Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 3 of 226
Found at i:877088 original size:7 final size:7
Alignment explanation
Indices: 877076--877125 Score: 82
Period size: 7 Copynumber: 7.0 Consensus size: 7
877066 CTTTATCTTT
877076 ACCCTAA
1 ACCCTAA
877083 ACCCTAAA
1 ACCCT-AA
877091 ACCCTAA
1 ACCCTAA
*
877098 ATCCTAA
1 ACCCTAA
877105 ACCCTAA
1 ACCCTAA
877112 ACCCTAA
1 ACCCTAA
877119 ACCCTAA
1 ACCCTAA
877126 TATAATATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
7 33 0.82
8 7 0.17
ACGTcount: A:0.44, C:0.40, G:0.00, T:0.16
Consensus pattern (7 bp):
ACCCTAA
Found at i:877133 original size:5 final size:5
Alignment explanation
Indices: 877123--877162 Score: 62
Period size: 5 Copynumber: 7.6 Consensus size: 5
877113 CCCTAAACCC
877123 TAATA TAATA TAATA TAATA TAATA TAATAA TATATA TAA
1 TAATA TAATA TAATA TAATA TAATA TAAT-A TA-ATA TAA
877163 AACATAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 25 0.76
6 6 0.18
7 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:879285 original size:24 final size:24
Alignment explanation
Indices: 879258--879304 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
879248 AGCCTATAAT
879258 GGGTAGCTCCAAAAAGCAATTAAC
1 GGGTAGCTCCAAAAAGCAATTAAC
* * *
879282 GGGTAGCTTCGAAGAGCAATTAA
1 GGGTAGCTCCAAAAAGCAATTAA
879305 TGGGAAGTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (24 bp):
GGGTAGCTCCAAAAAGCAATTAAC
Found at i:879414 original size:26 final size:25
Alignment explanation
Indices: 879350--879415 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
879340 ATACGAGCAC
* * *
879350 TAACGGGAAGCTTACAAAGAGCTTT
1 TAACGGGAAGCTCACAAAGAGCATA
*
879375 TAATCGGAAAGCTCACAAAGAGCCATA
1 TAA-CGGGAAGCTCACAAAGAG-CATA
*
879402 TAACGGGACGCTCA
1 TAACGGGAAGCTCA
879416 TAAGAGCTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 3 0.09
26 25 0.76
27 5 0.15
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (25 bp):
TAACGGGAAGCTCACAAAGAGCATA
Found at i:889082 original size:17 final size:18
Alignment explanation
Indices: 889046--889096 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
889036 TAGGGGTGTG
*
889046 CAAAATTCGGGTAAAACCGA
1 CAAAATTC-GGT-TAACCGA
889066 -AAAATTCGGTTAACCGA
1 CAAAATTCGGTTAACCGA
**
889083 CCGAATTCGGTTAA
1 CAAAATTCGGTTAA
889097 TCGGTCGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 6 0.22
18 14 0.52
19 7 0.26
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (18 bp):
CAAAATTCGGTTAACCGA
Found at i:889376 original size:9 final size:9
Alignment explanation
Indices: 889362--889437 Score: 107
Period size: 9 Copynumber: 8.4 Consensus size: 9
889352 GTAGTGATTC
*
889362 AATTTGGTT
1 AATTCGGTT
*
889371 AATTTGGTT
1 AATTCGGTT
*
889380 AATTCGGGT
1 AATTCGGTT
889389 AATTCGGTT
1 AATTCGGTT
*
889398 AATTCGGGT
1 AATTCGGTT
*
889407 AATTCGGAT
1 AATTCGGTT
889416 AATTCGGTT
1 AATTCGGTT
889425 AATTCGGTT
1 AATTCGGTT
889434 AATT
1 AATT
889438 TTTAACCAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 61 1.00
ACGTcount: A:0.25, C:0.08, G:0.24, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:890262 original size:12 final size:12
Alignment explanation
Indices: 890245--890270 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
890235 GATAAGTATT
890245 ATATTTATTTAA
1 ATATTTATTTAA
890257 ATATTTATTTAA
1 ATATTTATTTAA
890269 AT
1 AT
890271 TTTTTGTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATTTATTTAA
Found at i:898916 original size:8 final size:8
Alignment explanation
Indices: 898903--898943 Score: 73
Period size: 8 Copynumber: 5.0 Consensus size: 8
898893 TCTTTTATAT
898903 ATATAATA
1 ATATAATA
898911 ATATAATA
1 ATATAATA
898919 ATATAATA
1 ATATAATA
898927 ATATAATTA
1 ATATAA-TA
898936 ATATAATA
1 ATATAATA
898944 CTTATTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 24 0.75
9 8 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:908374 original size:28 final size:29
Alignment explanation
Indices: 908320--908374 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
908310 TTTCTATGTG
* * **
908320 TTTATAATGTTATTAATTAGTTTAATATT
1 TTTATAATGTAATTAATTAATCAAATATT
908349 TTTATAAT-TAATTAATTAATCAAATA
1 TTTATAATGTAATTAATTAATCAAATA
908375 GTTAATATCG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 14 0.64
29 8 0.36
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (29 bp):
TTTATAATGTAATTAATTAATCAAATATT
Found at i:914601 original size:7 final size:7
Alignment explanation
Indices: 914589--914616 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
914579 TTAGGATGAG
914589 TTTTAAA
1 TTTTAAA
914596 TTTTAAA
1 TTTTAAA
914603 TTTTAAA
1 TTTTAAA
914610 TTTTAAA
1 TTTTAAA
914617 ATAAATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTTTAAA
Found at i:916367 original size:44 final size:44
Alignment explanation
Indices: 916319--916408 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
916309 TAAATTTTAA
* *
916319 GATTCAAAAATTAAATCATTTAAATCTTACTTTTTAAGAATATG
1 GATTCAAAAATTAAATCACTTAAATCTTACTTTTTAAAAATATG
*
916363 GATTCAAAAATTAAATTACTTAAATCTTACTTTTTAAAAATATG
1 GATTCAAAAATTAAATCACTTAAATCTTACTTTTTAAAAATATG
916407 GA
1 GA
916409 GTTAAATACA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (44 bp):
GATTCAAAAATTAAATCACTTAAATCTTACTTTTTAAAAATATG
Found at i:917627 original size:25 final size:24
Alignment explanation
Indices: 917551--917652 Score: 90
Period size: 22 Copynumber: 4.3 Consensus size: 24
917541 CACTAATAAA
*
917551 CAGAGAGCACTA-AAGTACT-ATA-
1 CAGAGAGCAC-AGAAGTGCTAATAT
*
917573 CAGAGAGCACAGATGTGCTAA-A-
1 CAGAGAGCACAGAAGTGCTAATAT
* *
917595 CAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACAGAAGTGCT-AATAT
917620 CAGAGAGCACCA-AAGTGCTAATAAT
1 CAGAGAGCA-CAGAAGTGCTAAT-AT
917645 CAGAGAGC
1 CAGAGAGC
917653 GCGCTAAAGT
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.01
22 33 0.49
23 3 0.04
24 4 0.06
25 25 0.37
26 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.16
Consensus pattern (24 bp):
CAGAGAGCACAGAAGTGCTAATAT
Found at i:918758 original size:23 final size:22
Alignment explanation
Indices: 918725--918767 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
918715 TTCTTTTGTT
*
918725 TTATATATATAATAATATAATA
1 TTATATATATAATAAAATAATA
