTGT
1 TTTTAGATTATTTTAATGC
*
35698288 TTTTATATTATTTTTAATGC
1 TTTTAGATTA-TTTTAATGC
35698308 TTTTA
1 TTTTA
35698313 AATAAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (19 bp):
TTTTAGATTATTTTAATGC
Found at i:35703025 original size:24 final size:26
Alignment explanation
Indices: 35702982--35703039 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 26
35702972 GTATTACACC
*
35702982 CAAACCCAAACAGCCCAAAACT-AAA
1 CAAACCCAAACAGCACAAAACTAAAA
*
35703007 CAAACCC-AACAGCATAAAACTAAAAA
1 CAAACCCAAACAGCACAAAACT-AAAA
35703033 CAAACCC
1 CAAACCC
35703040 TAGCCCCCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 12 0.41
25 7 0.24
26 10 0.34
ACGTcount: A:0.57, C:0.34, G:0.03, T:0.05
Consensus pattern (26 bp):
CAAACCCAAACAGCACAAAACTAAAA
Done.