Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 169 of 240
Found at i:52529647 original size:24 final size:24
Alignment explanation
Indices: 52529620--52529675 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
52529610 TAATGATGTG
*
52529620 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
*
52529644 AAT-ATCAAAATATCAAAATATTAG
1 AATAAT-AAAATATCAAAATATTAA
52529668 AATAATAA
1 AATAATAA
52529676 TAATTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 8 0.30
24 17 0.63
25 2 0.07
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.29
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:52529671 original size:16 final size:15
Alignment explanation
Indices: 52529624--52529671 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
52529614 GATGTGAATA
52529624 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
*
52529640 ATAAAATATCAAAAT
1 ATAAAATATTAAAAT
*
52529655 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
52529671 A
1 A
52529672 ATAATAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:52529839 original size:20 final size:20
Alignment explanation
Indices: 52529787--52529843 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
52529777 ATACTACATC
*
52529787 AATATGTACATATATAAAAAA
1 AATATGTACATA-ATATAAAA
* * *
52529808 AATACGT-GATAATATTAAA
1 AATATGTACATAATATAAAA
52529827 AATATGTACATAATATA
1 AATATGTACATAATATA
52529844 GTGTTAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 12 0.43
20 10 0.36
21 6 0.21
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AATATGTACATAATATAAAA
Found at i:52529885 original size:22 final size:24
Alignment explanation
Indices: 52529822--52529886 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
52529812 CGTGATAATA
*
52529822 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
52529847 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
52529870 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
52529887 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:52529937 original size:33 final size:33
Alignment explanation
Indices: 52529875--52529939 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
52529865 TATAGTTAAG
*
52529875 ATATATACATAAGATAACATGTAAAATATATAT
1 ATATATAAATAAGATAACATGTAAAATATATAT
* *
52529908 ATATATAAATAATATAATAT-TAAAGATATATA
1 ATATATAAATAAGATAACATGTAAA-ATATATA
52529940 CATAAAATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 4 0.14
33 24 0.86
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (33 bp):
ATATATAAATAAGATAACATGTAAAATATATAT
Found at i:52529953 original size:16 final size:15
Alignment explanation
Indices: 52529896--52529953 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
52529886 AGATAACATG
52529896 TAAAATATATATATA
1 TAAAATATATATATA
52529911 TATAAATA-ATATAATA
1 TA-AAATATATAT-ATA
* * *
52529927 TTAAAGATATATACA
1 TAAAATATATATATA
52529942 TAAAATAGTATA
1 TAAAATA-TATA
52529954 AAATATATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
15 17 0.50
16 17 0.50
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (15 bp):
TAAAATATATATATA
Found at i:52530033 original size:22 final size:22
Alignment explanation
Indices: 52529969--52530040 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
52529959 TATATATACG
*
52529969 TAATATAA-ATTTA-AAATATA
1 TAATATAATATTAAGAAATATA
* *
52529989 CCTAATATATTA-AAAGAATATATA
1 --TAATATAATATTAAGAA-ATATA
52530013 TAATATAATATTAAGAAATATAA
1 TAATATAATATTAAGAAATAT-A
52530036 TAATA
1 TAATA
52530041 ACAAAAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
22 21 0.52
23 14 0.35
24 5 0.12
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (22 bp):
TAATATAATATTAAGAAATATA
Found at i:52530038 original size:23 final size:25
Alignment explanation
Indices: 52529995--52530040 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
52529985 TATACCTAAT
52529995 ATATTAAAAGAATATATATAATATA
1 ATATTAAAAGAATATATATAATATA
*
52530020 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
52530041 ACAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATATA
Found at i:52530446 original size:28 final size:28
Alignment explanation
Indices: 52530413--52530467 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
52530403 TTCTCTCCCA
52530413 AAAACTCTCCAAAAAAATCTCCC-CCTCC
1 AAAACTCTCCAAAAAAATC-CCCTCCTCC
52530441 AAAACTCTCCAAAAAAATCCCCTCCTC
1 AAAACTCTCCAAAAAAATCCCCTCCTC
52530468 TCTATATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.40, C:0.42, G:0.00, T:0.18
Consensus pattern (28 bp):
AAAACTCTCCAAAAAAATCCCCTCCTCC
Found at i:52530587 original size:30 final size:30
Alignment explanation
Indices: 52530551--52530725 Score: 287
Period size: 30 Copynumber: 5.8 Consensus size: 30
52530541 TAGGTACAAG
* *
52530551 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
* *
52530581 TGGTGGTGGAAAAAGAGTGGCTAGTGAAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
52530611 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
52530641 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
52530671 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
52530701 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGT
52530726 TGAGAAAAGT
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 133 1.00
ACGTcount: A:0.23, C:0.03, G:0.49, T:0.25
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
Found at i:52530644 original size:60 final size:60
Alignment explanation
Indices: 52530551--52530725 Score: 323
Period size: 60 Copynumber: 2.9 Consensus size: 60
52530541 TAGGTACAAG
*
52530551 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGAAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGAAGT
*
52530611 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGAAGT
*
52530671 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGT
52530726 TGAGAAAAGT
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 112 1.00
ACGTcount: A:0.23, C:0.03, G:0.49, T:0.25
Consensus pattern (60 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGAAGT
Found at i:52531511 original size:76 final size:76
Alignment explanation
Indices: 52531365--52531571 Score: 299
Period size: 76 Copynumber: 2.7 Consensus size: 76
52531355 TGATCCTGAA
** * ** * * *
52531365 CTCAACTCATTTCTCGCAATATGAATTGGCTTTTTTTGAAAAACAGAAATTTAAAAATACCTCAG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAACAACAGAAA-TTGAAAATACCTCAG
52531430 CGTGTCCTGAGG
65 CGTGTCCTGAGG
*
52531442 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAACAACAGAAATTGAAATTACCTCAGC
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAACAACAGAAATTGAAAATACCTCAGC
52531507 GTGTCCTGAGG
66 GTGTCCTGAGG
*
52531518 CTCAACTCACCTCTAGCAATATGAGTTGATTTTTTTTT-ACGAACAGAAATTGAA
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAC-AACAGAAATTGAA
52531572 GAACAGAAAT
Statistics
Matches: 119, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
75 2 0.02
76 75 0.63
77 42 0.35
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (76 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAACAACAGAAATTGAAAATACCTCAGC
GTGTCCTGAGG
Found at i:52531577 original size:14 final size:14
Alignment explanation
Indices: 52531558--52531585 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52531548 TTTTTTTTAC
52531558 GAACAGAAATTGAA
1 GAACAGAAATTGAA
52531572 GAACAGAAATTGAA
1 GAACAGAAATTGAA
52531586 AAGACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:52531704 original size:73 final size:74
Alignment explanation
Indices: 52531567--52531735 Score: 232
Period size: 73 Copynumber: 2.3 Consensus size: 74
52531557 CGAACAGAAA
* *
52531567 TTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCACAATAT
1 TTGAAAAACAGAAATTGAAAAGACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCACAATAT
*
52531632 GAGTTAATTT
65 GAGTCAATTT
* ** * **
52531642 TTGACAAACAGAAATTGAAATTACCTCAGC-GTGTCCCGAGGCTCAACTCACCTCTCGTAATATG
1 TTGAAAAACAGAAATTGAAAAGACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCACAATATG
*
52531706 AGTCGATTT
66 AGTCAATTT
52531715 TTGAAAAACAGAAATTGAAAA
1 TTGAAAAACAGAAATTGAAAA
52531736 CCAGAAATTG
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
73 56 0.68
75 26 0.32
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.25
Consensus pattern (74 bp):
TTGAAAAACAGAAATTGAAAAGACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCACAATATG
AGTCAATTT
Found at i:52531734 original size:14 final size:14
Alignment explanation
Indices: 52531715--52531749 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
52531705 GAGTCGATTT
52531715 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
*
52531729 TTGAAAACCAGAAA
1 TTGAAAAACAGAAA
52531743 TTGAAAA
1 TTGAAAA
52531750 TACCTCAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.60, C:0.09, G:0.14, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:52531794 original size:162 final size:160
Alignment explanation
Indices: 52531404--52531896 Score: 650
Period size: 162 Copynumber: 3.0 Consensus size: 160
52531394 CTTTTTTTGA
*
52531404 AAAACAGAAATTTAAAAATACCTCAGCGTGT---CCTGAGGCTCAACTCACCTCTCGCAATATGA
1 AAAACAGAAA-TTGAAAATACCTCAGCGTGTGAGCC-GAGGCTCAACTCACCTCTCGCAATATGA
* *
52531466 GTTGATTTTTTTTTAACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
64 GTT-A--ATTTTTGAA-AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
* * *
52531531 TAGCAATATGAGTTGATTTTTTTTTACGAACAGAAATTG
125 TCGCAATATGAGTTGA---TTTTTGACAAACAGAAATTG
* * *
52531570 AAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCACAATATGAG
1 AA-AACAGAAATTGAAAATACCTCAGCGTGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAG
* *
52531635 TTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGT
65 TTAATTTTTGA-AAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
* *
52531700 AATATGAGTCGATTTTTGAAAAACAGAAATTG
129 AATATGAGTTGATTTTTGACAAACAGAAATTG
* *
52531732 AAAACCAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATATGAG
1 AAAA-CAGAAATTGAAAATACCTCAGCGTGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAG
* * * * **
52531797 CTAATTTTTGATGAACATAAATTAAAACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
65 TTAATTTTTGA-AAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
*
52531862 AATATGAGTTGATTTTTGACAAACAAAAATTG
129 AATATGAGTTGATTTTTGACAAACAGAAATTG
52531894 AAA
1 AAA
52531897 TTACCTCAGC
Statistics
Matches: 291, Mismatches: 30, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
161 2 0.01
162 162 0.56
165 66 0.23
166 20 0.07
167 9 0.03
168 30 0.10
169 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (160 bp):
AAAACAGAAATTGAAAATACCTCAGCGTGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGT
TAATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
TATGAGTTGATTTTTGACAAACAGAAATTG
Found at i:52531804 original size:89 final size:87
Alignment explanation
Indices: 52531642--52531826 Score: 232
Period size: 89 Copynumber: 2.1 Consensus size: 87
52531632 GAGTTAATTT
* * *
52531642 TTGACAAA-CAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGTAATATG
1 TTGA-AAACCAGAAATTGAAAATACCTCAGCGTGTCCCAAGGCTCAACTCACCTCTCGCAATATG
*
52531706 AGTCGATTTTTGAAAAACAGAAA
65 AGTCAATTTTTGAAAAACAGAAA
* *
52531729 TTGAAAACCAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATAT
1 TTGAAAACCAGAAATTGAAAATACCTCAGCGTGT--CCCAAGGCTCAACTCACCTCTCGCAATAT
** *
52531794 GAG-CTAATTTTTGATGAACATAAA
64 GAGTC-AATTTTTGAAAAACAGAAA