918747 TTATATTATATAATAAAATAA
1 TTATA-TATATAATAAAATAA
918768 CATACTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTATATATATAATAAAATAATA
Found at i:919029 original size:13 final size:13
Alignment explanation
Indices: 919011--919048 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
919001 AACTAACTTC
919011 ATAAATATTTATA
1 ATAAATATTTATA
919024 ATAAATATTTATA
1 ATAAATATTTATA
919037 ATAAATATTTAT
1 ATAAATATTTAT
919049 GAATCTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATAAATATTTATA
Found at i:931990 original size:26 final size:26
Alignment explanation
Indices: 931961--932056 Score: 93
Period size: 26 Copynumber: 3.5 Consensus size: 26
931951 TTATATTAAG
931961 AATTTTATTAAATTATATTTAATAAT
1 AATTTTATTAAATTATATTTAATAAT
* * *
931987 AATTTTGTTAAAATATAGTTAAATTATTTAT
1 AATTTTATTAAATTATA-TTTAA-TA---AT
*
932018 AATTTTTATTAAATTATTTTTAATAAT
1 AA-TTTTATTAAATTATATTTAATAAT
*
932045 AAATTTATTAAA
1 AATTTTATTAAA
932057 ATTTAATAAC
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
26 24 0.43
27 8 0.14
28 2 0.04
30 2 0.04
31 8 0.14
32 12 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
AATTTTATTAAATTATATTTAATAAT
Found at i:932078 original size:58 final size:58
Alignment explanation
Indices: 931963--932078 Score: 135
Period size: 58 Copynumber: 2.0 Consensus size: 58
931953 ATATTAAGAA
* * * * ***
931963 TTTTATTAAATTATATTTAATAATAATTTTGTTAAAATATAGTTAAATTATTTATAAT
1 TTTTATTAAATTATATTTAATAATAAATTTATTAAAATATAGATAAAATAACAATAAT
* *
932021 TTTTATTAAATTATTTTTAATAATAAATTTATTAAAATTTA-ATAACAATAACAATAAT
1 TTTTATTAAATTATATTTAATAATAAATTTATTAAAATATAGATAA-AATAACAATAAT
932079 CATCTACCTA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
57 3 0.06
58 45 0.94
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (58 bp):
TTTTATTAAATTATATTTAATAATAAATTTATTAAAATATAGATAAAATAACAATAAT
Found at i:933398 original size:123 final size:123
Alignment explanation
Indices: 933170--933699 Score: 657
Period size: 123 Copynumber: 4.3 Consensus size: 123
933160 TTTCAAATCA
* * * *
933170 TGAACATGAACTATAAAATACACAT----AA-AAAAAAATTGAATGAGCTAATTGTATTAATCTG
1 TGAATATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAG
* *
933230 ATCCGATATGTAATTACTTAAAAAAGAAAATGCCTTTAAAAAAAATTGAATTGAAACCT
66 ATCCGATATATAATTACTT-AAAAAGAAAATGCCTTTTAAAAAAATTGAATTGAAACCT
** *
933289 TGAATATGAACTATAAAATAGAC-TGAAGAATGTAAAAATTGAATGAGTTAATTGTATTAATCAT
1 TGAATATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAG
*
933353 ATCCGATATATAATTACTTAAAAAAGAAGATGCCTTTTAAAAAAATTGAATTGAAACCT
66 ATCCGATATATAATTACTT-AAAAAGAAAATGCCTTTTAAAAAAATTGAATTGAAACCT
*
933412 TGAATATGAACTAGAACTATAAAATAGACATGAATAATAAAAAAATTGAATGAGTTAATTGTATT
1 TG-A-AT--A-T-GAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATT
* * **
933477 AATCGGATCCGATATGA-AATTACTTAAAAAGAAAATGCCTTTT--AAAAGTTGGCTTGAAACCT
60 AATCAGATCCGATAT-ATAATTACTTAAAAAGAAAATGCCTTTTAAAAAAATTGAATTGAAACCT
* * *
933539 TGAACATAAACTATAAAACAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAG
1 TGAATATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAG
* * * *
933604 ATCCGATATGTAATTACTTAAAAAGAAAATGTCTTTTAAAAAAATTGACTTGAAAACTT
66 ATCCGATATATAATTACTTAAAAAGAAAATGCCTTTTAAAAAAATTGAATTG-AAACCT
* * * * *
933663 TAAAAAT-AACTTTAAAATAAATATGAAGAATAAAAAA
1 TGAATATGAACTATAAAATAGACATGAAGAATAAAAAA
933700 TTAGTTATTG
Statistics
Matches: 359, Mismatches: 35, Indels: 30
0.85 0.08 0.07
Matches are distributed among these distances:
118 1 0.00
119 21 0.06
121 88 0.25
122 3 0.01
123 124 0.35
124 11 0.03
125 3 0.01
126 1 0.00
127 19 0.05
128 1 0.00
129 33 0.09
130 53 0.15
131 1 0.00
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (123 bp):
TGAATATGAACTATAAAATAGACATGAAGAATAAAAAAATTGAATGAGTTAATTGTATTAATCAG
ATCCGATATATAATTACTTAAAAAGAAAATGCCTTTTAAAAAAATTGAATTGAAACCT
Found at i:933572 original size:121 final size:122
Alignment explanation
Indices: 933197--933761 Score: 620
Period size: 123 Copynumber: 4.6 Consensus size: 122
933187 ATACACATAA
* * *
933197 AAAAAAATTGAATGAGCTAATTGTATTAATCTGATCCGATATGTAATTACTTAAAAAAGAAAATG
1 AAAAAAATTGAATGAGTTAATTGTATTAATCAGATCCGATATGAAATTACTTAAAAAAGAAAATG
* * *
933262 CCTTTAAAAAAAATTGAATTGAAACCTTGAATATGAACTATAAAATAGAC-TGAAGAAT
66 CCTTT--TAAAAATTGAATTGAAACCTTGAAAATAAACTATAAAATAGACATGAAGAAT
** * *
933320 GTAAAAATTGAATGAGTTAATTGTATTAATCATATCCGATAT-ATAATTACTTAAAAAAGAAGAT
1 AAAAAAATTGAATGAGTTAATTGTATTAATCAGATCCGATATGA-AATTACTTAAAAAAGAAAAT
*
933384 GCCTTTTAAAAAAATTGAATTGAAACCTTGAATATGAACTAGAACTATAAAATAGACATGAATAA
65 GCCTTTT--AAAAATTGAATTGAAACCTTG-A-A--AA-TA-AACTATAAAATAGACATGAAGAA
933449 T
122 T
*
933450 AAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCGATATGAAATTACTT-AAAAAGAAAATG
1 AAAAAAATTGAATGAGTTAATTGTATTAATCAGATCCGATATGAAATTACTTAAAAAAGAAAATG
* ** * *
933514 CCTTTTAAAAGTTGGCTTGAAACCTTGAACATAAACTATAAAACAGACATGAAGAAT
66 CCTTTTAAAAATTGAATTGAAACCTTGAAAATAAACTATAAAATAGACATGAAGAAT
*
933571 AAAAAAATTGAATGAGTTAATTGTATTAATCAGATCCGATATGTAATTACTT-AAAAAGAAAATG
1 AAAAAAATTGAATGAGTTAATTGTATTAATCAGATCCGATATGAAATTACTTAAAAAAGAAAATG
* * * * * * *
933635 TCTTTTAAAAAAATTGACTTGAAAACTTTAAAA-ATAACTTTAAAATAAATATGAAGAAT
66 CCTTTT--AAAAATTGAATTGAAACCTTGAAAATA-AACTATAAAATAGACATGAAGAAT
* * * *
933694 -AAAAAA-T---T-AGTT-ATTGTATTAATTAGATCCAATATGAAAATTTC-TATAAAA-AAAAT
1 AAAAAAATTGAATGAGTTAATTGTATTAATCAGATCCGATATG-AAATTACTTAAAAAAGAAAAT
933750 G-CTTTTAGAAAA
65 GCCTTTTA-AAAA
933762 AATTACTGTA
Statistics
Matches: 386, Mismatches: 39, Indels: 43
0.82 0.08 0.09
Matches are distributed among these distances:
113 1 0.00
114 4 0.01
115 5 0.01
116 29 0.08
117 13 0.03
118 1 0.00
121 90 0.23
122 9 0.02
123 124 0.32
124 1 0.00
125 2 0.01
126 1 0.00
127 19 0.05
128 1 0.00
129 32 0.08
130 53 0.14
131 1 0.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.31
Consensus pattern (122 bp):
AAAAAAATTGAATGAGTTAATTGTATTAATCAGATCCGATATGAAATTACTTAAAAAAGAAAATG
CCTTTTAAAAATTGAATTGAAACCTTGAAAATAAACTATAAAATAGACATGAAGAAT
Found at i:947040 original size:6 final size:6
Alignment explanation
Indices: 947029--947055 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
947019 AACAGTTATA
947029 CCAGCT CCAGCT CCAGCT CCAGCT CCA
1 CCAGCT CCAGCT CCAGCT CCAGCT CCA
