Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 30 of 126
Found at i:9319644 original size:14 final size:14
Alignment explanation
Indices: 9319627--9319692 Score: 55
Period size: 14 Copynumber: 4.7 Consensus size: 14
9319617 AGGTTTGAAA
9319627 ATTGAAAATTAAAG
1 ATTGAAAATTAAAG
9319641 ATTGAAAATATAAA-
1 ATTGAAAAT-TAAAG
* *
9319655 ATT-AGAAATTGAGG
1 ATTGA-AAATTAAAG
* *
9319669 ATTGAAAATTGAGG
1 ATTGAAAATTAAAG
*
9319683 ATTGAGAATT
1 ATTGAAAATT
9319693 TAGTAAGGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
13 3 0.07
14 37 0.82
15 5 0.11
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (14 bp):
ATTGAAAATTAAAG
Found at i:9319645 original size:21 final size:21
Alignment explanation
Indices: 9319621--9319692 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
9319611 AAATTGAGGT
9319621 TTGAAAATTGAAAATTAAAGA
1 TTGAAAATTGAAAATTAAAGA
9319642 TTGAAAATAT-AAAATTAGAA-A
1 TTGAAAAT-TGAAAATTA-AAGA
** * *
9319663 TTGAGGATTGAAAATTGAGGA
1 TTGAAAATTGAAAATTAAAGA
*
9319684 TTGAGAATT
1 TTGAAAATT
9319693 TAGTAAGGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
20 2 0.05
21 37 0.88
22 3 0.07
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (21 bp):
TTGAAAATTGAAAATTAAAGA
Found at i:9319655 original size:28 final size:28
Alignment explanation
Indices: 9319624--9319677 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
9319614 TTGAGGTTTG
9319624 AAAATT-GAAAATTAAAGATTGAAAATAT
1 AAAATTAG-AAATTAAAGATTGAAAATAT
* *
9319652 AAAATTAGAAATTGAGGATTGAAAAT
1 AAAATTAGAAATTAAAGATTGAAAAT
9319678 TGAGGATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.15, T:0.28
Consensus pattern (28 bp):
AAAATTAGAAATTAAAGATTGAAAATAT
Found at i:9322585 original size:31 final size:31
Alignment explanation
Indices: 9322550--9322623 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
9322540 AAATTTAAAT
* *
9322550 TAATAAAAATA-AAATTATGATCTCTTAAAAA
1 TAATAAAAATATAAATT-TAATATCTTAAAAA
*
9322581 TAATAAAAA-ATTAATTTAATATCTTAAAAA
1 TAATAAAAATATAAATTTAATATCTTAAAAA
*
9322611 TTATAAAAATATA
1 TAATAAAAATATA
9322624 GATAATTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 21 0.58
31 15 0.42
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (31 bp):
TAATAAAAATATAAATTTAATATCTTAAAAA
Found at i:9327848 original size:19 final size:20
Alignment explanation
Indices: 9327814--9327859 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
9327804 AATAACAATT
9327814 AAATTAAAGTTAATTAAACC
1 AAATTAAAGTTAATTAAACC
*
9327834 AAATTAAAG-TAATTAAACT
1 AAATTAAAGTTAATTAAACC
9327853 AAATTAA
1 AAATTAA
9327860 TTAGACTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (20 bp):
AAATTAAAGTTAATTAAACC
Found at i:9327857 original size:10 final size:10
Alignment explanation
Indices: 9327813--9327859 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
9327803 AAATAACAAT
*
9327813 TAAATTAAAG
1 TAAATTAAAC
*
9327823 TTAATTAAAC
1 TAAATTAAAC
* *
9327833 CAAATTAAAG
1 TAAATTAAAC
9327843 T-AATTAAAC
1 TAAATTAAAC
9327852 TAAATTAA
1 TAAATTAA
9327860 TTAGACTAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (10 bp):
TAAATTAAAC
Found at i:9328624 original size:30 final size:30
Alignment explanation
Indices: 9328588--9328644 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
9328578 GTAACCTCGA
*
9328588 TATAATGTCAATTTGTGTGAGAAACTTTAT
1 TATAATGTCAACTTGTGTGAGAAACTTTAT
* *
9328618 TATAATGTCAGCTTGTGTGAGCAACTT
1 TATAATGTCAACTTGTGTGAGAAACTT
9328645 GTTCCCGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (30 bp):
TATAATGTCAACTTGTGTGAGAAACTTTAT
Found at i:9330593 original size:29 final size:29
Alignment explanation
Indices: 9330530--9330594 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
9330520 ATTTTCGAGG
* * *
9330530 AATTTAGGGTTAAAATTGAAATTTTTGGAA
1 AATTT-GGGTTAAAATTCAAACTTTTGAAA
9330560 AATTTGGGATTAAAA-TCAAACTTTTGAAA
1 AATTTGGG-TTAAAATTCAAACTTTTGAAA
9330589 AATTTG
1 AATTTG
9330595 AGGTCGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.38
Consensus pattern (29 bp):
AATTTGGGTTAAAATTCAAACTTTTGAAA
Found at i:9330712 original size:88 final size:89
Alignment explanation
Indices: 9330620--9330781 Score: 215
Period size: 88 Copynumber: 1.8 Consensus size: 89
9330610 CTTTTGGAAA
* * * *
9330620 TTTAGGGG-CAAAATGGTAATTTTAGATG-AGTT-TAGTGGTCAAAATGTAATTTTTGAGAAGTT
1 TTTAGGGGTCAAAAT-GTAATTTTAGA-GAAGTTCGAG-GGTCAAAATGGAATTTTAGAAAAGTT
9330682 TA-GGGTTAAAACATATTTTTATGAAG
63 TAGGGGTTAAAACATATTTTTATGAAG
* *
9330708 TTTAGGGGTTAAAATGTAATTTTAGAGAAGTTCGAGGGTCAAAATGGGATTTTAGAAAAGTTTAG
1 TTTAGGGGTCAAAATGTAATTTTAGAGAAGTTCGAGGGTCAAAATGGAATTTTAGAAAAGTTTAG
9330773 GGGTTAAAA
66 GGGTTAAAA
9330782 TGTAATTTTG
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
87 1 0.02
88 47 0.73
89 16 0.25
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (89 bp):
TTTAGGGGTCAAAATGTAATTTTAGAGAAGTTCGAGGGTCAAAATGGAATTTTAGAAAAGTTTAG
GGGTTAAAACATATTTTTATGAAG
Found at i:9330911 original size:30 final size:30
Alignment explanation
Indices: 9330532--9330941 Score: 243
Period size: 30 Copynumber: 13.8 Consensus size: 30
9330522 TTTCGAGGAA
*
9330532 TTTA-GGGTTAAAATTGAAATTTTTGGAAAA-
1 TTTAGGGGTTAAAA-TGTAA-TTTTGGAAAAG
* ** *
9330562 TTT-GGGATTAAAATCAAACTTTT-GAAAAA
1 TTTAGGGGTTAAAATGTAA-TTTTGGAAAAG
* * *
9330591 TTT-GAGGTCGAAAATGTGACTTTTGG-AAA-
1 TTTAGGGGT-TAAAATGT-AATTTTGGAAAAG
* * **
9330620 TTTAGGGG-CAAAATGGTAATTTTAGATGAG
1 TTTAGGGGTTAAAAT-GTAATTTTGGAAAAG
* * * *
9330650 TTTAGTGGTCAAAATGTAATTTTTGAGAAG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
** * *
9330680 TTTA-GGGTTAAAACAT-ATTTT-TATGAAG
1 TTTAGGGGTTAAAATGTAATTTTGGA-AAAG
* *
9330708 TTTAGGGGTTAAAATGTAATTTTAGAGAAG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
* * ** *
9330738 -TTCGAGGGTCAAAATGGGATTTTAGAAAAG
1 TTTAG-GGGTTAAAATGTAATTTTGGAAAAG
*
9330768 TTTAGGGGTTAAAATGTAATTTTGGACAAG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
* * * *
9330798 TTTAAGGGTTAAAATATGATATTGGAAAAG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
*
9330828 TTTAGGGGTAAAAATGTAATTTTTGGAAAAG
1 TTTAGGGGTTAAAATGTAA-TTTTGGAAAAG
* ** * * **
9330859 CTCCGGGATTAACATGGGATTTTGGAAAAG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
* **
9330889 TTTGGGGGTTAAAATGTAATTTTAAAAAAG
1 TTTAGGGGTTAAAATGTAATTTTGGAAAAG
*
9330919 TTTTA-TGGTTAAAATGTAATTTT
1 -TTTAGGGGTTAAAATGTAATTTT
9330942 TGAAGAAAAT
Statistics
Matches: 295, Mismatches: 67, Indels: 36
0.74 0.17 0.09
Matches are distributed among these distances:
27 1 0.00
28 29 0.10
29 41 0.14
30 188 0.64
31 36 0.12
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.36
Consensus pattern (30 bp):
TTTAGGGGTTAAAATGTAATTTTGGAAAAG
Found at i:9330920 original size:121 final size:120
Alignment explanation
Indices: 9330628--9330933 Score: 314
Period size: 121 Copynumber: 2.5 Consensus size: 120
9330618 AATTTAGGGG
* ** * * ** *
9330628 CAAAATGGTAATTTTAGATGAGTTTAGTGGTCAAAATGTAATTTTTGAGAAGTTT-AGGGTTAAA
1 CAAAATGG-GATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTAAAAAAGTTTAAGGGTTAAA
* ** * * * * *
9330692 ACAT-AT-TTTTATGAAGTTTAGGGGTTAAAATGTAATTTTAGAGAAGTTCGAGGGT
65 ATATGATATTGGA-AAAGTTTAGGGGTAAAAATGTAATTTTAGAAAAGTCCGAGGAT
** *
9330747 CAAAATGGGATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTGGACAAGTTTAAGGGTTAAAA
1 CAAAATGGGATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTAAAAAAGTTTAAGGGTTAAAA
*
9330812 TATGATATTGGAAAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAAGCTCCG-GGAT
66 TATGATATTGGAAAAGTTTAGGGGTAAAAATGTAA-TTTTAGAAAAG-TCCGAGGAT
* * * * * *
9330868 TAACATGGGATTTTGGAAAAGTTTGGGGGTTAAAATGTAATTTTAAAAAAGTTTTATGGTTAAAA
1 CAAAATGGGATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTAAAAAAGTTTAAGGGTTAAAA
9330933 T
66 T
9330934 GTAATTTTTG
Statistics
Matches: 157, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
118 39 0.25
119 20 0.13
120 23 0.15
121 72 0.46
122 3 0.02
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (120 bp):
CAAAATGGGATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTAAAAAAGTTTAAGGGTTAAAA
TATGATATTGGAAAAGTTTAGGGGTAAAAATGTAATTTTAGAAAAGTCCGAGGAT
Found at i:9335736 original size:38 final size:38
Alignment explanation
Indices: 9335694--9335787 Score: 125
Period size: 38 Copynumber: 2.5 Consensus size: 38
9335684 ATGTATTACC
* * * *
9335694 GAATACATGTTAAGGATGCCTACTGTTACTGTTGAACT
1 GAATACATGTTAAGCATGCCTAATGCTACTGTTAAACT
* *
9335732 GAATACACGTTAAGCATGTCTAATGCTACTGTTAAACT
1 GAATACATGTTAAGCATGCCTAATGCTACTGTTAAACT
*
9335770 GAAAACATGTTAAGCATG
1 GAATACATGTTAAGCATG
9335788 TTTTACTATT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (38 bp):
GAATACATGTTAAGCATGCCTAATGCTACTGTTAAACT
Found at i:9337706 original size:20 final size:19
Alignment explanation
Indices: 9337663--9337731 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 19
9337653 AAAGTTAAAC
9337663 TTTTTTTTACAAATTCTTTGAA
1 TTTTTTTT-CAAATT-TTT-AA
9337685 TTTTTTTTCAGAATTTTTAA
1 TTTTTTTTCA-AATTTTTAA
*
9337705 TTATCTTTTT-AAATTTTAAA
1 TT-T-TTTTTCAAATTTTTAA
9337725 TTTTTTT
1 TTTTTTT
9337732 AAAAAAATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
18 4 0.09
19 1 0.02
20 14 0.33
21 7 0.16
22 17 0.40
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTTTTTCAAATTTTTAA
Found at i:9337788 original size:10 final size:10
Alignment explanation
Indices: 9337770--9337803 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
9337760 TTATAAATAT
9337770 TTTTAATTTA
1 TTTTAATTTA
*
9337780 TTTTGATTTA
1 TTTTAATTTA
9337790 TTTTAATTT-
1 TTTTAATTTA
9337799 TTTTA
1 TTTTA
9337804 GATAGACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 5 0.23
10 17 0.77
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (10 bp):
TTTTAATTTA
Found at i:9339338 original size:16 final size:16
Alignment explanation