52531818 TT-AAAACCA
1 TTGAAAACCA
52531827 CCTCAGCGTG
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
86 3 0.04
87 29 0.34
88 8 0.09
89 45 0.53
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.25
Consensus pattern (87 bp):
TTGAAAACCAGAAATTGAAAATACCTCAGCGTGTCCCAAGGCTCAACTCACCTCTCGCAATATGA
GTCAATTTTTGAAAAACAGAAA
Found at i:52531864 original size:73 final size:71
Alignment explanation
Indices: 52531769--52531968 Score: 256
Period size: 73 Copynumber: 2.8 Consensus size: 71
52531759 GTGTGAGCCA
* * *
52531769 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGATGAACATAAATTAAAACCACCTCAGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGATGAACATAAATTAAAACCACCTCAGC
52531834 GTGTCCTG
66 --GTCCTG
** * * **
52531842 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGATGAACATAAATTAAAACCACCTCAGC
*
52531907 GTCTTG
66 GTCCTG
* **
52531913 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAACATAAATTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGATG-AACATAAATTAAAA
52531969 AAACGAAAAT
Statistics
Matches: 109, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
71 41 0.38
72 12 0.11
73 56 0.51
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (71 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGATGAACATAAATTAAAACCACCTCAGC
GTCCTG
Found at i:52531894 original size:235 final size:232
Alignment explanation
Indices: 52531578--52532109 Score: 637
Period size: 235 Copynumber: 2.3 Consensus size: 232
52531568 TGAAGAACAG
* ** * *
52531578 AAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCACAATATGAGTTAATTTT
1 AAATTGAAAACACCTCAGC--GTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
* *
52531643 TGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGTAATATGAG
64 TGACAAACAAAAATTGAAATTACCTCAGC--GTCCCGAGGCTCAACTCACCTCTCGCAATATGAG
* *
52531708 TCGA-TTTTTGAAAAACAGAAATT--GAAAACCAGAAATTGAAAATACCTCAGCGTGTGAGCC-A
127 TCGATTTTTTGAAAAACAGAAATTAAAAAAACGA-AAATTGAAAATACCTCAGCGTGT---CCTA
* * ** *
52531769 AGGCTCAACTCACCTCTTGCAATATGAGCT-AATTTTTGATGA-ACAT
188 AGGCTCAACTCACCTCTCGCAATATGAGCTGAA--ATT-AAAACACAA
* *
52531815 AAATT-AAAACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAA-CACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
** * *
52531879 GACAAACAAAAATTGAAATTACCTCAGCGTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTG
65 GACAAACAAAAATTGAAATTACCTCAGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCG
*** * * *
52531944 ATTTTTTTTGAAACATAAATTAAAAAAACGAAAATTGAAAATACCTCAGCGTGTCCTGAGGTTCA
130 ATTTTTTGAAAAACAGAAATTAAAAAAACGAAAATTGAAAATACCTCAGCGTGTCCTAAGGCTCA
*
52532009 ACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAA
195 ACTCACCTCTCGCAATATGAGCTGAAATTAAAACACAA
* * *
52532047 AAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGATTTT
1 AAATTGAAAACACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
52532110 GAAAAAGTAG
Statistics
Matches: 256, Mismatches: 31, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
231 2 0.01
232 60 0.23
233 64 0.25
234 17 0.07
235 90 0.35
236 10 0.04
237 13 0.05
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (232 bp):
AAATTGAAAACACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
ACAAACAAAAATTGAAATTACCTCAGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGA
TTTTTTGAAAAACAGAAATTAAAAAAACGAAAATTGAAAATACCTCAGCGTGTCCTAAGGCTCAA
CTCACCTCTCGCAATATGAGCTGAAATTAAAACACAA
Found at i:52532082 original size:72 final size:73
Alignment explanation
Indices: 52531960--52532101 Score: 223
Period size: 72 Copynumber: 2.0 Consensus size: 73
52531950 TTTGAAACAT
* * * *
52531960 AAATTAAAAAAACGAAAATTGAAAATACCTCAGCGTGTCCTGAGGTTCAACTCACCTCTCGCAAT
1 AAATTAAAAAAACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAAT
52532025 ATGAGTTG
66 ATGAGTTG
* *
52532033 AAATT-AAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAAT
1 AAATTAAAAAAACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAAT
52532097 ATGAG
66 ATGAG
52532102 CTGATTTTGA
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
72 58 0.92
73 5 0.08
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (73 bp):
AAATTAAAAAAACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAAT
ATGAGTTG
Found at i:52532128 original size:160 final size:157
Alignment explanation
Indices: 52531826--52532115 Score: 406
Period size: 160 Copynumber: 1.8 Consensus size: 157
52531816 AATTAAAACC
** *
52531826 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAAAAA
1 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATAATTGAAAAACAAAAA
* ** * *
52531891 TTGAAATTACCTCAGCGTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAA
66 TTGAAAATACCTCAGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGA---TTTTTGAA
*
52531956 ACATAAATTAAAAAAACGAAAATTGAAAAT
128 AAATAAATTAAAAAAACGAAAATTGAAAAT
*
52531986 ACCTCAGCGTGTCCTGAGGTTCAACTCACCTCTCGCAATATGAGTTGA-AATT-AAAACACAAAA
1 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATAATTGAAAA-ACAAAA
*
52532049 ATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGA-TTTTGAA
65 ATTGAAAATACCTCAGCGT--CCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTGAA
52532113 AAA
128 AAA
52532116 GTAGAAATTA
Statistics
Matches: 116, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
157 9 0.08
158 3 0.03
159 26 0.22
160 47 0.41
161 31 0.27
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (157 bp):
ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATAATTGAAAAACAAAAA
TTGAAAATACCTCAGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTGAAAAA
TAAATTAAAAAAACGAAAATTGAAAAT
Found at i:52532500 original size:72 final size:72
Alignment explanation
Indices: 52532255--52532889 Score: 392
Period size: 72 Copynumber: 8.7 Consensus size: 72
52532245 AGTGTGTAAT
* * * * *
52532255 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTAAAAACAGAAATTGAAAATA
1 CTGAGGCTCAACTCATCTCTCGCAATATGAGTTGA-----ATTTTGAAAACAGAAATTGAAATTA
*
52532320 CCTCAGCATGTGAAC
61 CCTCAGC--GT-ATC
* * *
52532335 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAAATTGAAA-TA
1 CTGAGGCTCAACTCATCTCTCGCAATATGAGTTGA-----ATTTTGAAAACAGAAATTGAAATTA
* *
52532398 CCTCAACGTGTC
61 CCTCAGCGTATC
* * *
52532410 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCATCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
52532475 GCGTATC
66 GCGTATC
* * *
52532482 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTAACAACAGAAATTGAAATTACCT
1 CTGAGGCTCAACTCATCTCTCGCAATATGAGTTGA-ATTTTGAA-AACAGAAATTGAAATTACCT
*
52532547 CAGCGTGTC
64 CAGCGTATC
* * * ** * * *
52532556 CTGAGGCTCAACCCACCTCTAGCAATATGAGTTGAA---AAAAATACCA-CAGTGTGTAATT---
1 CTGAGGCTCAACTCATCTCTCGCAATATGAGTTGAATTTTGAAA-A-CAGAAAT-TGAAATTACC
* *
52532614 TGAAGC-TCA-A
63 T-CAGCGT-ATC
* * * * * * * *** * *
52532624 CTCA-CCTC-TCGCA-ATAT-G-AGT-TGA-TTTTTTTTTAAAAACAGAAATTGAAAATACCTCA
1 CTGAGGCTCAACTCATCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
*
52532682 GCATGTGAAC
66 GC--GT-ATC
* * *** *
52532692 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTTTTTTTTTTGAAAACAGAAATTGAAAATACCT
1 CTGAGGCTCAACTCATCTCTCGCAATATGAG--TTGAATTTTGAAAACAGAAATTGAAATTACCT
* *
52532756 CAACGTGTC
64 CAGCGTATC
* * *
52532765 ATGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAATAGAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCATCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
*
52532830 GCGTGTC
66 GCGTATC
* * *
52532837 CCGAGGCTCAACTCATCTCTAGCAATATGAGTTG-ATTTTGAAAAACAAAAATT
1 CTGAGGCTCAACTCATCTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATT
52532890 AAAAGGCTTA
Statistics
Matches: 448, Mismatches: 76, Indels: 70
0.75 0.13 0.12
Matches are distributed among these distances:
61 2 0.00
62 10 0.02
63 5 0.01
64 8 0.02
65 3 0.01
66 3 0.01
67 6 0.01
68 9 0.02
69 7 0.02
70 7 0.02
71 36 0.08
72 122 0.27
73 9 0.02
74 87 0.19
75 1 0.00
76 67 0.15
78 8 0.02
79 57 0.13
80 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (72 bp):
CTGAGGCTCAACTCATCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA
GCGTATC
Found at i:52532560 original size:74 final size:74
Alignment explanation
Indices: 52532255--52532590 Score: 403
Period size: 74 Copynumber: 4.5 Consensus size: 74
52532245 AGTGTGTAAT
* *
52532255 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTAAAAACAGAAATTGAAAATA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTT-AAAACAGAAATTGAAATTA
*
52532320 CCTCAGCATGTGAAC
63 CCTCAGC--GTG-TC
*
52532335 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAAATTGAAA-TA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTT-AAAACAGAAATTGAAATTA
*
52532398 CCTCAACGTGTC
63 CCTCAGCGTGTC
* ** * * *
52532410 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAACAGAAATTGAAATTACCT
*
52532473 CAGCGTATC
66 CAGCGTGTC
**
52532482 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTTTTAACAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAA-AACAGAAATTGAAATTACC
52532546 TCAGCGTGTC
65 TCAGCGTGTC
* *
52532556 CTGAGGCTCAACCCACCTCTAGCAATATGAGTTGA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
52532591 AAAAAATACC
Statistics
Matches: 231, Mismatches: 21, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
71 16 0.07
72 49 0.21
73 6 0.03
74 59 0.26
75 1 0.00
76 34 0.15
78 8 0.03
79 57 0.25
80 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Consensus pattern (74 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAAACAGAAATTGAAATTACCT
CAGCGTGTC
Found at i:52532836 original size:281 final size:279
Alignment explanation
Indices: 52532339--52532871 Score: 804
Period size: 281 Copynumber: 1.9 Consensus size: 279
52532329 GTGAACCGAG
*
52532339 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAAATTGAAATACCTCAA
1 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTAAAAACAGAAATTGAAATACCTCAA
* * ** *
52532404 CGTGTCTTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAATT
66 CGTGACTCGAGGCTCAACTCACCTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAAAT
* * * *
52532469 ACCTCAGCGTATCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTAACAACAGAA
131 ACCTCAACGTATCATGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTTGAACAACAGAA
*
52532534 ATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACCCACCTCTAGCAATATGAGTTGAAAAAAATA
196 ATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACCCACCTCTAGCAATATGAGTTGAAAAAAATA
52532599 CCACAGTGTGTAATTTGAA
261 CCACAGTGTGTAATTTGAA
*
52532618 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTTAAAAACAGAAATTGAAAATACCTCA
1 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTAAAAACAGAAATTG-AAATACCTCA
* ***
52532682 GCATGTGAAC-CGAGGCTCAACTCACCTCTCGCAATATAAGTTTTTTTTTTTGAAAACAGAAATT
65 --ACGTG-ACTCGAGGCTCAACTCACCTCTCGCAATATAAG--TTGAATTTTGAAAACAGAAATT
*
52532746 GAAAATACCTCAACGTGTCATGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAA-A
125 GAAAATACCTCAACGTATCATGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTTGAACA
* * *
52532809 ATAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCATCTCTAGCAATATGAGTTGA
190 ACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACCCACCTCTAGCAATATGAGTTGA
52532872 TTTTGAAAAA
Statistics
Matches: 228, Mismatches: 20, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
278 22 0.10
279 39 0.17
281 91 0.40
282 7 0.03
283 69 0.30
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (279 bp):
GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTAAAAACAGAAATTGAAATACCTCAA
CGTGACTCGAGGCTCAACTCACCTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAAAT
ACCTCAACGTATCATGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTTGAACAACAGAA
ATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACCCACCTCTAGCAATATGAGTTGAAAAAAATA
CCACAGTGTGTAATTTGAA
Found at i:52532869 original size:355 final size:358
Alignment explanation
Indices: 52532132--52532875 Score: 1284
Period size: 355 Copynumber: 2.1 Consensus size: 358
52532122 ATTAAAAGGT
* * * *
52532132 TCAACCCACCTCTCGCAATATGAGTTGA--TTCTTGACAAACAGAAATTGAAATTACCTCATCGT
1 TCAACTCATCTCTCGCAATATGAGTTGATTTTCTTAACAAACAGAAATTGAAATTACCTCAGCGT
* *
52532195 GTCCTGAGGCTCAACTCACCTCTCGCAATATGAATTGAAAAAAATACCACAGTGTGTAATCTGAA
66 GTCCTGAGGCTCAACCCACCTCTAGCAATATGAATTGAAAAAAATACCACAGTGTGTAATCTGAA
52532260 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTAAAAACAGAAATTGAAAATACCTCA
131 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTAAAAACAGAAATTGAAAATACCTCA
52532325 GCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAAA
196 GCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTT-ATTTTTTTTTTGAAAACAGAAA
*
52532390 TTGAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAA
260 TTGAAATACCTCAACGTGTCATGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAA
*
52532455 CAGAAATTGAAATTACCTCAGCGTATCCTGAGGC
325 CAGAAATTGAAATTACCTCAGCGTATCCCGAGGC
* *
52532489 TCAACTCATTTCTCGCAATATGAGTTGATTTTTTTAAC-AACAGAAATTGAAATTACCTCAGCGT
1 TCAACTCATCTCTCGCAATATGAGTTGATTTTCTTAACAAACAGAAATTGAAATTACCTCAGCGT
* *
52532553 GTCCTGAGGCTCAACCCACCTCTAGCAATATGAGTTGAAAAAAATACCACAGTGTGTAATTTGAA
66 GTCCTGAGGCTCAACCCACCTCTAGCAATATGAATTGAAAAAAATACCACAGTGTGTAATCTGAA
52532618 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTTAAAAACAGAAATTGAAAATACCTCA
131 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTAAAAACAGAAATTGAAAATACCTCA
52532682 GCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAG-T-TTTTTTTTTTGAAAACAGAAAT
196 GCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTATTTTTTTTTTGAAAACAGAAAT
*
52532745 TGAAAATACCTCAACGTGTCATGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA
261 TG-AAATACCTCAACGTGTCATGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAA
* *
52532810 TAGAAATTGAAATTACCTCAGCGTGTCCCGAGGC
325 CAGAAATTGAAATTACCTCAGCGTATCCCGAGGC
*
52532844 TCAACTCATCTCTAGCAATATGAGTTGATTTT
1 TCAACTCATCTCTCGCAATATGAGTTGATTTT
52532876 GAAAAACAAA
Statistics
Matches: 367, Mismatches: 17, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
354 24 0.07
355 121 0.33
356 1 0.00
357 99 0.27
358 116 0.32
359 6 0.02
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (358 bp):
TCAACTCATCTCTCGCAATATGAGTTGATTTTCTTAACAAACAGAAATTGAAATTACCTCAGCGT
GTCCTGAGGCTCAACCCACCTCTAGCAATATGAATTGAAAAAAATACCACAGTGTGTAATCTGAA
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTAAAAACAGAAATTGAAAATACCTCA
GCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTATTTTTTTTTTGAAAACAGAAAT
TGAAATACCTCAACGTGTCATGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAAC
AGAAATTGAAATTACCTCAGCGTATCCCGAGGC
Found at i:52533099 original size:121 final size:120
Alignment explanation
Indices: 52532768--52533131 Score: 488
Period size: 121 Copynumber: 3.0 Consensus size: 120
52532758 ACGTGTCATG
* ** * * * *
52532768 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAATAGAAATTGAAATTACCTCAGCG
1 AGGCTTAACTCACCTCTCGCAATATGAG-TCAA-TTT-AAAA-A-AAACTAAAAATACCTCAGCG
*
52532833 TGTCCCGAGGCTCAACTCA-TCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
61 TGCCCCGAGGCTCAACTCACT-TCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
* *
52532893 AGGCTTAACTCACCTCTCGCAGTATGAGTCACTTT----AAAACTAAAAATACCTCAGCGTGCCC
1 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAAAAAACTAAAAATACCTCAGCGTGCCC
*
52532954 CGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAA-AAAAATTAAA
66 CGAGGCTCAACTCACTTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
*
52533008 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
1 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAA-A-AAACTAAAAATACCTCAGCGTGC
*
52533073 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTTAAA
64 CCCGAGGCTCAACTCACTTCTAGCAATATGAGTTGATTTTGAAAAACAAAAA-TTAAA
52533131 A
1 A
52533132 TACCTCAGCG
Statistics
Matches: 214, Mismatches: 16, Indels: 20
0.86 0.06 0.08
Matches are distributed among these distances:
115 43 0.20
116 63 0.29
117 1 0.00
120 1 0.00
121 66 0.31
122 5 0.02
123 9 0.04
124 2 0.01
125 24 0.11
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (120 bp):
AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAAAAAACTAAAAATACCTCAGCGTGCCC
CGAGGCTCAACTCACTTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
Found at i:52533233 original size:75 final size:72
Alignment explanation
Indices: 52533008--52533344 Score: 430
Period size: 72 Copynumber: 4.7 Consensus size: 72
52532998 AAAAATTAAA
* * * * * * * *
52533008 AGGCTTAACTCACCTCTCGCAATATGAG-TCA-ATTT-AAAACATAAACTAAAAATACCTCGGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAACAGAAATTGAAATTACCTCAGCG
* *
52533070 TGCCCCG
66 TGTCCTG
* * * * *
52533077 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTTAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAACAGAAATTGAAATTACCTCAGCG
52533142 TGTCCTG
66 TGTCCTG
*
52533149 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTAAAAACAGAAATTGAAATTACCTCA
52533214 GCGTGTCCTG
63 GCGTGTCCTG
* *
52533224 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTAAAAACAGAAATCGAAATTACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAACAGAAATTGAAATTACCTCAGCG
52533289 TGTCC-G
66 TGTCCTG
* * *
52533295 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAACAGAAATT
52533345 AAAAGGCTTA
Statistics
Matches: 237, Mismatches: 25, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
69 26 0.11
70 2 0.01
71 48 0.20
72 94 0.40
75 67 0.28
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (72 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAACAGAAATTGAAATTACCTCAGCG
TGTCCTG
Found at i:52533283 original size:147 final size:146
Alignment explanation
Indices: 52533060--52533330 Score: 436
Period size: 147 Copynumber: 1.8 Consensus size: 146
52533050 AAACTAAAAA
* *
52533060 TACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAA
1 TACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAA
** *
52533125 TTTAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTA
66 TCGAAAATACCTCAGCGTGTCC-GAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTTTA
52533190 ACAACAGAAATTGAAAT
130 ACAACAGAAATTGAAAT
* * *
52533207 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTT-AAAAACAGAA
1 TACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTGAAAAACAAAA
*
52533271 ATCGAAATTACCTCAGCGTGTCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT
65 ATCGAAAATACCTCAGCGTGTCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT
52533331 GAAAAACAAA
Statistics
Matches: 114, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
146 36 0.32
147 73 0.64
148 5 0.04
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (146 bp):
TACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAAAAA
TCGAAAATACCTCAGCGTGTCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTTTAA
CAACAGAAATTGAAAT
Found at i:52533441 original size:120 final size:124
Alignment explanation
Indices: 52533224--52533456 Score: 348
Period size: 120 Copynumber: 1.9 Consensus size: 124
52533214 GCGTGTCCTG
* *
52533224 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTAAAAACAGAAATCGAAATTACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTTAAAAACAGAAATCGAAAATACCTCAGCG
*
52533289 TGTCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
66 TGCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
* * * *
52533348 AGGCTTAACTCACCTCTCGCAATATGAG-TCAA-TTT-AAAACATAAA-CTAAAATACCTCGGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTTAAAAACAGAAATCGAAAATACCTCAGCG
* * *
52533409 TGCCCGAGGTTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAA
66 TGCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAA
52533457 AATTAAAAAT
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
120 57 0.58
121 9 0.09
122 3 0.03
123 3 0.03
124 27 0.27
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (124 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTTAAAAACAGAAATCGAAAATACCTCAGCG
TGCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
Found at i:52533466 original size:67 final size:69
Alignment explanation
Indices: 52533348--52533518 Score: 190
Period size: 68 Copynumber: 2.5 Consensus size: 69
52533338 AAAAATTAAA
* * * * **
52533348 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAATACCTCGGCGTG-
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAACTAAAATACCTCAACGTGT
52533411 CCCG
66 CCCG
* * *
52533415 AGGTTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAA-A-AAATTAAAAATACCTCAACGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAACT-AAAATACCTCAACGTG
**
52533478 TCTTG
65 TCCCG
52533483 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
52533519 CCTTGGAAAG
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
66 4 0.05
67 41 0.47
68 43 0.49
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (69 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAACTAAAATACCTCAACGTGT
CCCG
Found at i:52546156 original size:23 final size:22
Alignment explanation
Indices: 52546130--52546183 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
52546120 TGTATACACG
52546130 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATA-ATACTAA
* *
52546153 TACATAATAATAATAATAGTAA
1 TACATAATAAAAATAATACTAA
52546175 TAC-TAATAA
1 TACATAATAA
52546184 TACTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.21
22 9 0.31
23 14 0.48
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (22 bp):
TACATAATAAAAATAATACTAA
Found at i:52546164 original size:3 final size:3
Alignment explanation
Indices: 52546133--52546203 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
52546123 ATACACGTAC
* * * *
52546133 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
52546180 ATA ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
52546204 CAAGGATATT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:52546694 original size:18 final size:18
Alignment explanation
Indices: 52546667--52546704 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
52546657 AGAAAAAAAA
*
52546667 AGAAGAGAGAGGGAAGAG
1 AGAAGAGAGAGAGAAGAG
*
52546685 AGAAGGGAGAGAGAAGAG
1 AGAAGAGAGAGAGAAGAG
52546703 AG
1 AG
52546705 GGGAATCCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (18 bp):
AGAAGAGAGAGAGAAGAG
Found at i:52546699 original size:11 final size:12
Alignment explanation
Indices: 52546668--52546700 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
52546658 GAAAAAAAAA
52546668 GAAGAGAG-AGG
1 GAAGAGAGAAGG
52546679 GAAGAGAGAAGG
1 GAAGAGAGAAGG
52546691 G-AGAGAGAAG
1 GAAGAGAGAAG
52546701 AGAGGGGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:52546820 original size:15 final size:16
Alignment explanation
Indices: 52546800--52546836 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
52546790 AGGTAAAAAA
*
52546800 TTTTATTT-TTTTATT
1 TTTTATTTCTTGTATT