947056 TGTTTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.52, G:0.15, T:0.15
Consensus pattern (6 bp):
CCAGCT
Found at i:947900 original size:37 final size:37
Alignment explanation
Indices: 947859--947976 Score: 93
Period size: 37 Copynumber: 3.2 Consensus size: 37
947849 GATTTGGCTT
947859 TAAATTTTTATAAAATTGTTTGATATATTACTTAAAA
1 TAAATTTTTATAAAATTGTTTGATATATTACTTAAAA
* * ** *
947896 TAAATTAATTACGAAACATAATTAG-T-T-TT--TTGATAAA
1 TAAATT-TTTA-TAAA-ATTGTTTGATATATTACTT-A-AAA
*
947933 TAAAGATTTTATAAAATTGTTTGATATATTACTTAAAA
1 TAAA-TTTTTATAAAATTGTTTGATATATTACTTAAAA
947971 TAAATT
1 TAAATT
947977 AATTACGAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 22
0.63 0.13 0.24
Matches are distributed among these distances:
35 7 0.12
36 5 0.09
37 20 0.34
38 14 0.24
39 5 0.09
40 7 0.12
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (37 bp):
TAAATTTTTATAAAATTGTTTGATATATTACTTAAAA
Found at i:947949 original size:75 final size:75
Alignment explanation
Indices: 947864--948018 Score: 301
Period size: 75 Copynumber: 2.1 Consensus size: 75
947854 GGCTTTAAAT
*
947864 TTTTATAAAATTGTTTGATATATTACTTAAAATAAATTAATTACGAAACATAATTAGTTTTTTGA
1 TTTTATAAAATTGTTTGATATATTACTTAAAATAAATTAATTACGAAACATAATCAGTTTTTTGA
947929 TAAATAAAGA
66 TAAATAAAGA
947939 TTTTATAAAATTGTTTGATATATTACTTAAAATAAATTAATTACGAAACATAATCAGTTTTTTGA
1 TTTTATAAAATTGTTTGATATATTACTTAAAATAAATTAATTACGAAACATAATCAGTTTTTTGA
948004 TAAATAAAGA
66 TAAATAAAGA
948014 TTTTA
1 TTTTA
948019 AATTATAAAA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 79 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.43
Consensus pattern (75 bp):
TTTTATAAAATTGTTTGATATATTACTTAAAATAAATTAATTACGAAACATAATCAGTTTTTTGA
TAAATAAAGA
Found at i:950020 original size:51 final size:51
Alignment explanation
Indices: 949941--950195 Score: 361
Period size: 51 Copynumber: 5.0 Consensus size: 51
949931 GATGCCGAAC
* *
949941 CAGCAAGGTGGAAACATCGAAT-CTCAAACATACACTCAGCTACCACAACAG
1 CAGCAAGGTGGAAACATTGAATAC-CAAACATATACTCAGCTACCACAACAG
* ** *
949992 CAGCAAGGTGGTAACATCAAATACCAAACATATACTCAACTACCACAACAG
1 CAGCAAGGTGGAAACATTGAATACCAAACATATACTCAGCTACCACAACAG
* * *
950043 CAGCAAGGTGGAAACGTTGAATACCAAACATATACTCAGCTGCCACAACAA
1 CAGCAAGGTGGAAACATTGAATACCAAACATATACTCAGCTACCACAACAG
* * *
950094 CAGCAAGGTGGAAACATTGAATCCCAAACTTATACTCAGCTACAACAACAG
1 CAGCAAGGTGGAAACATTGAATACCAAACATATACTCAGCTACCACAACAG
*
950145 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCCT-CCACAACAG
1 CAGCAAGGTGGAAACATTGAATACCAAACATATACTCAG-CTACCACAACAG
950196 TACTTAATGG
Statistics
Matches: 183, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
51 180 0.98
52 3 0.02
ACGTcount: A:0.42, C:0.27, G:0.15, T:0.16
Consensus pattern (51 bp):
CAGCAAGGTGGAAACATTGAATACCAAACATATACTCAGCTACCACAACAG
Found at i:952111 original size:51 final size:51
Alignment explanation
Indices: 952035--952137 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
952025 CCTTGGAACT
952035 TTTTACTGATTATAATTTGTTATTGATCCCTTTTGCCTATATCTGTTTGTG
1 TTTTACTGATTATAATTTGTTATTGATCCCTTTTGCCTATATCTGTTTGTG
952086 TTTTACTGATTATAATTTGTTATTGATCCCTTTTGCCTATATCTGTTTGTG
1 TTTTACTGATTATAATTTGTTATTGATCCCTTTTGCCTATATCTGTTTGTG
952137 T
1 T
952138 ATGTCCTTGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.55
Consensus pattern (51 bp):
TTTTACTGATTATAATTTGTTATTGATCCCTTTTGCCTATATCTGTTTGTG
Found at i:952126 original size:27 final size:27
Alignment explanation
Indices: 952045--952126 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 27
952035 TTTTACTGAT
952045 TATAATTTGTTATTGATCCCTTTTGCC
1 TATAATTTGTTATTGATCCCTTTTGCC
* **
952072 TAT-ATCTGTT-TGTG-T---TTTACTGAT
1 TATAATTTGTTAT-TGATCCCTTT--TGCC
952096 TATAATTTGTTATTGATCCCTTTTGCC
1 TATAATTTGTTATTGATCCCTTTTGCC
952123 TATA
1 TATA
952127 TCTGTTTGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
22 3 0.08
24 5 0.12
25 10 0.25
26 10 0.25
27 9 0.22
29 3 0.08
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.54
Consensus pattern (27 bp):
TATAATTTGTTATTGATCCCTTTTGCC
Found at i:958811 original size:3 final size:3
Alignment explanation
Indices: 958803--958840 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
958793 CAATGGGAGA
958803 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
958841 ATCGAAGAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:977133 original size:20 final size:21
Alignment explanation
Indices: 977101--977139 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
977091 ACTAAAGATA
977101 TTTAAAAATTTTAC-TATTAT
1 TTTAAAAATTTTACATATTAT
977121 TTTAATAAA-TTTACATATT
1 TTTAA-AAATTTTACATATT
977140 TAAATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAAAAATTTTACATATTAT
Found at i:978609 original size:33 final size:33
Alignment explanation
Indices: 978571--978672 Score: 145
Period size: 33 Copynumber: 3.2 Consensus size: 33
978561 AGATTAATTT
* * *
978571 ATATTTGATGTATCATTATATTAAATTATTTAA
1 ATATTTCATATATCATTCTATTAAATTATTTAA
978604 ATATTTCATATATCATTCTATTAAATTATTTAA
1 ATATTTCATATATCATTCTATTAAATTATTTAA
* *
978637 ATA--TCATTTACCATTCTATTAAATTATTTAA
1 ATATTTCATATATCATTCTATTAAATTATTTAA
978668 ATATT
1 ATATT
978673 ATATAACTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
31 29 0.47
33 33 0.53
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (33 bp):
ATATTTCATATATCATTCTATTAAATTATTTAA
Found at i:978655 original size:31 final size:31
Alignment explanation
Indices: 978584--978677 Score: 134
Period size: 31 Copynumber: 3.0 Consensus size: 31
978574 TTTGATGTAT
* *
978584 CATTATATTAAATTATTTAAATATTTCATATAT
1 CATTCTATTAAATTATTTAAATA--TCATATAC
*
978617 CATTCTATTAAATTATTTAAATATCATTTAC
1 CATTCTATTAAATTATTTAAATATCATATAC
*
978648 CATTCTATTAAATTATTTAAATATTATATA
1 CATTCTATTAAATTATTTAAATATCATATA
978678 ACTTAACTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 34 0.61
33 22 0.39
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (31 bp):
CATTCTATTAAATTATTTAAATATCATATAC
Found at i:982744 original size:26 final size:25
Alignment explanation
Indices: 982691--982762 Score: 85
Period size: 26 Copynumber: 2.9 Consensus size: 25
982681 CCCAGCCCAT
* *
982691 TTTTAAAAT-AAACATTAAAAATTA
1 TTTTAAAATAAAAAATTAAAAAGTA