Indices: 9339317--9339402 Score: 56
Period size: 16 Copynumber: 5.6 Consensus size: 16
9339307 ATTATTTTTA
9339317 AATTATATTTAATAAT
1 AATTATATTTAATAAT
9339333 AATTATA-TTAA-AAT
1 AATTATATTTAATAAT
* * *
9339347 ATGATTA-AATTATTTAT
1 A--ATTATATTTAATAAT
* * *
9339364 TATTAT-TTTTATTA-
1 AATTATATTTAATAAT
9339378 AATTATATTTAATAAT
1 AATTATATTTAATAAT
*
9339394 AATTCTATT
1 AATTATATT
9339403 AAAATTTAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
14 9 0.17
15 20 0.38
16 22 0.42
17 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (16 bp):
AATTATATTTAATAAT
Found at i:9355513 original size:30 final size:31
Alignment explanation
Indices: 9355435--9355523 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 31
9355425 GTAACTAATT
* *
9355435 TTTTTTATCTAATTTGGTA-TTCAAATTTGACA
1 TTTTTT-TCTAAGTTGGTACTT-AAACTTGACA
* *
9355467 TTTTTTTCTAATTTGGTACTTAAACTTGATA
1 TTTTTTTCTAAGTTGGTACTTAAACTTGACA
9355498 TTTTTTT-TAAGTTGGTACTTAAACTT
1 TTTTTTTCTAAGTTGGTACTTAAACTT
9355524 TTTGGGGTAC
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
30 18 0.34
31 27 0.51
32 8 0.15
ACGTcount: A:0.26, C:0.09, G:0.10, T:0.55
Consensus pattern (31 bp):
TTTTTTTCTAAGTTGGTACTTAAACTTGACA
Found at i:9356966 original size:76 final size:76
Alignment explanation
Indices: 9356840--9356993 Score: 308
Period size: 76 Copynumber: 2.0 Consensus size: 76
9356830 TGTTCTAAGA
9356840 ACAAATATGATAGGGAAATTGTTGATTCACCAATGTTTAATGTTAGGCAACTTATTTTAGAAGAT
1 ACAAATATGATAGGGAAATTGTTGATTCACCAATGTTTAATGTTAGGCAACTTATTTTAGAAGAT
9356905 AAAATGGTCGG
66 AAAATGGTCGG
9356916 ACAAATATGATAGGGAAATTGTTGATTCACCAATGTTTAATGTTAGGCAACTTATTTTAGAAGAT
1 ACAAATATGATAGGGAAATTGTTGATTCACCAATGTTTAATGTTAGGCAACTTATTTTAGAAGAT
9356981 AAAATGGTCGG
66 AAAATGGTCGG
9356992 AC
1 AC
9356994 TTCCATGTAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (76 bp):
ACAAATATGATAGGGAAATTGTTGATTCACCAATGTTTAATGTTAGGCAACTTATTTTAGAAGAT
AAAATGGTCGG
Found at i:9368592 original size:117 final size:118
Alignment explanation
Indices: 9368460--9368687 Score: 431
Period size: 118 Copynumber: 1.9 Consensus size: 118
9368450 CCTAAATCTA
* *
9368460 CTAAACTAAAAACCCTAAAACAGTTTTGC-AAAAAGCTCTTAAGCCTTGCCTTAACTTAACTATT
1 CTAAACTAAAAACCCTAAAACAGTTTTGCAAAAAAGCTCCTAAGCCTTGCCTCAACTTAACTATT
9368524 TATAAAAGAGTTTAGCAACCTTAATTAGGTCAAATACAAGCCCTAAACTAAAC
66 TATAAAAGAGTTTAGCAACCTTAATTAGGTCAAATACAAGCCCTAAACTAAAC
9368577 CTAAACTAAAAACCCTAAAACAGTTTTGCAAAAAAGCTCCTAAGCCTTGCCTCAACTTAACTATT
1 CTAAACTAAAAACCCTAAAACAGTTTTGCAAAAAAGCTCCTAAGCCTTGCCTCAACTTAACTATT
9368642 TATAAAAGAGTTTAGCAACCTTAATTAGGTCAAATACAAGCCCTAA
66 TATAAAAGAGTTTAGCAACCTTAATTAGGTCAAATACAAGCCCTAA
9368688 TTACATTAGT
Statistics
Matches: 108, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
117 29 0.27
118 79 0.73
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.27
Consensus pattern (118 bp):
CTAAACTAAAAACCCTAAAACAGTTTTGCAAAAAAGCTCCTAAGCCTTGCCTCAACTTAACTATT
TATAAAAGAGTTTAGCAACCTTAATTAGGTCAAATACAAGCCCTAAACTAAAC
Found at i:9375557 original size:15 final size:15
Alignment explanation
Indices: 9375537--9375586 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
9375527 CAAGTTTTTA
9375537 TTTTTCTTCTTCTTC
1 TTTTTCTTCTTCTTC
*
9375552 TTTTTCCTTC-TATTC
1 TTTTT-CTTCTTCTTC
*
9375567 TTTTTCTTTTTCTTC
1 TTTTTCTTCTTCTTC
9375582 TTTTT
1 TTTTT
9375587 TTTTCTCTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 3 0.10
15 23 0.77
16 4 0.13
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTCTTCTTCTTC
Found at i:9375595 original size:15 final size:15
Alignment explanation
Indices: 9375532--9375598 Score: 64
Period size: 15 Copynumber: 4.1 Consensus size: 15
9375522 TGGGACAAGT
9375532 TTTTATTTTTCTTCTTC
1 TTTT-TTTTTC-TCTTC
*
9375549 TTCTTTTTCCTTCTATTC
1 TT-TTTTT--TTCTCTTC
9375567 TTTTTCTTTT-TCTTC
1 TTTTT-TTTTCTCTTC
9375582 TTTTTTTTTCTCTTC
1 TTTTTTTTTCTCTTC
9375597 TT
1 TT
9375599 GTGCTTCAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
14 4 0.09
15 16 0.37
16 2 0.05
17 8 0.19
18 10 0.23
19 3 0.07
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTTTTCTCTTC
Found at i:9375595 original size:21 final size:21
Alignment explanation
Indices: 9375543--9375592 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
9375533 TTTATTTTTC
*
9375543 TTCTTCTTCTTTTTCCTTCTA
1 TTCTTTTTCTTTTTCCTTCTA
9375564 TTCTTTTTCTTTTT-CTTCT-
1 TTCTTTTTCTTTTTCCTTCTA
*
9375583 TTTTTTTTCT
1 TTCTTTTTCT
9375593 CTTCTTGTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 9 0.33
20 5 0.19
21 13 0.48
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (21 bp):
TTCTTTTTCTTTTTCCTTCTA
Found at i:9377416 original size:24 final size:24
Alignment explanation
Indices: 9377371--9377418 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
9377361 TGCAAAAACT
9377371 AAAGAAACAAATTAAAGTAAAATA
1 AAAGAAACAAATTAAAGTAAAATA
*
9377395 AAAGACAA-AAATTAACAGAAAAAT
1 AAAGA-AACAAATTAA-AGTAAAAT
9377419 TGCAATGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.15
Consensus pattern (24 bp):
AAAGAAACAAATTAAAGTAAAATA
Found at i:9389735 original size:28 final size:28
Alignment explanation
Indices: 9389681--9389736 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
9389671 AATATCCAAT
* *
9389681 TTACTCCCTGTTGACCCAAAAGTCATGC
1 TTACTCCCTATTGACCCAAAAGCCATGC
* *
9389709 TTACTCTCTATTGACCCAAAGGCCATGC
1 TTACTCCCTATTGACCCAAAAGCCATGC
9389737 CTGTTACCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.29
Consensus pattern (28 bp):
TTACTCCCTATTGACCCAAAAGCCATGC
Found at i:9389783 original size:19 final size:19
Alignment explanation
Indices: 9389761--9389799 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
9389751 CGATGCTGCT
*
9389761 TTCAGCCATCGATACGGTA
1 TTCAACCATCGATACGGTA
9389780 TTCAACCATCGATACGGTA
1 TTCAACCATCGATACGGTA
9389799 T
1 T
9389800 AATTGTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (19 bp):
TTCAACCATCGATACGGTA
Found at i:9397461 original size:16 final size:16
Alignment explanation
Indices: 9397417--9397461 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
9397407 GCTAATCAAA
9397417 AAATAAATATACA-TTC
1 AAATAAATATA-ATTTC
9397433 AAA-AAAT-TAATTTC
1 AAATAAATATAATTTC
9397447 AAATAAATATAATTT
1 AAATAAATATAATTT
9397462 AAACGTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.04
14 8 0.31
15 8 0.31
16 9 0.35
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATAAATATAATTTC
Found at i:9399729 original size:2 final size:2
Alignment explanation
Indices: 9399722--9399771 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
9399712 TGTTTGGAGA
9399722 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9399764 AT AT AT AT
1 AT AT AT AT
9399772 GCATATTTGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9399904 original size:131 final size:134
Alignment explanation
Indices: 9399757--9400039 Score: 430
Period size: 137 Copynumber: 2.1 Consensus size: 134
9399747 TATATATATA
* *
9399757 TATATATATATATATGCATATTTGGTGGCTGGAAATAAATAAATAAAT-A-CTTTTTGTC-TGAG
1 TATATATATATATATGCATATTTGGTGGCTAGAAATAAATAAATAAATAATCTTTTTGCCATGAG
* *
9399819 AATTATATTGAACATTTTGAATTGTTGAAATGAGTTGAATACAAAGGATTAATGAAAGATTTGAA
66 AAATATATTGAACATTTTGAATTGTTGAAATGAGTTGAATACAAAGGATTAATAAAAGATTTGAA
9399884 TTGT
131 TTGT
*
9399888 TATATATAT-TGATATGCATATTTGGTGGCTAGAAATAAATAAATAAATAAATGTTTTTTTGCCA
1 TATATATATAT-ATATGCATATTTGGTGGCTAGAAATAAATAAATAAAT-AA--TCTTTTTGCCA
* * *
9399952 TGTGAAATATATTGAACATTTTGGATTGTTGAAATGAGTTGAATACAATGGATTAATAAAAGATT
62 TGAGAAATATATTGAACATTTTGAATTGTTGAAATGAGTTGAATACAAAGGATTAATAAAAGATT
9400017 TGAATTGT
127 TGAATTGT
9400025 TATATATATATATAT
1 TATATATATATATAT
9400040 AGCAAGAAAC
Statistics
Matches: 136, Mismatches: 8, Indels: 10
0.88 0.05 0.06
Matches are distributed among these distances:
130 1 0.01
131 45 0.33
133 1 0.01
136 7 0.05
137 81 0.60
138 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.40
Consensus pattern (134 bp):
TATATATATATATATGCATATTTGGTGGCTAGAAATAAATAAATAAATAATCTTTTTGCCATGAG
AAATATATTGAACATTTTGAATTGTTGAAATGAGTTGAATACAAAGGATTAATAAAAGATTTGAA
TTGT
Found at i:9400992 original size:40 final size:41
Alignment explanation
Indices: 9400943--9401062 Score: 107
Period size: 41 Copynumber: 3.0 Consensus size: 41
9400933 ATGGTAAAGA
* * *
9400943 AATAACGGCGTTTCTAAAAAAACGCCGCAAAAGAT-AGAGC
1 AATAGCGGCGTTTATAAAAAAACGCCGCAAAAGATAAGACC
** * * *
9400983 AATAGCGGCGTTTATTTAAAAGCGCCGCTAAAGGTAAGACC
1 AATAGCGGCGTTTATAAAAAAACGCCGCAAAAGATAAGACC
* ** * * *
9401024 ATTAGCGGCGTTTATTTAAAAGCGCCGCTAAAGGTAAGA
1 AATAGCGGCGTTTATAAAAAAACGCCGCAAAAGATAAGA
9401063 GAATTATTCG
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 28 0.40
41 42 0.60
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (41 bp):
AATAGCGGCGTTTATAAAAAAACGCCGCAAAAGATAAGACC
Found at i:9401035 original size:41 final size:41
Alignment explanation
Indices: 9400985--9401062 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
9400975 GATAGAGCAA
9400985 TAGCGGCGTTTATTTAAAAGCGCCGCTAAAGGTAAGACCAT
1 TAGCGGCGTTTATTTAAAAGCGCCGCTAAAGGTAAGACCAT
9401026 TAGCGGCGTTTATTTAAAAGCGCCGCTAAAGGTAAGA
1 TAGCGGCGTTTATTTAAAAGCGCCGCTAAAGGTAAGA
9401063 GAATTATTCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (41 bp):
TAGCGGCGTTTATTTAAAAGCGCCGCTAAAGGTAAGACCAT
Found at i:9401147 original size:41 final size:41
Alignment explanation
Indices: 9401116--9401314 Score: 319
Period size: 41 Copynumber: 4.8 Consensus size: 41
9401106 AAGATCAGAT
* *
9401116 CAATAGCGGCGCATATGGAAAAGCGCTGCTAAAAGTCTAAG
1 CAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAAGTCTAAG
* *
9401157 CAATAGCCGCGCTTATGGAAAAGCGCCGGTAAAAGTCTAAG
1 CAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAAGTCTAAG
*
9401198 CAATTGCGGCGCTTATGGAAAAGCGCCG-TGAAAAGTCTAAG
1 CAATAGCGGCGCTTATGGAAAAGCGCCGCT-AAAAGTCTAAG