52546815 TTTTATTTCTTGTATT
1 TTTTATTTCTTGTATT
52546831 TTTTAT
1 TTTTAT
52546837 ATTATACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTATTTCTTGTATT
Found at i:52553627 original size:16 final size:16
Alignment explanation
Indices: 52553606--52553636 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52553596 TTAACTATTA
*
52553606 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
52553622 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
52553637 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:52555775 original size:19 final size:21
Alignment explanation
Indices: 52555751--52555790 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
52555741 ATTTTTCTGC
52555751 AACAAACT-GG-TTTCCAGAA
1 AACAAACTCGGTTTTCCAGAA
52555770 AACAAACTCGGTTTTCCAGAA
1 AACAAACTCGGTTTTCCAGAA
52555791 TATAATGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 2 0.11
21 9 0.47
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (21 bp):
AACAAACTCGGTTTTCCAGAA
Found at i:52565985 original size:39 final size:40
Alignment explanation
Indices: 52565942--52566030 Score: 99
Period size: 44 Copynumber: 2.1 Consensus size: 40
52565932 TTATTTTCTT
* *
52565942 CTTCTTCTAC-CCTACTTTAGGTTTTATTTTCTGCATTTA
1 CTTCTTCTACTACTACTTTAGGTTTCATTTTCTGCATTTA
* *
52565981 CTTCTTGAATTTACTATTACTTTAGGTTTCATTTTCTGCATTTA
1 CTTC-T---TCTACTACTACTTTAGGTTTCATTTTCTGCATTTA
52566025 CTTCTT
1 CTTCTT
52566031 GCATTTACTG
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
39 4 0.10
40 2 0.05
43 5 0.12
44 30 0.73
ACGTcount: A:0.17, C:0.20, G:0.08, T:0.55
Consensus pattern (40 bp):
CTTCTTCTACTACTACTTTAGGTTTCATTTTCTGCATTTA
Found at i:52566003 original size:44 final size:44
Alignment explanation
Indices: 52565954--52566045 Score: 157
Period size: 44 Copynumber: 2.1 Consensus size: 44
52565944 TCTTCTACCC
*
52565954 TACTTTAGGTTTTATTTTCTGCATTTACTTCTTGAATTTACTAT
1 TACTTTAGGTTTCATTTTCTGCATTTACTTCTTGAATTTACTAT
* *
52565998 TACTTTAGGTTTCATTTTCTGCATTTACTTCTTGCATTTACTGT
1 TACTTTAGGTTTCATTTTCTGCATTTACTTCTTGAATTTACTAT
52566042 TACT
1 TACT
52566046 AAGGTTTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.55
Consensus pattern (44 bp):
TACTTTAGGTTTCATTTTCTGCATTTACTTCTTGAATTTACTAT
Found at i:52566035 original size:22 final size:22
Alignment explanation
Indices: 52565967--52566036 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
52565957 TTTAGGTTTT
*
52565967 ATTTTCTGCATTTACTTCTTGA
1 ATTTTCTGCATTTACTTCTTGC
* * *
52565989 ATTTACT--A-TTACTTTAGGTTTC
1 ATTTTCTGCATTTAC-TT--CTTGC
52566011 ATTTTCTGCATTTACTTCTTGC
1 ATTTTCTGCATTTACTTCTTGC
52566033 ATTT
1 ATTT
52566037 ACTGTTACTA
Statistics
Matches: 35, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
19 4 0.11
20 3 0.09
22 21 0.60
24 3 0.09
25 4 0.11
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.56
Consensus pattern (22 bp):
ATTTTCTGCATTTACTTCTTGC
Found at i:52566415 original size:40 final size:40
Alignment explanation
Indices: 52566370--52566463 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 40
52566360 TGACTAAATC
** *
52566370 GTAATAAATTGGACTAAATTGAATAGAACTAAGAACTTAA
1 GTAATAAATTGGACTAAATCAAATACAACTAAGAACTTAA
*
52566410 GTAATAAATTGGACTAAATCAAATACAACTAAGAACTTAG
1 GTAATAAATTGGACTAAATCAAATACAACTAAGAACTTAA
52566450 GTAATAAATTGGAC
1 GTAATAAATTGGAC
52566464 CAAGGACTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.27
Consensus pattern (40 bp):
GTAATAAATTGGACTAAATCAAATACAACTAAGAACTTAA
Found at i:52575817 original size:14 final size:14
Alignment explanation
Indices: 52575798--52575825 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52575788 ATAACAAGAA
52575798 GTCATGCCATAAAT
1 GTCATGCCATAAAT
52575812 GTCATGCCATAAAT
1 GTCATGCCATAAAT
52575826 TATTGTACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (14 bp):
GTCATGCCATAAAT
Found at i:52578360 original size:19 final size:18
Alignment explanation
Indices: 52578336--52578376 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
52578326 AAAATATAAA
*
52578336 AAAAATCATTAAAATGATT
1 AAAAATCATAAAAAT-ATT
52578355 AAAAATCATAAAAATATT
1 AAAAATCATAAAAATATT
52578373 AAAA
1 AAAA
52578377 TTTATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAAATCATAAAAATATT
Found at i:52578393 original size:28 final size:28
Alignment explanation
Indices: 52578362--52578461 Score: 89
Period size: 28 Copynumber: 3.5 Consensus size: 28
52578352 ATTAAAAATC
* * *
52578362 ATAAAAA-TATTAAAATTTATATAATATT
1 ATAAAAATTATAAAAACTTAT-CAATATT
52578390 ATAAAAATTATAAAAACTTATCAATATT
1 ATAAAAATTATAAAAACTTATCAATATT
* *
52578418 ATAAAAGTTATAACAAA-TTAT-AATTTT
1 ATAAAAATTATAA-AAACTTATCAATATT
*
52578445 TTATAAAATTAATAAAA
1 ATA-AAAATT-ATAAAA
52578462 CATATTTAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
27 7 0.11
28 36 0.59
29 18 0.30
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (28 bp):
ATAAAAATTATAAAAACTTATCAATATT
Found at i:52578400 original size:19 final size:18
Alignment explanation
Indices: 52578388--52578440 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
52578378 TTATATAATA
52578388 TTATAAAAATTATAAAAAC
1 TTATAAAAATTAT-AAAAC
* * *
52578407 TTATCAATATTATAAAAG
1 TTATAAAAATTATAAAAC
52578425 TTATAACAAATTATAA
1 TTATAA-AAATTATAA
52578441 TTTTTTATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36
Consensus pattern (18 bp):
TTATAAAAATTATAAAAC
Found at i:52578419 original size:9 final size:9
Alignment explanation
Indices: 52578354--52578440 Score: 77
Period size: 9 Copynumber: 9.3 Consensus size: 9
52578344 TTAAAATGAT
*
52578354 TAAAAATCA
1 TAAAAATTA
52578363 TAAAAA-TA
1 TAAAAATTA
*
52578371 TTAAAATTTA
1 -TAAAAATTA
*
52578381 TATAATATTA
1 TA-AAAATTA
52578391 TAAAAATTA
1 TAAAAATTA
52578400 TAAAAACTTA
1 TAAAAA-TTA
* *
52578410 TCAATATTA
1 TAAAAATTA
*
52578419 TAAAAGTTA
1 TAAAAATTA
52578428 TAACAAATTA
1 TAA-AAATTA
52578438 TAA
1 TAA
52578441 TTTTTTATAA
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
8 1 0.02
9 37 0.60
10 24 0.39
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.36
Consensus pattern (9 bp):
TAAAAATTA
Found at i:52579373 original size:9 final size:9
Alignment explanation
Indices: 52579307--52579607 Score: 132
Period size: 9 Copynumber: 31.3 Consensus size: 9
52579297 TATATTTTTA
52579307 TTTATAATT
1 TTTATAATT
*
52579316 TATTAGAACTT
1 T-TTATAA-TT
* *
52579327 ATTATGATTT
1 TTTAT-AATT
*
52579337 TTTATAAGT
1 TTTATAATT
*
52579346 TTTACAATT
1 TTTATAATT
* *
52579355 AATGATAATT
1 -TTTATAATT
52579365 TTTATAATT
1 TTTATAATT
52579374 TGTATGATAATT
1 T-T-T-ATAATT
52579386 TATTATAACTT
1 T-TTATAA-TT
52579397 TTT-TGAATT
1 TTTAT-AATT
*
52579406 TTTATAAGCT
1 TTTATAA-TT
*
52579416 TTTATAATA
1 TTTATAATT
52579425 TTTATAAGTT
1 TTTATAA-TT
*
52579435 TTGATGAATT
1 TTTAT-AATT
*
52579445 CTTTATAAGT
1 -TTTATAATT
52579455 TTTA-AATAT
1 TTTATAAT-T
52579464 TTTA-AATAT
1 TTTATAAT-T
52579473 GTTT-TAA-T
1 -TTTATAATT
*
52579481 TTTATTATT
1 TTTATAATT
*
52579490 GTTATAATTATT
1 -TT-T-ATAATT
52579502 TTTATAATT
1 TTTATAATT
*
52579511 TATTAGAA-T
1 T-TTATAATT
*
52579520 TTTATAATG
1 TTTATAATT
*
52579529 TTTATAAGT
1 TTTATAATT
52579538 TTTATGAATTTT
1 TTTAT-AA--TT
52579550 TTTATAATT
1 TTTATAATT
52579559 TTTATAAGTT
1 TTTATAA-TT
* *
52579569 TATATAAAT
1 TTTATAATT
52579578 TTT-TAATAT
1 TTTATAAT-T
*
52579587 TTTAT-GTAT
1 TTTATAAT-T
52579596 TTTATAATT
1 TTTATAATT
52579605 TTT
1 TTT
52579608 TATGAAAAAT
Statistics
Matches: 224, Mismatches: 37, Indels: 62
0.69 0.11 0.19
Matches are distributed among these distances:
7 3 0.01
8 13 0.06
9 96 0.43
10 73 0.33
11 19 0.08
12 20 0.09
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.58
Consensus pattern (9 bp):
TTTATAATT
Found at i:52579451 original size:21 final size:19
Alignment explanation
Indices: 52579361--52579458 Score: 92
Period size: 19 Copynumber: 4.9 Consensus size: 19
52579351 AATTAATGAT
52579361 AATTTTTATAA-TTTGTATG
1 AATTTTTATAAGTTT-TATG
* *
52579380 ATAATTTATTATAACTTTTTTG
1 --AATTT-TTATAAGTTTTATG
52579402 AATTTTTATAAGCTTTTAT-
1 AATTTTTATAAG-TTTTATG
*
52579421 AATATTTATAAGTTTTGATG
1 AATTTTTATAAGTTTT-ATG
52579441 AATTCTTTATAAGTTTTA
1 AATT-TTTATAAGTTTTA
52579459 AATATTTTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
18 4 0.06
19 19 0.29
20 14 0.21
21 17 0.26
22 9 0.14
23 3 0.05
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (19 bp):
AATTTTTATAAGTTTTATG
Found at i:52579582 original size:104 final size:105
Alignment explanation
Indices: 52579415--52579608 Score: 249
Period size: 104 Copynumber: 1.9 Consensus size: 105
52579405 TTTTATAAGC
*
52579415 TTTTATAATATTTATAAGTTTTGATGAATTCTTTATAAGTTTTAAATATTTTAAATATGTTTT-A
1 TTTTATAATATTTATAAGTTTTGATGAATTCTTTATAAGTTTTAAATATTATAAATATGTTTTAA
52579479 -ATTTTAT-TATTGTTATAATTATTTTTATAATTTATTAGAA
66 TATTTTATGTATT-TTATAATT-TTTTTATAATTTATTAGAA
* * *
52579519 TTTTATAATGTTTATAAGTTTT-ATGAATTTTTTTATAATTTTTATAAGT-TTATATAA-AT-TT
1 TTTTATAATATTTATAAGTTTTGATGAA-TTCTTTATAAGTTTTA-AA-TATTATA-AATATGTT
52579580 TTAATATTTTATGTATTTTATAATTTTTT
62 TTAATATTTTATGTATTTTATAATTTTTT
52579609 ATGAAAAATA
Statistics
Matches: 79, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
103 5 0.06
104 39 0.49
105 13 0.16
106 18 0.23
107 4 0.05
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (105 bp):
TTTTATAATATTTATAAGTTTTGATGAATTCTTTATAAGTTTTAAATATTATAAATATGTTTTAA
TATTTTATGTATTTTATAATTTTTTTATAATTTATTAGAA
Found at i:52589983 original size:26 final size:26
Alignment explanation
Indices: 52589953--52590006 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
52589943 TTCTAATATA
52589953 AGATAATTGTAATTATTGTTTAATAC
1 AGATAATTGTAATTATTGTTTAATAC
52589979 AGATAATTGTAATTATTGTTTAATAC
1 AGATAATTGTAATTATTGTTTAATAC
52590005 AG
1 AG
52590007 CATAGTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.44
Consensus pattern (26 bp):
AGATAATTGTAATTATTGTTTAATAC
Found at i:52590051 original size:17 final size:17
Alignment explanation
Indices: 52590013--52590054 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
52590003 ACAGCATAGT
*
52590013 TTTTAATATATATTATA
1 TTTTAATATATAATATA
*
52590030 ATTTAATATA-AATATCA
1 TTTTAATATATAATAT-A
52590047 TTTTAATA
1 TTTTAATA
52590055 ATTTTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTAATATATAATATA
Found at i:52590699 original size:43 final size:43
Alignment explanation
Indices: 52590651--52590736 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
52590641 CAAAGAAAAA
52590651 ATGAGTGTGTAAAACATACTAGTACATAGTGCTATACCACAGT
1 ATGAGTGTGTAAAACATACTAGTACATAGTGCTATACCACAGT
52590694 ATGAGTGTGTAAAACATACTAGTACATAGTGCTATACCACAGT
1 ATGAGTGTGTAAAACATACTAGTACATAGTGCTATACCACAGT
52590737 CGGTCCATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (43 bp):
ATGAGTGTGTAAAACATACTAGTACATAGTGCTATACCACAGT
Found at i:52591161 original size:12 final size:12
Alignment explanation
Indices: 52591144--52591217 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
52591134 CTCTTCGTCT
52591144 TTCTTCTTCTCC
1 TTCTTCTTCTCC
*
52591156 TTCTTC-TCTTC
1 TTCTTCTTCTCC
*
52591167 TT-TCTCTTCACC
1 TTCT-TCTTCTCC
* *
52591179 TTCTACCTCATCC
1 TTCTTCTTC-TCC
*
52591192 TTCTTCATT-TCT
1 TTCTTC-TTCTCC
52591204 TTCTTCTTCTCC
1 TTCTTCTTCTCC
52591216 TT
1 TT
52591218 TGCCTCTTTG
Statistics
Matches: 46, Mismatches: 10, Indels: 12
0.68 0.15 0.18
Matches are distributed among these distances:
10 1 0.02
11 10 0.22
12 26 0.57
13 8 0.17
