Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 2 of 91
Found at i:64739 original size:47 final size:47
Alignment explanation
Indices: 64686--64927 Score: 222
Period size: 47 Copynumber: 5.1 Consensus size: 47
64676 AACCCTGCCG
* * *
64686 TGTCACAAATTCCCTCCATGGCATGTCACGAACTCTAAACACTAGCA
1 TGTCACAGATTCCCTCCATGGCGTGTCACGAACTCTAAACCCTAGCA
* * *
64733 TATCACAGATTTCTTCCATGGCGTGTCA-GAAACTCTAAACCCT-GCCA
1 TGTCACAGATTCCCTCCATGGCGTGTCACG-AACTCTAAACCCTAG-CA
* * * * *
64780 TGTCACAGATTCCCTCCATGGTGTGTCGCAAACTCTAAACCCTACCG
1 TGTCACAGATTCCCTCCATGGCGTGTCACGAACTCTAAACCCTAGCA
* * * * * * *
64827 TGTCACAGATTCCCTGCATGCCGTGTCACAAATTCTGAACGCT-GGA
1 TGTCACAGATTCCCTCCATGGCGTGTCACGAACTCTAAACCCTAGCA
* * * *
64873 GTGTCACGGATTCCCTCTATGGCGTGTCACAAACTTTAAACCCT-GCCA
1 -TGTCACAGATTCCCTCCATGGCGTGTCACGAACTCTAAACCCTAG-CA
64921 TGTCACA
1 TGTCACA
64928 ATGTGTCACA
Statistics
Matches: 155, Mismatches: 34, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
46 2 0.01
47 152 0.98
48 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (47 bp):
TGTCACAGATTCCCTCCATGGCGTGTCACGAACTCTAAACCCTAGCA
Found at i:64774 original size:94 final size:94
Alignment explanation
Indices: 64666--64927 Score: 272
Period size: 94 Copynumber: 2.8 Consensus size: 94
64656 ATGGAGTCTG
* * * * * *
64666 ACAAATTCTGAACCCTGCCGTGTCACAAATTCCCTCCATGGCATGTCACGAACTCTAAACACTAG
1 ACAAACTCTAAACCCTGCCGTGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTAAACACTAC
* * *
64731 CATATCACAGATTTCTTCCATGGCGTGTC
66 CATATCACAGATTCCCTCCATGCCGTGTC
* * * * *
64760 AGAAACTCTAAACCCTGCCATGTCACAGATTCCCTCCATGGTGTGTCGCAAACTCTAAACCCTAC
1 ACAAACTCTAAACCCTGCCGTGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTAAACACTAC
* * *
64825 CGTGTCACAGATTCCCTGCATGCCGTGTC
66 CATATCACAGATTCCCTCCATGCCGTGTC
* * * ** * * * * *
64854 ACAAATTCTGAACGCTGGAGTGTCACGGATTCCCTCTATGGCGTGTCACAAACTTTAAACCCTGC
1 ACAAACTCTAAACCCTGCCGTGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTAAACACTAC
*
64919 CATGTCACA
66 CATATCACA
64928 ATGTGTCACA
Statistics
Matches: 137, Mismatches: 31, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
94 137 1.00
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (94 bp):
ACAAACTCTAAACCCTGCCGTGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTAAACACTAC
CATATCACAGATTCCCTCCATGCCGTGTC
Found at i:64955 original size:23 final size:23
Alignment explanation
Indices: 64929--64973 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
64919 CATGTCACAA
*
64929 TGTGTCACACATTCCCACCATGT
1 TGTGTCACACATTCCCAACATGT
*
64952 TGTGTCACACATTTCCAACATG
1 TGTGTCACACATTCCCAACATG
64974 CTATTTCACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.31
Consensus pattern (23 bp):
TGTGTCACACATTCCCAACATGT
Found at i:64982 original size:23 final size:23
Alignment explanation
Indices: 64931--64983 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
64921 TGTCACAATG
* * *
64931 TGTCACACATTCCCACCATGTTG
1 TGTCACACATTCCCAACATGCTA
*
64954 TGTCACACATTTCCAACATGCTA
1 TGTCACACATTCCCAACATGCTA
*
64977 TTTCACA
1 TGTCACA
64984 AACTCTAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.26, C:0.32, G:0.09, T:0.32
Consensus pattern (23 bp):
TGTCACACATTCCCAACATGCTA
Found at i:65746 original size:29 final size:29
Alignment explanation
Indices: 65688--65748 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
65678 TAAATTCCTT
*
65688 TAATAAAATCCCTTATAGATATGCCCTAA
1 TAATAAAAGCCCTTATAGATATGCCCTAA
*
65717 TAATAAAAGCCTTTAATAGA-AT-CCCTTAA
1 TAATAAAAGCCCTT-ATAGATATGCCC-TAA
65746 TAA
1 TAA
65749 AAATCCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 3 0.11
29 20 0.71
30 5 0.18
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (29 bp):
TAATAAAAGCCCTTATAGATATGCCCTAA
Found at i:66246 original size:10 final size:9
Alignment explanation
Indices: 66209--66345 Score: 79
Period size: 9 Copynumber: 15.7 Consensus size: 9
66199 AAATCTAAAC
66209 AAAAAGAATT
1 AAAAA-AATT
*
66219 -AAGAAATT
1 AAAAAAATT
66227 AAAAAAATT
1 AAAAAAATT
66236 AAAACAAATT
1 AAAA-AAATT
66246 AAAAAAA--
1 AAAAAAATT
* *
66253 AAGAAATTT
1 AAAAAAATT
* *
66262 TATAAAATT
1 AAAAAAATT
*
66271 TAAAAAA-T
1 AAAAAAATT
66279 -AAAAAATT
1 AAAAAAATT
*
66287 CAAAAAATT
1 AAAAAAATT
* *
66296 -TAAATATT
1 AAAAAAATT
* *
66304 TAAAAATTT
1 AAAAAAATT
* *
66313 AAACAATTT
1 AAAAAAATT
66322 AAAAAAATT
1 AAAAAAATT
* *
66331 TAAAAATTT
1 AAAAAAATT
66340 AAAAAA
1 AAAAAA
66346 CTAATAAAAA
Statistics
Matches: 100, Mismatches: 20, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
7 11 0.11
8 12 0.12
9 68 0.68
10 9 0.09
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (9 bp):
AAAAAAATT
Found at i:68959 original size:18 final size:19
Alignment explanation
Indices: 68928--68974 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
68918 AACTTAAGTT
*
68928 GAAAAAAGATGAAGAGAAA
1 GAAAAAAGATGAAGACAAA
*
68947 GAAAAAAGA-GAAGCCAAA
1 GAAAAAAGATGAAGACAAA
68965 GATAAAAAGA
1 GA-AAAAAGA
68975 AGAACTTAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.68, C:0.04, G:0.23, T:0.04
Consensus pattern (19 bp):
GAAAAAAGATGAAGACAAA
Found at i:75675 original size:18 final size:19
Alignment explanation
Indices: 75652--75692 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
75642 ATGTATATTA
75652 TAATTGTACA-AATATAAT
1 TAATTGTACATAATATAAT
* *
75670 TAATTGTATATTATATAAT
1 TAATTGTACATAATATAAT
75689 TAAT
1 TAAT
75693 AATATAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (19 bp):
TAATTGTACATAATATAAT
Found at i:91526 original size:24 final size:23
Alignment explanation
Indices: 91495--91545 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
91485 TTTTAAAATA
91495 TAAT-TTCTATTCACTTCTTTTTG
1 TAATATTCTATTC-CTTCTTTTTG
* * *
91518 TAATATTCTCTTCCTTTTTTTTT
1 TAATATTCTATTCCTTCTTTTTG
91541 TAATA
1 TAATA
91546 CTCATTTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.20, C:0.16, G:0.02, T:0.63
Consensus pattern (23 bp):
TAATATTCTATTCCTTCTTTTTG
Found at i:97499 original size:26 final size:26
Alignment explanation
Indices: 97470--97570 Score: 86
Period size: 26 Copynumber: 3.9 Consensus size: 26
97460 TAAGGCATCC
97470 ATCCACTTTTGATGGTAAAATTATCT
1 ATCCACTTTTGATGGTAAAATTATCT
97496 ATCCACTTTT-AGTGGTAAAATTATTCT
1 ATCCACTTTTGA-TGGTAAAATTA-TCT
* * * **
97523 -T-AAATTTAGATGACAAAATTAT-T
1 ATCCACTTTTGATGGTAAAATTATCT
97546 CATCCACTTCTTG-TGGTAAAATTAT
1 -ATCCACTT-TTGATGGTAAAATTAT
97571 AATTAAAATA
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 15 0.26
26 36 0.62
27 5 0.09
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (26 bp):
ATCCACTTTTGATGGTAAAATTATCT
Found at i:97732 original size:56 final size:54
Alignment explanation
Indices: 97671--97798 Score: 161
Period size: 53 Copynumber: 2.4 Consensus size: 54
97661 TTAAATAATA
* * *
97671 TCGCATTCACTTCAGGGAATTG-ACGAATTTATAATTTTTTATTAGTAGCTCGTTTG
1 TCGCATTTACTTCAGGGAAATGAAC--ATTCATAA-TTTTTATTAGTAGCTCGTTTG
*
97727 TCGCATTTACTTCA-GGAAATGAACATTCATAATTTTTATTAGTAGCTTGTTTG
1 TCGCATTTACTTCAGGGAAATGAACATTCATAATTTTTATTAGTAGCTCGTTTG
* *
97780 TCACATTTACTTTAGGGAA
1 TCGCATTTACTTCAGGGAA
97799 CGGACAATTA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
53 32 0.50
54 11 0.17
55 6 0.09
56 15 0.23
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.42
Consensus pattern (54 bp):
TCGCATTTACTTCAGGGAAATGAACATTCATAATTTTTATTAGTAGCTCGTTTG
Found at i:98094 original size:80 final size:81
Alignment explanation
Indices: 97959--98131 Score: 276
Period size: 80 Copynumber: 2.1 Consensus size: 81
97949 ATTTTTTAAA
* *
97959 ATCAGAAATCAAAACCCCCAATCATTGAAATCCTTTTGAAGCTTGAAGATGATGAAAACATAATA
1 ATCAGAAATCAAAA-CCCCAATCATTGAAATCCTTTTAAAGCTTGAAGATGATGAAAACATAAAA
98024 ATTCTCAAACTTGAGAG
65 ATTCTCAAACTTGAGAG
* *
98041 ATCAGAAATCAAAA-CCTAATTATTGAAATCCTTTTAAAGCTTGAAGATGATGAAAACATAAAAA
1 ATCAGAAATCAAAACCCCAATCATTGAAATCCTTTTAAAGCTTGAAGATGATGAAAACATAAAAA
98105 TTCTCAAACTTGAGAG
66 TTCTCAAACTTGAGAG
*
98121 ATTAGAGAATC
1 ATCAGA-AATC
98132 GTGCTGATAA
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
80 67 0.79
81 4 0.05
82 14 0.16
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.27
Consensus pattern (81 bp):
ATCAGAAATCAAAACCCCAATCATTGAAATCCTTTTAAAGCTTGAAGATGATGAAAACATAAAAA
TTCTCAAACTTGAGAG
Found at i:98467 original size:25 final size:24
Alignment explanation
Indices: 98430--98487 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
98420 CATAACATTA
98430 TAAAAT-AAATAAAAAAAT-ATAAT
1 TAAAATAAAATAAAAAAATAAT-AT
*
98453 TAAAATAAAAGTAAATAAATAATAT
1 TAAAATAAAA-TAAAAAAATAATAT
*
98478 AAAAATAAAA
1 TAAAATAAAA
98488 AAGTTGAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 6 0.20
24 3 0.10
25 19 0.63
26 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (24 bp):
TAAAATAAAATAAAAAAATAATAT
Found at i:98470 original size:19 final size:19
Alignment explanation
Indices: 98432--98486 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
98422 TAACATTATA
98432 AAAT-AAATAAAAA-AATAT
1 AAATAAAATAAAAATAA-AT
* *
98450 AATTAAAATAAAAGTAAAT
1 AAATAAAATAAAAATAAAT
*
98469 AAATAATATAAAAATAAA
1 AAATAAAATAAAAATAAA
98487 AAAGTTGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 3 0.10
19 25 0.83
20 2 0.07
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
AAATAAAATAAAAATAAAT
Found at i:98615 original size:5 final size:5
Alignment explanation
Indices: 98607--98670 Score: 51
Period size: 5 Copynumber: 12.4 Consensus size: 5
98597 AAAAAAAATT
* * *
98607 ATAAA ATAAA TAAAAA AGAAA ATATAA GTAAA ATAAA AGT-AA AT-AA
1 ATAAA ATAAA -ATAAA ATAAA ATA-AA ATAAA ATAAA A-TAAA ATAAA
98653 ATAAA ATAAAA ATAAA AT
1 ATAAA AT-AAA ATAAA AT
98671 GATGTCCACT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
4 5 0.10
5 30 0.61
6 14 0.29
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:98639 original size:11 final size:11
Alignment explanation
Indices: 98607--98670 Score: 57
Period size: 11 Copynumber: 6.2 Consensus size: 11
98597 AAAAAAAATT
98607 ATAAAA-TAAA
1 ATAAAAGTAAA
*
98617 TAAAAAAG-AAA
1 -ATAAAAGTAAA
*
98628 ATATAAGTAAA
1 ATAAAAGTAAA
98639 ATAAAAGT-AA
1 ATAAAAGTAAA
98649 AT-AAA-TAAA
1 ATAAAAGTAAA
*
98658 ATAAAAATAAA
1 ATAAAAGTAAA
98669 AT
1 AT
98671 GATGTCCACT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
8 1 0.02
9 7 0.16
10 12 0.27
11 24 0.55
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (11 bp):
ATAAAAGTAAA
Found at i:99900 original size:39 final size:39
Alignment explanation
Indices: 99846--99929 Score: 159
Period size: 39 Copynumber: 2.2 Consensus size: 39
99836 ACCACCACTA
99846 AGAATCTTCATCCCTTAAAGTCTTACTTAATCTAACATT
1 AGAATCTTCATCCCTTAAAGTCTTACTTAATCTAACATT
99885 AGAATCTTCATCCCTTAAAGTCTTACTTAATCTAACATT
1 AGAATCTTCATCCCTTAAAGTCTTACTTAATCTAACATT
*
99924 AAAATC
1 AGAATC
99930 AATACTTAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.37
Consensus pattern (39 bp):
AGAATCTTCATCCCTTAAAGTCTTACTTAATCTAACATT
Found at i:107014 original size:9 final size:9
Alignment explanation
Indices: 107000--107026 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