9401239 CAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAAGTCTAAG
1 CAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAAGTCTAAG
*
9401280 CAATAGCGGTGCTTATGGAAAAAGCGCCGCTAAAA
1 CAATAGCGGCGCTTATGG-AAAAGCGCCGCTAAAA
9401315 TTTTTACATT
Statistics
Matches: 147, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
40 1 0.01
41 129 0.88
42 17 0.12
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.18
Consensus pattern (41 bp):
CAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAAGTCTAAG
Found at i:9403650 original size:34 final size:34
Alignment explanation
Indices: 9403612--9403679 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
9403602 TTAGAAAAAA
* * *
9403612 CAACCCAAATACTTCATTATTTAATTACTTAAAT
1 CAACCCAAATAATTAATTAATTAATTACTTAAAT
* *
9403646 CAACCCAATTAATTAATTAATTAATTATTTAAAT
1 CAACCCAAATAATTAATTAATTAATTACTTAAAT
9403680 ATTAAAAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (34 bp):
CAACCCAAATAATTAATTAATTAATTACTTAAAT
Found at i:9403724 original size:8 final size:8
Alignment explanation
Indices: 9403711--9403738 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
9403701 TAATTCAAAA
9403711 TATTTAAT
1 TATTTAAT
9403719 TATTTAAT
1 TATTTAAT
9403727 TATTTAAT
1 TATTTAAT
9403735 TATT
1 TATT
9403739 AAAAACAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATTTAAT
Found at i:9403743 original size:132 final size:136
Alignment explanation
Indices: 9403607--9403875 Score: 456
Period size: 135 Copynumber: 2.0 Consensus size: 136
9403597 TAAAATTAGA
**
9403607 AAAAACAACCCAAATACTTCATTATTTAATTACTTAAATCAACCCAATTAATTAA-T-TAATTAA
1 AAAAACAACCCAAATACTGAATTATTTAATTACTTAAATCAACCCAATTAATTAATTATAATTAA
9403670 TTATTTAAATATTAAAAACAACCCAAATATTTAATTCAAAATATTTAATTATTTAA-T-TATTTA
66 TTATTTAAATATTAAAAACAACCCAAATATTTAATTCAAAATATTTAATTATTTAATTATATTTA
9403733 ATTATT
131 ATTATT
* *
9403739 AAAAACAACCCAAATACTGAATTATTTAATTATTTAAATCAACTCAATTAATTAATTAATAATTA
1 AAAAACAACCCAAATACTGAATTATTTAATTACTTAAATCAACCCAATTAATTAATT-ATAATTA
*
9403804 ATTATTTAAATATTAAAAACAACTCAAATATTTAATTCAAAATATTTAATTATTTAATTATATTT
65 ATTATTTAAATATTAAAAACAACCCAAATATTTAATTCAAAATATTTAATTATTTAATTATATTT
9403869 AATTATT
130 AATTATT
9403876 TAATTAAATA
Statistics
Matches: 127, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
132 51 0.40
133 1 0.01
135 62 0.49
136 1 0.01
137 12 0.09
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (136 bp):
AAAAACAACCCAAATACTGAATTATTTAATTACTTAAATCAACCCAATTAATTAATTATAATTAA
TTATTTAAATATTAAAAACAACCCAAATATTTAATTCAAAATATTTAATTATTTAATTATATTTA
ATTATT
Found at i:9403796 original size:34 final size:34
Alignment explanation
Indices: 9403716--9403814 Score: 108
Period size: 34 Copynumber: 2.8 Consensus size: 34
9403706 CAAAATATTT
* * *
9403716 AATTATTTAATTATTTAATTATTAAAAACAACCC
1 AATTAATTAATTATTTAATTATTTAAATCAACCC
* * * *
9403750 AAATACTGAATTATTTAATTATTTAAATCAACTC
1 AATTAATTAATTATTTAATTATTTAAATCAACCC
9403784 AATTAATTAATTAATAATTAATTATTTAAAT
1 AATTAATTAATT-AT--TTAATTATTTAAAT
9403815 ATTAAAAACA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
34 37 0.70
35 2 0.04
37 14 0.26
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.43
Consensus pattern (34 bp):
AATTAATTAATTATTTAATTATTTAAATCAACCC
Found at i:9403827 original size:45 final size:46
Alignment explanation
Indices: 9403652--9403860 Score: 151
Period size: 45 Copynumber: 4.6 Consensus size: 46
9403642 AAATCAACCC
* *
9403652 AATTAATTAATTAATTAATTATTTAAATATTAAAAACAACCCAAAT
1 AATTAATTAAATAATTAATTATTTAAATATTAAAAACAACTCAAAT
* * * * ** *
9403698 ATTTAATTCAAAATATTTAATTATTTAATTATT--TAATTA-TTAAA-
1 AATTAATT--AAATAATTAATTATTTAAATATTAAAAACAACTCAAAT
* ** * * * * * *
9403742 AA-CAACCCAAATACTGAATTATTTAATTATTTAAATCAACTCAATT
1 AATTAA-TTAAATAATTAATTATTTAAATATTAAAAACAACTCAAAT
9403788 AATTAATT-AATAATTAATTATTTAAATATTAAAAACAACTCAAAT
1 AATTAATTAAATAATTAATTATTTAAATATTAAAAACAACTCAAAT
* *
9403833 ATTTAATTCAAAATATTTAATTATTTAA
1 AATTAATT--AAATAATTAATTATTTAA
9403861 TTATATTTAA
Statistics
Matches: 120, Mismatches: 32, Indels: 20
0.70 0.19 0.12
Matches are distributed among these distances:
42 21 0.17
43 2 0.02
44 3 0.03
45 44 0.37
46 12 0.10
47 2 0.02
48 36 0.30
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (46 bp):
AATTAATTAAATAATTAATTATTTAAATATTAAAAACAACTCAAAT
Found at i:9403857 original size:22 final size:20
Alignment explanation
Indices: 9403832--9403895 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 20
9403822 ACAACTCAAA
9403832 TATTTAATTCAAAATATTTAAT
1 TATTTAATT--AAATATTTAAT
9403854 TATTTAATT--ATATTTAAT
1 TATTTAATTAAATATTTAAT
9403872 TATTTAATTAAATATTTAAT
1 TATTTAATTAAATATTTAAT
9403892 TATT
1 TATT
9403896 AAAAACAACC
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
18 18 0.45
20 13 0.32
22 9 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTTAATTAAATATTTAAT
Found at i:9403895 original size:8 final size:8
Alignment explanation
Indices: 9403846--9403881 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
9403836 TAATTCAAAA
9403846 TATTTAAT
1 TATTTAAT
9403854 TATTTAATT
1 TATTTAA-T
9403863 ATATTTAAT
1 -TATTTAAT
9403872 TATTTAAT
1 TATTTAAT
9403880 TA
1 TA
9403882 AATATTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 17 0.65
9 2 0.08
10 7 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATTTAAT
Found at i:9403938 original size:33 final size:34
Alignment explanation
Indices: 9403876--9404110 Score: 111
Period size: 34 Copynumber: 6.6 Consensus size: 34
9403866 TTTAATTATT
* *
9403876 TAATTAAATATTTAATTATTAAAAACAACCCAAA
1 TAATTAATTAATTAATTATTAAAAACAACCCAAA
* *
9403910 TACTTAATT-ATTAATTAGTT-AAATCAACCCAATTAA
1 TAATTAATTAATTAATTA-TTAAAAACAACCC-A--AA
9403946 TTAATTAATTAATTATATAAATATTAAAAACAACCCAAA
1 -TAATTAATTAATTA-AT---TATTAAAAACAACCCAAA
* * * * *** ** **
9403985 TATTTAATTCAAAATATTTAATT-ATATTTA-TTATT
1 TAATTAATT--AATTAATT-ATTAAAAACAACCCAAA
* * *
9404020 TAATTAAATATTTAATTATTAAAAATAACCCAAA
1 TAATTAATTAATTAATTATTAAAAACAACCCAAA
* * * *
9404054 TACTTAATTATTTAATTAGTT-AAATCAACCCAAT
1 TAATTAATTAATTAATTA-TTAAAAACAACCCAAA
9404088 TAATTAATTAATTAATTAATTAA
1 TAATTAATTAATTAATT-ATTAA
9404111 TTATATAAAT
Statistics
Matches: 146, Mismatches: 36, Indels: 37
0.67 0.16 0.17
Matches are distributed among these distances:
32 3 0.02
33 25 0.17
34 54 0.37
35 12 0.08
36 6 0.04
37 11 0.08
38 12 0.08
39 5 0.03
40 4 0.03
41 3 0.02
42 11 0.08
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.40
Consensus pattern (34 bp):
TAATTAATTAATTAATTATTAAAAACAACCCAAA
Found at i:9404021 original size:17 final size:19
Alignment explanation
Indices: 9403999--9404039 Score: 59
Period size: 17 Copynumber: 2.2 Consensus size: 19
9403989 TAATTCAAAA
9403999 TATTTAATT-ATATTT-AT
1 TATTTAATTAATATTTAAT
9404016 TATTTAATTAAATATTTAAT
1 TATTTAATT-AATATTTAAT
9404036 TATT
1 TATT
9404040 AAAAATAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTAATTAATATTTAAT
Found at i:9404094 original size:4 final size:4
Alignment explanation
Indices: 9404085--9404113 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
9404075 AAATCAACCC
9404085 AATT AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT AATT A
9404114 TATAAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:9404186 original size:20 final size:18
Alignment explanation
Indices: 9404152--9404193 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 18
9404142 TAATTCAAAA
9404152 TATTTAATTATATTTAAT
1 TATTTAATTATATTTAAT
9404170 TATTTAATTAAATATTTAAT
1 TATTTAATT--ATATTTAAT
9404190 TATT
1 TATT
9404194 AAAAACAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTAATTATATTTAAT
Found at i:9404222 original size:34 final size:34
Alignment explanation
Indices: 9404174--9404259 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 34
9404164 TTTAATTATT
*
9404174 TAATTAAATATTTAATTA-TTAAAAACAACCCAAA
1 TAATTAATTATTTAATTAGTT-AAAACAACCCAAA
* * *
9404208 TACTTAATTATTTAATTAGTTAAATCAACCCAAT
1 TAATTAATTATTTAATTAGTTAAAACAACCCAAA
*
9404242 TAATTAATTAATTAATTA
1 TAATTAATTATTTAATTA
9404260 ATTATTTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 43 0.96
35 2 0.04
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.40
Consensus pattern (34 bp):
TAATTAATTATTTAATTAGTTAAAACAACCCAAA
Found at i:9404243 original size:154 final size:154
Alignment explanation
Indices: 9403710--9404372 Score: 968
Period size: 154 Copynumber: 4.3 Consensus size: 154
9403700 TTAATTCAAA
*
9403710 ATATTTAATTATTTAA-T---TATTTAATTATTAAAAACAACCCAAATACTGAATTATTTAATTA
1 ATATTTAATTATTTAATTAAATATTTAATTATTAAAAACAACCCAAATACTTAATTATTTAATTA
* * *
9403771 TTTAAATCAACTCAATTAATTAATTAA-TAATTAATT-A-T-T-TAAATATTAAAAACAACTCAA
66 GTTAAATCAACCCAATTAATTAATTAATTAATTAATTAATTATATAAATATTAAAAACAACCCAA
9403831 ATATTTAATTCAAAATATTTAATTATTTAATT
131 ATATTTAATTC---A-A---AA-TATTTAATT
9403863 ATATTTAATTATTTAATTAAATATTTAATTATTAAAAACAACCCAAATACTTAATTA-TTAATTA
1 ATATTTAATTATTTAATTAAATATTTAATTATTAAAAACAACCCAAATACTTAATTATTTAATTA
9403927 GTTAAATCAACCC--------AATTAATTAATTAATTAATTATATAAATATTAAAAACAACCCAA
66 GTTAAATCAACCCAATTAATTAATTAATTAATTAATTAATTATATAAATATTAAAAACAACCCAA
9403984 ATATTTAATTCAAAATATTTAATT
131 ATATTTAATTCAAAATATTTAATT
*
9404008 ATATTT-ATTATTTAATTAAATATTTAATTATTAAAAATAACCCAAATACTTAATTATTTAATTA
1 ATATTTAATTATTTAATTAAATATTTAATTATTAAAAACAACCCAAATACTTAATTATTTAATTA
9404072 GTTAAATCAACCCAATTAATTAATTAATTAATTAATTAATTATATAAATATTAAAAACAACCCAA
66 GTTAAATCAACCCAATTAATTAATTAATTAATTAATTAATTATATAAATATTAAAAACAACCCAA
9404137 ATATTTAATTCAAAATATTTAATT
131 ATATTTAATTCAAAATATTTAATT
9404161 ATATTTAATTATTTAATTAAATATTTAATTATTAAAAACAACCCAAATACTTAATTATTTAATTA
1 ATATTTAATTATTTAATTAAATATTTAATTATTAAAAACAACCCAAATACTTAATTATTTAATTA
* * *
9404226 GTTAAATCAACCCAATTAATTAATTAATTAATTAATTATTTATTTAACTATTAAAAACAACCCAA