14 1 0.02
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.57
Consensus pattern (12 bp):
TTCTTCTTCTCC
Found at i:52591271 original size:96 final size:96
Alignment explanation
Indices: 52591177--52592195 Score: 1404
Period size: 96 Copynumber: 10.7 Consensus size: 96
52591167 TTTCTCTTCA
* *
52591177 CCTTCTACCTCAT-C-CTTCTTCATTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTCTCTTCTTT
1 CCTTCTACCTCATCCTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
52591240 TCTTTCTTTCCCTCTTCTAATTCTTCATCTT
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTT
*
52591271 -CTTCTACCTCAT-C-CTTCTTTTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
1 CCTTCTACCTCATCCTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
*
52591333 TCTTTCTTTCCCTCTTCTAATTCTTCAGCTT
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTT
*
52591364 -CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTT
1 CCTTCTACCTCATCC-TCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT
*
52591428 TTCTTTCTTTCCCTCTTCTAATTCTTCAGCTT
65 TTCTTTCTTTCCCTCTTCTAATTCTTCATCTT
*
52591460 -CTTCTACCTTATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT
1 CCTTCTACCTCATCC-TCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT
52591524 TTCTTTCTTTCCCTCTTCTAATTCTTCATCTT
65 TTCTTTCTTTCCCTCTTCTAATTCTTCATCTT
*
52591556 -CATCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT
1 CCTTCTACCTCATCC-TCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT
52591620 TTCTTTCTTTCCCTCTTCTAATTCTTCATCTT
65 TTCTTTCTTTCCCTCTTCTAATTCTTCATCTT
* * *
52591652 -CTTCTACCTCATCCTTCTTCTTCTTTTCTTTTTTATTCTCCTTCGCCTCTTTGTCTTTCTTCTT
1 CCTTCTACCTCATCC-TCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT
*
52591716 TTCTTTCTTTCCCTCTTCTAATTCTTCAGCTT
65 TTCTTTCTTTCCCTCTTCTAATTCTTCATCTT
* *
52591748 -CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTATTCTCCTTCGCCTCTTTGTCTTTCTTCTT
1 CCTTCTACCTCATCC-TCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT
52591812 TTCTTTCTTTCCCTCTTCTAATTCTTCATCTTCAT
65 TTCTTTCTTTCCCTCTTCTAATTCTTCATC-T--T
* *
52591847 CTTCTTCTACCTCATCCTTCTTCTTCTTTCCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTC
1 C--CTTCTACCTCATCC-TCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTC
*
52591912 TTTTCTTTCTTTCCTTCTTCTAATTCTTCTTCATCTT
63 TTTTCTTTCTTTCCCTCTTCTAA---TTCTTCATCTT
* * *
52591949 -CTTCTACCTCATCCTTCTTCTTCTTCTCTTT-TGC--CT-CTTTG--TC-CT-TC-TTCTT-TT
1 CCTTCTACCTCATCC-TCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT
*
52592003 CT-TT-CTTTCCCTCTTCTAATTCTTCATCTT
65 TTCTTTCTTTCCCTCTTCTAATTCTTCATCTT
* **
52592033 CATCTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCCCCTTTGTTTCTTTGTCTTTCTTC
1 C--CTTCTACCTCATCC-TCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTC
*
52592098 TTTTCTTTCTTTCCCTCTTCTATTTCTTCATCTT
63 TTTTCTTTCTTTCCCTCTTCTAATTCTTCATCTT
* * * * * *
52592132 -CATCTTCTTC-TACTTTATCCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCCTTGTCTTTCTTCT
1 CCTTCTACCTCATCCTCT-T-CTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCT
52592195 T
64 T
52592196 CTCTGTCTCT
Statistics
Matches: 853, Mismatches: 43, Indels: 56
0.90 0.05 0.06
Matches are distributed among these distances:
84 11 0.01
87 44 0.05
88 4 0.00
89 3 0.00
90 6 0.01
91 7 0.01
92 1 0.00
93 105 0.12
94 4 0.00
95 9 0.01
96 503 0.59
97 4 0.00
98 4 0.00
99 55 0.06
102 83 0.10
104 1 0.00
105 9 0.01
ACGTcount: A:0.06, C:0.33, G:0.02, T:0.58
Consensus pattern (96 bp):
CCTTCTACCTCATCCTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
TCTTTCTTTCCCTCTTCTAATTCTTCATCTT
Found at i:52591398 original size:12 final size:12
Alignment explanation
Indices: 52591381--52591436 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
52591371 CTCATCCTTC
52591381 TTCTTCTTTTCT
1 TTCTTCTTTTCT
*
52591393 TTCTTCTTCTCCT
1 TTCTTCTT-TTCT
* *
52591406 TCGCCTCTTTGTCT
1 T-TCTTCTTT-TCT
52591420 TTCTTCTTTTCT
1 TTCTTCTTTTCT
52591432 TTCTT
1 TTCTT
52591437 TCCCTCTTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
12 16 0.46
13 11 0.31
14 8 0.23
ACGTcount: A:0.00, C:0.30, G:0.04, T:0.66
Consensus pattern (12 bp):
TTCTTCTTTTCT
Found at i:52591494 original size:12 final size:12
Alignment explanation
Indices: 52591477--52591628 Score: 72
Period size: 12 Copynumber: 11.4 Consensus size: 12
52591467 CTTATCCTTC
52591477 TTCTTCTTTTCT
1 TTCTTCTTTTCT
*
52591489 TTCTTCTTCTCCT
1 TTCTTCTT-TTCT
*
52591502 TTGCCTCTTTGTCT
1 TT-CTTCTTT-TCT
52591516 TTCTTCTTTTCT
1 TTCTTCTTTTCT
*
52591528 TTCTTTCCCTCTTCT
1 TTC-TT--CTTTTCT
*
52591543 AATTCTTCATCTTCAT
1 --TTCTTC-TTTTC-T
* * *
52591559 CTACCTCATCCTTC-
1 -TTCTTC-T-TTTCT
52591573 TTCTTCTTTTCT
1 TTCTTCTTTTCT
*
52591585 TTCTTCTTCTCCT
1 TTCTTCTT-TTCT
*
52591598 TTGCCTCTTTGTCT
1 TT-CTTCTTT-TCT
52591612 TTCTTCTTTTCT
1 TTCTTCTTTTCT
52591624 TTCTT
1 TTCTT
52591629 TCCCTCTTCT
Statistics
Matches: 110, Mismatches: 15, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
11 3 0.03
12 31 0.28
13 30 0.27
14 19 0.17
15 17 0.15
16 7 0.06
17 3 0.03
ACGTcount: A:0.04, C:0.32, G:0.03, T:0.62
Consensus pattern (12 bp):
TTCTTCTTTTCT
Found at i:52591657 original size:288 final size:288
Alignment explanation
Indices: 52591178--52592195 Score: 1572
Period size: 288 Copynumber: 3.6 Consensus size: 288
52591168 TTCTCTTCAC
* *
52591178 CTTCTACCTCAT-C--CTTCTTCATTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTCTCTTCTTT
1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
*
52591240 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCTTCTACCTCATCCTTC-T-TT-TTTTCTTTCTT
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTACCTCATCCTTCTTCTTCTTTTCTTTCTT
*
52591302 CTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCAGCTTCTT
131 CTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATCTTCTT
52591367 CTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCT
196 CTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCT
52591432 TTCTTTCCCTCTTCTAATTCTTCAGCTT
261 TTCTTTCCCTCTTCTAATTCTTCAGCTT
*
52591460 CTTCTACCTTATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
52591525 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTACCTCATCCTTCTTCTTCTTTTCTTTCTT
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTACCTCATCCTTCTTCTTCTTTTCTTTCTT
52591590 CTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATCTTCTT
131 CTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATCTTCTT
* *
52591655 CTACCTCATCCTTCTTCTTCTTTTCTTTTTTATTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCT
196 CTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCT
52591720 TTCTTTCCCTCTTCTAATTCTTCAGCTT
261 TTCTTTCCCTCTTCTAATTCTTCAGCTT
* *
52591748 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTATTCTCCTTCGCCTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
*
52591813 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTTCTTCTACCTCATCCTTCTTCTTCTTTCC
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCA------TCTACCTCATCCTTCTTCTTCTTTTC
* *
52591878 TTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCTTCTTCTAATTCTTCTT
125 TTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAA---TTCTT
*
52591943 CATCTTCTTCTACCTCAT-C--CTTCTTC--TTC-TTC-TC-T-T--TT-GCCTCTTTGTCCTTC
187 CATCTTCTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTC
*
52591996 TTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATCTTCAT
252 TTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCAGC-T--T
* **
52592036 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCCCCTTTGTTTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
* * * *
52592101 TCTTTCTTTCCCTCTTCTATTTCTTCATCTTCATCTTCTTC-TACTT-TATCCTTCTTTTCTTTC
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTACCTCATCCTTCT-T-CTTCTTTTCTTTC
*
52592164 TTCTTCTCCTTTGCCTCCTTGTCTTTCTTCTT
129 TTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT
52592196 CTCTGTCTCT
Statistics
Matches: 687, Mismatches: 29, Indels: 40
0.91 0.04 0.05
Matches are distributed among these distances:
280 1 0.00
281 5 0.01
282 59 0.09
283 1 0.00
285 142 0.21
286 4 0.01
287 2 0.00
288 355 0.52
289 1 0.00
290 1 0.00
291 2 0.00
292 3 0.00
294 87 0.13
296 1 0.00
297 23 0.03
ACGTcount: A:0.06, C:0.33, G:0.02, T:0.59
Consensus pattern (288 bp):
CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTACCTCATCCTTCTTCTTCTTTTCTTTCTT
CTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATCTTCTT
CTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCT
TTCTTTCCCTCTTCTAATTCTTCAGCTT
Found at i:52592196 original size:27 final size:28
Alignment explanation
Indices: 52592134--52592198 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 28
52592124 TTCATCTTCA
* * * *
52592134 TCTTCTTCTACTTTATCCTTCTTTTCTT
1 TCTTCTTCTCCTTTAGCCTCCTTGTCTT
52592162 TCTTCTTCTCCTTT-GCCTCCTTGTCTT
1 TCTTCTTCTCCTTTAGCCTCCTTGTCTT
52592189 TCTTCTTCTC
1 TCTTCTTCTC
52592199 TGTCTCTGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 20 0.61
28 13 0.39
ACGTcount: A:0.03, C:0.34, G:0.03, T:0.60
Consensus pattern (28 bp):
TCTTCTTCTCCTTTAGCCTCCTTGTCTT
Found at i:52592394 original size:12 final size:13
Alignment explanation
Indices: 52592365--52592409 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
52592355 CTTCTCCTTG
52592365 TCTTTCTTCTTC-
1 TCTTTCTTCTTCA
*
52592377 TGTTTCTTC-TCA
1 TCTTTCTTCTTCA
52592389 TCTTTC-TCTTCA
1 TCTTTCTTCTTCA
52592401 TC-TTCTTCT
1 TCTTTCTTCT
52592410 CCCTCCACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 7 0.25
12 21 0.75
ACGTcount: A:0.04, C:0.31, G:0.02, T:0.62
Consensus pattern (13 bp):
TCTTTCTTCTTCA
Found at i:52592604 original size:25 final size:22
Alignment explanation
Indices: 52592567--52592623 Score: 55
Period size: 25 Copynumber: 2.5 Consensus size: 22
52592557 TTCTCATCAT
52592567 CTTCTTCAT-CTTTGTGCATCTTCTC
1 CTTCTTC-TCCTTT-TGC-TCTT-TC
*
52592592 CTTCTTCTCCTTTTTCTCTTTC
1 CTTCTTCTCCTTTTGCTCTTTC
52592614 CTT-TTCTCCT
1 CTTCTTCTCCT
52592624 CTTTATTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 7 0.23
22 5 0.17
23 4 0.13
24 3 0.10
25 11 0.37
ACGTcount: A:0.04, C:0.35, G:0.04, T:0.58
Consensus pattern (22 bp):
CTTCTTCTCCTTTTGCTCTTTC
Found at i:52594766 original size:2 final size:2
Alignment explanation
Indices: 52594759--52594793 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
52594749 TCTACCTTCT
52594759 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52594794 ATTTTAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52595437 original size:19 final size:18
Alignment explanation
Indices: 52595415--52595451 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
52595405 AACATGAAAA
52595415 TTAAAATAAATATCGATAC
1 TTAAAATAAATAT-GATAC
*
52595434 TTAAAATATATATGATAC
1 TTAAAATAAATATGATAC
52595452 CAATTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.35
Consensus pattern (18 bp):
TTAAAATAAATATGATAC
Found at i:52596428 original size:15 final size:16
Alignment explanation
Indices: 52596408--52596438 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
52596398 TAATTTGCTT
52596408 TATATAAAAA-TAATA
1 TATATAAAAATTAATA
52596423 TATATAAAAATTAATA
1 TATATAAAAATTAATA
52596439 CGGACAGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TATATAAAAATTAATA
Found at i:52599364 original size:6 final size:6
Alignment explanation
Indices: 52599353--52599381 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