106990 AATACCTAGC
107000 GATTTTGCT
1 GATTTTGCT
107009 GATTTTGCT
1 GATTTTGCT
107018 GATTTTGCT
1 GATTTTGCT
107027 ACTTCCGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.22, T:0.56
Consensus pattern (9 bp):
GATTTTGCT
Found at i:109369 original size:16 final size:18
Alignment explanation
Indices: 109347--109384 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
109337 TTCATTAAAA
*
109347 AGAAAAAAAGGGA-AGAG
1 AGAAAATAAGGGAGAGAG
*
109364 AGAAAATGAGGGAGAGAG
1 AGAAAATAAGGGAGAGAG
109382 AGA
1 AGA
109385 GGAAAGAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.39, T:0.03
Consensus pattern (18 bp):
AGAAAATAAGGGAGAGAG
Found at i:113574 original size:3 final size:3
Alignment explanation
Indices: 113566--113595 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
113556 ATAAAATTTG
113566 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
113596 GACATACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:114718 original size:40 final size:40
Alignment explanation
Indices: 114674--114753 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
114664 CCTTATACAG
114674 TGATTTTTATAGTTTGAAACTATATCTTCAAGCCCGAATT
1 TGATTTTTATAGTTTGAAACTATATCTTCAAGCCCGAATT
114714 TGATTTTTATAGTTTGAAACTATATCTTCAAGCCCGAATT
1 TGATTTTTATAGTTTGAAACTATATCTTCAAGCCCGAATT
114754 ATGTTAGATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (40 bp):
TGATTTTTATAGTTTGAAACTATATCTTCAAGCCCGAATT
Found at i:119370 original size:9 final size:8
Alignment explanation
Indices: 119329--119372 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
119319 TATTGATATA
119329 TATTTTTT
1 TATTTTTT
119337 TA-TTTTT
1 TATTTTTT
*
119344 GATCTTATTT
1 TAT-TT-TTT
119354 TATTTTTT
1 TATTTTTT
119362 TATTTTTT
1 TATTTTTT
119370 TAT
1 TAT
119373 AGATCTCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 6 0.19
8 16 0.52
9 4 0.13
10 5 0.16
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (8 bp):
TATTTTTT
Found at i:124318 original size:795 final size:806
Alignment explanation
Indices: 122548--124432 Score: 2296
Period size: 795 Copynumber: 2.3 Consensus size: 806
122538 CCCAACCCTC
* * * * * * * *
122548 AGTTGTT-AAGCTACAAATTTTGAGTTCAGTGAGGAATTTAGCAAGTCAGTTATGAGTCTTTTTG
1 AGTTGTTAAAGCTACAAATTTTGAGTTTAATAAAGAATTTAGCAACTCAATTATGAATCTTTCTG
* ** * * *
122612 CGAGATTCTTTAATGGTTTTGGAGTCA-A-AGGTTTTCTTCTTCAGACATCATTTCAAAC-AGGA
66 CAAGATTCTTCGATGGTTTTGGAGTCACAGAAGTATTC--C-TCAAACATCATTTCAAACAAGG-
* ** *
122674 TTGTAATTTGGGTGAGTTTAATCAA-TTGGAGGAGGAGGAGGAAGAGGAAAAGAAGAGGAAGAAG
127 TTGTAATTCGGGCAAG-TGAAT-AAGTT------GGA-GAGG-A-A-GAAAAGAAGAGGAAG-A-
*
122738 AGTAGAGACTACTTGCTAATCAAACACATGCAGTAACAAGTACTCAATCTATTGTGCTAAAAACA
178 A-TAGAGACTACTTGCTAATCAAACACATGCAGTAACAAGTACTCAATCTATTGTGCTAGAAACA
* * *
122803 GAGACTAAGTTTATATTTCTCAAAATCAAATACCTTTGACTTGATAAATTACCCAAATTGAAAAC
242 GAAACTAAGATTATATTTCCCAAAATCAAATACCTTTGACTTGATAAATTACCCAAATTGAAAAC
*
122868 TTTTTACTCTAGGATACATGCAGAGAGTTAGATTGAAATCTCAAATCAACAACCCTTATTTTGGG
307 TTTTTACTCTAGGATACATGCAGAGAGTAAGATTGAAATCTCAAATCAACAACCC-TA--TT--G
* ** * *
122933 TGATATCATGTAAATCAACAAGAGAAGGAAGAAACCCACACAAATCAATAGGAGAAGTAGGAAAT
367 TGATATCA-GCAAATCAACAAGAGAAACAAGAAACCCACACAAATCAATAAGAGAAATAGGAAAT
** * * * * ** * *
122998 TTAGGCAACAAAACCCAAACAAAAAATACTACAAGATTCTCAGGCCAAAACCTCAATAGACGAAT
431 CCAGGCAACAAAACCAAAACAAAAAACACTAAAAAATTCTCAAACCAAAACCTCAATAGACAAAC
* * *
123063 GAAGAATAAAATCCTTAAAACCACCATACCTTAGCAAGCAAAATCTCAAAAGCAACAAAACCCAA
496 GAAGAATAAAATCCCTAAAACCACCATACCCTAGCAAGCAAAATCCCAAAAGCAACAAAACCCAA
* * * * *
123128 GTAGCAGAAGCAAGAAGCCACCACAAACAAAATTGATATCACGGAAATCAACTAGAGAAGCAACA
561 GCAACAGAAGCAAGAAGCCACCACAAACAAAACTGATATCACGAAAATCAACTAAAGAAGCAACA
* * *
123193 AACCTAAGCGATGAAACCCACAACCAAAACAGTAGAAAAACCTCAAGCGAAAACCCAAACTGACC
626 AACCTAAGCGACGAAACCCAAAACCAAAACAGTAGAAAAACCTCAAACGAAAACCCAAACTGACC
* * *
123258 CTTATATTCGGAGTGGAAAGACCAAATGAAGAATTTCATGGCAAAAACCTGAAAATGTCCTCTCA
691 CTTATATTCGAAGCGGAAAGACCAAATGAAGAATTTCATGGCAAAAACCCGAAAATGTCCTCTCA
* * * *
123323 CATTCATCAGAATACTAAGACAGGTGTTAGACTTTAGACCCCTTTTTACCT
756 CATTCATCAAAATACTAAGACAGGTGTCAGACTCTAGACCCCTTTGTACCT
*
123374 AGTTGTTAAAGTTACAAATTTTGAGTTTAATAAAGAATTTAGCAACTCAATTATGAATCTTTCTG
1 AGTTGTTAAAGCTACAAATTTTGAGTTTAATAAAGAATTTAGCAACTCAATTATGAATCTTTCTG
* *
123439 CAAGATTCTTCGATGGTTTTGGAGTCACAGAAGTGTTCCTCAGACATCATTTCAAACAAGGTTGT
66 CAAGATTCTTCGATGGTTTTGGAGTCACAGAAGTATTCCTCAAACATCATTTCAAACAAGGTTGT
* *
123504 AATTCGGGCAAGTGAATAAGTT-G-GATG-AGAAAA-AAGAGGAAGAATAGAGACTGCTTGCTAA
131 AATTCGGGCAAGTGAATAAGTTGGAGAGGAAGAAAAGAAGAGGAAGAATAGAGACTACTTGCTAA
* * * *
123565 TCAAACACATGCAGTAACAAGTACTCAATCTATTGTGTTAGAGATAGAAACTATA-ATTATGTTT
196 TCAAACACATGCAGTAACAAGTACTCAATCTATTGTGCTAGAAACAGAAACTA-AGATTATATTT
* * *
123629 CCCAAAATCACATACCTTTGCCTTGATAAATTGCCCAAATTGAAAACTTTTTACTCTAAGG-TAC
260 CCCAAAATCAAATACCTTTGACTTGATAAATTACCCAAATTGAAAACTTTTTACTCT-AGGATAC
123693 ATGCAGAGAGTCAAG-TTGAAATCTCAAATCAACAA-CC-A-T-TG-T-TC-GCAAATCAACAAG
324 ATGCAGAGAGT-AAGATTGAAATCTCAAATCAACAACCCTATTGTGATATCAGCAAATCAACAAG
* **
123750 AGAAACAAGAAACGCATGCAAATCAATAAGAGAAATAGGAAATCCAGG-AGACAAAACCTAAAAC
388 AGAAACAAGAAACCCACACAAATCAATAAGAGAAATAGGAAATCCAGGCA-ACAAAACC-AAAAC
* *
123814 -AAAAACACTAAAAAATTCTCAAACTAAAACCTCAATAGACAAACGAAGAATTGAAA-CCCTAAA
451 AAAAAACACTAAAAAATTCTCAAACCAAAACCTCAATAGACAAACGAAGAA-TAAAATCCCTAAA
* * * * * *
123877 ACCACC-TCACCCTAGCAAGTAGAATCCCAAATGCAACAAAACCGAAGCAACAGATGTAAGAAGC
515 ACCACCAT-ACCCTAGCAAGCAAAATCCCAAAAGCAACAAAACCCAAGCAACAGAAGCAAGAAGC
*
123941 CACCACATAA-AAAACTGATATCACGAAAATCAA-TCAAAGAAGCAACAAACCTAAGCGGCGAAA
579 CACCACA-AACAAAACTGATATCACGAAAATCAACT-AAAGAAGCAACAAACCTAAGCGACGAAA
* * * *
124004 CCCAAAACCAAAACAGTAGAAAAACCTCAAAC-ATTATCCCAAACTGACCCTTATGTTTGAAGCG
642 CCCAAAACCAAAACAGTAGAAAAACCTCAAACGA-AAACCCAAACTGACCCTTATATTCGAAGCG
* * * *
124068 GAAATACCAAATGAAGACTTTTATGGCAAAAACCCGAAAATGTCCTCTTACATTCATCAAAATAC
706 GAAAGACCAAATGAAGAATTTCATGGCAAAAACCCGAAAATGTCCTCTCACATTCATCAAAATAC
*
124133 TAAGATAGGTGTCAGACTCTAGACCCCTTTGTACCT
771 TAAGACAGGTGTCAGACTCTAGACCCCTTTGTACCT
* * *
124169 AGTTGTTAAAGCTACAAATTTTGAGTTTAGT-GAGAAATTTAGCAACTCGATTATGAATCTTTCT
1 AGTTGTTAAAGCTACAAATTTTGAGTTTAATAAAG-AATTTAGCAACTCAATTATGAATCTTTCT
* * *
124233 GCAAGATTCTTCGATGGTTTT-TAGTCACAGAGGTATTCCTCAAACATCATTTCCAACAAGGTTG
65 GCAAGATTCTTCGATGGTTTTGGAGTCACAGAAGTATTCCTCAAACATCATTTCAAACAAGGTTG
124297 TAATTCGGGCAAGTCGAATAAGTTGGAAGAGGAAAAAGAGGAAAGAAGAGGAAAGAGAATAGAGA
130 TAATTCGGGCAAGT-GAATAAGTTGG-AGAGG---AAGA--AAAGAAGAGG--A-AGAATAGAGA
124362 CTACTTGCTAATCAAACACATGCAGTAACAAGTACTCAATCTATTGTGCTAGAAACAGAAACTAA
185 CTACTTGCTAATCAAACACATGCAGTAACAAGTACTCAATCTATTGTGCTAGAAACAGAAACTAA
*
124427 GTTTAT
250 GATTAT
124433 GTTTATCTAA
Statistics
Matches: 927, Mismatches: 101, Indels: 80
0.84 0.09 0.07
Matches are distributed among these distances:
794 58 0.06
795 444 0.48
796 11 0.01
797 2 0.00
798 4 0.00
799 2 0.00
802 4 0.00
804 3 0.00
805 7 0.01
807 4 0.00
808 232 0.25
809 7 0.01
810 1 0.00
811 9 0.01
812 5 0.01
813 1 0.00
816 3 0.00
818 1 0.00
824 2 0.00
825 6 0.01
826 38 0.04
827 76 0.08
828 1 0.00
829 6 0.01
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (806 bp):
AGTTGTTAAAGCTACAAATTTTGAGTTTAATAAAGAATTTAGCAACTCAATTATGAATCTTTCTG
CAAGATTCTTCGATGGTTTTGGAGTCACAGAAGTATTCCTCAAACATCATTTCAAACAAGGTTGT
AATTCGGGCAAGTGAATAAGTTGGAGAGGAAGAAAAGAAGAGGAAGAATAGAGACTACTTGCTAA
TCAAACACATGCAGTAACAAGTACTCAATCTATTGTGCTAGAAACAGAAACTAAGATTATATTTC
CCAAAATCAAATACCTTTGACTTGATAAATTACCCAAATTGAAAACTTTTTACTCTAGGATACAT
GCAGAGAGTAAGATTGAAATCTCAAATCAACAACCCTATTGTGATATCAGCAAATCAACAAGAGA
AACAAGAAACCCACACAAATCAATAAGAGAAATAGGAAATCCAGGCAACAAAACCAAAACAAAAA
ACACTAAAAAATTCTCAAACCAAAACCTCAATAGACAAACGAAGAATAAAATCCCTAAAACCACC
ATACCCTAGCAAGCAAAATCCCAAAAGCAACAAAACCCAAGCAACAGAAGCAAGAAGCCACCACA
AACAAAACTGATATCACGAAAATCAACTAAAGAAGCAACAAACCTAAGCGACGAAACCCAAAACC
AAAACAGTAGAAAAACCTCAAACGAAAACCCAAACTGACCCTTATATTCGAAGCGGAAAGACCAA
ATGAAGAATTTCATGGCAAAAACCCGAAAATGTCCTCTCACATTCATCAAAATACTAAGACAGGT
GTCAGACTCTAGACCCCTTTGTACCT
Found at i:124347 original size:10 final size:10
Alignment explanation
Indices: 124322--124352 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
124312 GAATAAGTTG
124322 GAAGAGGAAA
1 GAAGAGGAAA
124332 -AAGAGGAAA
1 GAAGAGGAAA
124341 GAAGAGGAAA
1 GAAGAGGAAA
124351 GA
1 GA
124353 GAATAGAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (10 bp):
GAAGAGGAAA
Found at i:126026 original size:822 final size:815
Alignment explanation
Indices: 124441--127267 Score: 3404
Period size: 822 Copynumber: 3.5 Consensus size: 815
124431 ATGTTTATCT
* * * * ** * *
124441 AAGCGGCAAAACCTAAAACAAAAACACTAGAAAATTCTCAGGTTGAAACCTCAATAGACAAAC-A
1 AAGCGACAAAACCCAAAACAAAAACACTAGAAGATTCTCAAGCCGAAACCTCAACAGACGAACGA
* * *
124505 AGAATAGAAAC-CCTAAAACCACCCTGGCC-TAGCAAGCAGAATCCCAAATGCAACAAAACCCAA
66 AGAATAAAAACTCC-AAAACCACCCT-ACCTTGGCAAGCAGAATCCCAAATGCAACAAAACCCAA
* * ** * * * * * *
124568 GCAGCAGATTTAAGAAGCCACCACATAGAAAACTAATATCATGACAATCAATCAAAGAAGCAATA
129 GCAACAAATGCAAGAAGCCACCACATAGAAAATTGATATCACGAAAATCAACCAAAGAAGCAACA
* ** * *
124633 AACCTAAGCGGCGAAACCCAAAACCAAAACAGTAGAAAAACCTCAAGCAAAAACCCAAAATG-GC
194 AACCTAACCGGCGAAACCCAAAACCAAAACAACAGAAAAACCTCAAGCAAAAACCCAAACTGACC
* * ** ** **
124697 GTTAATGTTTTGAG-CAAAAAGACCAAATAAAGACTTTCATGGCAAAAACCTGAAAATGTCCTCT
259 CTT-ATATTCAGAGTGGAAAAGACCAAATAAAGACTTTCATGGCAAAAACCCAAAAATGTCCTCT
* * *
124761 TGCATTCATCAAAATACTAGGACAGGTGTCAAACTCTAGACCCCTCTATATCC-AGTTGTTAAAG
323 TACATTCATCAAAAGACTAGGACAGGTGTCAAACTCTAGACCCCTCTGTA-CCTAGTTGTTAAAG
* * * * * * *
124825 CTATAAATTTTGAGTTCAGTGAGAAATTTAGCAACTCGGTTATGAATATTTTTACGAGATTTTTG
387 CTACAAATTTTGAGTTCAGTGAGGAATTTAGCAACTCGGTTATGAATCTTTCTGCAAGATTTTTT
* * * *
124890 GATGGTTTTGGAGCCATGGAGGTGTTCCTCAGACATCATTTTAAACAAGGTTGTAATTCGGGCAA
452 GATGGTTTTGGAGTCACGGAGGTGTTCCTCAG--ATCATTTCAAACAGGGTTGTAATTCGGGCAA
* * * **
124955 GTTGAATAAGTTGGAAGAGGAAGA--AAAG---AGGAAAAATAGTAAAGACTGCATGGTAATCAA
515 GTTGAATAAGTTGGAGGAGGAAGAGGAAAGAAAAGGAAAAAAAGTAGAGACTGC-TTATAATCAA
*
125015 ACACATGTAGTAACAGGTACTCAATCTATTGTGCTAGAAACAGAGACTAAGTTTATATTTCCTAA
579 ACACATGTAGTAACAAGTACTCAATCTATTGTGCTAGAAACAGAGACTAAGTTTATATTTCC-AA
125080 AATCACATACCTTTGACTTGATAAATTGCCCAAATTGAAAACTTTTTACTTTAAGATACATGCAG
643 AATCACATACCTTTGACTTGATAAATTGCCCAAATTGAAAACTTTTTACTTTAAGATACATGCAG
* * *
125145 AGAGTCAAGTTGAAATCTCAAATCAACAACCCTTATTTCAGGTAAAATCAC-GTAAATCAACAAG
708 AGAGTCAGGTTGAAATCTCAAATCAACAACCCTTA-TTCAGGTGATATCACTG-AAATCAACAAG
* * * *
125209 AAAAGCAAGAAACTCAAGAAAATCAATAGAAGAAGTAGAAAATCC
771 AAAAGCAAGAAACCCAACAAAATCAATAGAAGAAGCAGGAAATCC
* * * * * *
125254 AAGCAACAAAACCTAAAACAAAGACACTAGGAGATTCTCAAGTCGAAACCTCAACAGACGAATGA
1 AAGCGACAAAACCCAAAACAAAAACACTAGAAGATTCTCAAGCCGAAACCTCAACAGACGAACGA
* * *
125319 ATAATAAAAACTCCAAAACCACCCTGCCTTGGCAAGTAGAATCCCAAATGCAACAAAACCCAA-C
66 AGAATAAAAACTCCAAAACCACCCTACCTTGGCAAGCAGAATCCCAAATGCAACAAAACCCAAGC
* * * *
125383 AGCAGAA-GCAAGAAGCCACCACATAGAAAATTGATATCACATAAAAATCAACTAGAGAAGCAAC