66 GTTAAATCAACCCAATTAATTAATTAATTAATTAATTAATTATATAAATATTAAAAACAACCCAA
9404291 ATATTTAATTCAAAATATTTAATT
131 ATATTTAATTCAAAATATTTAATT
9404315 ATTTAATTATATTTACTTATTTAATTAAATATTTAATTATTAAAAAACAACCCAAATA
1 A--T-ATT-TA---A-TTATTTAATTAAATATTTAATTATT-AAAAACAACCCAAATA
9404373 ATTTTGATGA
Statistics
Matches: 473, Mismatches: 9, Indels: 46
0.90 0.02 0.09
Matches are distributed among these distances:
144 49 0.10
145 35 0.07
146 2 0.00
148 6 0.01
149 10 0.02
150 2 0.00
151 1 0.00
152 1 0.00
153 121 0.26
154 145 0.31
156 19 0.04
157 38 0.08
158 2 0.00
161 1 0.00
162 25 0.05
163 16 0.03
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.42
Consensus pattern (154 bp):
ATATTTAATTATTTAATTAAATATTTAATTATTAAAAACAACCCAAATACTTAATTATTTAATTA
GTTAAATCAACCCAATTAATTAATTAATTAATTAATTAATTATATAAATATTAAAAACAACCCAA
ATATTTAATTCAAAATATTTAATT
Found at i:9404248 original size:4 final size:4
Alignment explanation
Indices: 9404239--9404263 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
9404229 AAATCAACCC
9404239 AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT A
9404264 TTTATTTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:9404317 original size:22 final size:20
Alignment explanation
Indices: 9404292--9404355 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 20
9404282 ACAACCCAAA
9404292 TATTTAATTCAAAATATTTAAT
1 TATTTAATT--AAATATTTAAT
*
9404314 TATTTAATT--ATATTTACT
1 TATTTAATTAAATATTTAAT
9404332 TATTTAATTAAATATTTAAT
1 TATTTAATTAAATATTTAAT
9404352 TATT
1 TATT
9404356 AAAAAACAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 17 0.45
20 12 0.32
22 9 0.24
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTTAATTAAATATTTAAT
Found at i:9410553 original size:86 final size:85
Alignment explanation
Indices: 9410401--9410671 Score: 289
Period size: 86 Copynumber: 3.2 Consensus size: 85
9410391 ATCTGTTAAT
* * * * * * *
9410401 TTTAGCGGCGTTTGTGGAAAAAACGCCGTTAAAGAACACT-AT-TTATAGCGGCATTTCTGGAG-
1 TTTAGCGGCGTTTGTAGAAAAAGCGCCGCTAAAGAACA-TGGTCTT-TAGAGGC-GTT-TGTAGC
*
9410463 TAAGCGTCGCTAAAGACCATGTTC
62 TAAGCGCCGCTAAAGACCATGTTC
* * *
9410487 TTTAGCGGCGTTTGTTGAAAAAAGCGCCGCTAAAG-ACTATGTTCTTTAGAGGCGTTTGTATCTA
1 TTTAGCGGCGTTTGTAG-AAAAAGCGCCGCTAAAGAAC-ATGGTCTTTAGAGGCGTTTGTAGCTA
* * *
9410551 AGCACCGCTAAAGAACATGGTC
64 AGCGCCGCTAAAGACCATGTTC
* * *
9410573 TTTAGCGGCGTTTGTAGAAGAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTGTAGGTAAA
1 TTTAGCGGCGTTTGTAGAAAAAGCGCCGCTAAAGAACATGGTCTTTAGAGGCGTTTGTAGCT-AA
9410638 GCGCCGCTAAAGACCATGTTC
65 GCGCCGCTAAAGACCATGTTC
*
9410659 TTTTGCGGCGTTT
1 TTTAGCGGCGTTT
9410672 TTTTTTTATA
Statistics
Matches: 156, Mismatches: 22, Indels: 14
0.81 0.11 0.07
Matches are distributed among these distances:
85 40 0.26
86 91 0.58
87 23 0.15
88 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (85 bp):
TTTAGCGGCGTTTGTAGAAAAAGCGCCGCTAAAGAACATGGTCTTTAGAGGCGTTTGTAGCTAAG
CGCCGCTAAAGACCATGTTC
Found at i:9410661 original size:43 final size:43
Alignment explanation
Indices: 9410401--9410671 Score: 255
Period size: 43 Copynumber: 6.3 Consensus size: 43
9410391 ATCTGTTAAT
* * * *
9410401 TTTAGCGGCGTTTGT-GGAAAAAACGCCGTTAAAGAACACTATT-
1 TTTAGCGGCGTTTGTAGG-AAAAGCGCCGCTAAAGACCA-TGTTC
* * * * *
9410444 TATAGCGGCATTTCT-GGAGTAAGCGTCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTAGGA-AAAGCGCCGCTAAAGACCATGTTC
* * *
9410487 TTTAGCGGCGTTTGTTGAAAAAAGCGCCGCTAAAGACTATGTTC
1 TTTAGCGGCGTTTGTAG-GAAAAGCGCCGCTAAAGACCATGTTC
* *** * * *
9410531 TTTAGAGGCGTTTGTA-TCTAAGCACCGCTAAAGAACATGGTC
1 TTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTC
* *
9410573 TTTAGCGGCGTTTGTA-GAAGAAGCGCCGCTAAAGAACATGGTC
1 TTTAGCGGCGTTTGTAGGAA-AAGCGCCGCTAAAGACCATGTTC
*
9410616 TTTAGCGGCGTTTGTAGGTAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTC
*
9410659 TTTTGCGGCGTTT
1 TTTAGCGGCGTTT
9410672 TTTTTTTATA
Statistics
Matches: 188, Mismatches: 34, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
42 38 0.20
43 111 0.59
44 38 0.20
45 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTC
Found at i:9413252 original size:3 final size:3
Alignment explanation
Indices: 9413244--9413297 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
9413234 TATATCCCAA
9413244 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9413292 AA- AAT A
1 AAT AAT A
9413298 GAATAGAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:9414353 original size:7 final size:7
Alignment explanation
Indices: 9414330--9414458 Score: 95
Period size: 7 Copynumber: 19.0 Consensus size: 7
9414320 TTCGAAAAAA
9414330 GTCAACG
1 GTCAACG
*
9414337 GTCAA-A
1 GTCAACG
9414343 GTCAACG
1 GTCAACG
**
9414350 GTCAGTG
1 GTCAACG
9414357 GTCAACG
1 GTCAACG
**
9414364 GTCAGTG
1 GTCAACG
9414371 GTCAACG
1 GTCAACG
*
9414378 GTCAA-A
1 GTCAACG
*
9414384 GTCAACA
1 GTCAACG
*
9414391 GTCAATG
1 GTCAACG
*
9414398 GTCAA-A
1 GTCAACG
9414404 GTCAACG
1 GTCAACG
**
9414411 GTCAGTG
1 GTCAACG
9414418 GTCAACG
1 GTCAACG
9414425 GTCAACG
1 GTCAACG
* *
9414432 ATCAA-A
1 GTCAACG
9414438 GTCAACG
1 GTCAACG
**
9414445 GTCAGTG
1 GTCAACG
9414452 GTCAACG
1 GTCAACG
9414459 TCGGTCAATG
Statistics
Matches: 91, Mismatches: 27, Indels: 8
0.72 0.21 0.06
Matches are distributed among these distances:
6 19 0.21
7 72 0.79
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:9414359 original size:20 final size:20
Alignment explanation
Indices: 9414336--9414456 Score: 103
Period size: 20 Copynumber: 6.3 Consensus size: 20
9414326 AAAAGTCAAC
9414336 GGTCAAAGTCAACGGTCAGT
1 GGTCAAAGTCAACGGTCAGT
* ** **
9414356 GGTCAACGGTCAGTGGTCAAC
1 GGTCAA-AGTCAACGGTCAGT
* *
9414377 GGTCAAAGTCAACAGTCAAT
1 GGTCAAAGTCAACGGTCAGT
9414397 GGTCAAAGTCAACGGTCAGT
1 GGTCAAAGTCAACGGTCAGT
*
9414417 GGTCAACGGTCAAC-G--A--
1 GGTCAA-AGTCAACGGTCAGT
9414433 --TCAAAGTCAACGGTCAGT
1 GGTCAAAGTCAACGGTCAGT
9414451 GGTCAA
1 GGTCAA
9414457 CGTCGGTCAA
Statistics
Matches: 78, Mismatches: 14, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
13 6 0.08
14 5 0.06
16 1 0.01
18 1 0.01
20 44 0.56
21 21 0.27
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.19
Consensus pattern (20 bp):
GGTCAAAGTCAACGGTCAGT
Found at i:9414411 original size:47 final size:47
Alignment explanation
Indices: 9414338--9414448 Score: 161
Period size: 47 Copynumber: 2.3 Consensus size: 47
9414328 AAGTCAACGG
**
9414338 TCAAAGTCAACGGTCAGTGGTCAACGGTCAGTGGTCAACGGTCAAAG-
1 TCAAAGTCAACGGTCA-AAGTCAACGGTCAGTGGTCAACGGTCAAAGA
* *
9414385 TCAACAGTCAATGGTCAAAGTCAACGGTCAGTGGTCAACGGTCAACGA
1 TCAA-AGTCAACGGTCAAAGTCAACGGTCAGTGGTCAACGGTCAAAGA
9414433 TCAAAGTCAACGGTCA
1 TCAAAGTCAACGGTCA
9414449 GTGGTCAACG
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
47 42 0.74
48 15 0.26
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (47 bp):
TCAAAGTCAACGGTCAAAGTCAACGGTCAGTGGTCAACGGTCAAAGA
Found at i:9414458 original size:34 final size:34
Alignment explanation
Indices: 9414371--9414458 Score: 124
Period size: 34 Copynumber: 2.6 Consensus size: 34
9414361 ACGGTCAGTG
** * * *
9414371 GTCAACGGTCA-AAGTCAACAGTCAATGGTCAAA
1 GTCAACGGTCAGTGGTCAACGGTCAACGATCAAA
9414404 GTCAACGGTCAGTGGTCAACGGTCAACGATCAAA
1 GTCAACGGTCAGTGGTCAACGGTCAACGATCAAA
9414438 GTCAACGGTCAGTGGTCAACG
1 GTCAACGGTCAGTGGTCAACG
9414459 TCGGTCAATG
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 11 0.22
34 38 0.78
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (34 bp):
GTCAACGGTCAGTGGTCAACGGTCAACGATCAAA
Found at i:9414477 original size:54 final size:52
Alignment explanation
Indices: 9414356--9414465 Score: 123
Period size: 54 Copynumber: 2.1 Consensus size: 52
9414346 AACGGTCAGT
* ** *
9414356 GGTCAACGGTCAGTGGTCAACGGTCAAAGTCAACAGTCAATGGTCAAAGTCAAC
1 GGTCAGCGGTCAACGGTCAACGATCAAAGTCAACAGTCAATGGTCAAAGT--AC
* * * *
9414410 GGTCAGTGGTCAACGGTCAACGATCAAAGTCAACGGTCAGTGGTCAACGT-C
1 GGTCAGCGGTCAACGGTCAACGATCAAAGTCAACAGTCAATGGTCAAAGTAC
9414461 GGTCA
1 GGTCA
9414466 ATGCCGGTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
51 6 0.12
54 42 0.88
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.19
Consensus pattern (52 bp):
GGTCAGCGGTCAACGGTCAACGATCAAAGTCAACAGTCAATGGTCAAAGTAC
Found at i:9414531 original size:14 final size:15
Alignment explanation
Indices: 9414512--9414546 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
9414502 TGGGTTGGAC
9414512 TTGGTTCAATT-GGT
1 TTGGTTCAATTGGGT
9414526 TTGGTTCAATTGGGT
1 TTGGTTCAATTGGGT
9414541 TTGGTT
1 TTGGTT
9414547 AGGTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.11, C:0.06, G:0.31, T:0.51
Consensus pattern (15 bp):
TTGGTTCAATTGGGT
Found at i:9414562 original size:21 final size:21
Alignment explanation
Indices: 9414536--9414579 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
9414526 TTGGTTCAAT
9414536 TGGGTTTGGTTAGGTTTTAAA
1 TGGGTTTGGTTAGGTTTTAAA
*
9414557 TGGGTTTGGTTTGGTTTTAAA
1 TGGGTTTGGTTAGGTTTTAAA
9414578 TG
1 TG
9414580 AATGTGGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (21 bp):
TGGGTTTGGTTAGGTTTTAAA
Found at i:9414609 original size:22 final size:23
Alignment explanation
Indices: 9414543--9414609 Score: 79
Period size: 21 Copynumber: 3.1 Consensus size: 23
9414533 AATTGGGTTT
* *
9414543 GGTTAGGTTTTAAATG-GGTTT-
1 GGTTTGGTTTTAAATGAGATTTG
*
9414564 GGTTTGGTTTTAAATGA-ATGTG
1 GGTTTGGTTTTAAATGAGATTTG
9414586 GGTTTGG-TTTAAATGAGATTTG
1 GGTTTGGTTTTAAATGAGATTTG
9414608 GG
1 GG
9414610 CTTGATGGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
21 26 0.67
22 13 0.33
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (23 bp):
GGTTTGGTTTTAAATGAGATTTG
Found at i:9415094 original size:10 final size:10
Alignment explanation
Indices: 9415079--9415112 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
9415069 AAGGCAAGGA
9415079 AAAAAGAAAG
1 AAAAAGAAAG
9415089 AAAAAG-AA-
1 AAAAAGAAAG
9415097 AAAAAGAAAG