52599343 TAAATTATTT
52599353 TTTTAA TTTTAA TTTTAA TTTTAA TTTTA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTA
52599382 TCAAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:52604597 original size:4 final size:4
Alignment explanation
Indices: 52604590--52604639 Score: 59
Period size: 4 Copynumber: 13.0 Consensus size: 4
52604580 TTAATTTGTT
* * *
52604590 TGTA TGTA TGTA TGTA TGTA TG-- TGTG TGTG TGTG TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
52604636 TGTA
1 TGTA
52604640 AATATATGTG
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
2 2 0.05
4 41 0.95
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:52611362 original size:20 final size:20
Alignment explanation
Indices: 52611337--52611384 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
52611327 CTTAAAAGGG
*
52611337 ACTTCTA-CCAATACAAGTCC
1 ACTTCTATCC-ATACAAATCC
52611357 ACTTCTATCCATACAAATCC
1 ACTTCTATCCATACAAATCC
52611377 ACTTCTAT
1 ACTTCTAT
52611385 TTGTAACACC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.31
Consensus pattern (20 bp):
ACTTCTATCCATACAAATCC
Found at i:52612758 original size:20 final size:20
Alignment explanation
Indices: 52612733--52612772 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
52612723 ACTTTAAAAT
*
52612733 CAAGTTAAAATTATTTTAAC
1 CAAGTTAAAATGATTTTAAC
52612753 CAAGTTAAAATGATTTTAAC
1 CAAGTTAAAATGATTTTAAC
52612773 AAATCAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (20 bp):
CAAGTTAAAATGATTTTAAC
Found at i:52615995 original size:23 final size:23
Alignment explanation
Indices: 52615964--52616016 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
52615954 AGAGTTAGGA
*
52615964 TGATAAAATAGGATTTGTCAACT
1 TGATTAAATAGGATTTGTCAACT
52615987 TGATTAAATAGGATTTGTCAACT
1 TGATTAAATAGGATTTGTCAACT
52616010 TGATTAA
1 TGATTAA
52616017 CTCAAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (23 bp):
TGATTAAATAGGATTTGTCAACT
Found at i:52619187 original size:24 final size:25
Alignment explanation
Indices: 52619160--52619216 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
52619150 TAGCTCAGAG
* *
52619160 GAGCTTACCG-TTTACAGCTCGTAA
1 GAGCATACCGATTCACAGCTCGTAA
* *
52619184 GAGCATACCGATTCAGAGCTCGTAT
1 GAGCATACCGATTCACAGCTCGTAA
52619209 GAGCATAC
1 GAGCATAC
52619217 ATGTTTAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (25 bp):
GAGCATACCGATTCACAGCTCGTAA
Found at i:52620850 original size:16 final size:16
Alignment explanation
Indices: 52620825--52620858 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52620815 ATGAATATAT
* *
52620825 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
52620841 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
52620857 AT
1 AT
52620859 TGAATATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:52624240 original size:40 final size:39
Alignment explanation
Indices: 52624177--52624290 Score: 122
Period size: 40 Copynumber: 2.9 Consensus size: 39
52624167 CGTCAGATAG
* *
52624177 ACCG-AACACACCACACAAAAGCTCATAAGAGTTGATCCA
1 ACCGAAACACACCA-ATAGAAGCTCATAAGAGTTGATCCA
* ** * * *
52624216 ACCGAAATATGCCAAATAGAAGCTCGTAAGAGCTGGTCCA
1 ACCGAAACACACC-AATAGAAGCTCATAAGAGTTGATCCA
*
52624256 CCCGAAACACACCAATAGAAGCTCATAAGAGTTGA
1 ACCGAAACACACCAATAGAAGCTCATAAGAGTTGA
52624291 ACAGAAGCTC
Statistics
Matches: 58, Mismatches: 15, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
39 23 0.40
40 34 0.59
41 1 0.02
ACGTcount: A:0.41, C:0.26, G:0.18, T:0.15
Consensus pattern (39 bp):
ACCGAAACACACCAATAGAAGCTCATAAGAGTTGATCCA
Found at i:52625932 original size:17 final size:15
Alignment explanation
Indices: 52625907--52625950 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
52625897 TTATTTTTTT
*
52625907 AAATCTATAAAATATAA
1 AAATATATAAAAT-T-A
*
52625924 AAATATATACAATTA
1 AAATATATAAAATTA
52625939 AAATATATAAAA
1 AAATATATAAAA
52625951 AGCTTATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.50
16 1 0.04
17 11 0.46
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATATATAAAATTA
Found at i:52626099 original size:9 final size:9
Alignment explanation
Indices: 52626079--52626108 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
52626069 ATTCTTGAAC
52626079 TTTTAT-TA
1 TTTTATATA
52626087 TTTTATATA
1 TTTTATATA
52626096 TTTTATATA
1 TTTTATATA
52626105 TTTT
1 TTTT
52626109 TATTAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.29
9 15 0.71
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTATATA
Found at i:52628996 original size:29 final size:29
Alignment explanation
Indices: 52628933--52629000 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
52628923 TAATCAACCA
52628933 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
52628962 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
52628991 CGCACACTTA
1 CGCACACTTA
52629001 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:52629113 original size:174 final size:174
Alignment explanation
Indices: 52628822--52629149 Score: 550
Period size: 174 Copynumber: 1.9 Consensus size: 174
52628812 AACTCAAGGT
* *
52628822 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTTAT
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTTAT
* * *
52628887 AGAAAATATATATTGGGTTGCACGCATAACGTTTAGTAATCAACCACGCACACTTAGTGCCATGC
66 AGAAAATATATATTGGGTTGCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCATGC
52628952 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
52628996 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAA-TTTAT
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTTAT
** *
52629060 AGAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATG
66 AGAAAATATATATTGGGTT-GCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCATG
* *
52629125 TACTTTAAACTCGCACACTTAGTGC
130 CACTTTAAACTCACACACTTAGTGC
52629150 TGTACAATTT
Statistics
Matches: 143, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
173 24 0.17
174 119 0.83
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTTAT
AGAAAATATATATTGGGTTGCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:52629141 original size:29 final size:30
Alignment explanation
Indices: 52629102--52629180 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
52629092 CTTAATAATC
52629102 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
52629132 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
52629161 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
52629181 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:52637154 original size:29 final size:29
Alignment explanation
Indices: 52637091--52637158 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
52637081 TAATCAACCA
52637091 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
52637120 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
52637149 CGCACACTTA
1 CGCACACTTA
52637159 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:52637299 original size:29 final size:30
Alignment explanation
Indices: 52637260--52637338 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
52637250 CTTAATAATC
52637260 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
52637290 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
52637319 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
52637339 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:52643208 original size:14 final size:15
Alignment explanation
Indices: 52643183--52643211 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
52643173 ATAATAGAGA
52643183 GAGAGAAAGAAAAAT
1 GAGAGAAAGAAAAAT
52643198 GAGAG-AAGAAAAAT
1 GAGAGAAAGAAAAAT
52643212 AAAGAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.66, C:0.00, G:0.28, T:0.07
Consensus pattern (15 bp):
GAGAGAAAGAAAAAT
Found at i:52646333 original size:23 final size:24
Alignment explanation
Indices: 52646301--52646348 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
52646291 TTGAACATCA
*
52646301 ATAATTTTAG-TTTAAAATATGTC
1 ATAATCTTAGATTTAAAATATGTC
*
52646324 ATAATCTTAGCATTTTAAATATGTC
1 ATAATCTTAG-ATTTAAAATATGTC
52646349 TTAAGTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
25 12 0.57
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (24 bp):
ATAATCTTAGATTTAAAATATGTC
Found at i:52647907 original size:39 final size:39
Alignment explanation
Indices: 52647856--52648065 Score: 210
Period size: 39 Copynumber: 5.4 Consensus size: 39
52647846 TTTTCAATCA
* * *
52647856 CACCAGCACACAGCCTGCTAGGCATATAGTCCGAATAAT
1 CACCGGCACACAGCCTGCTAGGCACATAGACCGAATAAT
** *
52647895 CACCGGCACACAGTTTGCTAGGCACATAGCCCGAATAAT
1 CACCGGCACACAGCCTGCTAGGCACATAGACCGAATAAT
* * ** * *
52647934 TACTGGCACACAGTTTGCTAAGTACATA-ACCTGAATAAT
1 CACCGGCACACAGCCTGCTAGGCACATAGACC-GAATAAT
* *
52647973 TACTGGCACACAGCCTGCTAGGCACATA-ACACGAATAAT
1 CACCGGCACACAGCCTGCTAGGCACATAGAC-CGAATAAT
* * *
52648012 CACTGGTACACAG-CTCGCTAGGCACATAGCCCGAATAAT
1 CACCGGCACACAGCCT-GCTAGGCACATAGACCGAATAAT
*
52648051 CACCGGTACACAGCC
1 CACCGGCACACAGCC
52648066 CAAATAATCA
Statistics
Matches: 148, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
38 4 0.03
39 141 0.95
40 3 0.02
ACGTcount: A:0.33, C:0.30, G:0.19, T:0.19
Consensus pattern (39 bp):
CACCGGCACACAGCCTGCTAGGCACATAGACCGAATAAT
Found at i:52648088 original size:23 final size:23
Alignment explanation
Indices: 52648033--52648088 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
52648023 AGCTCGCTAG
* *
52648033 GCACATAGCCCGAATAATCACCG
1 GCACATAGCCCAAATAATCACCA
* *
52648056 GTACACAGCCCAAATAATCACCA
1 GCACATAGCCCAAATAATCACCA
52648079 GCACATAGCC
1 GCACATAGCC
52648089 TGCTAGGCAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.36, G:0.14, T:0.12
Consensus pattern (23 bp):
GCACATAGCCCAAATAATCACCA
Found at i:52653965 original size:24 final size:24
Alignment explanation
Indices: 52653938--52653989 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
52653928 TTAGTAAGTC
*
52653938 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
52653962 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
52653986 AAAT
1 AAAT
52653990 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:52655935 original size:24 final size:24
Alignment explanation
Indices: 52655908--52655959 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
52655898 TTAGTAAGTC
*
52655908 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
52655932 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
52655956 AAAT
1 AAAT
52655960 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:52657404 original size:12 final size:12
Alignment explanation
Indices: 52657387--52657414 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
52657377 CATCAAAAAC
52657387 ATTAAAATAAAT
1 ATTAAAATAAAT
52657399 ATTAAAATAAAT
1 ATTAAAATAAAT
52657411 ATTA
1 ATTA
52657415 CCCAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATTAAAATAAAT
Found at i:52658994 original size:26 final size:26
Alignment explanation
Indices: 52658965--52659016 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
52658955 TTATCGGTCA
* *
52658965 ATTTATTTTTATTTCAATAGATCTTT
1 ATTTATTTTTATTCCAATACATCTTT
52658991 ATTTATTTTTATTCCAATACATCTTT
1 ATTTATTTTTATTCCAATACATCTTT
52659017 TTCTTACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.12, G:0.02, T:0.60
Consensus pattern (26 bp):
ATTTATTTTTATTCCAATACATCTTT
Found at i:52662524 original size:21 final size:21