131 AACA-AATGCAAGAAGCCACCACATAGAAAATTGATATCAC--GAAAATCAACCAAAGAAGCAAC
* * * * * * *
125447 AAACCTCACCGACGAAACCTAAAACC-AAACAACAGAAAAACCTTAAGCAGAAACCTAAATTGAC
193 AAACCTAACCGGCGAAACCCAAAACCAAAACAACAGAAAAACCTCAAGCAAAAACCCAAACTGAC
* * * * *
125511 CTTTATATTCGGAGTGGAAAA-ACCAACTAAAGACTTTCATGGTAAAAACCCAAAAATGTCCCCT
258 CCTTATATTCAGAGTGGAAAAGACCAAATAAAGACTTTCATGGCAAAAACCCAAAAATGTCCTCT
* * * *
125575 TACATTCATTAAAATACTAGGACAGGTGTCAAACTTTAGACCCCTATGTACCTAGTTGTTAAAGC
323 TACATTCATCAAAAGACTAGGACAGGTGTCAAACTCTAGACCCCTCTGTACCTAGTTGTTAAAGC
* *** * *
125640 TACAAATTTTGAGTTTAACAAGGAATTTAGCAACTCGATAATGAATCTTTCTGCAAGATTTTTTG
388 TACAAATTTTGAGTTCAGTGAGGAATTTAGCAACTCGGTTATGAATCTTTCTGCAAGATTTTTTG
* * * *
125705 ATGATTTTGGAGTCACGGAGGTGTTTCTCATGATCAATTCAAATAGGGTTGTAATTCGGGCAAGT
453 ATGGTTTTGGAGTCACGGAGGTGTTCCTCA-GATCATTTCAAACAGGGTTGTAATTCGGGCAAGT
125770 TGAATAAGTTGAAGGAGGAGGAAGAGGAAGAGAAAAGGAAAAAAAGTAGAGACTGCTTACTAATC
517 TGAATAAGTT---GGAGGAGGAAGAGGAA-AGAAAAGGAAAAAAAGTAGAGACTGCTTA-TAATC
* *
125835 AAACACATGCAGTAACAAGTACTCAATCTATTGTGCTAGAAACAGAAACTAAGTTTATATTTTCC
577 AAACACATGTAGTAACAAGTACTCAATCTATTGTGCTAGAAACAGAGACTAAGTTTATA-TTTCC
** * *
125900 AAAATCACATACCTTTGACTTGATAAACCGCCCAAATTGAAAACCTTTTACTTTAAAATACATGC
641 AAAATCACATACCTTTGACTTGATAAATTGCCCAAATTGAAAACTTTTTACTTTAAGATACATGC
* * *
125965 AGAGAGTGAGGTTGAAATTTCAAATCAACAACCCTTACTTCAAGTGATATC-CTGCAAATCAACA
706 AGAGAGTCAGGTTGAAATCTCAAATCAACAACCCTTA-TTCAGGTGATATCACTG-AAATCAACA
* * * * *
126029 AGAGAAGTAAGAAACCCATCCAAATCAATAGGAGAAGCAGGAAATCC
769 AGAAAAGCAAGAAACCCAACAAAATCAATAGAAGAAGCAGGAAATCC
* * * * *
126076 AGGCGATAAAACCCAAAACAAAAACACTAGAAGATTCTCAAACCGAAACTTCAACAAACGAACGA
1 AAGCGACAAAACCCAAAACAAAAACACTAGAAGATTCTCAAGCCGAAACCTCAACAGACGAACGA
* *
126141 AGAATAAAAA-TCCCAAAACCACCCTACCTTGACAAGCAGAATCCCAAATGCAATAAAACCCAAG
66 AGAATAAAAACT-CCAAAACCACCCTACCTTGGCAAGCAGAATCCCAAATGCAACAAAACCCAAG
* * *
126205 CAACAAATGCAAAAAGCCACCACATATAAAATTGATATCACGAAAATCAACCAAAGAAGCAATAA
130 CAACAAATGCAAGAAGCCACCACATAGAAAATTGATATCACGAAAATCAACCAAAGAAGCAACAA
* * * * * * ** *
126270 ACCTAAGCTGCGAAACCCAAAGCCAAAACAATAGAATAACCTCAAGCAGAAACTTAAACTAACCC
195 ACCTAACCGGCGAAACCCAAAACCAAAACAACAGAAAAACCTCAAGCAAAAACCCAAACTGACCC
* * * * **
126335 TTGTGTTCAGAGT-GAAAAGACCAAATGAAGACTTTCATGGTAAAAAAGCAAAAATGTCCTCTTA
260 TTATATTCAGAGTGGAAAAGACCAAATAAAGACTTTCATGGCAAAAACCCAAAAATGTCCTCTTA
* * *
126399 CATTCATTAAAAGAATAGGACAGGTGTCAAACTCTTGACCCCTCTGTACCTAGTTGTTAAAGCTA
325 CATTCATCAAAAGACTAGGACAGGTGTCAAACTCTAGACCCCTCTGTACCTAGTTGTTAAAGCTA
* ** * *
126464 CAAATTTTGAGTTCAGTGAGGAATTTAGCAACTTGGTTATGGGTCTTTCTGCAAGATTCTTTAAT
390 CAAATTTTGAGTTCAGTGAGGAATTTAGCAACTCGGTTATGAATCTTTCTGCAAGATTTTTTGAT
* * *
126529 GGTTTTGGAGTCACAGAGGTGTTCCTCAAACATCATTTCAAACAGGGTTGTAATTCGGTCAAGTT
455 GGTTTTGGAGTCACGGAGGTGTTCCTC--AGATCATTTCAAACAGGGTTGTAATTCGGGCAAGTT
* * * ** * * *
126594 GAATCAGTTGGAGAAAGAAGAGGAAAAGAAAAGGAAGGAGAGTAGAGATTGCTTGATAATTAAAC
518 GAATAAGTTGGAGGAGGAAGAGG-AAAGAAAAGGAAAAAAAGTAGAGACTGCTT-ATAATCAAAC
* * *
126659 ACATGTAGTAACAAGTACTCAATCTATTATGTTAGAAACAGAGACTAAGTTTATATTTCTCGAAA
581 ACATGTAGTAACAAGTACTCAATCTATTGTGCTAGAAACAGAGACTAAGTTTATATTTC-CAAAA
* * *
126724 TCACATACCTTTGACTTGATAAATTGCCCAAATTAAAAACTTTTTACTATAAGATACATGTAGAG
645 TCACATACCTTTGACTTGATAAATTGCCCAAATTGAAAACTTTTTACTTTAAGATACATGCAGAG
* ** *
126789 AGTCTGGTTGAAATCTCAAATCAACAACCCTTATTTTGGATGATATCACAT-AAATCAATAAGAA
710 AGTCAGGTTGAAATCTCAAATCAACAACCCTTATTCAGG-TGATATCAC-TGAAATCAACAAGAA
126853 AAGCAAGAAACCCACACAAAA-CAATAGGAA-AAGCAGGAAATCC
773 AAGCAAGAAACCCA-ACAAAATCAATA-GAAGAAGCAGGAAATCC
** * * *
126896 AATTGACAAAACCCAAAACAACAACACTAGAAGATTCTCAAGCCGAAACCTTAACAGACGAACAA
1 AAGCGACAAAACCCAAAACAAAAACACTAGAAGATTCTCAAGCCGAAACCTCAACAGACGAACGA
* * * * *
126961 AGAATAGAAACCCCAAAACCACCATACCTTGGCAAGTAGAATCCCAAATGCAGCAAAACCCAAGC
66 AGAATAAAAACTCCAAAACCACCCTACCTTGGCAAGCAGAATCCCAAATGCAACAAAACCCAAGC
* *
127026 AACAAATGCAAGACA-CCACCATATA-AAACATTGATATCACGAAAATCAACCAGAGAAGCAACA
131 AACAAATGCAAGA-AGCCACCACATAGAAA-ATTGATATCACGAAAATCAACCAAAGAAGCAACA
* * * * *
127089 AACCTAAGCGGCGAAACCTAAAACCAAAATAACAAAAAAACCTCAAGAAAAAACCCAAACTGACC
194 AACCTAACCGGCGAAACCCAAAACCAAAACAACAGAAAAACCTCAAGCAAAAACCCAAACTGACC
* * ** *
127154 CTTGTATTCAGAGTGG-AAAGACCAAATGAAGACTTTCATGGCAAAAA-ATAAAAACCGTCCTCT
259 CTTATATTCAGAGTGGAAAAGACCAAATAAAGACTTTCATGGCAAAAACCCAAAAA-TGTCCTCT
* * *
127217 TACATTCATCAAAAGA-TCAAGACAGGTGTCAGACTCTAGATCCCTCTGTAC
323 TACATTCATCAAAAGACT-AGGACAGGTGTCAAACTCTAGACCCCTCTGTAC
127268 ATGAGATTCA
Statistics
Matches: 1726, Mismatches: 245, Indels: 79
0.84 0.12 0.04
Matches are distributed among these distances:
813 130 0.08
814 264 0.15
815 48 0.03
816 11 0.01
818 2 0.00
819 18 0.01
820 548 0.32
821 58 0.03
822 567 0.33
823 79 0.05
824 1 0.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (815 bp):
AAGCGACAAAACCCAAAACAAAAACACTAGAAGATTCTCAAGCCGAAACCTCAACAGACGAACGA
AGAATAAAAACTCCAAAACCACCCTACCTTGGCAAGCAGAATCCCAAATGCAACAAAACCCAAGC
AACAAATGCAAGAAGCCACCACATAGAAAATTGATATCACGAAAATCAACCAAAGAAGCAACAAA
CCTAACCGGCGAAACCCAAAACCAAAACAACAGAAAAACCTCAAGCAAAAACCCAAACTGACCCT
TATATTCAGAGTGGAAAAGACCAAATAAAGACTTTCATGGCAAAAACCCAAAAATGTCCTCTTAC
ATTCATCAAAAGACTAGGACAGGTGTCAAACTCTAGACCCCTCTGTACCTAGTTGTTAAAGCTAC
AAATTTTGAGTTCAGTGAGGAATTTAGCAACTCGGTTATGAATCTTTCTGCAAGATTTTTTGATG
GTTTTGGAGTCACGGAGGTGTTCCTCAGATCATTTCAAACAGGGTTGTAATTCGGGCAAGTTGAA
TAAGTTGGAGGAGGAAGAGGAAAGAAAAGGAAAAAAAGTAGAGACTGCTTATAATCAAACACATG
TAGTAACAAGTACTCAATCTATTGTGCTAGAAACAGAGACTAAGTTTATATTTCCAAAATCACAT
ACCTTTGACTTGATAAATTGCCCAAATTGAAAACTTTTTACTTTAAGATACATGCAGAGAGTCAG
GTTGAAATCTCAAATCAACAACCCTTATTCAGGTGATATCACTGAAATCAACAAGAAAAGCAAGA
AACCCAACAAAATCAATAGAAGAAGCAGGAAATCC
Found at i:126884 original size:30 final size:30
Alignment explanation
Indices: 126835--126892 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
126825 TGGATGATAT
* *
126835 CACATAAATCAATAAGAAAAGCAAGAAACC
1 CACACAAAACAATAAGAAAAGCAAGAAACC
* *
126865 CACACAAAACAATAGGAAAAGCAGGAAA
1 CACACAAAACAATAAGAAAAGCAAGAAA
126893 TCCAATTGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.60, C:0.19, G:0.14, T:0.07
Consensus pattern (30 bp):
CACACAAAACAATAAGAAAAGCAAGAAACC
Found at i:126924 original size:820 final size:816
Alignment explanation
Indices: 124441--127267 Score: 3397
Period size: 820 Copynumber: 3.5 Consensus size: 816
124431 ATGTTTATCT
* * * * ** * *
124441 AAGCGGCAAAACCTAAAACAAAAACACTAGAAAATTCTCAGGTTGAAACCTCAATAGACAAAC-A
1 AAGCGACAAAACCCAAAACAAAAACACTAGAAGATTCTCAAGCCGAAACCTCAACAGACGAACGA
* * *
124505 AGAATAGAAACCCTAAAACCACCCTGGCC-TAGCAAGCAGAATCCCAAATGCAACAAAACCCAAG
66 AGAATAAAAACCC-AAAACCACCCT-ACCTTGGCAAGCAGAATCCCAAATGCAACAAAACCCAAG
* * ** * * * * * * *
124569 CAGCAGATTTAAGAAGCCACCACATAGAAAACTAATATCATGACAATCAATCAAAGAAGCAATAA
129 CAACAAATGCAAAAAGCCACCACATAGAAAATTGATATCACGAAAATCAACCAAAGAAGCAACAA
** * * *
124634 ACCTAAGCGGCGAAACCCAAAACCAAAACAGTAGAAAAACCTCAAGCAAAAACCCAAAATG-GCG
194 ACCTAAGCGGCGAAACCCAAAACCAAAACAACAGAAAAACCTCAAGCAAAAACCCAAACTGACCC
* ** ** * *
124698 TTAATGTTTTGAGCAAAAAGACCAAATAAAGACTTTCATGG-CAAAAACCTGAAAATGTCCTCTT
259 TT-ATATTCAGAGTGAAAAGACCAAATAAAGACTTTCATGGTAAAAAACC-AAAAATGTCCTCTT
* * * *
124762 GCATTCATCAAAATACTAGGACAGGTGTCAAACTCTAGACCCCTCTATATCC-AGTTGTTAAAGC
322 ACATTCATCAAAAGAATAGGACAGGTGTCAAACTCTAGACCCCTCTGTA-CCTAGTTGTTAAAGC
* * * * * *
124826 TATAAATTTTGAGTTCAGTGAGAAATTTAGCAACTCGGTTATGAATATTTTTACGAGATTTTTGG
386 TACAAATTTTGAGTTCAGTGAGGAATTTAGCAACTCGGTTATGAATCTTTCTGCAAGATTTTT-G
* * * * *
124891 ATGGTTTTGGAGCCATGGAGGTGTTCCTCAGACATCATTTTAAACAAGGTTGTAATTCGGGCAAG
450 ATGGTTTTGGAGTCACGGAGGTGTTCCTCAAACATCATTTCAAACAGGGTTGTAATTCGGGCAAG
* * * * * *
124956 TTGAATAAGTT-G-GAAGAGGAAGAAAAG---AGGAAAAATAGTAAAGACTGCATGGTAATCAAA
515 TTGAATAAGTTGGAGAAGAAGAGGAAAAGAAAAGGAAAAAAAGTAGAGACTGCTTGATAATCAAA
*
125016 CACATGTAGTAACAGGTACTCAATCTATTGTGCTAGAAACAGAGACTAAGTTTATATTTC-CTAA
580 CACATGTAGTAACAAGTACTCAATCTATTGTGCTAGAAACAGAGACTAAGTTTATATTTCTC-AA
125080 AATCACATACCTTTGACTTGATAAATTGCCCAAATTGAAAACTTTTTACTTTAAGATACATGCAG
644 AATCACATACCTTTGACTTGATAAATTGCCCAAATTGAAAACTTTTTACTTTAAGATACATGCAG
* * * *
125145 AGAGTCAAGTTGAAATCTCAAATCAACAACCCTTATTTCAGG-TAAAATCACGTAAATCAACAAG
709 AGAGTCAGGTTGAAATCTCAAATCAACAACCCTTATTT-TGGATGATATCAC-TAAATCAACAAG
* * * *
125209 AAAAGCAAGAAACTCA-AGAAAATCAATA-GAAGAAGTAGAAAATCC
772 AAAAGCAAGAAACCCACACAAAA-CAATAGGAA-AAGCAGGAAATCC
* * * * * *
125254 AAGCAACAAAACCTAAAACAAAGACACTAGGAGATTCTCAAGTCGAAACCTCAACAGACGAATGA
1 AAGCGACAAAACCCAAAACAAAAACACTAGAAGATTCTCAAGCCGAAACCTCAACAGACGAACGA
* * *
125319 ATAATAAAAACTCCAAAACCACCCTGCCTTGGCAAGTAGAATCCCAAATGCAACAAAACCCAA-C
66 AGAATAAAAAC-CCAAAACCACCCTACCTTGGCAAGCAGAATCCCAAATGCAACAAAACCCAAGC
* * * * *
125383 AGCAGAA-GCAAGAAGCCACCACATAGAAAATTGATATCACATAAAAATCAACTAGAGAAGCAAC
130 AACA-AATGCAAAAAGCCACCACATAGAAAATTGATATCAC--GAAAATCAACCAAAGAAGCAAC
* * * * * * * *
125447 AAACCTCACCGACGAAACCTAAAACC-AAACAACAGAAAAACCTTAAGCAGAAACCTAAATTGAC
192 AAACCTAAGCGGCGAAACCCAAAACCAAAACAACAGAAAAACCTCAAGCAAAAACCCAAACTGAC
* * * * *
125511 CTTTATATTCGGAGTGGAAAA-ACCAACTAAAGACTTTCATGGTAAAAACCCAAAAATGTCCCCT
257 CCTTATATTCAGAGT-GAAAAGACCAAATAAAGACTTTCATGGTAAAAAACCAAAAATGTCCTCT
* * * * *
125575 TACATTCATTAAAATACTAGGACAGGTGTCAAACTTTAGACCCCTATGTACCTAGTTGTTAAAGC
321 TACATTCATCAAAAGAATAGGACAGGTGTCAAACTCTAGACCCCTCTGTACCTAGTTGTTAAAGC
* *** * *
125640 TACAAATTTTGAGTTTAACAAGGAATTTAGCAACTCGATAATGAATCTTTCTGCAAGATTTTTTG
386 TACAAATTTTGAGTTCAGTGAGGAATTTAGCAACTCGGTTATGAATCTTTCTGCAAGA-TTTTTG
* * ** * *
125705 ATGATTTTGGAGTCACGGAGGTGTTTCTC-ATGATCAATTCAAATAGGGTTGTAATTCGGGCAAG
450 ATGGTTTTGGAGTCACGGAGGTGTTCCTCAAACATCATTTCAAACAGGGTTGTAATTCGGGCAAG
* *
125769 TTGAATAAGTTGAAGGAGGAGGAAGAGGAAGAGAAAAGGAAAAAAAGTAGAGACTGCTT-ACTAA
515 TTGAATAAGTT---GGA-GAAGAAGAGGAAAAGAAAAGGAAAAAAAGTAGAGACTGCTTGA-TAA
* *
125833 TCAAACACATGCAGTAACAAGTACTCAATCTATTGTGCTAGAAACAGAAACTAAGTTTATATTT-
575 TCAAACACATGTAGTAACAAGTACTCAATCTATTGTGCTAGAAACAGAGACTAAGTTTATATTTC
** * *
125897 TCCAAAATCACATACCTTTGACTTGATAAACCGCCCAAATTGAAAACCTTTTACTTTAAAATACA
640 T-CAAAATCACATACCTTTGACTTGATAAATTGCCCAAATTGAAAACTTTTTACTTTAAGATACA
* * * **
125962 TGCAGAGAGTGAGGTTGAAATTTCAAATCAACAACCCTTA-CTTCAAGTGATATC-CTGCAAATC
704 TGCAGAGAGTCAGGTTGAAATCTCAAATCAACAACCCTTATTTTGGA-TGATATCACT--AAATC
* * * *
126025 AACAAGAGAAGTAAGAAACCCATC-CAAATCAATAGGAGAAGCAGGAAATCC
766 AACAAGAAAAGCAAGAAACCCA-CACAAAACAATAGGAAAAGCAGGAAATCC
* * * * *
126076 AGGCGATAAAACCCAAAACAAAAACACTAGAAGATTCTCAAACCGAAACTTCAACAAACGAACGA
1 AAGCGACAAAACCCAAAACAAAAACACTAGAAGATTCTCAAGCCGAAACCTCAACAGACGAACGA
* *
126141 AGAATAAAAATCCCAAAACCACCCTACCTTGACAAGCAGAATCCCAAATGCAATAAAACCCAAGC
66 AGAATAAAAA-CCCAAAACCACCCTACCTTGGCAAGCAGAATCCCAAATGCAACAAAACCCAAGC
* *
126206 AACAAATGCAAAAAGCCACCACATATAAAATTGATATCACGAAAATCAACCAAAGAAGCAATAAA
130 AACAAATGCAAAAAGCCACCACATAGAAAATTGATATCACGAAAATCAACCAAAGAAGCAACAAA
* * * * * ** *
126271 CCTAAGCTGCGAAACCCAAAGCCAAAACAATAGAATAACCTCAAGCAGAAACTTAAACTAACCCT
195 CCTAAGCGGCGAAACCCAAAACCAAAACAACAGAAAAACCTCAAGCAAAAACCCAAACTGACCCT