1 AAAAAGAAAG
9415107 AAAAAG
1 AAAAAG
9415113 GTTTGGGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 6 0.27
9 4 0.18
10 12 0.55
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:9415101 original size:18 final size:18
Alignment explanation
Indices: 9415078--9415112 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
9415068 TAAGGCAAGG
9415078 AAAAAAGAAAGAAAAAGA
1 AAAAAAGAAAGAAAAAGA
9415096 AAAAAAGAAAGAAAAAG
1 AAAAAAGAAAGAAAAAG
9415113 GTTTGGGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAGAAAAAGA
Found at i:9417506 original size:17 final size:17
Alignment explanation
Indices: 9417484--9417517 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
9417474 TCATTTACGT
9417484 GGCAAGTTAACTAGCCA
1 GGCAAGTTAACTAGCCA
9417501 GGCAAGTTAACTAGCCA
1 GGCAAGTTAACTAGCCA
9417518 CATCAACTAG
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:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (17 bp):
GGCAAGTTAACTAGCCA
Found at i:9418229 original size:3 final size:3
Alignment explanation
Indices: 9418223--9418275 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
9418213 AATACATTTA
*
9418223 ATT ATT ATT ATT ATT ATT ATT ATT ATT -TG A-T ATT ATAT AGTT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T A-TT ATT
9418267 ATT ATT ATT
1 ATT ATT ATT
9418276 TGATTTTAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
2 4 0.09
3 35 0.81
4 3 0.07
5 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:9418450 original size:23 final size:24
Alignment explanation
Indices: 9418408--9418461 Score: 85
Period size: 23 Copynumber: 2.3 Consensus size: 24
9418398 TATTCTTTCA
9418408 ATTATTTTCAAAATTAATAAATAT
1 ATTATTTTCAAAATTAATAAATAT
9418432 A-TATTTT-AAAATTATATAAATAT
1 ATTATTTTCAAAATTA-ATAAATAT
9418455 ATTATTT
1 ATTATTT
9418462 AATAAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.25
23 15 0.54
24 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTATTTTCAAAATTAATAAATAT
Found at i:9419494 original size:21 final size:22
Alignment explanation
Indices: 9419470--9419515 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
9419460 AAGTGTTACC
* *
9419470 AAATTTA-TTGCATTAAATTTA
1 AAATTTAGTTGCAGTAAATTGA
*
9419491 AAATTTAGTTGGAGTAAATTGA
1 AAATTTAGTTGCAGTAAATTGA
9419513 AAA
1 AAA
9419516 CTTTTGAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.46, C:0.02, G:0.13, T:0.39
Consensus pattern (22 bp):
AAATTTAGTTGCAGTAAATTGA
Found at i:9422003 original size:6 final size:6
Alignment explanation
Indices: 9421994--9422026 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
9421984 ATAGTATACA
9421994 CACACG CACACG CACACG CACACG CACACG CAC
1 CACACG CACACG CACACG CACACG CACACG CAC
9422027 TTAGTTTAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
CACACG
Found at i:9426226 original size:21 final size:22
Alignment explanation
Indices: 9426202--9426243 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
9426192 TTTTAATTAG
9426202 ATATTAT-TTATTACAAAATAT
1 ATATTATCTTATTACAAAATAT
*
9426223 ATATTATCTTATTATAAAATA
1 ATATTATCTTATTACAAAATA
9426244 AACTTCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATTATCTTATTACAAAATAT
Found at i:9427871 original size:3 final size:3
Alignment explanation
Indices: 9427863--9427902 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
9427853 AAATACTTTC
9427863 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9427903 TTAATAAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:9428218 original size:34 final size:35
Alignment explanation
Indices: 9428155--9428220 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 35
9428145 TGTACAAATC
* *
9428155 CAAACCCAAAAAACAAAATCTTAACTCTCATAATG
1 CAAACCCAAAAAACAAAACCCTAACTCTCATAATG
* *
9428190 CAAACCC-AAAAATAAAACCCTAATTCTCATA
1 CAAACCCAAAAAACAAAACCCTAACTCTCATA
9428221 GAGTTCTCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 20 0.74
35 7 0.26
ACGTcount: A:0.52, C:0.27, G:0.02, T:0.20
Consensus pattern (35 bp):
CAAACCCAAAAAACAAAACCCTAACTCTCATAATG
Found at i:9430567 original size:17 final size:18
Alignment explanation
Indices: 9430545--9430578 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
9430535 TAAGGGTCAA
9430545 TATATAATT-TTATTTTT
1 TATATAATTGTTATTTTT
*
9430562 TATATATTTGTTATTTT
1 TATATAATTGTTATTTT
9430579 AGAATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
TATATAATTGTTATTTTT
Found at i:9431033 original size:26 final size:27
Alignment explanation
Indices: 9430993--9431051 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
9430983 TTTATAAAAT
9430993 TTTAAATTAATAATAAT-AAAATTATAA
1 TTTAAATTAATAATAATAAAAATT-TAA
*
9431020 TTTAATTTAA-AATAATAAAAATTTAA
1 TTTAAATTAATAATAATAAAAATTTAA
9431046 TTTAAA
1 TTTAAA
9431052 CCTATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
TTTAAATTAATAATAATAAAAATTTAA
Found at i:9431044 original size:21 final size:21
Alignment explanation
Indices: 9431018--9431064 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
9431008 ATAAAATTAT
9431018 AATTTAATTTAAA-ATAATAAA
1 AATTTAATTTAAACAT-ATAAA
*
9431039 AATTTAATTTAAACCTATAAA
1 AATTTAATTTAAACATATAAA
9431060 AATTT
1 AATTT
9431065 TCAAGAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTTAATTTAAACATATAAA
Found at i:9436320 original size:43 final size:43
Alignment explanation
Indices: 9436259--9436452 Score: 250
Period size: 43 Copynumber: 4.5 Consensus size: 43
9436249 AAAAAATGCT
*
9436259 GCTAAAGAACATGTTCTTTAGCGGCGCTTACCA-CACAAACGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTT-CCACCACAAACGCC
* * *
9436302 GCTAAAGAACATGGTCTTTAGCGGCGCTTCTACCATAAACACC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTCCACCACAAACGCC
* * * *
9436345 GTTAAAGAATATGGTCTTTAACAGCGCTTTCCA-CACAAACGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGC-TTCCACCACAAACGCC
*
9436388 GCTAAAGAACATGGTCTTTAGCGGCGCTTCTACCACAAACGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTCCACCACAAACGCC
*
9436431 GCTAAAGACCAT-GTGCTTTAGC
1 GCTAAAGAACATGGT-CTTTAGC
9436453 AAACGCCGCT
Statistics
Matches: 130, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
42 8 0.06
43 118 0.91
44 4 0.03
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
GCTAAAGAACATGGTCTTTAGCGGCGCTTCCACCACAAACGCC
Found at i:9436406 original size:86 final size:86
Alignment explanation
Indices: 9436259--9436443 Score: 289
Period size: 86 Copynumber: 2.2 Consensus size: 86
9436249 AAAAAATGCT
* * *
9436259 GCTAAAGAACATGTTCTTTAGCGGCGCTTACCACACAAACGCCGCTAAAGAACATGGTCTTTAGC
1 GCTAAAGAACATGGTCTTTAACAGCGCTTACCACACAAACGCCGCTAAAGAACATGGTCTTTAGC
*
9436324 GGCGCTTCTACCATAAACACC
66 GGCGCTTCTACCACAAACACC
* * *
9436345 GTTAAAGAATATGGTCTTTAACAGCGCTTTCCACACAAACGCCGCTAAAGAACATGGTCTTTAGC
1 GCTAAAGAACATGGTCTTTAACAGCGCTTACCACACAAACGCCGCTAAAGAACATGGTCTTTAGC
*
9436410 GGCGCTTCTACCACAAACGCC
66 GGCGCTTCTACCACAAACACC
*
9436431 GCTAAAGACCATG
1 GCTAAAGAACATG
9436444 TGCTTTAGCA
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 88 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (86 bp):
GCTAAAGAACATGGTCTTTAACAGCGCTTACCACACAAACGCCGCTAAAGAACATGGTCTTTAGC
GGCGCTTCTACCACAAACACC
Found at i:9436472 original size:29 final size:29
Alignment explanation
Indices: 9436423--9436480 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
9436413 GCTTCTACCA
9436423 CAAACGCCGCTAAAGACCAT-GTGCTTTAG
1 CAAACGCCGCTAAAGACCATGGT-CTTTAG
9436452 CAAACGCCGCTAAAG-CACATGGTCTTTAG
1 CAAACGCCGCTAAAGAC-CATGGTCTTTAG
9436481 TTGCGCTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 1 0.04
29 24 0.89
30 2 0.07
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.21
Consensus pattern (29 bp):
CAAACGCCGCTAAAGACCATGGTCTTTAG
Found at i:9436497 original size:72 final size:72
Alignment explanation
Indices: 9436380--9436526 Score: 233
Period size: 72 Copynumber: 2.0 Consensus size: 72
9436370 GCTTTCCACA
*
9436380 CAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCTACCACAAACGCCGCTAAAGACCAT-G
1 CAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCTACCACAAACGCCGCTAAAGAACATGG
9436444 TGCTTTAG
66 T-CTTTAG
* ** *
9436452 CAAACGCCGCTAAAGCACATGGTCTTTAGTTGCGCTTCTACCACAAACGCCTCTAAAGAACATGG
1 CAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCTACCACAAACGCCGCTAAAGAACATGG
9436517 TCTTTAG
66 TCTTTAG
9436524 CAA
1 CAA
9436527 CGCTTTCCAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
72 67 0.97
73 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (72 bp):
CAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCTACCACAAACGCCGCTAAAGAACATGG
TCTTTAG
Found at i:9436515 original size:43 final size:42
Alignment explanation
Indices: 9436452--9436639 Score: 164
Period size: 43 Copynumber: 4.4 Consensus size: 42
9436442 TGTGCTTTAG
* **
9436452 CAAACGCCGCTAAAGCACATGGTCTTTAGTTGCGCTTCTACCA
1 CAAACGCCGCTAAAGAACATGGTCTTTAGCAGCGCTT-TACCA
* *
9436495 CAAACGCCTCTAAAGAACATGGTCTTTAGCAACGCTTT-CCATA
1 CAAACGCCGCTAAAGAACATGGTCTTTAGCAGCGCTTTACC--A
* * *
9436538 CAAACGCCGCTGAAGAACATGATCTTTAGCGGCGCTTTTACCCA
1 CAAACGCCGCTAAAGAACATGGTCTTTAGCAGCGC-TTTA-CCA
* * * * * *
9436582 CAAACGCCGCTATAGATA-ATGTTCTTCAGCGGCGTTTTTTCCA
1 CAAACGCCGCTAAAGA-ACATGGTCTTTAGCAGCG-CTTTACCA
*
9436625 TAAACGCCGCTAAAG
1 CAAACGCCGCTAAAG
9436640 CAAAACAGAT
Statistics
Matches: 120, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 79 0.66
44 35 0.29
45 1 0.01
46 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (42 bp):
CAAACGCCGCTAAAGAACATGGTCTTTAGCAGCGCTTTACCA
Found at i:9436634 original size:87 final size:85
Alignment explanation
Indices: 9436453--9436639 Score: 198
Period size: 87 Copynumber: 2.2 Consensus size: 85
9436443 GTGCTTTAGC
* * ** *
9436453 AAACGCCGCTAAAGCACATGGTCTTTAGTTGCGCTTCTACCACAAACGCCTCTAAAGAACATGGT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTCTACCACAAACGCCGCTAAAGAACATGGT