*
982715 TTTTAAAATAAAAAAATTTAAAAGTA
1 TTTTAAAAT-AAAAAATTAAAAAGTA
982741 TTTTAAAATTAAAAAA-TAAAAA
1 TTTTAAAA-TAAAAAATTAAAAA
982763 TAAAAAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 9 0.22
25 5 0.12
26 26 0.63
27 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (25 bp):
TTTTAAAATAAAAAATTAAAAAGTA
Found at i:984676 original size:24 final size:25
Alignment explanation
Indices: 984648--984706 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
984638 ATTGGCTTGT
* *
984648 ATGAGCTTCCCGTTA-ATGGCTCTC
1 ATGAGCTTCCCATTACATGGCTCAC
*
984672 CTGAGCTTCCCATTACATGGCTCAC
1 ATGAGCTTCCCATTACATGGCTCAC
984697 ATGAGCTTCC
1 ATGAGCTTCC
984707 TCTTATGTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.19, C:0.32, G:0.19, T:0.31
Consensus pattern (25 bp):
ATGAGCTTCCCATTACATGGCTCAC
Found at i:987045 original size:18 final size:18
Alignment explanation
Indices: 987022--987059 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
987012 TTTTGCTAAC
987022 ACATAACCCAACTATTAT
1 ACATAACCCAACTATTAT
987040 ACATAACCCAACTATTAT
1 ACATAACCCAACTATTAT
987058 AC
1 AC
987060 TTTTATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (18 bp):
ACATAACCCAACTATTAT
Found at i:990328 original size:110 final size:109
Alignment explanation
Indices: 990152--990354 Score: 327
Period size: 110 Copynumber: 1.9 Consensus size: 109
990142 AAGTTAAGAA
*
990152 GATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTCAAAT
1 GATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTCTCTCAAAT
990217 TT-CCAAACGCAAAACATTGCCTTATTTTAAAATTTTTTAAAAG
66 TTCCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTTAAAAG
* * *
990260 GATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
1 GATATTTAGCTATTTGGTCGAACGAG--AAATCGAAACCCAGCACATTAGGGCACGTTCTCTCAA
* *
990325 ATTTCCCAAACGCTAAATATTGCCTTATTT
64 ATTTCCCAAACGCAAAACATTGCCTTATTT
990355 AGAAAAACCT
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
108 25 0.29
110 38 0.44
111 23 0.27
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (109 bp):
GATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTCTCTCAAAT
TTCCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTTAAAAG
Found at i:992720 original size:8 final size:8
Alignment explanation
Indices: 992707--992762 Score: 53
Period size: 8 Copynumber: 6.8 Consensus size: 8
992697 TTTTTTTTAG
992707 TATATTAT
1 TATATTAT
992715 TATATTAT
1 TATATTAT
992723 TATATTGTAAAT
1 TATA-T-T--AT
*
992735 TATATTAA
1 TATATTAT
992743 T-TA-TAT
1 TATATTAT
992749 TATATTAT
1 TATATTAT
992757 TATATT
1 TATATT
992763 TTAAATAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
6 3 0.08
7 4 0.10
8 23 0.57
9 1 0.03
10 2 0.05
11 1 0.03
12 6 0.15
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (8 bp):
TATATTAT
Found at i:993817 original size:15 final size:14
Alignment explanation
Indices: 993781--993821 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
993771 ATATTGAATT
993781 AAATGAATTAAA-A
1 AAATGAATTAAATA
*
993794 ATATGAATTAAATA
1 AAATGAATTAAATA
993808 AAAGTGAATTAAAT
1 AAA-TGAATTAAAT
993822 TATGATTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 11 0.46
14 3 0.12
15 10 0.42
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (14 bp):
AAATGAATTAAATA
Found at i:994211 original size:41 final size:37
Alignment explanation
Indices: 994163--994267 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 37
994153 TCGACCTCGA
994163 GTCGATGAGACACTGGGTGTCATACTGTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCA-A-T-TTACTTCGGATAG
* ** ** * *
994203 ATTCGATGAGGTACTGGGTACCAATTTACTTCGGCTTG
1 -GTCGATGAGACACTGGGTGTCAATTTACTTCGGATAG
* *
994241 GCCGATGAGACACTGGGTGTCACTTTA
1 GTCGATGAGACACTGGGTGTCAATTTA
994268 TTGCGTCGAA
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
37 20 0.40
38 11 0.22
39 1 0.02
40 1 0.02
41 17 0.34
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (37 bp):
GTCGATGAGACACTGGGTGTCAATTTACTTCGGATAG
Found at i:1003510 original size:26 final size:26
Alignment explanation
Indices: 1003452--1003504 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1003442 TGATTCCTTG
*
1003452 TGGAACTCTAAGGGAATTGCCTACCT
1 TGGAACTCTAAGGGAATTGCCCACCT
* *
1003478 TGGAACTCTAAGGGAGTTGCCCCCCT
1 TGGAACTCTAAGGGAATTGCCCACCT
1003504 T
1 T
1003505 TTAACTTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (26 bp):
TGGAACTCTAAGGGAATTGCCCACCT
Found at i:1012233 original size:34 final size:34
Alignment explanation
Indices: 1012190--1012257 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1012180 TAAGCAATAC
1012190 ATAACCTTCCATTTTTGTAAACTTACCCTTCAAG
1 ATAACCTTCCATTTTTGTAAACTTACCCTTCAAG
1012224 ATAACCTTCCATTTTTGTAAACTTACCCTTCAAG
1 ATAACCTTCCATTTTTGTAAACTTACCCTTCAAG
1012258 CAACCATTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.38
Consensus pattern (34 bp):
ATAACCTTCCATTTTTGTAAACTTACCCTTCAAG
Found at i:1016837 original size:72 final size:73
Alignment explanation
Indices: 1016688--1016888 Score: 260
Period size: 72 Copynumber: 2.7 Consensus size: 73
1016678 CAATATTATT
* * *
1016688 AACTACTCTAACATTACTAAATATATTTCACTTAAATTGCAATTTAAATTTATACAATTTTGTTC
1 AACTACTCTGACATTACTAAATATATTTCATTTAAATTGCAATTCAAATTTATACAATTTTGTTC
**
1016753 ATCCATGG
66 ATCCATAA
* * * *
1016761 AACTACTCTGACATTATTAAATATATTTTATTTAAA-TACAATTCAAATTTATACAATTTTGTTG
1 AACTACTCTGACATTACTAAATATATTTCATTTAAATTGCAATTCAAATTTATACAATTTTGTTC
1016825 ATCCATAA
66 ATCCATAA
* * **
1016833 AACTATTGTTTGACATTACTAAATGCATTTCATTTAAATTGCAATTCAAATTTATA
1 AACTA--CTCTGACATTACTAAATATATTTCATTTAAATTGCAATTCAAATTTATA
1016889 AGAAATTTAA
Statistics
Matches: 109, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
72 36 0.33
73 32 0.29
74 25 0.23
75 16 0.15
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.42
Consensus pattern (73 bp):
AACTACTCTGACATTACTAAATATATTTCATTTAAATTGCAATTCAAATTTATACAATTTTGTTC
ATCCATAA
Found at i:1017386 original size:2 final size:2
Alignment explanation
Indices: 1017374--1017402 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1017364 GTTGATTAAA
1017374 AT AT A- 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
1017403 GTAAATGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1029579 original size:2 final size:2