* * * *
126336 TGTGTTCAGAGTGAAAAGACCAAATGAAGACTTTCATGGTAAAAAAGCAAAAATGTCCTCTTACA
260 TATATTCAGAGTGAAAAGACCAAATAAAGACTTTCATGGTAAAAAACCAAAAATGTCCTCTTACA
* *
126401 TTCATTAAAAGAATAGGACAGGTGTCAAACTCTTGACCCCTCTGTACCTAGTTGTTAAAGCTACA
325 TTCATCAAAAGAATAGGACAGGTGTCAAACTCTAGACCCCTCTGTACCTAGTTGTTAAAGCTACA
* ** *
126466 AATTTTGAGTTCAGTGAGGAATTTAGCAACTTGGTTATGGGTCTTTCTGCAAGATTCTTTAATGG
390 AATTTTGAGTTCAGTGAGGAATTTAGCAACTCGGTTATGAATCTTTCTGCAAGATT-TTTGATGG
* *
126531 TTTTGGAGTCACAGAGGTGTTCCTCAAACATCATTTCAAACAGGGTTGTAATTCGGTCAAGTTGA
454 TTTTGGAGTCACGGAGGTGTTCCTCAAACATCATTTCAAACAGGGTTGTAATTCGGGCAAGTTGA
* ** * * *
126596 ATCAGTTGGAGAAAGAAGAGGAAAAGAAAAGGAAGGAGAGTAGAGATTGCTTGATAATTAAACAC
519 ATAAGTTGGAG-AAGAAGAGGAAAAGAAAAGGAAAAAAAGTAGAGACTGCTTGATAATCAAACAC
* * *
126661 ATGTAGTAACAAGTACTCAATCTATTATGTTAGAAACAGAGACTAAGTTTATATTTCTCGAAATC
583 ATGTAGTAACAAGTACTCAATCTATTGTGCTAGAAACAGAGACTAAGTTTATATTTCTCAAAATC
* * *
126726 ACATACCTTTGACTTGATAAATTGCCCAAATTAAAAACTTTTTACTATAAGATACATGTAGAGAG
648 ACATACCTTTGACTTGATAAATTGCCCAAATTGAAAACTTTTTACTTTAAGATACATGCAGAGAG
* *
126791 TCTGGTTGAAATCTCAAATCAACAACCCTTATTTTGGATGATATCACATAAATCAATAAGAAAAG
713 TCAGGTTGAAATCTCAAATCAACAACCCTTATTTTGGATGATATCAC-TAAATCAACAAGAAAAG
126856 CAAGAAACCCACACAAAACAATAGGAAAAGCAGGAAATCC
777 CAAGAAACCCACACAAAACAATAGGAAAAGCAGGAAATCC
** * * *
126896 AATTGACAAAACCCAAAACAACAACACTAGAAGATTCTCAAGCCGAAACCTTAACAGACGAACAA
1 AAGCGACAAAACCCAAAACAAAAACACTAGAAGATTCTCAAGCCGAAACCTCAACAGACGAACGA
* * * *
126961 AGAATAGAAACCCCAAAACCACCATACCTTGGCAAGTAGAATCCCAAATGCAGCAAAACCCAAGC
66 AGAATA-AAAACCCAAAACCACCCTACCTTGGCAAGCAGAATCCCAAATGCAACAAAACCCAAGC
* * *
127026 AACAAATGCAAGACA-CCACCATATA-AAACATTGATATCACGAAAATCAACCAGAGAAGCAACA
130 AACAAATGCAA-AAAGCCACCACATAGAAA-ATTGATATCACGAAAATCAACCAAAGAAGCAACA
* * * *
127089 AACCTAAGCGGCGAAACCTAAAACCAAAATAACAAAAAAACCTCAAGAAAAAACCCAAACTGACC
193 AACCTAAGCGGCGAAACCCAAAACCAAAACAACAGAAAAACCTCAAGCAAAAACCCAAACTGACC
* * * * * *
127154 CTTGTATTCAGAGTGGAAAGACCAAATGAAGACTTTCATGGCAAAAAA-TAAAAACCGTCCTCTT
258 CTTATATTCAGAGTGAAAAGACCAAATAAAGACTTTCATGGTAAAAAACCAAAAA-TGTCCTCTT
* * *
127218 ACATTCATCAAAAG-ATCAAGACAGGTGTCAGACTCTAGATCCCTCTGTAC
322 ACATTCATCAAAAGAAT-AGGACAGGTGTCAAACTCTAGACCCCTCTGTAC
127268 ATGAGATTCA
Statistics
Matches: 1717, Mismatches: 248, Indels: 91
0.84 0.12 0.04
Matches are distributed among these distances:
813 130 0.08
814 251 0.15
815 58 0.03
817 1 0.00
819 23 0.01
820 558 0.32
821 58 0.03
822 556 0.32
823 82 0.05
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (816 bp):
AAGCGACAAAACCCAAAACAAAAACACTAGAAGATTCTCAAGCCGAAACCTCAACAGACGAACGA
AGAATAAAAACCCAAAACCACCCTACCTTGGCAAGCAGAATCCCAAATGCAACAAAACCCAAGCA
ACAAATGCAAAAAGCCACCACATAGAAAATTGATATCACGAAAATCAACCAAAGAAGCAACAAAC
CTAAGCGGCGAAACCCAAAACCAAAACAACAGAAAAACCTCAAGCAAAAACCCAAACTGACCCTT
ATATTCAGAGTGAAAAGACCAAATAAAGACTTTCATGGTAAAAAACCAAAAATGTCCTCTTACAT
TCATCAAAAGAATAGGACAGGTGTCAAACTCTAGACCCCTCTGTACCTAGTTGTTAAAGCTACAA
ATTTTGAGTTCAGTGAGGAATTTAGCAACTCGGTTATGAATCTTTCTGCAAGATTTTTGATGGTT
TTGGAGTCACGGAGGTGTTCCTCAAACATCATTTCAAACAGGGTTGTAATTCGGGCAAGTTGAAT
AAGTTGGAGAAGAAGAGGAAAAGAAAAGGAAAAAAAGTAGAGACTGCTTGATAATCAAACACATG
TAGTAACAAGTACTCAATCTATTGTGCTAGAAACAGAGACTAAGTTTATATTTCTCAAAATCACA
TACCTTTGACTTGATAAATTGCCCAAATTGAAAACTTTTTACTTTAAGATACATGCAGAGAGTCA
GGTTGAAATCTCAAATCAACAACCCTTATTTTGGATGATATCACTAAATCAACAAGAAAAGCAAG
AAACCCACACAAAACAATAGGAAAAGCAGGAAATCC
Found at i:135544 original size:2 final size:2
Alignment explanation
Indices: 135537--135562 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
135527 GAATGATATA
135537 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
135563 ACCTCTTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:146753 original size:2 final size:2
Alignment explanation
Indices: 146746--146782 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
146736 GAAATCAAAC
146746 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
146783 TGATTAATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:147648 original size:11 final size:11
Alignment explanation
Indices: 147632--147657 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
147622 ATAATGCACA
147632 AGATTAATTAC
1 AGATTAATTAC
147643 AGATTAATTAC
1 AGATTAATTAC
147654 AGAT
1 AGAT
147658 AAGAGAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (11 bp):
AGATTAATTAC
Found at i:155307 original size:4 final size:4
Alignment explanation
Indices: 155298--155333 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
155288 TGAATATGGA
155298 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
155334 CTAAGAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:162906 original size:18 final size:17
Alignment explanation
Indices: 162885--163045 Score: 55
Period size: 17 Copynumber: 9.1 Consensus size: 17
162875 TAATGTCATA
*
162885 TATTTTATTTTTATTTCT
1 TATTTTATTTTTATAT-T
* *
162903 TATTATAATTTTATATT
1 TATTTTATTTTTATATT
*
162920 T-TTTTATTTTT-TAATA
1 TATTTTATTTTTAT-ATT
* * *
162936 TAATTT-TTTATATTATA
1 TATTTTATTTTTA-TATT
162953 TATTTTA-TTTTA-ATT
1 TATTTTATTTTTATATT
* * *
162968 TTTTTTACTTATACTATATA
1 TATTTTA-TT-T-TTATATT
*
162988 AATTTTAATTTCTTATATTT
1 TATTTT-ATTT-TTATA-TT
* *
163008 TATTTTATTTTAATTTT
1 TATTTTATTTTTATATT
163025 TATATTATATATTTTAT-TT
1 TAT-TT-TAT-TTTTATATT
163044 TA
1 TA
163046 ATATTTTTTA
Statistics
Matches: 105, Mismatches: 23, Indels: 29
0.67 0.15 0.18
Matches are distributed among these distances:
15 9 0.09
16 15 0.14
17 23 0.22
18 20 0.19
19 18 0.17
20 19 0.18
21 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTTATTTTTATATT
Found at i:162917 original size:68 final size:70
Alignment explanation
Indices: 162826--162968 Score: 166
Period size: 68 Copynumber: 2.1 Consensus size: 70
162816 AATATACTTA
* *
162826 TATTTTTTATTATTAATTTTTATATAATATCATCTTTTAAATAT-ATTTTTAATGTCATATATTT
1 TATTTCTTATTATTAATTTTTATATAATATCAT-TTTTAAATATAATTTTTAATATCATATATTT
162890 TATTTT
65 TATTTT
** * * * * *
162896 TATTTCTTATTA-TAA-TTTTATATTTTTTTATTTTTTAATATAATTTTTTATATTATATATTTT
1 TATTTCTTATTATTAATTTTTATATAATATCATTTTTAAATATAATTTTTAATATCATATATTTT
162959 ATTTT
66 ATTTT
*
162964 AATTT
1 TATTT
162969 TTTTTACTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
67 9 0.15
68 39 0.63
69 3 0.05
70 11 0.18
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (70 bp):
TATTTCTTATTATTAATTTTTATATAATATCATTTTTAAATATAATTTTTAATATCATATATTTT
ATTTT
Found at i:162986 original size:68 final size:67
Alignment explanation
Indices: 162860--162986 Score: 148
Period size: 68 Copynumber: 1.9 Consensus size: 67
162850 TAATATCATC
* * **
162860 TTTTAAATATATTTTTAATGTCATATATTTTATTTTTATTTCTTATTATAATTTTATATTTTTTT
1 TTTTAAATATATTTTTAATATCATATATTTTATTTTAATTTCTTATTATAATACTATATTTTTTT
162925 AT
66 AT
* * * * *
162927 TTTTTAATATAATTTTTTATATTATATATTTTATTTTAATTT-TTTTTACTTATACTATAT
1 TTTTAAATAT-ATTTTTAATATCATATATTTTATTTTAATTTCTTATTA-TAATACTATAT
162987 AAATTTTAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
67 14 0.29
68 35 0.71
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (67 bp):
TTTTAAATATATTTTTAATATCATATATTTTATTTTAATTTCTTATTATAATACTATATTTTTTT
AT
Found at i:163002 original size:24 final size:24
Alignment explanation
Indices: 162975--163035 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
162965 ATTTTTTTTA
*
162975 CTTATACTATATAAATTTTAATTT
1 CTTATATTATATAAATTTTAATTT
* **
162999 CTTATATTTTATTTTATTTTAATTT
1 CTTATATTATA-TAAATTTTAATTT
163024 -TTATATTATATA
1 CTTATATTATATA
163036 TTTTATTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 1 0.03
24 18 0.60
25 11 0.37
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (24 bp):
CTTATATTATATAAATTTTAATTT
Found at i:172460 original size:30 final size:29
Alignment explanation
Indices: 172417--172474 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
172407 AATCTTTTTA
*
172417 TTATATTTAATTTT-TATTCAAATAAATTC
1 TTATATTTAATTTTAAATT-AAATAAATTC
*
172446 TTATATTTTTATTTTAAATTAAATAAATT
1 TTATA-TTTAATTTTAAATTAAATAAATT
172475 TTTAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 17 0.68
31 3 0.12
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (29 bp):
TTATATTTAATTTTAAATTAAATAAATTC
Found at i:175982 original size:40 final size:38
Alignment explanation
Indices: 175884--175989 Score: 135
Period size: 38 Copynumber: 2.7 Consensus size: 38
175874 ATAGTGCCCG
*
175884 TGTGCACGATGTGGGGGGATGTACACGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACTGAT
* *
175922 TGTGTACGATGTGGGGGGATGCACATGATGATGC-C-GACT
1 TGTGCACGATGTGGGGGGATGTACATGATG--GCACTGA-T
175961 ATGTGCACGATGTGGGGGGATGTACATGA
1 -TGTGCACGATGTGGGGGGATGTACATGA
175990 GTCGGGTGTG
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
38 29 0.49
39 2 0.03
40 28 0.47
ACGTcount: A:0.22, C:0.14, G:0.40, T:0.25
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGTACATGATGGCACTGAT
Found at i:189337 original size:21 final size:21
Alignment explanation
Indices: 189298--189337 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
189288 ACCCTTATTT
*
189298 GCTCCTCTCTCACTACCTCCA
1 GCTCCTCTCTCACAACCTCCA
189319 GCTCCTC-CTCACAATCCTC
1 GCTCCTCTCTCACAA-CCTC
189338 TAAGAACCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.15, C:0.53, G:0.05, T:0.28
Consensus pattern (21 bp):
GCTCCTCTCTCACAACCTCCA
Found at i:214982 original size:23 final size:24
Alignment explanation
Indices: 214946--214992 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
214936 TATATATACA
214946 TATATATAATTGTA-TAAATATAT
1 TATATATAATTGTATTAAATATAT
*
214969 TATATATACA-TGTATTTAATATAT
1 TATATATA-ATTGTATTAAATATAT
214993 ATAGAATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (24 bp):
TATATATAATTGTATTAAATATAT
Found at i:214995 original size:23 final size:22
Alignment explanation
Indices: 214936--214995 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
214926 GTTATGTATA
* *
214936 TATATATACATATATATAATTG
1 TATAAATATATATATATAATTG
214958 TATAAATATATTATATATACA-TG
1 TATAAATATA-TATATATA-ATTG
*
214981 TATTTAATATATATA
1 TA-TAAATATATATA
214996 GAATCATTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 8 0.25
23 16 0.50
24 8 0.25
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (22 bp):
TATAAATATATATATATAATTG
Found at i:215208 original size:26 final size:25
Alignment explanation
Indices: 215150--215208 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 25
215140 AGTTGTATCA
215150 TAATTTCATATATATATATAATAAAG
1 TAATTT-ATATATATATATAATAAAG
*
215176 TAA--TATAT-TATATATACATATATG
1 TAATTTATATATATATATA-ATA-AAG
215200 TAATTTATA
1 TAATTTATA
215209 CATAAGCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
22 8 0.29
23 7 0.25
24 6 0.21
26 7 0.25
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (25 bp):
TAATTTATATATATATATAATAAAG
Found at i:215465 original size:218 final size:214
Alignment explanation
Indices: 214962--215481 Score: 699
Period size: 215 Copynumber: 2.4 Consensus size: 214
214952 TAATTGTATA
* * * * * *