*
9436518 CTTTAGCAACGCTTTCCATA
66 CTTCAGCAACGCTTTCCATA
* * *
9436538 CAAACGCCGCTGAAGAACATGATCTTTAGCGGCGCTTTTACCCACAAACGCCGCTATAGATA-AT
1 -AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTCTA-CCACAAACGCCGCTAAAGA-ACAT
* ** *
9436602 GTTCTTCAGCGGCGTTTTTTCCAT-
63 GGTCTTCAGCAACG--CTTTCCATA
9436626 AAACGCCGCTAAAG
1 AAACGCCGCTAAAG
9436640 CAAAACAGAT
Statistics
Matches: 83, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
86 33 0.40
87 42 0.51
88 1 0.01
89 7 0.08
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (85 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTCTACCACAAACGCCGCTAAAGAACATGGT
CTTCAGCAACGCTTTCCATA
Found at i:9438463 original size:32 final size:32
Alignment explanation
Indices: 9438425--9438490 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
9438415 ATTTAAATTT
*
9438425 AAAAATATATATTAGTGACAACATTTTACTTA
1 AAAAATATATATTAATGACAACATTTTACTTA
9438457 AAAAATATATATTAATGACAACATTTTACTTA
1 AAAAATATATATTAATGACAACATTTTACTTA
9438489 AA
1 AA
9438491 TATTTAGGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (32 bp):
AAAAATATATATTAATGACAACATTTTACTTA
Found at i:9438590 original size:8 final size:8
Alignment explanation
Indices: 9438579--9438670 Score: 54
Period size: 8 Copynumber: 12.2 Consensus size: 8
9438569 ATTAAATATT
9438579 TAATTAAA
1 TAATTAAA
9438587 TAATTAAA
1 TAATTAAA
**
9438595 T-ATTTTA
1 TAATTAAA
9438602 -AATTAAA
1 TAATTAAA
* *
9438609 TATTTAAT
1 TAATTAAA
*
9438617 TAACT-AA
1 TAATTAAA
* **
9438624 TATTGTTTA
1 TAAT-TAAA
9438633 TAATTAAA
1 TAATTAAA
9438641 T-ATT---
1 TAATTAAA
9438645 TAATTAAA
1 TAATTAAA
9438653 TAATTAAA
1 TAATTAAA
9438661 TAATTAAA
1 TAATTAAA
9438669 TA
1 TA
9438671 TAATTATTTA
Statistics
Matches: 61, Mismatches: 15, Indels: 16
0.66 0.16 0.17
Matches are distributed among these distances:
4 1 0.02
5 3 0.05
7 14 0.23
8 39 0.64
9 4 0.07
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (8 bp):
TAATTAAA
Found at i:9438652 original size:66 final size:61
Alignment explanation
Indices: 9438565--9438716 Score: 209
Period size: 66 Copynumber: 2.4 Consensus size: 61
9438555 TATAATTAAA
*
9438565 TATAATTAAATATTTAATTAAATAATTAAATATTTTAAAT-TAAATATTTAATTAACTAATATTG
1 TATAATTAAATATTTAATTAAATAATTAAATA-ATTAAATATAAATATTTAATT-A--AATA-T-
9438629 TT
60 TT
*
9438631 TATAATTAAATATTTAATTAAATAATTAAATAATTAAATATAATTATTTAATTAAATATTT
1 TATAATTAAATATTTAATTAAATAATTAAATAATTAAATATAAATATTTAATTAAATATTT
*
9438692 TA-AATTAAATATTTAATTAACTAAT
1 TATAATTAAATATTTAATTAAATAAT
9438717 ACTGTTTATA
Statistics
Matches: 82, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
60 22 0.27
61 4 0.05
62 1 0.01
63 4 0.05
65 7 0.09
66 44 0.54
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (61 bp):
TATAATTAAATATTTAATTAAATAATTAAATAATTAAATATAAATATTTAATTAAATATTT
Found at i:9438671 original size:60 final size:59
Alignment explanation
Indices: 9438602--9438716 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 59
9438592 AAATATTTTA
9438602 AATTAAATAT-TTAATTAACT-AATATTGTTTATAATTAAATATTTAATTAAATAATTAAAT
1 AATTAAATATATTAATTAACTAAATA-T-TTTA-AATTAAATATTTAATTAAATAATTAAAT
* * *
9438662 AATTAAATATAATTATTTAATTAAATATTTTAAATTAAATATTTAATTAACTAAT
1 AATTAAATAT-ATTAATTAACTAAATATTTTAAATTAAATATTTAATTAAATAAT
9438717 ACTGTTTATA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
60 32 0.65
61 4 0.08
62 9 0.18
63 4 0.08
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (59 bp):
AATTAAATATATTAATTAACTAAATATTTTAAATTAAATATTTAATTAAATAATTAAAT
Found at i:9438682 original size:26 final size:26
Alignment explanation
Indices: 9438632--9438716 Score: 91
Period size: 26 Copynumber: 3.2 Consensus size: 26
9438622 AATATTGTTT
**
9438632 ATAATTAAATATTTAATTAAATAATTAA
1 ATAATTAAATA--TAATTATTTAATTAA
9438660 ATAATTAAATATAATTATTTAATTAA
1 ATAATTAAATATAATTATTTAATTAA
* *
9438686 ATATTTTAAAT-TAAATATTTAATTAA
1 ATA-ATTAAATATAATTATTTAATTAA
*
9438712 CTAAT
1 ATAAT
9438717 ACTGTTTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
25 1 0.02
26 32 0.64
27 6 0.12
28 11 0.22
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
ATAATTAAATATAATTATTTAATTAA
Found at i:9438688 original size:92 final size:95
Alignment explanation
Indices: 9438556--9438732 Score: 297
Period size: 92 Copynumber: 1.9 Consensus size: 95
9438546 ATTGTTTTTT
9438556 ATAATTAAATATAATTAAATATTTAATTAAATAATTAAATATTTTAAATTAAATATTTAATTAAC
1 ATAATTAAATATAATTAAATA-TTAATTAAATAATTAAATATTTTAAATTAAATATTTAATTAAC
*
9438621 TAATATTGTTTATAATTAAATATTTAATTAA
65 TAATACTGTTTATAATTAAATATTTAATTAA
**
9438652 ATAATT-AA-ATAATTAAATA-TAATTATTTAATTAAATATTTTAAATTAAATATTTAATTAACT
1 ATAATTAAATATAATTAAATATTAATTAAATAATTAAATATTTTAAATTAAATATTTAATTAACT
9438714 AATACTGTTTATAATTAAA
66 AATACTGTTTATAATTAAA
9438733 AAAATTTGTG
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
92 59 0.76
94 11 0.14
95 2 0.03
96 6 0.08
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (95 bp):
ATAATTAAATATAATTAAATATTAATTAAATAATTAAATATTTTAAATTAAATATTTAATTAACT
AATACTGTTTATAATTAAATATTTAATTAA
Found at i:9438699 original size:18 final size:18
Alignment explanation
Indices: 9438644--9438699 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
9438634 AATTAAATAT
9438644 TTAATTAAATA-ATTAAA
1 TTAATTAAATATATTAAA
*
9438661 -TAATTAAATATAATT-AT
1 TTAATTAAATAT-ATTAAA
*
9438678 TTAATTAAATATTTTAAA
1 TTAATTAAATATATTAAA
9438696 TTAA
1 TTAA
9438700 ATATTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 10 0.31
17 3 0.09
18 19 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAATTAAATATATTAAA
Found at i:9451167 original size:50 final size:50
Alignment explanation
Indices: 9451083--9451212 Score: 161
Period size: 50 Copynumber: 2.6 Consensus size: 50
9451073 GATAAAACGA
** * * * * *
9451083 CAAATCTTTTACACCTAAAGTTATGGAGGTGCAGATTGAAACCGCAATGG
1 CAAATCTCATACACCTAAAGTTGTAGAGGGGCAGAATGAAACCACAATGG
* *
9451133 CAAATCTCATACACCTAAAGTTGTAGAGGGGCAGAATGAAGCCACAATTG
1 CAAATCTCATACACCTAAAGTTGTAGAGGGGCAGAATGAAACCACAATGG
* *
9451183 CAAATCTCATTCACCTAAAGCTGTAGAGGG
1 CAAATCTCATACACCTAAAGTTGTAGAGGG
9451213 ACAAATTAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (50 bp):
CAAATCTCATACACCTAAAGTTGTAGAGGGGCAGAATGAAACCACAATGG
Found at i:9451239 original size:50 final size:50
Alignment explanation
Indices: 9451127--9451229 Score: 136
Period size: 50 Copynumber: 2.1 Consensus size: 50
9451117 ATTGAAACCG
* * *
9451127 CAATGGCAAATCTCATACACCTAAAGTTGTAGAGGGGCAGAATGAAGCCA
1 CAATGGCAAATCTCATACACCTAAAGCTGTAGAGGGACAGAATAAAGCCA
* * *
9451177 CAATTGCAAATCTCATTCACCTAAAGCTGTAGAGGGACA-AATTAAAGTCA
1 CAATGGCAAATCTCATACACCTAAAGCTGTAGAGGGACAGAA-TAAAGCCA
9451227 CAA
1 CAA
9451230 GGACGAATCT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 2 0.04
50 44 0.96
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (50 bp):
CAATGGCAAATCTCATACACCTAAAGCTGTAGAGGGACAGAATAAAGCCA
Found at i:9451321 original size:40 final size:40
Alignment explanation
Indices: 9451277--9451611 Score: 347
Period size: 40 Copynumber: 8.4 Consensus size: 40
9451267 AGTTGCAACC
* * *
9451277 TCCAATCTCTTACCCTAACCAGAGGGCAAATTGAAGACAA
1 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
**
9451317 TCCAATCTTTTACCCCGATCATG-GGGCAGATTGAA-AGCAA
1 TCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAGA-CAA
*
9451357 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAA
1 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
* ** *
9451397 TCTAATCTTTTACCCCGATCATG-GGGTAGATTGAA-AGCAA
1 TCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAGA-CAA
* * *
9451437 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCCCA
1 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
** * ** * * *
9451477 TCTGATCTCTTACCCCGATCATG-GGGCAAATTGAAAACTA
1 TCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAGACAA
* * * * *
9451517 TCCAATCTATTACCCAAATTAGAGGGTAGATTGAAGACCA
1 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
*
9451557 TCCAATCTTTTACCCTAATCAGAGGGCAAATTGAAGACAA
1 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
9451597 TCCAATCTTTTACCC
1 TCCAATCTTTTACCC
9451612 CTAAAGTTAT
Statistics
Matches: 239, Mismatches: 46, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
39 5 0.02
40 230 0.96
41 4 0.02
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (40 bp):
TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
Found at i:9451407 original size:80 final size:80
Alignment explanation
Indices: 9451277--9451611 Score: 449
Period size: 80 Copynumber: 4.2 Consensus size: 80
9451267 AGTTGCAACC
* *
9451277 TCCAATCTCTTACCCTAACCAGAGGGCAAATTGAAGACAATCCAATCTTTTACCCCGATCATGGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCCGATCATGGG
*
9451342 GCAGATTGAAAGCAA
66 GCAAATTGAAAGCAA
*
9451357 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCTAATCTTTTACCCCGATCATGGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCCGATCATGGG
* *
9451422 GTAGATTGAAAGCAA
66 GCAAATTGAAAGCAA
* * ** *
9451437 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCCCATCTGATCTCTTACCCCGATCATGGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCCGATCATGGG
* *
9451502 GCAAATTGAAAACTA
66 GCAAATTGAAAGCAA
* * ** * * **
9451517 TCCAATCTATTACCCAAATTAGAGGGTAGATTGAAGACCATCCAATCTTTTACCCTAATCA-GAG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCCGATCATG-G
9451581 GGCAAATTG-AAGACAA
65 GGCAAATTGAAAG-CAA
9451597 TCCAATCTTTTACCC
1 TCCAATCTTTTACCC
9451612 CTAAAGTTAT
Statistics
Matches: 227, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
79 3 0.01
80 224 0.99
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (80 bp):
TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCCGATCATGGG
GCAAATTGAAAGCAA
Found at i:9453403 original size:30 final size:30
Alignment explanation