Alignment explanation
Indices: 1029572--1029598 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1029562 ATTCAAGGGT
1029572 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1029599 TTATGGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1030221 original size:19 final size:19
Alignment explanation
Indices: 1030197--1030239 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1030187 TGATACATAA
*
1030197 TTTATA-TTAAAATCTCAAT
1 TTTATAGTT-AAATCACAAT
1030216 TTTATAGTTAAATCACAAT
1 TTTATAGTTAAATCACAAT
1030235 TTTAT
1 TTTAT
1030240 TTACTAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (19 bp):
TTTATAGTTAAATCACAAT
Found at i:1032679 original size:30 final size:32
Alignment explanation
Indices: 1032631--1032693 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
1032621 TAATAAAGTT
*
1032631 AAAATTATACTTTGATTTTTTAAAAATAATAA
1 AAAATTATACTTTAATTTTTTAAAAATAATAA
*
1032663 AAAATTA-A-TTTAATTTTTTAAAAATTATAA
1 AAAATTATACTTTAATTTTTTAAAAATAATAA
1032693 A
1 A
1032694 GATAAGGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 21 0.72
31 1 0.03
32 7 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (32 bp):
AAAATTATACTTTAATTTTTTAAAAATAATAA
Found at i:1033434 original size:24 final size:25
Alignment explanation
Indices: 1033384--1033437 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
1033374 ATTATATACA
* *
1033384 AATAAATTTAACAAAAATAAAACAC
1 AATAAATTCAACAAAAAGAAAACAC
*
1033409 AATAAATTCAAC-ACAAGAAAACAC
1 AATAAATTCAACAAAAAGAAAACAC
1033433 AATAA
1 AATAA
1033438 CCCATCAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.67, C:0.15, G:0.02, T:0.17
Consensus pattern (25 bp):
AATAAATTCAACAAAAAGAAAACAC
Found at i:1036333 original size:3 final size:3
Alignment explanation
Indices: 1036325--1036351 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1036315 TATATTGATG
1036325 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1036352 GTTATGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:1047614 original size:75 final size:75
Alignment explanation
Indices: 1047491--1047633 Score: 216
Period size: 75 Copynumber: 1.9 Consensus size: 75
1047481 CAGGCTATGC
* * *
1047491 TCCTCCTCCAAGGCCAAGTCCTCAAGCGCCACCACCAGGACCTGGTCATCCTCCAAGTCCACCAC
1 TCCTCCTCCAAGGCCAAGTCCTCAAGAGCCACCACCAAGACCAGGTCATCCTCCAAGTCCACCAC
1047556 ATGCCGGGCA
66 ATGCCGGGCA
* * *
1047566 TCCTCCTCCAAGGCCAAGT-CTCTATGAGCCACCACCAAGACCAGGTCATCCTCCAGGTCCACTA
1 TCCTCCTCCAAGGCCAAGTCCTC-AAGAGCCACCACCAAGACCAGGTCATCCTCCAAGTCCACCA
1047630 CATG
65 CATG
1047634 AGCATCCTCC
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 3 0.05
75 58 0.95
ACGTcount: A:0.24, C:0.42, G:0.17, T:0.17
Consensus pattern (75 bp):
TCCTCCTCCAAGGCCAAGTCCTCAAGAGCCACCACCAAGACCAGGTCATCCTCCAAGTCCACCAC
ATGCCGGGCA
Found at i:1047670 original size:27 final size:24
Alignment explanation
Indices: 1047612--1047657 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1047602 AAGACCAGGT
* *
1047612 CATCCTCCAGGTCCACTACATGAG
1 CATCCTCCAAGTCCACCACATGAG
1047636 CATCCTCCAAGTCCACCACATG
1 CATCCTCCAAGTCCACCACATG
1047658 TTGAGCATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.41, G:0.13, T:0.20
Consensus pattern (24 bp):
CATCCTCCAAGTCCACCACATGAG
Found at i:1047697 original size:99 final size:99
Alignment explanation
Indices: 1047537--1047719 Score: 251
Period size: 99 Copynumber: 1.8 Consensus size: 99
1047527 AGGACCTGGT
* * *
1047537 CATCCTCCAAGTCCACCACATGCCGGGCATCCTCCTCCAAGGCCAAGTCTCTATGAGCCACCACC
1 CATCCTCCAAGTCCACCACATGCCGAGCATCCTCCTCCAAGGCCAAGTCCCCATGAGCCACCACC
1047602 AAGACCAGGTCATCCTCCAGGTCCACTACATGAG
66 AAGACCAGGTCATCCTCCAGGTCCACTACATGAG
** * * **
1047636 CATCCTCCAAGTCCACCACATGTTGAGCATCCTCCTCCAAGG-CTAGATCCCCATGCGCCACCGT
1 CATCCTCCAAGTCCACCACATGCCGAGCATCCTCCTCCAAGGCCAAG-TCCCCATGAGCCACCAC
* *
1047700 TAGGACCAGGTCATCCTCCA
65 CAAGACCAGGTCATCCTCCA
1047720 AGCCCACCAC
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
98 3 0.04
99 69 0.96
ACGTcount: A:0.24, C:0.40, G:0.17, T:0.19
Consensus pattern (99 bp):
CATCCTCCAAGTCCACCACATGCCGAGCATCCTCCTCCAAGGCCAAGTCCCCATGAGCCACCACC
AAGACCAGGTCATCCTCCAGGTCCACTACATGAG
Found at i:1047914 original size:90 final size:90
Alignment explanation
Indices: 1047703--1047937 Score: 226
Period size: 90 Copynumber: 2.6 Consensus size: 90
1047693 CCACCGTTAG
* * *
1047703 GACCAGGTCATCCTCCAAGCCCACCACATAATGATCA-TCTTCATCCAGACCATGCTCCCCCTCC
1 GACCAGGTCATCCTCCAAG-TCACCACATAATGAGCATTC-TCATCCAGGCCATGCT--CCCTCC
* * **
1047767 AGGGCCAGGTCCCCATGTGCCACCACCAA
62 AGGACCAAGTCCCCATACGCCACCACCAA
* * * * **
1047796 GACCTGGACATCCTCCAGGTGCATCACATGCTGAGCATTCTCATCCAGGCCATGCT-CCTCCAGG
1 GACCAGGTCATCCTCCAAGT-CACCACATAATGAGCATTCTCATCCAGGCCATGCTCCCTCCAGG
1047860 ACCAAGTCCCCATACGCCACCACC-A
65 ACCAAGTCCCCATACGCCACCACCAA
* * *
1047885 GAACCAGGTCATCTTCCAAGTCAACCACATATTG-GTCATCCTCATCCAGGCCA
1 G-ACCAGGTCATCCTCCAAGTC-ACCACATAATGAG-CATTCTCATCCAGGCCA
1047938 GATCCCCATG
Statistics
Matches: 116, Mismatches: 21, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
89 4 0.03
90 67 0.58
93 43 0.37
94 2 0.02
ACGTcount: A:0.25, C:0.40, G:0.16, T:0.19
Consensus pattern (90 bp):
GACCAGGTCATCCTCCAAGTCACCACATAATGAGCATTCTCATCCAGGCCATGCTCCCTCCAGGA
CCAAGTCCCCATACGCCACCACCAA
Found at i:1049450 original size:26 final size:27
Alignment explanation
Indices: 1049421--1049474 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
1049411 CATAGTTTAG
1049421 TGTCTGCC-GTTTTTGGCACGTTTCTT
1 TGTCTGCCAGTTTTTGGCACGTTTCTT
*
1049447 TGTCTGCCATTTTTTGGCACGTTTCTT
1 TGTCTGCCAGTTTTTGGCACGTTTCTT
1049474 T
1 T
1049475 ATTGTTCTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.06, C:0.22, G:0.20, T:0.52
Consensus pattern (27 bp):
TGTCTGCCAGTTTTTGGCACGTTTCTT
Found at i:1051643 original size:3 final size:3
Alignment explanation
Indices: 1051635--1051736 Score: 61
Period size: 3 Copynumber: 33.0 Consensus size: 3
1051625 TAAGAGAAAT
* *
1051635 ATA ATA ATA ATA GTA ATA ATA ATGCA A-A ATTA ATTA AT- TTA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA AT--A ATA A-TA A-TA ATA ATA ATA ATA
* *
1051681 ATA ATA ATA ACA AGTAA ATAA ATAA ATA AT- ATA A-A ATA ATA ATA GTA