214962 AATATATTATATATACATGTATTTAATATATATAGAATCATTCTTATAACTTATAATAAATTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGCATTATTATAACTTATAATAAATTTTA
*
215027 TTTATATGATTACACTTAATAACTTTATTAGGTATCACCTTAGTTTTTATAACATATTGTTTATA
66 TTTATATGATTACACTTAATAACTTCATTAGGTATCACCTTAGTTTTTATAACATATTGTTTATA
* * *
215092 ATTAGCTTTTATTTATATAAACTTTGATATAAAACATTATAACATGTAAGTTGTATCATAATTTC
131 ATTAGCTTTTATTTATACAAACTTTGATATAAAACATTATAACATATAAATTGTATCATAATTT-
215157 ATATATATATATAATAAAGT
195 ATATATATATATAATAAAGT
* * *
215177 AATATATTATATATACATATATGTAATTTATACATAAGCATTATTATAAGTTATAATAAATCTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGCATTATTATAACTTATAATAAATTTTA
* * *
215242 TTTATATGATTACACTTAATAACTTCATTAGTTATCGCTTTAGTTTTTATAACATATTGTTTATA
66 TTTATATGATTACACTTAATAACTTCATTAGGTATCACCTTAGTTTTTATAACATATTGTTTATA
*
215307 ATTAG-TTATTATTTAT-CAAACTTTGATATAAAAATTAAAACATTATAACATATAAATTGTGTC
131 ATTAGCTT-TTATTTATACAAACTTTG--AT----A-TAAAACATTATAACATATAAATTGTATC
*
215370 ATTAA-TT-T-TATATATGTAATAAAGT
188 A-TAATTTATATATATATATAATAAAGT
* * * * *
215395 AATATATCATATATACACATATTTAATTTATACATAAGCATTATTATAATTTATATTAATTTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGCATTATTATAACTTATAATAAATTTTA
*
215460 TTTATATGACTACACTTAATAA
66 TTTATATGATTACACTTAATAA
215482 TTATGTGAGT
Statistics
Matches: 270, Mismatches: 26, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
214 10 0.04
215 130 0.48
216 2 0.01
218 95 0.35
219 1 0.00
220 1 0.00
221 28 0.10
222 3 0.01
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (214 bp):
AATATATTATATATACATATATTTAATTTATACATAAGCATTATTATAACTTATAATAAATTTTA
TTTATATGATTACACTTAATAACTTCATTAGGTATCACCTTAGTTTTTATAACATATTGTTTATA
ATTAGCTTTTATTTATACAAACTTTGATATAAAACATTATAACATATAAATTGTATCATAATTTA
TATATATATATAATAAAGT
Found at i:222656 original size:16 final size:16
Alignment explanation
Indices: 222619--222654 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
222609 CAATATTGAT
222619 CCTTTCATTTATTTTG
1 CCTTTCATTTATTTTG
*
222635 CCTTTCA-TTATTTTT
1 CCTTTCATTTATTTTG
222650 CCTTT
1 CCTTT
222655 TCCATATCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.11, C:0.22, G:0.03, T:0.64
Consensus pattern (16 bp):
CCTTTCATTTATTTTG
Found at i:227119 original size:3 final size:3
Alignment explanation
Indices: 227111--227142 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
227101 TTTCTTTTAC
*
227111 ATT ATT ATT ATT AAT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
227143 ATCTCTTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:237249 original size:43 final size:43
Alignment explanation
Indices: 237187--237297 Score: 143
Period size: 43 Copynumber: 2.6 Consensus size: 43
237177 ATTGACTCGG
** * *
237187 CTATGTGCGAGTAAAGAGTGCGCATAAGCCGAG-GATGACCCAG
1 CTATGTGCGAGTAGGGAGTGCGCATAA-CCCAGTGATGACCCAA
* *
237230 TTATGTGCGAGTAGGGAGTGTGCATAACCCAGTGATGACCCAA
1 CTATGTGCGAGTAGGGAGTGCGCATAACCCAGTGATGACCCAA
*
237273 CCATGTGCGAGTAGGGAGTGCGCAT
1 CTATGTGCGAGTAGGGAGTGCGCAT
237298 GAGCTGGTGA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 4 0.07
43 54 0.93
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.20
Consensus pattern (43 bp):
CTATGTGCGAGTAGGGAGTGCGCATAACCCAGTGATGACCCAA
Found at i:237308 original size:43 final size:43
Alignment explanation
Indices: 237189--237310 Score: 138
Period size: 43 Copynumber: 2.8 Consensus size: 43
237179 TGACTCGGCT
** ***
237189 ATGTGCGAGTAAAGAGTGCGCATAAGCCGAG-GATGACCCAGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAACC
* * *
237232 ATGTGCGAGTAGGGAGTGTGCATAACCCAGTGATGACCCAACC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAACC
* *
237275 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
237311 TGATGATGAT
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 1 0.02
43 64 0.98
ACGTcount: A:0.27, C:0.18, G:0.35, T:0.20
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAACC
Found at i:237328 original size:23 final size:23
Alignment explanation
Indices: 237302--237346 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
237292 GCGCATGAGC
237302 TGGTGATG-ATGATGATGATGGGA
1 TGGTG-TGCATGATGATGATGGGA
237325 TGGTGTGCATGATGATGATGGG
1 TGGTGTGCATGATGATGATGGG
237347 TACACGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.22, C:0.02, G:0.44, T:0.31
Consensus pattern (23 bp):
TGGTGTGCATGATGATGATGGGA
Found at i:253910 original size:90 final size:90
Alignment explanation
Indices: 253628--253934 Score: 234
Period size: 90 Copynumber: 3.4 Consensus size: 90
253618 GACCGATCGA
* * *
253628 CGCCGCCAGATCTGTCGCCGCAAGGAAGAGCCGACCCAGGCGAGGAGCGACGCCACCGGTTGGGG
1 CGCCACCAGATCTGTCGCCGGAAGGAAGAGCCGACCCAGGCGAGGAGCGACGCAACCGGTTGGGG
*
253693 AGACCGACCGTAAGAGAACCAGTCG
66 AGACCGACCGTAAGAGAACCCGTCG
** * ** * ** * **
253718 CGCCACCAGATCTGTCGCCGGTTGGGGAGAGCCGA-CTTGAC--CCA-CGCCGCAAGGAAGAGTT
1 CGCCACCAGATCTGTCGCCGG-AAGGAAGAGCCGACCCAGGCGAGGAGCGACGCAA--CCG-GTT
** * ** *
253779 CGCCGATACC-A--G-AAGGAGCCCGACCATCG
62 -GGGGAGACCGACCGTAA-GAGAAC--CCGTCG
* *
253808 ACGCCGCCAGATCTGTCGCCGGAAGGAAGAGCCGACCCAGGCGAGGAGCGACGCTACCGGTTGGG
1 -CGCCACCAGATCTGTCGCCGGAAGGAAGAGCCGACCCAGGCGAGGAGCGACGCAACCGGTTGGG
*
253873 GAGGCCGACCGTAAGAGAACCCGTCG
65 GAGACCGACCGTAAGAGAACCCGTCG
**
253899 CGCCACCAGATCTGTCGCCGGTGGGAGAGAGCCGAC
1 CGCCACCAGATCTGTCGCCGGAAGGA-AGAGCCGAC
253935 TTGACCCACG
Statistics
Matches: 155, Mismatches: 44, Indels: 35
0.66 0.19 0.15
Matches are distributed among these distances:
87 8 0.05
88 6 0.04
89 1 0.01
90 68 0.44
91 57 0.37
92 1 0.01
93 6 0.04
94 8 0.05
ACGTcount: A:0.23, C:0.32, G:0.35, T:0.10
Consensus pattern (90 bp):
CGCCACCAGATCTGTCGCCGGAAGGAAGAGCCGACCCAGGCGAGGAGCGACGCAACCGGTTGGGG
AGACCGACCGTAAGAGAACCCGTCG
Found at i:253931 original size:181 final size:182
Alignment explanation
Indices: 253618--254020 Score: 675
Period size: 181 Copynumber: 2.2 Consensus size: 182
253608 GGCCAGAGAA
*
253618 GACCGATCGACGCCGCCAGATCTGTCGCCGCAAGGAAGAGCCGACCCAGGCGAGGAGCGACGCCA
1 GACC-ATCGACGCCGCCAGATCTGTCGCCGGAAGGAAGAGCCGACCCAGGCGAGGAGCGACGCCA
253683 CCGGTTGGGGAGACCGACCGTAAGAGAACCAGTCGCGCCACCAGATCTGTCGCCGGTTGGGGAGA
65 CCGGTTGGGGAGACCGACCGTAAGAGAACCAGTCGCGCCACCAGATCTGTCGCCGGTTGGGGAGA
*
253748 GCCGACTTGACCCACGCCGCAAGGAAGAGTTCGCCGATACCAGAAGGAG-CCC
130 GCCGACTTGACCCACGCCGCAAGGAAGAGTTCGCCGACACCAGAAGGAGCCCC
*
253800 GACCATCGACGCCGCCAGATCTGTCGCCGGAAGGAAGAGCCGACCCAGGCGAGGAGCGACGCTAC
1 GACCATCGACGCCGCCAGATCTGTCGCCGGAAGGAAGAGCCGACCCAGGCGAGGAGCGACGCCAC
* *
253865 CGGTTGGGGAGGCCGACCGTAAGAGAACCCGTCGCGCCACCAGATCTGTCGCCGG-TGGGAGAGA
66 CGGTTGGGGAGACCGACCGTAAGAGAACCAGTCGCGCCACCAGATCTGTCGCCGGTTGGG-GAGA
* * *
253929 GCCGACTTGACCCACGCCGCAAGGAAGAGTTCGCCGACGCGAGAAGGGGCCCC
130 GCCGACTTGACCCACGCCGCAAGGAAGAGTTCGCCGACACCAGAAGGAGCCCC
* * *
253982 GACCATCGACGCCACCAGATCTGTCGTCGGAAAGAAGAG
1 GACCATCGACGCCGCCAGATCTGTCGCCGGAAGGAAGAG
254021 TGTAGAGAGA
Statistics
Matches: 208, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
180 4 0.02
181 161 0.77
182 43 0.21
ACGTcount: A:0.24, C:0.32, G:0.34, T:0.10
Consensus pattern (182 bp):
GACCATCGACGCCGCCAGATCTGTCGCCGGAAGGAAGAGCCGACCCAGGCGAGGAGCGACGCCAC
CGGTTGGGGAGACCGACCGTAAGAGAACCAGTCGCGCCACCAGATCTGTCGCCGGTTGGGGAGAG
CCGACTTGACCCACGCCGCAAGGAAGAGTTCGCCGACACCAGAAGGAGCCCC
Found at i:254819 original size:13 final size:13
Alignment explanation
Indices: 254803--254832 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
254793 ATTATACAAA
254803 AAAATTACTTGAT
1 AAAATTACTTGAT
254816 AAAATTACTTGAT
1 AAAATTACTTGAT
254829 AAAA
1 AAAA
254833 ATAAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (13 bp):
AAAATTACTTGAT
Found at i:254852 original size:18 final size:18
Alignment explanation
Indices: 254831--254868 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
254821 TACTTGATAA
254831 AAATAAATAAT-AAGTAAT
1 AAAT-AATAATAAAGTAAT
*
254849 AAATAATGATAAAGTAAT
1 AAATAATAATAAAGTAAT
254867 AA
1 AA
254869 CAATTCAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (18 bp):
AAATAATAATAAAGTAAT
Found at i:254932 original size:4 final size:4
Alignment explanation
Indices: 254923--254962 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
254913 TACATGACAT
254923 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T-AA T-AA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
254963 TAACTAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 6 0.17
4 29 0.83
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:254965 original size:16 final size:18
Alignment explanation
Indices: 254925--254962 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
254915 CATGACATTA
254925 AATAAATAAATAAATAAAT
1 AATAAATAAAT-AATAAAT
254944 AAATAAAT-AATAATAAAT
1 -AATAAATAAATAATAAAT
254962 A
1 A
254963 TAACTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 7 0.39
19 3 0.17
20 7 0.39
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AATAAATAAATAATAAAT
Found at i:255127 original size:25 final size:26
Alignment explanation
Indices: 255099--255147 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
255089 ATTGCTTATG
*
255099 AAAAATATATA-ATAATAAAAATATA
1 AAAAATATATATAAAATAAAAATATA
255124 AAAAATATATATAAAATAAAAATA
1 AAAAATATATATAAAATAAAAATA
255148 ATATAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (26 bp):
AAAAATATATATAAAATAAAAATATA
Found at i:255141 original size:20 final size:19
Alignment explanation
Indices: 255099--255158 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 19
255089 ATTGCTTATG
255099 AAAAATATATAATAATAAAAAT
1 AAAAATA-AT-ATAAT-AAAAT
255121 ATAAAA-AATATATATAAAAT
1 A-AAAATAATATA-ATAAAAT
255141 AAAAATAATATAATAAAA
1 AAAAATAATATAATAAAA
255159 AAATATATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
19 10 0.29
20 15 0.43
21 4 0.11
22 2 0.06
23 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAATAATATAATAAAAT
Found at i:255141 original size:29 final size:31
Alignment explanation
Indices: 255099--255168 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
255089 ATTGCTTATG
255099 AAAAATATAT--AATAATAAA-AATAT-A-AA
1 AAAAATATATAAAATAA-AAATAATATAATAA
*
255126 AAATATATATAAAATAAAAATAATATAATAA
1 AAAAATATATAAAATAAAAATAATATAATAA
255157 AAAAATATATAA
1 AAAAATATATAA
255169 TTTTTATTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 9 0.25
28 3 0.08
29 10 0.28
30 1 0.03
31 13 0.36
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (31 bp):
AAAAATATATAAAATAAAAATAATATAATAA
Found at i:255142 original size:18 final size:18
Alignment explanation
Indices: 255121--255167 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 18
255111 TAATAAAAAT
255121 ATAAAAAATATATATAAA
1 ATAAAAAATATATATAAA
*
255139 AT-AAAAATA-ATATAAT
1 ATAAAAAATATATATAAA
255155 A-AAAAAATATATA
1 ATAAAAAATATATA
255168 ATTTTTATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 14 0.54
17 10 0.38
18 2 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAAAAATATATATAAA
Found at i:255281 original size:20 final size:21
Alignment explanation
Indices: 255258--255332 Score: 52