Indices: 9453347--9453532 Score: 216
Period size: 30 Copynumber: 6.1 Consensus size: 30
9453337 TTATTTTTTG
* *
9453347 CCCCTCAAAGTTTTCAAAACTTCAAATTTGA
1 CCCCT-AAAGTTTTCAAAAATTCAAATTTAA
* * * *
9453378 CCCCTAAATTTTTTAAAAATGCAAATTTCA
1 CCCCTAAAGTTTTCAAAAATTCAAATTTAA
9453408 CCACC-AAA-TTTTCCAAAAATTCAAATTTAA
1 CC-CCTAAAGTTTT-CAAAAATTCAAATTTAA
* *
9453438 TCCCTAAAGTTTTCAAACATTCAAATTTAA
1 CCCCTAAAGTTTTCAAAAATTCAAATTTAA
9453468 CCCCCTAAA-TTTTCCAAAAATTCAAATTTAA
1 -CCCCTAAAGTTTT-CAAAAATTCAAATTTAA
* *
9453499 CCCCTAAAGTTTTCAAAAATTAAAATCTAA
1 CCCCTAAAGTTTTCAAAAATTCAAATTTAA
9453529 CCCC
1 CCCC
9453533 ATTTTAATAT
Statistics
Matches: 134, Mismatches: 14, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
29 6 0.04
30 90 0.67
31 38 0.28
ACGTcount: A:0.41, C:0.24, G:0.03, T:0.32
Consensus pattern (30 bp):
CCCCTAAAGTTTTCAAAAATTCAAATTTAA
Found at i:9453495 original size:61 final size:61
Alignment explanation
Indices: 9453347--9453532 Score: 241
Period size: 61 Copynumber: 3.0 Consensus size: 61
9453337 TTATTTTTTG
* * * * * *
9453347 CCCCTCAAAGTTTT-CAAAACTTCAAATTTGACCCCTAAATTTTTTAAAAATGCAAATTTCAC
1 CCCCT-AAA-TTTTCCAAAAATTCAAATTTAACCCCTAAAGTTTTCAAAAATTCAAATTTAAC
* * *
9453409 CACC-AAATTTTCCAAAAATTCAAATTTAATCCCTAAAGTTTTCAAACATTCAAATTTAAC
1 CCCCTAAATTTTCCAAAAATTCAAATTTAACCCCTAAAGTTTTCAAAAATTCAAATTTAAC
* *
9453469 CCCCTAAATTTTCCAAAAATTCAAATTTAACCCCTAAAGTTTTCAAAAATTAAAATCTAAC
1 CCCCTAAATTTTCCAAAAATTCAAATTTAACCCCTAAAGTTTTCAAAAATTCAAATTTAAC
9453530 CCC
1 CCC
9453533 ATTTTAATAT
Statistics
Matches: 108, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
59 4 0.04
60 46 0.43
61 55 0.51
62 3 0.03
ACGTcount: A:0.41, C:0.24, G:0.03, T:0.32
Consensus pattern (61 bp):
CCCCTAAATTTTCCAAAAATTCAAATTTAACCCCTAAAGTTTTCAAAAATTCAAATTTAAC
Found at i:9459699 original size:6 final size:6
Alignment explanation
Indices: 9459674--9459712 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
9459664 ACAATTCATA
* * *
9459674 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
9459713 ATTTTGCTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:9462163 original size:5 final size:5
Alignment explanation
Indices: 9462153--9462179 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
9462143 CGATGAAGTC
9462153 AACAA AACAA AACAA AACAA AACAA AA
1 AACAA AACAA AACAA AACAA AACAA AA
9462180 TTAACTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AACAA
Found at i:9463876 original size:41 final size:42
Alignment explanation
Indices: 9463786--9463971 Score: 225
Period size: 41 Copynumber: 4.5 Consensus size: 42
9463776 GCAGCGCTTT
* * *
9463786 CTAATAACCTGACCTTTAGCGGCGTTTATGATAAAAGCGCCG
1 CTAATGACCTGACCTTTAGCGGCGCTTATGGTAAAAGCGCCG
* * *
9463828 CTAATGACCTGACCTTTAGAGGTGCTTATGGT-AAAGCGTCG
1 CTAATGACCTGACCTTTAGCGGCGCTTATGGTAAAAGCGCCG
* * * *
9463869 CTAATGACATGACCTTTAGCGCCACTAAT-GTAAAAGCGCCG
1 CTAATGACCTGACCTTTAGCGGCGCTTATGGTAAAAGCGCCG
* * *
9463910 CTAATAACCTGACCTTTAGCGACGCTTATGGGAAAA-CGCCG
1 CTAATGACCTGACCTTTAGCGGCGCTTATGGTAAAAGCGCCG
*
9463951 CTAATGACCTAACCTTTAGCG
1 CTAATGACCTGACCTTTAGCG
9463972 ACAATTTTCC
Statistics
Matches: 121, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
40 2 0.02
41 87 0.72
42 32 0.26
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (42 bp):
CTAATGACCTGACCTTTAGCGGCGCTTATGGTAAAAGCGCCG
Found at i:9463988 original size:82 final size:82
Alignment explanation
Indices: 9463818--9463992 Score: 206
Period size: 82 Copynumber: 2.1 Consensus size: 82
9463808 CGTTTATGAT
* ** * * * *
9463818 AAAAGCGCCGCTAATGACCTGACCTTTAGAGGTGCTTATGGTAAAGCGTCGCTAATGACATGACC
1 AAAAGCGCCGCTAATAACCTGACCTTTAGAGACGCTTATGGGAAAACGCCGCTAATGACATAACC
* * **
9463883 TTTAGCGCCACTAATGT
66 TTTAGCGACAATAATCC
* *
9463900 AAAAGCGCCGCTAATAACCTGACCTTTAGCGACGCTTATGGGAAAACGCCGCTAATGACCTAACC
1 AAAAGCGCCGCTAATAACCTGACCTTTAGAGACGCTTATGGGAAAACGCCGCTAATGACATAACC
**
9463965 TTTAGCGACAATTTTCC
66 TTTAGCGACAATAATCC
*
9463982 ATAAGCGCCGC
1 AAAAGCGCCGC
9463993 AAAAGGTGAA
Statistics
Matches: 77, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.23
Consensus pattern (82 bp):
AAAAGCGCCGCTAATAACCTGACCTTTAGAGACGCTTATGGGAAAACGCCGCTAATGACATAACC
TTTAGCGACAATAATCC
Found at i:9463991 original size:41 final size:41
Alignment explanation
Indices: 9463786--9463992 Score: 101
Period size: 41 Copynumber: 5.0 Consensus size: 41
9463776 GCAGCGCTTT
* * ** **
9463786 CTAATAACCTGACCTTTAGCGGCGTTTATGATAAAAGCGCCG
1 CTAATAACCTAACCTTTAGCGACAATTATG-CCAAAGCGCCG
* * * **** ** *
9463828 CTAATGACCTGACCTTTAGAGGTGCTTATGGTAAAGCGTCG
1 CTAATAACCTAACCTTTAGCGACAATTATGCCAAAGCGCCG
* * * * * * **
9463869 CTAATGACATGACCTTTAGCGCCACTAATGTAAAAGCGCCG
1 CTAATAACCTAACCTTTAGCGACAATTATGCCAAAGCGCCG
* ** ** *
9463910 CTAATAACCTGACCTTTAGCGACGCTTATGGGAAAACGCCG
1 CTAATAACCTAACCTTTAGCGACAATTATGCCAAAGCGCCG
* *
9463951 CTAATGACCTAACCTTTAGCGACAATT-TTCCATAAGCGCCG
1 CTAATAACCTAACCTTTAGCGACAATTATGCCA-AAGCGCCG
9463992 C
1 C
9463993 AAAAGGTGAA
Statistics
Matches: 132, Mismatches: 32, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
40 2 0.02
41 104 0.79
42 26 0.20
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.25
Consensus pattern (41 bp):
CTAATAACCTAACCTTTAGCGACAATTATGCCAAAGCGCCG
Found at i:9470148 original size:22 final size:20
Alignment explanation
Indices: 9470113--9470163 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 20
9470103 CCCATTTGCT
9470113 AAAAATAAATAATT-TAGTCAAA
1 AAAAAT-AATAATTATA-T-AAA
9470135 AGAAAATAATAATTATATAAA
1 A-AAAATAATAATTATATAAA
9470156 AAAAATAA
1 AAAAATAA
9470164 AAACAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 7 0.26
21 4 0.15
22 9 0.33
23 7 0.26
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (20 bp):
AAAAATAATAATTATATAAA
Found at i:9474626 original size:31 final size:31
Alignment explanation
Indices: 9474591--9474683 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 31
9474581 ATTAAGATCT
9474591 AAATTAGGAAAAAGTATCAAGTTTAAGTACC
1 AAATTAGGAAAAAGTATCAAGTTTAAGTACC
* * *
9474622 AAATTGGGTAAAA--A--AAGTTTAGGTACC
1 AAATTAGGAAAAAGTATCAAGTTTAAGTACC
* * * *
9474649 AAATTAAGAAAAAGTGTCAAATTTAAATACC
1 AAATTAGGAAAAAGTATCAAGTTTAAGTACC
9474680 AAAT
1 AAAT
9474684 GTTATATTAA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
27 22 0.46
29 1 0.02
31 25 0.52
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.26
Consensus pattern (31 bp):
AAATTAGGAAAAAGTATCAAGTTTAAGTACC
Found at i:9474661 original size:27 final size:27
Alignment explanation
Indices: 9474609--9474661 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
9474599 AAAAAGTATC
** *
9474609 AAGTTTAAGTACCAAATTGGGTAAAAA
1 AAGTTTAAGTACCAAATTAAGAAAAAA
*
9474636 AAGTTTAGGTACCAAATTAAGAAAAA
1 AAGTTTAAGTACCAAATTAAGAAAAA
9474662 GTGTCAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.51, C:0.08, G:0.17, T:0.25
Consensus pattern (27 bp):
AAGTTTAAGTACCAAATTAAGAAAAAA
Found at i:9482798 original size:3 final size:3
Alignment explanation
Indices: 9482792--9482818 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9482782 ATACCGGTCC
9482792 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
9482819 TTTGTTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:9483102 original size:83 final size:83
Alignment explanation
Indices: 9482963--9483129 Score: 255
Period size: 83 Copynumber: 2.0 Consensus size: 83
9482953 GAAATTAAAG
* * * * *
9482963 ATAAAAAACTAAACCAAACAAAAATCAAACAACAATCCACAAAAAATTAAACCCCAATTTCAAAA
1 ATAAAAAACCAAACAAAACAAAAATCAAACAACAACCCACAAAAAATTAAACCCCAAGTCCAAAA
*
9483028 TGGATCGCTTCAATTTCA
66 TGGATCACTTCAATTTCA
9483046 ATAAAAAACCAAACAAAACAAAAAATCAAACAACAACCCA-AAAAAATTAAACCCCAAGTCCAAA
1 ATAAAAAACCAAACAAAAC-AAAAATCAAACAACAACCCACAAAAAATTAAACCCCAAGTCCAAA
*
9483110 ATGGGTCACTTCAATTTCA
65 ATGGATCACTTCAATTTCA
9483129 A
1 A
9483130 GAAAGAAATC
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
83 57 0.75
84 19 0.25
ACGTcount: A:0.56, C:0.23, G:0.04, T:0.17
Consensus pattern (83 bp):
ATAAAAAACCAAACAAAACAAAAATCAAACAACAACCCACAAAAAATTAAACCCCAAGTCCAAAA
TGGATCACTTCAATTTCA
Found at i:9486130 original size:18 final size:16
Alignment explanation
Indices: 9486109--9486154 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
9486099 TTTTATTTAA
9486109 TATTAAATTTAAATTATT
1 TATTAAA-TT-AATTATT
*
9486127 TATTTAATTAATTATT
1 TATTAAATTAATTATT
9486143 T-TT-AATTAATTA
1 TATTAAATTAATTA
9486155 AATAATTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 9 0.33
15 2 0.07
16 8 0.30
17 2 0.07
18 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTAAATTAATTATT
Found at i:9486133 original size:13 final size:12
Alignment explanation
Indices: 9486115--9486166 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
9486105 TTAATATTAA
*
9486115 ATTTAAATTATTT
1 ATTT-AATTAATT
9486128 ATTTAATTAATT
1 ATTTAATTAATT
9486140 ATTTTTAATTAATT
1 A--TTTAATTAATT
**
9486154 AAATAATTAATT
1 ATTTAATTAATT
9486166 A
1 A
9486167 AAACTAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 18 0.53
13 4 0.12
14 12 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTAATTAATT
Found at i:9492986 original size:4 final size:4
Alignment explanation
Indices: 9492973--9493012 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
9492963 TGATTTGAAG
*
9492973 GAAA -AAA GAAA GAAA -AAA GAAA GAAA GAAA -AAA GGAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
9493013 TGACAAGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
3 9 0.29
4 22 0.71
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:9492997 original size:15 final size:15
Alignment explanation
Indices: 9492977--9493012 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
9492967 TTGAAGGAAA
9492977 AAAGAAAGAAAAAAG
1 AAAGAAAGAAAAAAG
9492992 AAAGAAAGAAAAAAG
1 AAAGAAAGAAAAAAG
*
9493007 GAAGAA