1 ATA ATA ATA ATA A-T-A AT-A AT-A ATA ATA ATA ATA ATA ATA ATA ATA
1051728 ATA ATA ATA
1 ATA ATA ATA
1051737 TTAAATTAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 20
0.74 0.07 0.18
Matches are distributed among these distances:
2 9 0.11
3 53 0.65
4 15 0.19
5 4 0.05
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1066037 original size:82 final size:82
Alignment explanation
Indices: 1065900--1066061 Score: 279
Period size: 82 Copynumber: 2.0 Consensus size: 82
1065890 GAAGACTCAT
* *
1065900 AATTTGATAAGCTTCTTCCACTGTAAAGGTTGAATAAATGATGTCTCTATTCCATCGCTTAGGAT
1 AATTTGATAAGCTTCTTCCACTGTAAAGGTTGAATAAATGAGGTATCTATTCCATCGCTTAGGAT
*
1065965 TCTGCAAAATTAAATGC
66 TCTGCAAAATCAAATGC
* *
1065982 AATTTGATAATCTTCTTCCACTGTAAAGGTTGAATAAATGAGGTATCTATTCCATCGTTTAGGAT
1 AATTTGATAAGCTTCTTCCACTGTAAAGGTTGAATAAATGAGGTATCTATTCCATCGCTTAGGAT
1066047 TCTGCAAAATCAAAT
66 TCTGCAAAATCAAAT
1066062 CAGACACAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 75 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (82 bp):
AATTTGATAAGCTTCTTCCACTGTAAAGGTTGAATAAATGAGGTATCTATTCCATCGCTTAGGAT
TCTGCAAAATCAAATGC
Found at i:1067216 original size:27 final size:27
Alignment explanation
Indices: 1067184--1067237 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1067174 TAAACTGAGC
1067184 CGTAAATATTTTTATAAATATTTACGG
1 CGTAAATATTTTTATAAATATTTACGG
1067211 CGTAAATATTTTTATAAATATTTACGG
1 CGTAAATATTTTTATAAATATTTACGG
1067238 AGTGTCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (27 bp):
CGTAAATATTTTTATAAATATTTACGG
Found at i:1067410 original size:17 final size:17
Alignment explanation
Indices: 1067388--1067448 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
1067378 TAAAGAATGA
1067388 CCTAAATAGCAATTATG
1 CCTAAATAGCAATTATG
** * *
1067405 CCTAAATAAAAAGATAAGG
1 CCTAAAT-AGCA-ATTATG
1067424 CCTAAATAGCAATTATG
1 CCTAAATAGCAATTATG
1067441 CCTAAATA
1 CCTAAATA
1067449 AAAAGATGAG
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
17 19 0.56
18 4 0.12
19 11 0.32
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (17 bp):
CCTAAATAGCAATTATG
Found at i:1067431 original size:36 final size:36
Alignment explanation
Indices: 1067388--1067460 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1067378 TAAAGAATGA
1067388 CCTAAATAGCAATTATGCCTAAATAAAAAGATAAGG
1 CCTAAATAGCAATTATGCCTAAATAAAAAGATAAGG
*
1067424 CCTAAATAGCAATTATGCCTAAATAAAAAGATGAGG
1 CCTAAATAGCAATTATGCCTAAATAAAAAGATAAGG
1067460 C
1 C
1067461 AACATAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (36 bp):
CCTAAATAGCAATTATGCCTAAATAAAAAGATAAGG
Found at i:1072322 original size:23 final size:23
Alignment explanation
Indices: 1072272--1072315 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1072262 AATAGTTCAG
*
1072272 AAGAAAAAGCGCGTCAAAAGACA
1 AAGAAAAAACGCGTCAAAAGACA
*
1072295 AAGAAAAAACGTGTCAAAAGA
1 AAGAAAAAACGCGTCAAAAGA
1072316 TAGAGAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.59, C:0.14, G:0.20, T:0.07
Consensus pattern (23 bp):
AAGAAAAAACGCGTCAAAAGACA
Found at i:1077671 original size:81 final size:80
Alignment explanation
Indices: 1077495--1077672 Score: 191
Period size: 81 Copynumber: 2.2 Consensus size: 80
1077485 AGAAAACTAC
* *
1077495 TAGGAAAAGCCTAAAGGCTAAGCTAGGAAGATGCCTGACAATGATATAGTAAATTGGCAGATAGT
1 TAGG-AAAGACTAAAGGCTAAGCTACGAAGATGCCTGACAATGATATAGTAAATTGGCAGATAGT
* *
1077560 AATAAGGGTTGAGATT
65 AATAAGGATCGAGATT
* * * * *
1077576 TAGGAAAAGCCTAAATGCTAAGCTACGAAGATGCCTGACAATGATTTTATTTCAAATT-TCTA-A
1 TAGG-AAAGACTAAAGGCTAAGCTACGAAGATGCCTGACAATGA-TATA-GT-AAATTGGC-AGA
*
1077639 TAGTAATAAGGATCGAGTTT
61 TAGTAATAAGGATCGAGATT
1077659 TAGG-AAGACTAAAG
1 TAGGAAAGACTAAAG
1077673 CAAAGCGTTA
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
81 50 0.60
82 3 0.04
83 24 0.29
84 6 0.07
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.26
Consensus pattern (80 bp):
TAGGAAAGACTAAAGGCTAAGCTACGAAGATGCCTGACAATGATATAGTAAATTGGCAGATAGTA
ATAAGGATCGAGATT
Found at i:1079477 original size:42 final size:42
Alignment explanation
Indices: 1079424--1079547 Score: 124
Period size: 42 Copynumber: 3.0 Consensus size: 42
1079414 AGGCTGCACA
* * * * *
1079424 GAAGCACATAAGTGCTAAACAGAAACCCGTAAGAGTTGAGC-
1 GAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTAAACT
* *
1079465 GAAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAAACT
1 G-AAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTAAACT
* * * * *
1079508 GAAGCTCAAAAGAGCTAAACGGAAACTCATTAGGGTTAAA
1 GAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTAAA
1079548 TAGAAACTCA
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.01
42 67 0.97
43 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.16
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTAAACAGAAACCCATAAGAGTTAAACT
Found at i:1079536 original size:21 final size:21
Alignment explanation
Indices: 1079421--1079559 Score: 82
Period size: 21 Copynumber: 6.6 Consensus size: 21
1079411 CGAAGGCTGC
* * *
1079421 ACAGAAGCACATAAGTGCTAA
1 ACAGAAACTCATAAGAGCTAA
* * * *
1079442 ACAGAAACCCGTAAGAGTTGA
1 ACAGAAACTCATAAGAGCTAA
* *
1079463 GC-GAAAGCTCATAAGAGCTGA
1 ACAGAAA-CTCATAAGAGCTAA
* * *
1079484 ACAGAAACCCATAAGGGTTAA
1 ACAGAAACTCATAAGAGCTAA
* * *
1079505 ACTGAAGCTCAAAAGAGCTAA
1 ACAGAAACTCATAAGAGCTAA
* * * *
1079526 ACGGAAACTCATTAGGGTTAA
1 ACAGAAACTCATAAGAGCTAA
*
1079547 ATAGAAACTCATA
1 ACAGAAACTCATA
1079560 TAAGTTAACA
Statistics
Matches: 86, Mismatches: 30, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
20 4 0.05
21 78 0.91
22 4 0.05
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.17
Consensus pattern (21 bp):
ACAGAAACTCATAAGAGCTAA
Found at i:1084603 original size:21 final size:21
Alignment explanation
Indices: 1084509--1084619 Score: 64
Period size: 21 Copynumber: 5.3 Consensus size: 21
1084499 AACTCATATA
* *
1084509 AGTTTTCGTTCAACCCTAATG
1 AGTTTCCGTTCAACCCTTATG
* * * *
1084530 GGTTTCCATT-AAGCTCTTTTG
1 AGTTTCCGTTCAA-CCCTTATG
* * * *
1084551 AGCTTCTGTTTAACCCTTTTG
1 AGTTTCCGTTCAACCCTTATG
* * *
1084572 AGATTT-TGTTCAGCTCTTATG
1 AG-TTTCCGTTCAACCCTTATG
1084593 AGTTTCCGTTCAACCCTTATG
1 AGTTTCCGTTCAACCCTTATG
*
1084614 GGTTTC
1 AGTTTC
1084620 TGTTTAGCAT
Statistics