Alignment explanation
Indices: 52662481--52662653 Score: 188
Period size: 21 Copynumber: 8.3 Consensus size: 21
52662471 GTACATTGTT
* *
52662481 AACAGAAACTCGT-A-AGCTG
1 AACAGAAGCTCGTAAGAGCTA
*
52662500 AACAGAAGCTTGTAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTA
*
52662521 AACAGAAGCTCATAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTA
* * *
52662542 AATAGAAGCTTGAAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTA
* * *
52662563 AACAGAAACTCATAAGAGTTA
1 AACAGAAGCTCGTAAGAGCTA
*
52662584 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTA
* * *
52662605 AACAGAAACTCGTAAAAGTTA
1 AACAGAAGCTCGTAAGAGCTA
*
52662626 AATAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTA
*
52662647 AATAGAA
1 AACAGAA
52662654 AGTAAAACAC
Statistics
Matches: 125, Mismatches: 27, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
19 11 0.09
20 1 0.01
21 113 0.90
ACGTcount: A:0.47, C:0.15, G:0.21, T:0.17
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTA
Found at i:52662551 original size:42 final size:42
Alignment explanation
Indices: 52662503--52662654 Score: 214
Period size: 42 Copynumber: 3.6 Consensus size: 42
52662493 TAAGCTGAAC
* * *
52662503 AGAAGCTTGTAAGAGCTAAACAGAAGCTCATAAGAGCTAAAT
1 AGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGTTAAAT
* * *
52662545 AGAAGCTTGAAAGAGCTAAACAGAAACTCATAAGAGTTAAAC
1 AGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGTTAAAT
* * *
52662587 AGAAGCTCGTAAGAGCTGAACAGAAACTCGTAAAAGTTAAAT
1 AGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGTTAAAT
*
52662629 AGAAGCTCGTAAGAGCTAAATAGAAA
1 AGAAGCTCGTAAGAGCTAAACAGAAA
52662655 GTAAAACACG
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 98 1.00
ACGTcount: A:0.47, C:0.14, G:0.21, T:0.18
Consensus pattern (42 bp):
AGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGTTAAAT
Found at i:52670551 original size:25 final size:25
Alignment explanation
Indices: 52670531--52670638 Score: 101
Period size: 25 Copynumber: 4.3 Consensus size: 25
52670521 AAGCTCCTCT
52670531 AAGCTGAATAACAGTAAGCTCATGC
1 AAGCTGAATAACAGTAAGCTCATGC
* *
52670556 GAGCTGAATAACGGTAAGCTCATGC
1 AAGCTGAATAACAGTAAGCTCATGC
* * * * *
52670581 GAGATGAGTATCAGTAAGCTCATAC
1 AAGCTGAATAACAGTAAGCTCATGC
* * * *
52670606 GAGCTGAGTATC-GATAAGCTCATAC
1 AAGCTGAATAACAG-TAAGCTCATGC
52670631 AAGCTGAA
1 AAGCTGAA
52670639 ATCACTAACC
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
24 1 0.01
25 71 0.99
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (25 bp):
AAGCTGAATAACAGTAAGCTCATGC
Found at i:52670575 original size:50 final size:50
Alignment explanation
Indices: 52670499--52670638 Score: 133
Period size: 50 Copynumber: 2.8 Consensus size: 50
52670489 ATACATGTAT
* * *
52670499 GCTCATAAGAGCT--ATAAACGGTAAGCTCCT-CTAAGCTGAATAACAGTAA
1 GCTCATACGAGCTGAAT-AACGGTAAGCTCATGC-AAGATGAATAACAGTAA
* * * *
52670548 GCTCATGCGAGCTGAATAACGGTAAGCTCATGCGAGATGAGTATCAGTAA
1 GCTCATACGAGCTGAATAACGGTAAGCTCATGCAAGATGAATAACAGTAA
* * * * *
52670598 GCTCATACGAGCTGAGTATCGATAAGCTCATACAAGCTGAA
1 GCTCATACGAGCTGAATAACGGTAAGCTCATGCAAGATGAA
52670639 ATCACTAACC
Statistics
Matches: 73, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
49 11 0.15
50 59 0.81
51 3 0.04
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (50 bp):
GCTCATACGAGCTGAATAACGGTAAGCTCATGCAAGATGAATAACAGTAA
Found at i:52674634 original size:32 final size:32
Alignment explanation
Indices: 52674598--52674662 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
52674588 ACTAATTTCT
*
52674598 TTCCCAATCTGCAGAAAACCTTGCTATTCAAC
1 TTCCCAATCTGCAGAAAACCCTGCTATTCAAC
*
52674630 TTCCCAATCTGCAGAAAACCCTGCTCTTCAAC
1 TTCCCAATCTGCAGAAAACCCTGCTATTCAAC
52674662 T
1 T
52674663 CATGTTCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.29, C:0.34, G:0.09, T:0.28
Consensus pattern (32 bp):
TTCCCAATCTGCAGAAAACCCTGCTATTCAAC
Found at i:52676727 original size:24 final size:24
Alignment explanation
Indices: 52676699--52676746 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
52676689 CGGTTCTTGG
*
52676699 CATTAAATAAGTAATGGAATAAAA
1 CATTAAATAAATAATGGAATAAAA
52676723 CATTAAATAAATAATGGAATAAAA
1 CATTAAATAAATAATGGAATAAAA
52676747 TATACCTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.60, C:0.04, G:0.10, T:0.25
Consensus pattern (24 bp):
CATTAAATAAATAATGGAATAAAA
Found at i:52681418 original size:21 final size:21
Alignment explanation
Indices: 52681385--52681437 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
52681375 CATTATTTCT
* * *
52681385 AATCTTACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
* *
52681406 AATCTCACCGCTATAGTAACT
1 AATCTCACCGCTACAGTAACC
52681427 AATCTCACCGC
1 AATCTCACCGC
52681438 CACCGCTGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.32, G:0.09, T:0.28
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:52685396 original size:21 final size:21
Alignment explanation
Indices: 52685372--52685411 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
52685362 ATTGTCAATA
52685372 ACTTTTTAATATTTTTTTTTT
1 ACTTTTTAATATTTTTTTTTT
*
52685393 ACTTTTTTATATTTTTTTT
1 ACTTTTTAATATTTTTTTT
52685412 GTAAATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (21 bp):
ACTTTTTAATATTTTTTTTTT
Found at i:52689704 original size:26 final size:27
Alignment explanation
Indices: 52689675--52689732 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
52689665 ATTATATTCA
*
52689675 TATTTAATAT-ATTTTCTTATCCAATT
1 TATTTAATATGATTTTCTAATCCAATT
* *
52689701 TATTTAATATGTTTTTCTAATTCAATT
1 TATTTAATATGATTTTCTAATCCAATT
52689728 TATTT
1 TATTT
52689733 TTCAAGTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.60
Consensus pattern (27 bp):
TATTTAATATGATTTTCTAATCCAATT
Found at i:52691207 original size:22 final size:22
Alignment explanation
Indices: 52691179--52691226 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
52691169 TTTTACTTTT
*
52691179 TCAATTCACTCTAAATTCTCTC
1 TCAATTCACTCTAAATACTCTC
* * *
52691201 TCAATTCATTTTCAATACTCTC
1 TCAATTCACTCTAAATACTCTC
52691223 TCAA
1 TCAA
52691227 CTCTCAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (22 bp):
TCAATTCACTCTAAATACTCTC
Found at i:52697407 original size:26 final size:26
Alignment explanation
Indices: 52697363--52697413 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
52697353 TAAGTGTTCT
52697363 GAAACTGATACATGCTATGATATTCA
1 GAAACTGATACATGCTATGATATTCA
* * *
52697389 GAAATTGATATATGTTATGATATTC
1 GAAACTGATACATGCTATGATATTC
52697414 TGAAGCTACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (26 bp):
GAAACTGATACATGCTATGATATTCA
Found at i:52700784 original size:18 final size:18
Alignment explanation
Indices: 52700761--52700796 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
52700751 TAAAAGATGA
52700761 AATCAAATTTTATTGAGT
1 AATCAAATTTTATTGAGT
52700779 AATCAAATTTTATTGAGT
1 AATCAAATTTTATTGAGT
52700797 CTAGTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (18 bp):
AATCAAATTTTATTGAGT
Found at i:52705746 original size:68 final size:69
Alignment explanation
Indices: 52705605--52705748 Score: 184
Period size: 68 Copynumber: 2.1 Consensus size: 69
52705595 TTGATCACTT
* * * *
52705605 TAATATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAGATAATT
1 TAATATTAAATTAATAAAATACTTATAAAGATAAATATTAAATTAAATTTAATATTAAAATAATT
***
52705670 ACTT
66 AAAA
* *
52705674 TAATATTAAATTAATAAAATAC-TATAAAGATAATTATTAAATTTAATTTAATATTAAAACT-AT
1 TAATATTAAATTAATAAAATACTTATAAAGATAAATATTAAATTAAATTTAATATTAAAA-TAAT
52705737 TAAAA
65 TAAAA
52705742 TAATATT
1 TAATATT
52705749 GTTTTTGAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
68 43 0.66
69 22 0.34
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (69 bp):
TAATATTAAATTAATAAAATACTTATAAAGATAAATATTAAATTAAATTTAATATTAAAATAATT
AAAA
Found at i:52710663 original size:37 final size:37
Alignment explanation
Indices: 52710600--52710678 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 37
52710590 TTATTACGAA
*
52710600 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACATAATCTCCACACGAAGTCATCGG
*
52710637 GTCTTACCCGGACGA-AATC-CCTACACGTAGTCATCGG
1 GTCTTACCCGGAC-ATAATCTCC-ACACGAAGTCATCGG
52710674 GTCTT
1 GTCTT
52710679 TAGAGCTCAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
36 2 0.05
37 35 0.92
38 1 0.03
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGAAGTCATCGG
Found at i:52710875 original size:47 final size:47
Alignment explanation
Indices: 52710797--52711494 Score: 1200
Period size: 47 Copynumber: 14.7 Consensus size: 47
52710787 CCCTTCGGGA
* * * * * *
52710797 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
52710844 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52710891 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52710938 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52710985 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52711032 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52711079 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52711126 CTTATCACATATATACACTTTCACATTCATCACCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCA-CATCGGCCATTAGGC
52711174 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52711221 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52711270 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52711317 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
52711366 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52711413 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
52711460 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
52711495 AGAATCCTAA
Statistics
Matches: 624, Mismatches: 21, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
46 1 0.00
47 483 0.77
48 47 0.08
49 93 0.15
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:52717890 original size:26 final size:27
Alignment explanation
Indices: 52717856--52717906 Score: 63
Period size: 26 Copynumber: 1.9 Consensus size: 27
52717846 AATATTTCAA
52717856 ACATGAAA-TATAGTCT-TCAAATACAGT
1 ACATGAAATTATA-TCTAT-AAATACAGT
52717883 ACAT-AAATTATATCTATAAATACA
1 ACATGAAATTATATCTATAAATACA
52717907 TCGATAGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (27 bp):
ACATGAAATTATATCTATAAATACAGT
Found at i:52721610 original size:158 final size:158
Alignment explanation
Indices: 52721322--52721634 Score: 518
Period size: 158 Copynumber: 2.0 Consensus size: 158
52721312 TCTTTGATCC
* ** * *
52721322 ATGGTCTTACTCATTATTCTTGGCTGTCATAGCATCTTACCATAAATCCCACGAGTGAGTCTGTA
1 ATGGTCTTACTCATTATACCCGGCTATCATAGCATCTTACCACAAATCCCACGAGTGAGTCTGTA
52721387 AATATTATTATTTAATATTTATGAGCCAAATATAGTATAATATTAAAATTTTATATGATAAATTT
66 AATATTATTATTTAATATTTATGAGCCAAATATAGTATAATATTAAAATTTTATATGATAAATTT
52721452 TGTTAATTGAATGAATAATTAAGTACAA
131 TGTTAATTGAATGAATAATTAAGTACAA
* * *
52721480 ATGGTCTTACTCATTATACCCGGTTATCATAGCATCTTACCACAAATTCCACGAGTGAGTTTGTA
1 ATGGTCTTACTCATTATACCCGGCTATCATAGCATCTTACCACAAATCCCACGAGTGAGTCTGTA
* * *
52721545 AATATTATTATTTAATATTTATGAGTCAAATATAGTATAATATTGAATTTTTATATGATAAATTT
66 AATATTATTATTTAATATTTATGAGCCAAATATAGTATAATATTAAAATTTTATATGATAAATTT
*
52721610 TGTTAATTGAATGAATAGTTAAGTA
131 TGTTAATTGAATGAATAATTAAGTA
52721635 TAAGTGGTTT
Statistics
Matches: 143, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
158 143 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (158 bp):