1 AAAGAA
9493013 TGACAAGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAAAAG
Found at i:9493006 original size:11 final size:11
Alignment explanation
Indices: 9492973--9492998 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9492963 TGATTTGAAG
9492973 GAAAAAAGAAA
1 GAAAAAAGAAA
9492984 GAAAAAAGAAA
1 GAAAAAAGAAA
9492995 GAAA
1 GAAA
9492999 GAAAAAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:9493185 original size:18 final size:18
Alignment explanation
Indices: 9493162--9493196 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
9493152 CGAAGAAAGA
9493162 TAAG-TTTGATTAATTTTT
1 TAAGTTTTG-TTAATTTTT
9493180 TAAGTTTTGTTAATTTT
1 TAAGTTTTGTTAATTTT
9493197 AAATTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (18 bp):
TAAGTTTTGTTAATTTTT
Found at i:9493394 original size:21 final size:20
Alignment explanation
Indices: 9493368--9493410 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
9493358 TAATTTACTT
9493368 TAATTTAATTTTGTTAGTTAG
1 TAATTTAATTTTGTTAG-TAG
*
9493389 TAATTTTATTTTGTTAGTAG
1 TAATTTAATTTTGTTAGTAG
9493409 TA
1 TA
9493411 GTAAGTAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (20 bp):
TAATTTAATTTTGTTAGTAG
Found at i:9493941 original size:12 final size:11
Alignment explanation
Indices: 9493909--9493933 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9493899 GTAAAATTAG
9493909 TTATAAAAAAA
1 TTATAAAAAAA
9493920 TTATAAAAAAA
1 TTATAAAAAAA
9493931 TTA
1 TTA
9493934 ATATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TTATAAAAAAA
Found at i:9494163 original size:16 final size:15
Alignment explanation
Indices: 9494117--9494165 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
9494107 TAAATCTAAC
9494117 TAATTAATTATCAAAA
1 TAATTAATTA-CAAAA
9494133 T-A-TAATATA-AAAA
1 TAATTAAT-TACAAAA
9494146 TAATTAATTACCAAAA
1 TAATTAATTA-CAAAA
9494162 TAAT
1 TAAT
9494166 ATCTCTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 5 0.18
14 7 0.25
15 7 0.25
16 9 0.32
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
TAATTAATTACAAAA
Found at i:9494245 original size:30 final size:29
Alignment explanation
Indices: 9494209--9494304 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 29
9494199 AATAAATTAA
*
9494209 TAAATAATTATTTATTTTGTACCATTTTGG
1 TAAATAA-TATATATTTTGTACCATTTTGG
** * * *
9494239 TAAATAAT-GGTGTGTGGATACCATTTTGG
1 TAAATAATATATATTTTG-TACCATTTTGG
* *
9494268 TATATAAATATATATTTTGTACCATTTTAG
1 TAAAT-AATATATATTTTGTACCATTTTGG
9494298 TAAATAA
1 TAAATAA
9494305 CTCATTTTGG
Statistics
Matches: 50, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
28 4 0.08
29 18 0.36
30 24 0.48
31 4 0.08
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (29 bp):
TAAATAATATATATTTTGTACCATTTTGG
Found at i:9495556 original size:43 final size:43
Alignment explanation
Indices: 9495474--9495562 Score: 108
Period size: 43 Copynumber: 2.1 Consensus size: 43
9495464 ATTAACATGT
* * *
9495474 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTACATGTTAC
** *
9495517 TAAATTATATTACTTTTCTCTTATTAATAT-CTTAACATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTT-ACATGTTAC
9495560 TAA
1 TAA
9495563 TTGTGCAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 2 0.05
43 37 0.95
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTACATGTTAC
Found at i:9496171 original size:45 final size:45
Alignment explanation
Indices: 9496107--9496243 Score: 193
Period size: 45 Copynumber: 3.0 Consensus size: 45
9496097 CCTTAGCTCA
* *
9496107 TCAAGCCAAGTATATCAGCCTCAGTTTGACGAGGCACCACAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATAC
*
9496152 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCATAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATAC
** ** * *
9496197 TCAAGGGAAGGATATCAGGTTGAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATAC
9496242 TC
1 TC
9496244 TACTCCTCCC
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.20
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATAC
Found at i:9496528 original size:21 final size:21
Alignment explanation
Indices: 9496504--9496590 Score: 68
Period size: 21 Copynumber: 4.1 Consensus size: 21
9496494 TCATAATATT
9496504 AACCCTAAAACCTAAACCTAA
1 AACCCTAAAACCTAAACCTAA
* * *
9496525 AA-CCTTAAACTTAAAACTATA
1 AACCCTAAAACCTAAACCTA-A
* ** *
9496546 AACCTTAAGCCCTAAACTTAA
1 AACCCTAAAACCTAAACCTAA
* * *
9496567 AACCCTAAATCCTATACATAA
1 AACCCTAAAACCTAAACCTAA
9496588 AAC
1 AAC
9496591 ATTTTTAAAA
Statistics
Matches: 49, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
20 14 0.29
21 25 0.51
22 10 0.20
ACGTcount: A:0.49, C:0.28, G:0.01, T:0.22
Consensus pattern (21 bp):
AACCCTAAAACCTAAACCTAA
Found at i:9496533 original size:14 final size:14
Alignment explanation
Indices: 9496502--9496580 Score: 63
Period size: 14 Copynumber: 5.6 Consensus size: 14
9496492 TTTCATAATA
*
9496502 TTAACCCTAAAACC
1 TTAAACCTAAAACC
9496516 -TAAACCTAAAACC
1 TTAAACCTAAAACC
*
9496529 TTAAACTTAAAA-C
1 TTAAACCTAAAACC
* *
9496542 TATAAACCTTAAGCC
1 T-TAAACCTAAAACC
* *
9496557 CTAAACTTAAAACC
1 TTAAACCTAAAACC
*
9496571 CTAAATCCTA
1 TTAAA-CCTA
9496581 TACATAAAAC
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
13 14 0.27
14 33 0.65
15 4 0.08
ACGTcount: A:0.47, C:0.28, G:0.01, T:0.24
Consensus pattern (14 bp):
TTAAACCTAAAACC
Found at i:9496575 original size:28 final size:28
Alignment explanation
Indices: 9496509--9496580 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
9496499 ATATTAACCC
*
9496509 TAAAA-CCTAAACCTAAAACCTTAAACT
1 TAAAACCCTAAACCTAAAACCCTAAACT
** * *
9496536 TAAAACTATAAACCTTAAGCCCTAAACT
1 TAAAACCCTAAACCTAAAACCCTAAACT
9496564 TAAAACCCTAAATCCTA
1 TAAAACCCTAAA-CCTA
9496581 TACATAAAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 5 0.14
28 27 0.77
29 3 0.09
ACGTcount: A:0.49, C:0.26, G:0.01, T:0.24
Consensus pattern (28 bp):
TAAAACCCTAAACCTAAAACCCTAAACT
Found at i:9496904 original size:45 final size:44
Alignment explanation
Indices: 9496840--9496976 Score: 193
Period size: 45 Copynumber: 3.0 Consensus size: 44
9496830 CCCTAGCTCA
*
9496840 TCAAGCCAAGTATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAG-ATATCAGCCTCAGTTTGACGAGCCACCGTAATAC
9496885 TCAAGCCAAGAATATCAGCCTCAGTTTGACGAGCCACCGTAATAC
1 TCAAGCCAAG-ATATCAGCCTCAGTTTGACGAGCCACCGTAATAC
** ** *
9496930 TCAAGGGAATGATATCAGGTTGAGTTTGACGAGCCACCGTAATAC
1 TCAAGCCAA-GATATCAGCCTCAGTTTGACGAGCCACCGTAATAC
9496975 TC
1 TC
9496977 TACTCCTCCC
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 83 0.99
46 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (44 bp):
TCAAGCCAAGATATCAGCCTCAGTTTGACGAGCCACCGTAATAC
Found at i:9497254 original size:14 final size:14
Alignment explanation
Indices: 9497235--9497308 Score: 64
Period size: 14 Copynumber: 5.3 Consensus size: 14
9497225 TTCATAATGT
9497235 TAAACCTTAAAACC
1 TAAACCTTAAAACC
*
9497249 TAAACC-CAAAACC
1 TAAACCTTAAAACC
*
9497262 TTAAA-CTTAAAACTA
1 -TAAACCTTAAAAC-C
**
9497277 TAAACCTTAAGCCC
1 TAAACCTTAAAACC
9497291 TAAA-CTTAAAACCC
1 TAAACCTTAAAA-CC
9497305 TAAA
1 TAAA
9497309 TCCTATACAT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
13 12 0.26
14 29 0.62
15 6 0.13
ACGTcount: A:0.50, C:0.27, G:0.01, T:0.22
Consensus pattern (14 bp):
TAAACCTTAAAACC
Found at i:9497280 original size:28 final size:27
Alignment explanation
Indices: 9497234--9497302 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
9497224 TTTCATAATG
*
9497234 TTAAACCTTAAAACCTAAACCCAAAACC
1 TTAAA-CTTAAAACATAAACCCAAAACC
** *
9497262 TTAAACTTAAAACTATAAACCTTAAGCC
1 TTAAACTTAAAAC-ATAAACCCAAAACC
*
9497290 CTAAACTTAAAAC
1 TTAAACTTAAAAC
9497303 CCTAAATCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 8 0.23
28 27 0.77
ACGTcount: A:0.49, C:0.26, G:0.01, T:0.23
Consensus pattern (27 bp):
TTAAACTTAAAACATAAACCCAAAACC
Found at i:9497281 original size:21 final size:21
Alignment explanation
Indices: 9497235--9497286 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
9497225 TTCATAATGT
*
9497235 TAAACCTTAAAACCTAAACCCA
1 TAAACCTT-AAACCTAAAACCA
* *
9497257 -AAACCTTAAACTTAAAACTA
1 TAAACCTTAAACCTAAAACCA
9497277 TAAACCTTAA
1 TAAACCTTAA
9497287 GCCCTAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.52, C:0.25, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACCTTAAACCTAAAACCA
Found at i:9497483 original size:26 final size:26
Alignment explanation
Indices: 9497440--9497489 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
9497430 TCCAAAACCA
* *
9497440 AAATGCAAATATAAAAATTATTAATT
1 AAATACAAATATAAAAATAATTAATT
**
9497466 AAATACAAATATTGAAATAATTAA
1 AAATACAAATATAAAAATAATTAA
9497490 ATTCAAATTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (26 bp):
AAATACAAATATAAAAATAATTAATT
Found at i:9500880 original size:21 final size:21
Alignment explanation
Indices: 9500851--9500893 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
9500841 CTCACCTTTG
*
9500851 TTTCCCCAATTAAATC-CACAA
1 TTTCACCAATT-AATCACACAA
9500872 TTTCACCAATTAATCACACAA
1 TTTCACCAATTAATCACACAA
9500893 T
1 T
9500894 CAATCTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (21 bp):
TTTCACCAATTAATCACACAA
Found at i:9503083 original size:20 final size:18
Alignment explanation
Indices: 9503051--9503120 Score: 69
Period size: 16 Copynumber: 4.1 Consensus size: 18
9503041 AACACATTAC
*
9503051 CTTTCTCTCCTTCTACTTT
1 CTTTCTTTCCTTCT-CTTT
9503070 CTTTCCTTTCC-T-TCTTT
1 CTTT-CTTTCCTTCTCTTT
9503087 CTTTCTTT-CTT-TCTTT
1 CTTTCTTTCCTTCTCTTT
*
9503103 CTTTCTTTTCTT-TCTTT
1 CTTTCTTTCCTTCTCTTT
9503120 C
1 C
9503121 ATGTTTATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
15 1 0.02
16 18 0.38
17 17 0.36
18 1 0.02
19 5 0.11
20 5 0.11
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.67
Consensus pattern (18 bp):
CTTTCTTTCCTTCTCTTT
Done.