Period size: 20 Copynumber: 3.6 Consensus size: 21
255248 AAATGTAAAG
255258 ATAAAGATAAAAAAATA-ATA
1 ATAAAGATAAAAAAATAGATA
255278 ATAATAAGA-AATAAAAATAGGA-A
1 AT-A-AAGATAA-AAAAATA-GATA
* * *
255301 AT-ATGATAATAAAATATATA
1 ATAAAGATAAAAAAATAGATA
255321 ATAAA-ATAAAAA
1 ATAAAGATAAAAA
255333 TAATTAATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 16
0.67 0.08 0.25
Matches are distributed among these distances:
19 1 0.02
20 20 0.48
21 6 0.14
22 11 0.26
23 3 0.07
24 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.23
Consensus pattern (21 bp):
ATAAAGATAAAAAAATAGATA
Found at i:255323 original size:12 final size:13
Alignment explanation
Indices: 255299--255328 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
255289 TAAAAATAGG
255299 AAATATGATAATA
1 AAATATGATAATA
255312 AAATAT-ATAATA
1 AAATATGATAATA
255324 AAATA
1 AAATA
255329 AAAATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
AAATATGATAATA
Found at i:256720 original size:60 final size:60
Alignment explanation
Indices: 256625--256757 Score: 239
Period size: 60 Copynumber: 2.2 Consensus size: 60
256615 TAGAAGACAA
256625 AAACAGAAGGTTTTTCGCTACAACGAGATTCAATCTCGCTGTAGCGAAATTGTGACCCAG
1 AAACAGAAGGTTTTTCGCTACAACGAGATTCAATCTCGCTGTAGCGAAATTGTGACCCAG
* *
256685 AAACAGAAGGTTTTTCGCTACAACGAGATTTAATCTCGTTGTAGCGAAATTGTGACCCAG
1 AAACAGAAGGTTTTTCGCTACAACGAGATTCAATCTCGCTGTAGCGAAATTGTGACCCAG
*
256745 AAACAGAATGTTT
1 AAACAGAAGGTTT
256758 CTCGTTGTAG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 70 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (60 bp):
AAACAGAAGGTTTTTCGCTACAACGAGATTCAATCTCGCTGTAGCGAAATTGTGACCCAG
Found at i:256772 original size:39 final size:39
Alignment explanation
Indices: 256718--256809 Score: 148
Period size: 39 Copynumber: 2.4 Consensus size: 39
256708 CGAGATTTAA
* *
256718 TCTCGTTGTAGCGAAATTGTGACCCAGAAACAGAATGTT
1 TCTCGTTGTAGCGAAATTGTAACCCAGAAACAGAAAGTT
256757 TCTCGTTGTAGCGAAATTGTAACCCAGAAACAGAAAGTT
1 TCTCGTTGTAGCGAAATTGTAACCCAGAAACAGAAAGTT
* *
256796 TCTCGCTGCAGCGA
1 TCTCGTTGTAGCGA
256810 GAATGAATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (39 bp):
TCTCGTTGTAGCGAAATTGTAACCCAGAAACAGAAAGTT
Found at i:257248 original size:43 final size:43
Alignment explanation
Indices: 257187--257310 Score: 155
Period size: 43 Copynumber: 2.9 Consensus size: 43
257177 CCCATCATCA
* * **
257187 TCATCACTAGCTTATGCGCACTCCCTACTCGCACAT-GGCTGGG
1 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAATC-GGG
*
257230 TCATCACCAGGTTATGCGCACTCCCTACTCACACATAATCGGG
1 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAATCGGG
257273 TCATC-CTC-GGCTTATGCGCACTCCCTACTCGCACATAA
1 TCATCAC-CAGG-TTATGCGCACTCCCTACTCGCACATAA
257311 CCGAGTCAAT
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
42 3 0.04
43 68 0.94
44 1 0.01
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (43 bp):
TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAATCGGG
Found at i:259529 original size:20 final size:21
Alignment explanation
Indices: 259499--259537 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
259489 AAAAACGTAA
259499 TTTTCCCTTTGAATTTTCTAG
1 TTTTCCCTTTGAATTTTCTAG
*
259520 TTTT-CCTTTGATTTTTCT
1 TTTTCCCTTTGAATTTTCT
259538 CTTTTCTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.10, C:0.18, G:0.08, T:0.64
Consensus pattern (21 bp):
TTTTCCCTTTGAATTTTCTAG
Found at i:262170 original size:2 final size:2
Alignment explanation
Indices: 262163--262193 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
262153 NNNNNNNNNN
262163 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
262194 TAAAAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:262306 original size:24 final size:24
Alignment explanation
Indices: 262257--262306 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
262247 AAAAATTACA
* *
262257 AATATGATTTTTCTATATGAATTT
1 AATATGATCTTTCTATATGAAATT
*
262281 AATATTATCTTTCTATCAT-AAATT
1 AATATGATCTTTCTAT-ATGAAATT
262305 AA
1 AA
262307 AATCGTTACT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (24 bp):
AATATGATCTTTCTATATGAAATT
Found at i:273031 original size:18 final size:17
Alignment explanation
Indices: 273002--273035 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
272992 AAAAAAAAAA
273002 AAGAAAGAAAGAAGAAT
1 AAGAAAGAAAGAAGAAT
273019 AAGAAATGAAAGAAGAA
1 AAGAAA-GAAAGAAGAA
273036 CTGTCAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.06
Consensus pattern (17 bp):
AAGAAAGAAAGAAGAAT
Found at i:273435 original size:15 final size:17
Alignment explanation
Indices: 273417--273449 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
273407 ATTATAATAA
273417 ATAA-TTTTATAA-GTT
1 ATAATTTTTATAATGTT
273432 ATAATTTTTATAATGTT
1 ATAATTTTTATAATGTT
273449 A
1 A
273450 ACCCGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
ATAATTTTTATAATGTT
Found at i:273495 original size:17 final size:17
Alignment explanation
Indices: 273465--273505 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
273455 AAATAAAAAG
*
273465 TAAA-TATATTTATATT
1 TAAAGTATATATATATT
273481 TAAAGTATATATATATT
1 TAAAGTATATATATATT
*
273498 AAAAGTAT
1 TAAAGTAT
273506 TTTAGTGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (17 bp):
TAAAGTATATATATATT
Found at i:273528 original size:3 final size:3
Alignment explanation
Indices: 273520--273555 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
273510 GTGTGTATAT
273520 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
273556 TTCCTTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:273803 original size:15 final size:15
Alignment explanation
Indices: 273783--273814 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
273773 AATATATATA
*
273783 TTATAATTAATAATT
1 TTATAAGTAATAATT
273798 TTATAAGTAATAATT
1 TTATAAGTAATAATT
273813 TT
1 TT
273815 TGTAATGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTATAAGTAATAATT
Found at i:274275 original size:330 final size:323
Alignment explanation
Indices: 273620--274265 Score: 810
Period size: 330 Copynumber: 2.0 Consensus size: 323
273610 AAGAATTAAT
* *
273620 AATCATAGTTTCATGAATTAATTTAATTAATTATATGGATTTGTCCTTAATTACATGAAATTAAA
1 AATCATAATTGCATGAATTAATTTAATTAATTATATGGATTTGTCCTTAATTACATGAAATTAAA
* * * **
273685 AAAAAATAACTAAGTTTCAAAACTTTTCTAATCTCATAACTTCTTTTTAGATAATTAAGTTTATA
66 AAAAAATAACTAAATTTCAAAACTATTCTAATCTCACAACTTCTACTTA-ATAATTAAGTTTATA
* *
273750 TATTATAAGTTTATATAAACAAAAATATATATATTATAATTAATAATTTTATAAGTAATAATTTT
130 TATTATAAGTTTATATAAACAAAAATATATATATTATAATTAATAATTTTACAAGTAATAATTTA
* **
273815 TGTAATGTTAACACAAAATAGAAAGTAAATATGTTTATATTTAATATATATATATATACACACAC
195 TGTAATGTTAACACAAAATAAAAAGTAAATAAATTTATATTTAATATATATATATAT------A-
*
273880 ACTAAAAGTATTTTAGAATATATATAATAGTAAGTATCTTCTTTATAAATGAATCCAATATATAT
253 ACTAAAAGTATTGTAGAATATATATAATAGTAAGTATCTTCTTTATAAATGAATCCAATATATAT
273945 AAAGTA
318 AAAGTA
* * *
273951 AATCATAATTGCATGAATTAATTTAATTAATTATATGGGTTTGTCCTTAATTATATGAAATT-TA
1 AATCATAATTGCATGAATTAATTTAATTAATTATATGGATTTGTCCTTAATTACATGAAATTAAA
* * * *
274015 AAAAAATAGCTAAATTTCAAAACTATTCTAATCTCACAACTTCTCAACTT-CT-CTTAAGGTTTG
66 AAAAAATAACTAAATTTCAAAACTATTCTAATCTCACAACTTCT--ACTTAATAATTAA-GTTTA
* * ** *
274078 TATATTATAAGTTTGTATAAATAAAGGTGTATATATTATAATTAATAATTTTACAAGT-ATAATT
128 TATATTATAAGTTTATATAAACAAAAATATATATATTATAATTAATAATTTTACAAGTAATAATT
* *
274142 TATGTAATGTTAACATAAAATAAAAAGTAAATAAATTTATATTTAA-A-GTATATATAT-ACTAA
193 TATGTAATGTTAACACAAAATAAAAAGTAAATAAATTTATATTTAATATATATATATATAACTAA
* * *
274204 AAGTATTAGT-GTATATATA-ATATAGTAATTATATT-TCTTATAAATGAA-CTCAATATATATA
258 AAGTATT-GTAGAATATATATA-ATAGTAAGTATCTTCT-TTATAAATGAATC-CAATATATATA
274265 A
319 A
274266 TGTATATATA
Statistics
Matches: 278, Mismatches: 30, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
318 3 0.01
319 55 0.20
320 1 0.00
327 9 0.03
328 1 0.00
329 51 0.18
330 98 0.35
331 58 0.21
332 2 0.01
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (323 bp):
AATCATAATTGCATGAATTAATTTAATTAATTATATGGATTTGTCCTTAATTACATGAAATTAAA
AAAAAATAACTAAATTTCAAAACTATTCTAATCTCACAACTTCTACTTAATAATTAAGTTTATAT
ATTATAAGTTTATATAAACAAAAATATATATATTATAATTAATAATTTTACAAGTAATAATTTAT
GTAATGTTAACACAAAATAAAAAGTAAATAAATTTATATTTAATATATATATATATAACTAAAAG
TATTGTAGAATATATATAATAGTAAGTATCTTCTTTATAAATGAATCCAATATATATAAAGTA
Found at i:281085 original size:19 final size:20
Alignment explanation
Indices: 281061--281098 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
281051 CTAACATCAT
*
281061 ACTG-AAAACAAGTACATTG
1 ACTGAAAAACAAGCACATTG
281080 ACTGAAAAACAAGCACATT
1 ACTGAAAAACAAGCACATT
281099 AGTGTCGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.50, C:0.18, G:0.13, T:0.18
Consensus pattern (20 bp):
ACTGAAAAACAAGCACATTG
Found at i:288859 original size:44 final size:44
Alignment explanation
Indices: 288796--288890 Score: 190
Period size: 44 Copynumber: 2.2 Consensus size: 44
288786 AGGATGACAA
288796 CCCTCCCCCAATGGGTCACCATATATAAAAGCTTTCAGACCCAC
1 CCCTCCCCCAATGGGTCACCATATATAAAAGCTTTCAGACCCAC
288840 CCCTCCCCCAATGGGTCACCATATATAAAAGCTTTCAGACCCAC
1 CCCTCCCCCAATGGGTCACCATATATAAAAGCTTTCAGACCCAC
288884 CCCTCCC
1 CCCTCCC
288891 TTTTTAGTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.27, C:0.42, G:0.11, T:0.20
Consensus pattern (44 bp):
CCCTCCCCCAATGGGTCACCATATATAAAAGCTTTCAGACCCAC
Found at i:295063 original size:26 final size:27
Alignment explanation
Indices: 295004--295057 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
294994 AGAATCACAA
*
295004 AGCCAAAAATGTACAAGTACATGAAAT
1 AGCCAAAAAGGTACAAGTACATGAAAT
*
295031 AGCCAAAAAGGTATAAGTACATGAAAT
1 AGCCAAAAAGGTACAAGTACATGAAAT
295058 TGCAAATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.52, C:0.13, G:0.17, T:0.19
Consensus pattern (27 bp):
AGCCAAAAAGGTACAAGTACATGAAAT
Found at i:300008 original size:3 final size:3
Alignment explanation
Indices: 300000--300061 Score: 97
Period size: 3 Copynumber: 20.7 Consensus size: 3
299990 CAAGACGACC
***
300000 AAG AAG AAG AAG AAG GTC AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
300048 AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AA
300062 ACGAGCAGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.65, C:0.02, G:0.32, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:303817 original size:26 final size:26
Alignment explanation
Indices: 303787--303837 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
303777 GATTCTTCAC
*
303787 TTTCCATTTCTCTCTTTTTCTTTTAT
1 TTTCCACTTCTCTCTTTTTCTTTTAT
*
303813 TTTCCACTTCTGTCTTTTTCTTTTA
1 TTTCCACTTCTCTCTTTTTCTTTTA
303838 CCGTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.08, C:0.24, G:0.02, T:0.67
Consensus pattern (26 bp):
TTTCCACTTCTCTCTTTTTCTTTTAT
Found at i:307405 original size:3 final size:3
Alignment explanation
Indices: 307397--307425 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
307387 AAAAGAACGA
307397 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
307426 TTCTTCTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:309784 original size:14 final size:15