ATGGTCTTACTCATTATACCCGGCTATCATAGCATCTTACCACAAATCCCACGAGTGAGTCTGTA
AATATTATTATTTAATATTTATGAGCCAAATATAGTATAATATTAAAATTTTATATGATAAATTT
TGTTAATTGAATGAATAATTAAGTACAA
Found at i:52723314 original size:13 final size:13
Alignment explanation
Indices: 52723296--52723454 Score: 83
Period size: 13 Copynumber: 11.8 Consensus size: 13
52723286 AGAAAAATAA
*
52723296 TATATGAATTGGT
1 TATATGAAATGGT
*
52723309 TATATGAATTGGT
1 TATATGAAATGGT
*
52723322 TATATGGATAAAT-GA
1 TATAT-G--AAATGGT
*
52723337 TATATGAAATGGG
1 TATATGAAATGGT
* *
52723350 TATATGAAAATAGA
1 TATATG-AAATGGT
52723364 TATATGAAATGGT
1 TATATGAAATGGT
*
52723377 TATATG-AATCAGT
1 TATATGAAAT-GGT
**
52723390 TATATGTAAA-AAT
1 TATATG-AAATGGT
*
52723403 GATATGTATAATGGT
1 TATATG-A-AATGGT
*
52723418 TATATG-AATCAGT
1 TATATGAAAT-GGT
* *
52723431 TATATGGAAATAGA
1 TATAT-GAAATGGT
52723445 TATATGAAAT
1 TATATGAAAT
52723455 AAAACATTGG
Statistics
Matches: 118, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
12 10 0.08
13 65 0.55
14 23 0.19
15 17 0.14
16 3 0.03
ACGTcount: A:0.42, C:0.01, G:0.19, T:0.37
Consensus pattern (13 bp):
TATATGAAATGGT
Found at i:52723367 original size:14 final size:13
Alignment explanation
Indices: 52723331--52723372 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
52723321 TTATATGGAT
52723331 AAATGATATATG-
1 AAATGATATATGA
*
52723343 AAATGGGTATATGA
1 AAAT-GATATATGA
52723357 AAATAGATATATGA
1 AAAT-GATATATGA
52723371 AA
1 AA
52723373 TGGTTATATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 4 0.16
13 7 0.28
14 14 0.56
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.29
Consensus pattern (13 bp):
AAATGATATATGA
Found at i:52723372 original size:27 final size:26
Alignment explanation
Indices: 52723309--52723384 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 26
52723299 ATGAATTGGT
*
52723309 TATATGAATTGGTTATATGGATAAATGA
1 TATATGAAATGGTTATAT-GA-AAATGA
*
52723337 TATATGAAATGGGTATATGAAAATAGA
1 TATATGAAATGGTTATATGAAAAT-GA
52723364 TATATGAAATGGTTATATGAA
1 TATATGAAATGGTTATATGAA
52723385 TCAGTTATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.09
27 24 0.55
28 16 0.36
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (26 bp):
TATATGAAATGGTTATATGAAAATGA
Found at i:52723403 original size:68 final size:67
Alignment explanation
Indices: 52723289--52723425 Score: 186
Period size: 68 Copynumber: 2.0 Consensus size: 67
52723279 TCGGATGAGA
* ** *
52723289 AAAATAATATATGAATTGGTTATATGAATTGGTTATATGGATAAATGATATATGA-AATGGGTAT
1 AAAATAATATATGAAATGGTTATATGAATCAGTTATATGGAAAAATGATATAT-ATAATGGGTAT
52723353 ATG
65 ATG
* * *
52723356 AAAATAGATATATGAAATGGTTATATGAATCAGTTATATGTAAAAATGATATGTATAATGGTTAT
1 AAAATA-ATATATGAAATGGTTATATGAATCAGTTATATGGAAAAATGATATATATAATGGGTAT
52723421 ATG
65 ATG
52723424 AA
1 AA
52723426 TCAGTTATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
67 7 0.11
68 54 0.89
ACGTcount: A:0.44, C:0.01, G:0.19, T:0.36
Consensus pattern (67 bp):
AAAATAATATATGAAATGGTTATATGAATCAGTTATATGGAAAAATGATATATATAATGGGTATA
TG
Found at i:52723441 original size:68 final size:67
Alignment explanation
Indices: 52723290--52723452 Score: 179
Period size: 68 Copynumber: 2.4 Consensus size: 67
52723280 CGGATGAGAA
* ** *
52723290 AAATA-ATATATGAATTGGTTATATGAATTGGTTATATGGATAAATGATATATGAAATGGGTATA
1 AAATAGATATATGAAATGGTTATATGAATCAGTTATATGGAAAAATGATATATGAAATGGGTATA
52723354 TG
66 TG
* * *
52723356 AAAATAGATATATGAAATGGTTATATGAATCAGTTATATGTAAAAATGATATGT-ATAATGGTTA
1 -AAATAGATATATGAAATGGTTATATGAATCAGTTATATGGAAAAATGATATATGA-AATGGGTA
52723420 TATG
64 TATG
* * *
52723424 -AATCAGTTATATGGAAATAGATATATGAA
1 AAAT-AGATATAT-GAAATGGTTATATGAA
52723453 ATAAAACATT
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
66 3 0.04
67 13 0.16
68 66 0.80
ACGTcount: A:0.44, C:0.01, G:0.19, T:0.36
Consensus pattern (67 bp):
AAATAGATATATGAAATGGTTATATGAATCAGTTATATGGAAAAATGATATATGAAATGGGTATA
TG
Found at i:52723991 original size:25 final size:25
Alignment explanation
Indices: 52723963--52724012 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
52723953 AATCCTTAAT
*
52723963 GTTATTTTTGTTGGTTTAGTAATTG
1 GTTATTTTGGTTGGTTTAGTAATTG
*
52723988 GTTATTTTGGTTGGTTTGGTAATTG
1 GTTATTTTGGTTGGTTTAGTAATTG
52724013 ATGGCATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.58
Consensus pattern (25 bp):
GTTATTTTGGTTGGTTTAGTAATTG
Found at i:52724176 original size:87 final size:87
Alignment explanation
Indices: 52724073--52724243 Score: 342
Period size: 87 Copynumber: 2.0 Consensus size: 87
52724063 GAATTGGTAC
52724073 ATACATGATAGGATAATTGATGAAATTCAATTGGTGATAAACTATCATTAGAGGCTTGGTATAAA
1 ATACATGATAGGATAATTGATGAAATTCAATTGGTGATAAACTATCATTAGAGGCTTGGTATAAA
52724138 TGATTGATAATAGCATATGATA
66 TGATTGATAATAGCATATGATA
52724160 ATACATGATAGGATAATTGATGAAATTCAATTGGTGATAAACTATCATTAGAGGCTTGGTATAAA
1 ATACATGATAGGATAATTGATGAAATTCAATTGGTGATAAACTATCATTAGAGGCTTGGTATAAA
52724225 TGATTGATAATAGCATATG
66 TGATTGATAATAGCATATG
52724244 TTAGTTGGAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (87 bp):
ATACATGATAGGATAATTGATGAAATTCAATTGGTGATAAACTATCATTAGAGGCTTGGTATAAA
TGATTGATAATAGCATATGATA
Found at i:52726393 original size:52 final size:52
Alignment explanation
Indices: 52726315--52726418 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
52726305 GCTTATAGTG
52726315 TTTGTACCTTAATCAATCATGTTTCCAATTAAGCTCAAGTATGTATTTCGTT
1 TTTGTACCTTAATCAATCATGTTTCCAATTAAGCTCAAGTATGTATTTCGTT
52726367 TTTGTACCTTAATCAATCATGTTTCCAATTAAGCTCAAGTATGTATTTCGTT
1 TTTGTACCTTAATCAATCATGTTTCCAATTAAGCTCAAGTATGTATTTCGTT
52726419 CATACATGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (52 bp):
TTTGTACCTTAATCAATCATGTTTCCAATTAAGCTCAAGTATGTATTTCGTT
Found at i:52733244 original size:23 final size:22
Alignment explanation
Indices: 52733204--52733246 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
52733194 AAATTATAAA
*
52733204 ATATAAAAATATATATATGTAC
1 ATATAAAAAAATATATATGTAC
52733226 ATATAAGAAAAATATATATGT
1 ATATAA-AAAAATATATATGT
52733247 GTGTGAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:52733285 original size:12 final size:12
Alignment explanation
Indices: 52733268--52733330 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
52733258 AAAAAATAAA
52733268 AAATATATATAT
1 AAATATATATAT
*
52733280 AAATATACATATTT
1 AAATAT--ATATAT
* *
52733294 TAATATGTA-A-
1 AAATATATATAT
52733304 AAATATATATAT
1 AAATATATATAT
*
52733316 AAGTATATATAT
1 AAATATATATAT
52733328 AAA
1 AAA
52733331 ATTATGAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
10 7 0.18
11 1 0.03
12 21 0.54
14 10 0.26
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (12 bp):
AAATATATATAT
Found at i:52733997 original size:21 final size:21
Alignment explanation
Indices: 52733971--52734025 Score: 96
Period size: 19 Copynumber: 2.7 Consensus size: 21
52733961 AATCATATAT
52733971 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
52733992 TCTAAGATTG--TATATCATA
1 TCTAAGATTGCATATATCATA
52734011 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
52734026 CCTTGAAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 19 0.59
21 13 0.41
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:52735714 original size:20 final size:20
Alignment explanation
Indices: 52735689--52735736 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
52735679 ATTTTCAAGG
* *
52735689 TATCGATAAAAGTTATAAAT
1 TATCGATAAAAGGTAAAAAT
**
52735709 TATCGATACTAGGTAAAAAT
1 TATCGATAAAAGGTAAAAAT
52735729 TATCGATA
1 TATCGATA
52735737 CCAATTTTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.33
Consensus pattern (20 bp):
TATCGATAAAAGGTAAAAAT
Found at i:52737943 original size:39 final size:39
Alignment explanation
Indices: 52737914--52738041 Score: 152
Period size: 39 Copynumber: 3.3 Consensus size: 39
52737904 GCTACTCGTT
*
52737914 CAAATGCCTTCGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGACATAACCCGGTTATAGTAACTCGCA
* *
52737953 CAAATGCCTTCGGACTTAACCCGGATT-TAGTAAGTCGCA
1 CAAATGCCTTCGGACATAACCCGG-TTATAGTAACTCGCA
* * * * *
52737992 CCAATGCCTTCGGGCTTAGCCCGG-AATTAGTAACTCGCA
1 CAAATGCCTTCGGACATAACCCGGTTA-TAGTAACTCGCA
52738031 CAAATGCCTTC
1 CAAATGCCTTC
52738042 AGATCTTAGT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
39 75 0.97
40 2 0.03
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGACATAACCCGGTTATAGTAACTCGCA
Found at i:52739404 original size:85 final size:85
Alignment explanation
Indices: 52739261--52739439 Score: 358
Period size: 85 Copynumber: 2.1 Consensus size: 85
52739251 TATTTTATTG
52739261 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
52739326 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
52739346 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
52739411 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
52739431 CCCATGCTC
1 CCCATGCTC
52739440 ATGGCCGGCC
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 94 1.00
ACGTcount: A:0.26, C:0.27, G:0.08, T:0.38
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:52746084 original size:79 final size:80
Alignment explanation
Indices: 52745907--52746090 Score: 198
Period size: 79 Copynumber: 2.3 Consensus size: 80
52745897 GCTACTCGTT
** *
52745907 CAAATGCCTTCGGGACACAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAA-GCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGACTTAACCCG
* *
52745971 GATTTAGTAAGTCGCAC
64 GATATAGTAAGTAGCAC
* **
52745988 CAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GATCTTAGTCCGG
1 CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGA-CTTAACCCGG
* **
52746050 ATATGGTCACTTAGCA-
65 ATATAGT-AAGTAGCAC
52746066 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
52746091 CATCATTGAA
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
77 2 0.02
78 25 0.29
79 47 0.54
80 10 0.11
81 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGACTTAACCCGGA
TATAGTAAGTAGCAC
Found at i:52746090 original size:40 final size:40
Alignment explanation
Indices: 52745888--52746090 Score: 211
Period size: 40 Copynumber: 5.1 Consensus size: 40
52745878 CGGAATTTAA
** **
52745888 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACACAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
52745928 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
52745968 CCGGATTTAGTAAGTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
52746007 CCGGA-ATTAGTAACTCGCACAAATGCCTTC--GATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
52746046 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
52746086 CCGGA
1 CCGGA
52746091 CATCATTGAA
Statistics
Matches: 136, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
37 1 0.01
39 53 0.39
40 80 0.59
41 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:52747397 original size:85 final size:85
Alignment explanation
Indices: 52747254--52747432 Score: 358
Period size: 85 Copynumber: 2.1 Consensus size: 85
52747244 TATTTTATTG
52747254 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
52747319 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
52747339 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
52747404 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
52747424 CCCATGCTC
1 CCCATGCTC
52747433 ATGGCCGACC
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 94 1.00
ACGTcount: A:0.26, C:0.27, G:0.08, T:0.38
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Done.