Alignment explanation
Indices: 309765--309793 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
309755 GCAGATGATG
309765 AGAGGAAGA-GAGGA
1 AGAGGAAGATGAGGA
309779 AGAGGAAGATGAGGA
1 AGAGGAAGATGAGGA
309794 GATTGATTGG
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:0.48, C:0.00, G:0.48, T:0.03
Consensus pattern (15 bp):
AGAGGAAGATGAGGA
Found at i:325179 original size:2 final size:2
Alignment explanation
Indices: 325172--325205 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
325162 AATGAAACTC
* *
325172 AT AT AT AT AT AT AT AT AT AT AT CT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
325206 CTAAAACGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:325206 original size:12 final size:12
Alignment explanation
Indices: 325172--325208 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
325162 AATGAAACTC
*
325172 ATATATATATAT
1 ATATATATATCT
325184 ATATATATATCT
1 ATATATATATCT
*
325196 ATATTTATATCT
1 ATATATATATCT
325208 A
1 A
325209 AAACGTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (12 bp):
ATATATATATCT
Found at i:325947 original size:9 final size:9
Alignment explanation
Indices: 325933--325966 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
325923 TTAAACTCAA
325933 AGGAAAGAG
1 AGGAAAGAG
325942 AGGAAAGAG
1 AGGAAAGAG
*
325951 AAGAAAGA-
1 AGGAAAGAG
325959 AGGAAAGA
1 AGGAAAGA
325967 TGATGGAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (9 bp):
AGGAAAGAG
Found at i:333487 original size:35 final size:35
Alignment explanation
Indices: 333379--333487 Score: 130
Period size: 35 Copynumber: 3.1 Consensus size: 35
333369 TGTTGTACAG
* * * * *
333379 AGAACAACCAAAATAAATGAAGT-GTTACTTTACGT
1 AGAATAACCAAAACAAGTGAA-TCGTTACTTCACGC
* *
333414 AGAATAACTAAAACAAGTGAATCGTTACTTCATGC
1 AGAATAACCAAAACAAGTGAATCGTTACTTCACGC
*
333449 AGAATAACCAAAACAAGTGAATCGTTACTTCACAC
1 AGAATAACCAAAACAAGTGAATCGTTACTTCACGC
333484 AGAA
1 AGAA
333488 CAAGTAAAGC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
34 1 0.02
35 62 0.98
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (35 bp):
AGAATAACCAAAACAAGTGAATCGTTACTTCACGC
Found at i:333500 original size:26 final size:26
Alignment explanation
Indices: 333460--333518 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
333450 GAATAACCAA
* *
333460 AACAAGTGAATCGTTACTTCACACAG
1 AACAAGTAAAGCGTTACTTCACACAG
*
333486 AACAAGTAAAGCGTTACTTCACGCAG
1 AACAAGTAAAGCGTTACTTCACACAG
*
333512 AATAAGT
1 AACAAGT
333519 GAAGTACTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (26 bp):
AACAAGTAAAGCGTTACTTCACACAG
Found at i:333830 original size:29 final size:29
Alignment explanation
Indices: 333796--333852 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
333786 TGTTCTCGTA
333796 TACTTATTCAT-GTACAACTTATTCTCTTG
1 TACTTATTC-TCGTACAACTTATTCTCTTG
* *
333825 TACTTATTCTCGTACAGCTTCTTCTCTT
1 TACTTATTCTCGTACAACTTATTCTCTT
333853 ACACCTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.19, C:0.25, G:0.07, T:0.49
Consensus pattern (29 bp):
TACTTATTCTCGTACAACTTATTCTCTTG
Found at i:361942 original size:14 final size:14
Alignment explanation
Indices: 361923--361954 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
361913 CAGTCATCTG
361923 TTTTCTCTTTTTCT
1 TTTTCTCTTTTTCT
*
361937 TTTTCTTTTTTTCT
1 TTTTCTCTTTTTCT
361951 TTTT
1 TTTT
361955 TTTCCTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTCTCTTTTTCT
Found at i:369739 original size:2 final size:2
Alignment explanation
Indices: 369732--369773 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
369722 TGTACTCAAC
369732 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
369774 TTATATGAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:371506 original size:2 final size:2
Alignment explanation
Indices: 371499--371532 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
371489 TATACGCATG
371499 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
371533 ATAAAATTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:372439 original size:31 final size:31
Alignment explanation
Indices: 372396--372465 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 31
372386 ATCATTAATC
372396 ATAAATAATTATTTAATTCAAAAT-AAAAAAT
1 ATAAA-AATTATTTAATTCAAAATAAAAAAAT
*
372427 ATAAAAATTTATTTAATTTAAAATAAAAAAAT
1 ATAAAAA-TTATTTAATTCAAAATAAAAAAAT
372459 ATAAAAA
1 ATAAAAA
372466 CTCGATTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 2 0.06
31 20 0.56
32 14 0.39
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (31 bp):
ATAAAAATTATTTAATTCAAAATAAAAAAAT
Found at i:374383 original size:41 final size:41
Alignment explanation
Indices: 374333--374418 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 41
374323 ATTAACATAT
* * * *
374333 TAAGTTATTGAATTAAATTATTGATATATAATATGATATGA
1 TAAGCTATTGAATTAAACTATTAAAATATAATATGATATGA
* * * *
374374 TAAGCTATTGAGTTGAACTGTTAAAATATAATATGTTATGA
1 TAAGCTATTGAATTAAACTATTAAAATATAATATGATATGA
374415 TAAG
1 TAAG
374419 TTTATATTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.42, C:0.02, G:0.15, T:0.41
Consensus pattern (41 bp):
TAAGCTATTGAATTAAACTATTAAAATATAATATGATATGA
Found at i:384245 original size:22 final size:22
Alignment explanation
Indices: 384220--384267 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
384210 TGACTTAATA
384220 ATTGCG-TCTTTGATTTTTAAGC
1 ATTGCGTTCTTTG-TTTTTAAGC
* * *
384242 ATTGTGTTTTTTGTTTTTAAGT
1 ATTGCGTTCTTTGTTTTTAAGC
384264 ATTG
1 ATTG
384268 TGTGACTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.17, C:0.06, G:0.19, T:0.58
Consensus pattern (22 bp):
ATTGCGTTCTTTGTTTTTAAGC
Found at i:384268 original size:22 final size:23
Alignment explanation
Indices: 384228--384270 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
384218 TAATTGCGTC
384228 TTTGATTTTTAAGCATTGTGTTT
1 TTTGATTTTTAAGCATTGTGTTT
*
384251 TTTG-TTTTTAAGTATTGTGT
1 TTTGATTTTTAAGCATTGTGT
384271 GACTGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.16, C:0.02, G:0.19, T:0.63
Consensus pattern (23 bp):
TTTGATTTTTAAGCATTGTGTTT
Found at i:384305 original size:22 final size:22
Alignment explanation
Indices: 384255--384305 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
384245 GTGTTTTTTG
* ** *
384255 TTTTTAAGTATTGTGTGACTGA
1 TTTTTAGGTATTACGTGACTAA
384277 TTTTTAGGTATTACGTGACTAA
1 TTTTTAGGTATTACGTGACTAA
384299 TTTTTAG
1 TTTTTAG
384306 ATAATGCTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.06, G:0.20, T:0.51
Consensus pattern (22 bp):
TTTTTAGGTATTACGTGACTAA
Found at i:384364 original size:23 final size:22
Alignment explanation
Indices: 384316--384470 Score: 71
Period size: 22 Copynumber: 7.0 Consensus size: 22
384306 ATAATGCTTA
384316 AGTCACGCAATGCCTAAAAACT
1 AGTCACGCAATGCCTAAAAACT
* **
384338 AGTCACGCAATGCTTGACTAACT
1 AGTCACGCAATGCCT-AAAAACT
*** * **
384361 AGTCATATAATGCTTATCAA-T
1 AGTCACGCAATGCCTAAAAACT
* * **
384382 AATTCACGTAATGCCCTATCAACT
1 -AGTCACGCAATG-CCTAAAAACT
* *** *
384406 AGTCACGTAATATTTAAAAATT
1 AGTCACGCAATGCCTAAAAACT
* *
384428 AGTCACGCAATGTCTACAAACT
1 AGTCACGCAATGCCTAAAAACT
*
384450 AGTCACACAATGTCC-AAAAAC
1 AGTCACGCAATG-CCTAAAAAC
384471 CAATTACGTA
Statistics
Matches: 101, Mismatches: 27, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
21 1 0.01
22 64 0.63
23 35 0.35
24 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (22 bp):
AGTCACGCAATGCCTAAAAACT
Found at i:384689 original size:51 final size:51
Alignment explanation
Indices: 384602--384717 Score: 135
Period size: 51 Copynumber: 2.3 Consensus size: 51
384592 AGAATACTCA
* * *
384602 AAAGA-TTTTTTTCATGTATAAAAAACCATTCCAAAATGCTTAAAATGCTC
1 AAAGATTTTTTTTCATGTATAAAAAACCACTCCAAAATACTCAAAATGCTC
* * * * *
384652 AAAGATTTTTTTTCATGTATCAAAAATCACTCTAAAATACTCAAAATGTTT
1 AAAGATTTTTTTTCATGTATAAAAAACCACTCCAAAATACTCAAAATGCTC
*
384703 AAAAATTTCTTTTTC
1 AAAGATTT-TTTTTC
384718 TGGTAAGGAA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 5 0.09
51 44 0.80
52 6 0.11
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.39
Consensus pattern (51 bp):
AAAGATTTTTTTTCATGTATAAAAAACCACTCCAAAATACTCAAAATGCTC
Found at i:384975 original size:15 final size:15
Alignment explanation
Indices: 384952--384982 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
384942 TTCACGTGAG
384952 AATGCAAATGAATCA
1 AATGCAAATGAATCA
*
384967 AATGTAAATGAATCA
1 AATGCAAATGAATCA
384982 A
1 A
384983 GTTATGTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.10, G:0.13, T:0.23
Consensus pattern (15 bp):
AATGCAAATGAATCA
Found at i:396441 original size:119 final size:121
Alignment explanation
Indices: 396298--396552 Score: 433
Period size: 119 Copynumber: 2.1 Consensus size: 121
396288 GAGGAGAGTT
* * * *
396298 GATGAGTCATGAATCTCACTTCGAAGAAACGCTCTCAAGAGGGGAGTCGACGAGCCATATATCCG
1 GATGAGCCATAAATCTCACTTCGAAGAAACGCTCTCAAGAGGGGAGTCGAAGAGCCATATATCCC
* * *
396363 ACATCGAAGAAAAGCTC-T-CGAGAGGATGTTATGGTTTTAGAAGGGAGCCGATGA
66 ACATCGAAGAAAAGCTCTTAAGAGAGGATGTTATGGTCTTAGAAGGGAGCCAATGA
396417 GATGAGCCATAAATCTCACTTCGAAGAAACGCTCTCAAGAGGGGAGTCGAAGAGCCATATATCCC
1 GATGAGCCATAAATCTCACTTCGAAGAAACGCTCTCAAGAGGGGAGTCGAAGAGCCATATATCCC
396482 ACATCGAAGAAAAGCTCTTAAGAGAGGATGTTATGGTCTTAGAAGGGAGCCAATGA
66 ACATCGAAGAAAAGCTCTTAAGAGAGGATGTTATGGTCTTAGAAGGGAGCCAATGA
396538 GATGAGCCATAAATC
1 GATGAGCCATAAATC
396553 CCACGGGGAA
Statistics
Matches: 127, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
119 78 0.61
120 1 0.01
121 48 0.38
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.20
Consensus pattern (121 bp):
GATGAGCCATAAATCTCACTTCGAAGAAACGCTCTCAAGAGGGGAGTCGAAGAGCCATATATCCC
ACATCGAAGAAAAGCTCTTAAGAGAGGATGTTATGGTCTTAGAAGGGAGCCAATGA
Found at i:396611 original size:73 final size:73
Alignment explanation
Indices: 396468--396604 Score: 211
Period size: 73 Copynumber: 1.9 Consensus size: 73
396458 GGGAGTCGAA
* * *
396468 GAGCCATATATCCCACATCGAAGAAAAGCTCTTAAGAGAGGATGTTATGGTCTTAGAAGGGAGCC
1 GAGCCATAAATCCCACAGCGAAGAAAAGCTCTTAAGAGAAGATGTTATGGTCTTAGAAGGGAGCC
396533 AATGAGAT
66 AATGAGAT
* * * *
396541 GAGCCATAAATCCCACGGGGAAGAAAAGCTTTTGAGAGAAGATGTTATGGTCTTAGAAGGGAGC
1 GAGCCATAAATCCCACAGCGAAGAAAAGCTCTTAAGAGAAGATGTTATGGTCTTAGAAGGGAGC
396605 TGATGAGCCA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 57 1.00
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.21
Consensus pattern (73 bp):
GAGCCATAAATCCCACAGCGAAGAAAAGCTCTTAAGAGAAGATGTTATGGTCTTAGAAGGGAGCC
AATGAGAT
Found at i:396899 original size:97 final size:96
Alignment explanation
Indices: 396739--396934 Score: 277
Period size: 97 Copynumber: 2.0 Consensus size: 96
396729 TTCACAAAAT
* *
396739 ATAAAATTTTGAAGAGTCATTTGTTGTTGAATTACAGTGATAAGTGACAAGAGTACTACAGGCAA
1 ATAAAATTTTGAAGAGCCATTTGTTCTTGAATTACAGTGATAAGTGACAAGAGTACTACAGGCAA
396804 ACTACCCTT-AAGATGAACCGAATCCAGTTC
66 ACTACCCTTAAAGATGAACCGAATCCAGTTC
* * * * *
396834 ATAAAATTTTGAGGAGCCATTTGTTCTTGAGAATTGCAGTGATAAGTGACTAGAGTATTTCAGGC
1 ATAAAATTTTGAAGAGCCATTTGTTCTT--GAATTACAGTGATAAGTGACAAGAGTACTACAGGC
** *
396899 AAACTACCCTTAAAGATGAGTCTAATCCAGTTC
64 AAACTACCCTTAAAGATGAACCGAATCCAGTTC
396932 ATA
1 ATA
396935 CAAAGTAGCA
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
95 25 0.28
97 42 0.48
98 21 0.24
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.30
Consensus pattern (96 bp):
ATAAAATTTTGAAGAGCCATTTGTTCTTGAATTACAGTGATAAGTGACAAGAGTACTACAGGCAA
ACTACCCTTAAAGATGAACCGAATCCAGTTC
Found at i:408336 original size:110 final size:110
Alignment explanation
Indices: 408143--408361 Score: 393
Period size: 110 Copynumber: 2.0 Consensus size: 110
408133 TTAGATTGTT
* *
408143 TTATTTATACTTCTGTTTGCATCTATTTGCAAGGTTCTTGTAGCGTGTTGATGTATTGTATGATC
1 TTATTTATACTTCTGTTTCCATCTATTTGCAAGGTTCTTGTAGCATGTTGATGTATTGTATGATC
408208 TTGCTCAAATCCTCTTCAGCTTCATCTTTTCTCTAGAGAAGATGC
66 TTGCTCAAATCCTCTTCAGCTTCATCTTTTCTCTAGAGAAGATGC
* * *
408253 TTATTTATACTTCTGTTTCCCTTTATTTGGAAGGTTCTTGTAGCATGTTGATGTATTGTATGATC
1 TTATTTATACTTCTGTTTCCATCTATTTGCAAGGTTCTTGTAGCATGTTGATGTATTGTATGATC
408318 TTGCTCAAATCCTCTTCAGCTTCATCTTTTCTCTAGAGAAGATG
66 TTGCTCAAATCCTCTTCAGCTTCATCTTTTCTCTAGAGAAGATG
408362 TCAACTGTTT
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 104 1.00
ACGTcount: A:0.20, C:0.18, G:0.17, T:0.45
Consensus pattern (110 bp):
TTATTTATACTTCTGTTTCCATCTATTTGCAAGGTTCTTGTAGCATGTTGATGTATTGTATGATC
TTGCTCAAATCCTCTTCAGCTTCATCTTTTCTCTAGAGAAGATGC
Found at i:415725 original size:2 final size:2
Alignment explanation
Indices: 415720--415769 Score: 70
Period size: 2 Copynumber: 26.0 Consensus size: 2
415710 AATAATTAAG
415720 TA TA TA T- TA TA TA TA TA TA TA TA TA GT- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
415761 TA -A TA TA TA
1 TA TA TA TA TA
415770 AGNNNNNNNN
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.07
2 40 0.91
3 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:420687 original size:2 final size:2
Alignment explanation
Indices: 420680--420728 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
420670 NNNNNNACAT
*
420680 TA TA TA TA TA TG TA TA TA TA -A TA TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
420720 T- TA TA TA TA
1 TA TA TA TA TA
420729 ATTATATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:420706 original size:9 final size:9
Alignment explanation
Indices: 420681--420735 Score: 67
Period size: 9 Copynumber: 5.9 Consensus size: 9
420671 NNNNNACATT
420681 ATATATATA
1 ATATATATA
*
420690 TGTATATATA
1 -ATATATATA
420700 ATATATATA
1 ATATATATA
420709 ATATATATA
1 ATATATATA
420718 TATTATATATA
1 -A-TATATATA
420729 AT-TATAT
1 ATATATAT
420736 TTTGGTACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
8 5 0.12
9 18 0.44
10 10 0.24
11 8 0.20
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (9 bp):
ATATATATA
Found at i:423569 original size:2 final size:2
Alignment explanation
Indices: 423556--423608 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
423546 AATTTTTAGA
*
423556 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
423598 AT AT AT GT AT A
1 AT AT AT AT AT A
423609 AATTAAATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:430590 original size:23 final size:23
Alignment explanation
Indices: 430564--430609 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
430554 ATACAATAAC
**
430564 CTTATCCTAATTTAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
430587 CTTATCCTAATAGAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
430610 TGTTATTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAGGAAT
Found at i:436287 original size:23 final size:23
Alignment explanation
Indices: 436256--436303 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
436246 TACCTGGTTC
436256 TCCTAGTTTTGCTCCAACATTTA
1 TCCTAGTTTTGCTCCAACATTTA
* * *
436279 TCCTGGTTTTGTTCCAACGTTTA
1 TCCTAGTTTTGCTCCAACATTTA
436302 TC
1 TC
436304 TGACTTAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.25, G:0.12, T:0.46
Consensus pattern (23 bp):
TCCTAGTTTTGCTCCAACATTTA
Found at i:444622 original size:23 final size:23
Alignment explanation
Indices: 444596--444639 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
444586 AGTTCTCCTA
444596 GTTTTGCTCCAATGTTTATCTTG
1 GTTTTGCTCCAATGTTTATCTTG
444619 GTTTTGCTCCAATGTTTATCT
1 GTTTTGCTCCAATGTTTATCT
444640 GACTTAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.14, C:0.18, G:0.16, T:0.52
Consensus pattern (23 bp):
GTTTTGCTCCAATGTTTATCTTG
Found at i:445235 original size:22 final size:21
Alignment explanation
Indices: 445207--445247 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
445197 CAATTTGAAC
445207 TTGGAGACAAACCAAGATCAGT
1 TTGGAGACAAACCAA-ATCAGT
445229 TTGGAGACAAACCAAATCA
1 TTGGAGACAAACCAAATCA
445248 AACACCATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.17
Consensus pattern (21 bp):
TTGGAGACAAACCAAATCAGT
Found at i:446763 original size:19 final size:20
Alignment explanation
Indices: 446740--446788 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
446730 AAGAAATATA
*
446740 AAAATTAATAAATAATAAC-T
1 AAAATTAA-AAAGAATAACAT
446760 -AAATTAAAAAGAATAACAT
1 AAAATTAAAAAGAATAACAT
446779 AAAATTAAAA
1 AAAATTAAAA
446789 TAACTCACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 9 0.35
19 8 0.31
20 9 0.35
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAATTAAAAAGAATAACAT
Found at i:448709 original size:9 final size:9
Alignment explanation
Indices: 448695--448721 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
448685 AATAAGGCTG
448695 AAGTGTGAA
1 AAGTGTGAA
448704 AAGTGTGAA
1 AAGTGTGAA
448713 AAGTGTGAA
1 AAGTGTGAA
448722 GAGTAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (9 bp):
AAGTGTGAA
Found at i:455290 original size:21 final size:21
Alignment explanation
Indices: 455264--455303 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
455254 GAAAAGCCAC
*
455264 GTTTTTATTTCTTTGCTGTAT
1 GTTTTTATTTCTTAGCTGTAT
*
455285 GTTTTTCTTTCTTAGCTGT
1 GTTTTTATTTCTTAGCTGT
455304 TGAAGGCCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.12, G:0.15, T:0.65
Consensus pattern (21 bp):
GTTTTTATTTCTTAGCTGTAT
Found at i:459833 original size:21 final size:21
Alignment explanation
Indices: 459807--459846 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
459797 GAAAAGCCAC
459807 GTTTTTATTTCCTT-GCTGTAT
1 GTTTTTATTT-CTTAGCTGTAT
*
459828 GTTTTTCTTTCTTAGCTGT
1 GTTTTTATTTCTTAGCTGT
459847 TGAAGGTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.07, C:0.15, G:0.15, T:0.62
Consensus pattern (21 bp):
GTTTTTATTTCTTAGCTGTAT
Found at i:461648 original size:17 final size:17
Alignment explanation
Indices: 461626--461661 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
461616 CGTCCATACA
461626 TTTTTGCTCTATATTCC
1 TTTTTGCTCTATATTCC
461643 TTTTTGCTCTATATTCC
1 TTTTTGCTCTATATTCC
461660 TT
1 TT
461662 GTTCATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.22, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTTTGCTCTATATTCC
Found at i:502231 original size:2 final size:2
Alignment explanation
Indices: 502224--502253 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
502214 TTTAACGACA
502224 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
502254 CTTCAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:519964 original size:80 final size:80
Alignment explanation
Indices: 519745--519968 Score: 322
Period size: 80 Copynumber: 2.8 Consensus size: 80
519735 GAGAGCTGAG
* * * *
519745 GCATCTTTCTTTGTCATGTGTGCTTCCAAGTCGTACCACAAAAAATTTGTGGAGCTAGGTTAATT
1 GCATCTTTCTTTGTCATGTGTACCTCCAATTCGTACCACAAAAAATTTGTGGAGCTAGGTTAATG
*
519810 AGCTACTTCGGTTAT
66 AGCTACTTCAGTTAT
* * * * * *
519825 GCATCTTTCTTTGCCATGTGTACCTCCAATTCCTACCACAAAAAGTTAGAGGACCTAGGTTAATG
1 GCATCTTTCTTTGTCATGTGTACCTCCAATTCGTACCACAAAAAATTTGTGGAGCTAGGTTAATG
519890 AGCTACTTCAGTTAT
66 AGCTACTTCAGTTAT
* * *
519905 GCATCTTTCTTTTTCATGTGTACCTCCAATTCGTACCATAAAAAATTTGTGGAGTTAGGTTAAT
1 GCATCTTTCTTTGTCATGTGTACCTCCAATTCGTACCACAAAAAATTTGTGGAGCTAGGTTAAT
519969 TATCTATTCT
Statistics
Matches: 124, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 124 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (80 bp):
GCATCTTTCTTTGTCATGTGTACCTCCAATTCGTACCACAAAAAATTTGTGGAGCTAGGTTAATG
AGCTACTTCAGTTAT
Found at i:526505 original size:8 final size:8
Alignment explanation
Indices: 526494--526545 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
526484 ATAAAACTGA
526494 AAAATAAT
1 AAAATAAT
526502 AAAAATAAGT
1 -AAAATAA-T
*
526512 AAAACAAT
1 AAAATAAT
526520 AAAATAAT
1 AAAATAAT
*
526528 AAAAT-CT
1 AAAATAAT
526535 AAAATAA-
1 AAAATAAT
526542 AAAA
1 AAAA
526546 AGGAAGAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 10 0.27
8 13 0.35
9 13 0.35
10 1 0.03
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (8 bp):
AAAATAAT
Found at i:527674 original size:13 final size:14
Alignment explanation
Indices: 527627--527678 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
527617 AAGTTAATCC
* *
527627 TATAAATTATTTTT
1 TATAAATAATTATT
*
527641 TATAAAAATATTTATT
1 TAT--AAATAATTATT
527657 TATAAATAATTA-T
1 TATAAATAATTATT
527670 TATAAATAA
1 TATAAATAA
527679 AAAATTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 10 0.31
14 11 0.34
16 11 0.34
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATAAATAATTATT
Found at i:528795 original size:18 final size:18
Alignment explanation
Indices: 528738--528795 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
528728 ACGATTAATG
*
528738 ACACGTTTAACATGATTA
1 ACACGTTTAACACGATTA
* * * *
528756 ACATGTGTAACACAATTC
1 ACACGTTTAACACGATTA
* *
528774 ACACGATTAACACGTTTA
1 ACACGTTTAACACGATTA
528792 ACAC
1 ACAC
528796 AATTAAATAA
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (18 bp):
ACACGTTTAACACGATTA
Found at i:532986 original size:28 final size:24
Alignment explanation
Indices: 532928--532978 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
532918 TTGTGGAACA
532928 TTGCTTGAATGAGTCTTGAGTTGT
1 TTGCTTGAATGAGTCTTGAGTTGT
532952 TTGCTTGAATGAGTCTTGAGTTGT
1 TTGCTTGAATGAGTCTTGAGTTGT
532976 TTG
1 TTG
532979 TTGGCTTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.16, C:0.08, G:0.29, T:0.47
Consensus pattern (24 bp):
TTGCTTGAATGAGTCTTGAGTTGT
Found at i:538639 original size:21 final size:19
Alignment explanation
Indices: 538613--538655 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
538603 AACTAAACCA
*
538613 AAATATAAATTAACAAATATT
1 AAATATAAACTAA-AAAT-TT
*
538634 AAATATCAACTAAAAATTT
1 AAATATAAACTAAAAATTT
538653 AAA
1 AAA
538656 AAACACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 4 0.20
21 11 0.55
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATATAAACTAAAAATTT
Found at i:538903 original size:20 final size:20
Alignment explanation
Indices: 538880--538917 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
538870 TCTCTTCATA
538880 ATGAA-ATTGATTATAATTTT
1 ATGAACATTGA-TATAATTTT
*
538900 ATGAACATTTATATAATT
1 ATGAACATTGATATAATT
538918 AAGTACCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (20 bp):
ATGAACATTGATATAATTTT
Done.