Matches: 66, Mismatches: 20, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
20 5 0.08
21 57 0.86
22 4 0.06
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (21 bp):
AGTTTCCGTTCAACCCTTATG
Found at i:1084634 original size:42 final size:42
Alignment explanation
Indices: 1084491--1084623 Score: 117
Period size: 42 Copynumber: 3.2 Consensus size: 42
1084481 TCTCTCGAGC
* * * *
1084491 TTCTGTTTAA-CTCATATAAGTTTTCGTTCAACCCTAATGGGT
1 TTCTG-TTAAGCTCTTATGAGTTTCCGTTCAACCCTTATGGGT
** * * * * * *
1084533 TTCCATTAAGCTCTTTTGAGCTTCTGTTTAACCCTTTTGAGAT
1 TTCTGTTAAGCTCTTATGAGTTTCCGTTCAACCCTTATG-GGT
*
1084576 TT-TGTTCAGCTCTTATGAGTTTCCGTTCAACCCTTATGGGT
1 TTCTGTTAAGCTCTTATGAGTTTCCGTTCAACCCTTATGGGT
1084617 TTCTGTT
1 TTCTGTT
1084624 TAGCATTTAT
Statistics
Matches: 67, Mismatches: 21, Indels: 6
0.71 0.22 0.06
Matches are distributed among these distances:
41 8 0.12
42 55 0.82
43 4 0.06
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.46
Consensus pattern (42 bp):
TTCTGTTAAGCTCTTATGAGTTTCCGTTCAACCCTTATGGGT
Found at i:1085668 original size:20 final size:20
Alignment explanation
Indices: 1085639--1085686 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1085629 CTGCATCTAA
*
1085639 GAAAAATTTTGAACTTTTGG
1 GAAAAATTTTGAAATTTTGG
*
1085659 GAAAATTTTTGAAATTTTGG
1 GAAAAATTTTGAAATTTTGG
1085679 GAAAAATT
1 GAAAAATT
1085687 CTCTAAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (20 bp):
GAAAAATTTTGAAATTTTGG
Found at i:1086977 original size:27 final size:28
Alignment explanation
Indices: 1086926--1087001 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 28
1086916 TGACTATTTT
**
1086926 TTAAAAGATTAAT-A-ATTAATTTAAAC-
1 TTAAAA-ATTAATAATATTAAAATAAACA
1086952 TTAAAAATTAATAATATTAAAATAAACA
1 TTAAAAATTAATAATATTAAAATAAACA
**
1086980 AAAAAAATT-ATAAATATTAAAA
1 TTAAAAATTAAT-AATATTAAAA
1087002 ACTAAAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
25 6 0.14
26 7 0.17
27 12 0.29
28 17 0.40
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (28 bp):
TTAAAAATTAATAATATTAAAATAAACA
Found at i:1093648 original size:5 final size:5
Alignment explanation
Indices: 1093638--1093663 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1093628 TGAGCATTCG
1093638 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
1093664 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:1094449 original size:31 final size:30
Alignment explanation
Indices: 1094414--1094473 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1094404 GGAGGTGGGA
*
1094414 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
1094445 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
1094474 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:1094702 original size:9 final size:9
Alignment explanation
Indices: 1094688--1094724 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1094678 TATAGTTTGA
1094688 TATTCGAAT
1 TATTCGAAT
1094697 TATTCGAAT
1 TATTCGAAT
*
1094706 TATTCGAGT
1 TATTCGAAT
1094715 TATTCGAAT
1 TATTCGAAT
1094724 T
1 T
1094725 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:1101385 original size:33 final size:32
Alignment explanation
Indices: 1101324--1101392 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 32
1101314 TTTTAAAATG
*
1101324 AAAATTTTTTATTTAAGGCTTTATAATTT-AT
1 AAAATTTTTTATTTAAGGCTTTAAAATTTAAT
*
1101355 AAAATTATTTTAATTTAA-TCTATTAAAATTTAAT
1 AAAATT-TTTT-ATTTAAGGCT-TTAAAATTTAAT
1101389 AAAA
1 AAAA
1101393 ATATAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 6 0.19
32 6 0.19
33 14 0.44
34 6 0.19
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (32 bp):
AAAATTTTTTATTTAAGGCTTTAAAATTTAAT
Found at i:1109398 original size:19 final size:18
Alignment explanation
Indices: 1109376--1109439 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
1109366 TTGTAAAATT
*
1109376 TTATAAAGTCATAAGAAAA
1 TTATAAAAT-ATAAGAAAA
1109395 TTATAAAAATATAAGAAAA
1 TTAT-AAAATATAAGAAAA
*
1109414 TT-TAAAATTCTAA-AAAA
1 TTATAAAA-TATAAGAAAA
1109431 TATATAAAA
1 T-TATAAAA
1109440 ATTATTGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 9 0.23
18 6 0.15
19 20 0.51
20 4 0.10
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (18 bp):
TTATAAAATATAAGAAAA
Found at i:1109427 original size:26 final size:27
Alignment explanation
Indices: 1109391--1109442 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1109381 AAGTCATAAG
1109391 AAAATTAT-AAAAATATA-AGAAAATTT
1 AAAATTATAAAAAATATATA-AAAATTT
*
1109417 AAAATTCTAAAAAATATATAAAAATT
1 AAAATTATAAAAAATATATAAAAATT
1109443 ATTGTATCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 15 0.65
28 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (27 bp):
AAAATTATAAAAAATATATAAAAATTT
Found at i:1109439 original size:10 final size:9
Alignment explanation
Indices: 1109351--1109444 Score: 52
Period size: 10 Copynumber: 10.1 Consensus size: 9
1109341 AAGGCTCTTT
1109351 TAAAAATTA
1 TAAAAATTA
*
1109360 TAAAAATTG
1 TAAAAATTA
*
1109369 T-AAAATTT
1 TAAAAATTA
* *
1109377 TATAAAGTCA
1 TA-AAAATTA
1109387 TAAGAAAATTA
1 T-A-AAAATTA
1109398 TAAAAA-TA
1 TAAAAATTA
1109406 TAAGAAAATT-
1 T-A-AAAATTA
*
1109416 T-AAAATTC
1 TAAAAATTA
1109424 TAAAAAATATA
1 T-AAAAAT-TA
1109435 TAAAAATTA
1 TAAAAATTA
1109444 T
1 T
1109445 TGTATCCCAT
Statistics
Matches: 66, Mismatches: 9, Indels: 20
0.69 0.09 0.21
Matches are distributed among these distances:
7 6 0.09
8 11 0.17
9 17 0.26
10 22 0.33
11 10 0.15
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (9 bp):
TAAAAATTA
Found at i:1109936 original size:10 final size:10
Alignment explanation
Indices: 1109923--1110033 Score: 51
Period size: 9 Copynumber: 11.4 Consensus size: 10
1109913 TTTTACATAC
1109923 TTTTTTT-AA
1 TTTTTTTAAA
1109932 TTTTTTTAAA
1 TTTTTTTAAA
*
1109942 ---TTTAAAA
1 TTTTTTTAAA
*
1109949 TATTTTTAAAA
1 T-TTTTTTAAA
*
1109960 TACTTTTTTTAA
1 T--TTTTTTAAA
1109972 TTTTTTT-AA
1 TTTTTTTAAA
1109981 TTTTTTT-AA
1 TTTTTTTAAA
*
1109990 --TTTTAAAA
1 TTTTTTTAAA
*
1109998 TATTTTTAAAA
1 T-TTTTTTAAA
*
1110009 TACTTTTTTTAA
1 T--TTTTTTAAA
1110021 TTTTTTT-AA
1 TTTTTTTAAA
1110030 TTTT
1 TTTT
1110034 AAAATACTTT
Statistics
Matches: 83, Mismatches: 8, Indels: 22
0.73 0.07 0.19
Matches are distributed among these distances:
7 10 0.12
8 2 0.02
9 24 0.29
10 14 0.17
11 17 0.20
12 16 0.19
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:1109936 original size:40 final size:40
Alignment explanation
Indices: 1109892--1110039 Score: 170
Period size: 40 Copynumber: 3.5 Consensus size: 40
1109882 TAATAAATAT
1109892 TTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTTAA
1 TTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTTAA
* * *
1109932 TTTTTTTAAATTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAA
1 TTTTTTTAATTTTAAAATATTTTT----TAC-----ATACTTTTTTTAA
* *
1109981 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
1 TTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTTAA
1110021 TTTTTTTAATTTTAAAATA
1 TTTTTTTAATTTTAAAATA
1110040 CTTTAAAATA
Statistics
Matches: 91, Mismatches: 8, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
40 53 0.58
44 3 0.03
45 1 0.01
49 34 0.37
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.64
Consensus pattern (40 bp):
TTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTTAA
Found at i:1109977 original size:9 final size:9
Alignment explanation
Indices: 1109963--1110033 Score: 63
Period size: 9 Copynumber: 7.4 Consensus size: 9
1109953 TTTAAAATAC
1109963 TTTTTTTAA
1 TTTTTTTAA
1109972 TTTTTTTAA
1 TTTTTTTAA
1109981 TTTTTTTAA
1 TTTTTTTAA
**
1109990 -TTTTAAAA
1 TTTTTTTAA
*
1109998 TATTTTTAAAATAC
1 T-TTTTT----TAA
1110012 TTTTTTTAA
1 TTTTTTTAA
1110021 TTTTTTTAA
1 TTTTTTTAA
1110030 TTTT
1 TTTT
1110034 AAAATACTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
8 6 0.12
9 33 0.66
10 4 0.08
13 5 0.10
14 2 0.04
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:1109995 original size:49 final size:49
Alignment explanation
Indices: 1109901--1110075 Score: 239
Period size: 49 Copynumber: 3.5 Consensus size: 49
1109891 TTTTTTTTAA
* *
1109901 TTTTAAAATA-TTTTTTACATACTTTTTTTAATTTTTTTAAATTTAAAATAT
1 TTTTAAAATACTTTTTT---TAATTTTTTTAATTTTTTTAATTTTAAAATAT
1109952 TTTTAAAATACTTTTTTTAATTTTTTTAATTTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTTTTAATTTTTTTAATTTTTTTAATTTTAAAATAT
**
1110001 TTTTAAAATACTTTTTTTAATTTTTTTAA-TTTTAAAATACTTTAAAATA-
1 TTTTAAAATACTTTTTTTAATTTTTTTAATTTTTTTAAT--TTTAAAATAT
1110050 TTTTAAAATACTTTTTTTTAATTTTT
1 TTTTAAAATAC-TTTTTTTAATTTTT
1110076 AAAAATAAAA
Statistics
Matches: 116, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
48 7 0.06
49 70 0.60
50 23 0.20
51 10 0.09
52 6 0.05
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (49 bp):
TTTTAAAATACTTTTTTTAATTTTTTTAATTTTTTTAATTTTAAAATAT
Found at i:1110036 original size:89 final size:87
Alignment explanation
Indices: 1109892--1110053 Score: 270
Period size: 89 Copynumber: 1.8 Consensus size: 87
1109882 TAATAAATAT
* * *
1109892 TTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTTAATTTTTTTAAATTTAAAATATTTTTA
1 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAAATTTAAAATA-CTTTA
1109957 AAATACTTTTTTTAATTTTTTTAA
65 AAATA-TTTTTTTAATTTTTTTAA
*
1109981 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATACTTTAA
1 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAAATTTAAAATACTTTAA
1110046 AATATTTT
66 AATATTTT
1110054 AAAATACTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
87 4 0.06
88 9 0.13
89 56 0.81
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (87 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAAATTTAAAATACTTTAA
AATATTTTTTTAATTTTTTTAA
Found at i:1110044 original size:10 final size:10
Alignment explanation
Indices: 1110031--1110063 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
1110021 TTTTTTTAAT
1110031 TTTAAAATAC
1 TTTAAAATAC
*
1110041 TTTAAAATAT
1 TTTAAAATAC
1110051 TTTAAAATAC
1 TTTAAAATAC
1110061 TTT
1 TTT
1110064 TTTTTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (10 bp):
TTTAAAATAC
Found at i:1110065 original size:40 final size:41
Alignment explanation
Indices: 1109981--1110079 Score: 114
Period size: 40 Copynumber: 2.4 Consensus size: 41
1109971 ATTTTTTTAA
* **
1109981 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA-
1 TTTTTTTAATTTTAAAATATCTTTAAAATACTTTTAATAAT
*
1110021 TTTTTTTAATTTTAAAATA-CTTTAAAATA-TTTTAAAATACT
1 TTTTTTTAATTTTAAAATATCTTTAAAATACTTTT--AATAAT
1110062 TTTTTTTAATTTTTAAAA
1 TTTTTTTAA-TTTTAAAA
1110080 ATAAAAATGG
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
38 4 0.08
39 9 0.18
40 21 0.41
41 9 0.18
42 8 0.16
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (41 bp):
TTTTTTTAATTTTAAAATATCTTTAAAATACTTTTAATAAT
Found at i:1110065 original size:89 final size:90
Alignment explanation
Indices: 1109892--1110075 Score: 266
Period size: 89 Copynumber: 2.1 Consensus size: 90
1109882 TAATAAATAT
* * *
1109892 TTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTTAATTTTTTTAAATTTAAAATATTTTTA
1 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAAATTTAAAATATCTTTA
**
1109957 AAATACTTTTTTTAA-TTTTTTTAA
66 AAATACTTTTAATAATTTTTTTTAA
*
1109981 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATA-CTTTA
1 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAAATTTAAAATATCTTTA
*
1110045 AAATA-TTTTAAAATACTTTTTTTTAA
66 AAATACTTTT--AATAATTTTTTTTAA
1110071 TTTTT
1 TTTTT
1110076 AAAAATAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
87 4 0.05
88 9 0.11
89 58 0.68
90 14 0.16
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (90 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAAATTTAAAATATCTTTA
AAATACTTTTAATAATTTTTTTTAA
Found at i:1110300 original size:19 final size:19
Alignment explanation
Indices: 1110276--1110332 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1110266 ATTTTTGATG
* *
1110276 TATTTTTATAGATTTTTAC
1 TATTTTTATAAAATTTTAC
1110295 TATTTTTATAAAATTTTAC
1 TATTTTTATAAAATTTTAC
*
1110314 AATTTTTTATAAATATTTT
1 TA-TTTTTATAAA-ATTTT
1110333 TATAATTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.55
20 10 0.30
21 5 0.15
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (19 bp):
TATTTTTATAAAATTTTAC
Found at i:1118733 original size:21 final size:21
Alignment explanation
Indices: 1118707--1118749 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1118697 ATTTTAAAAG
1118707 TAAAAAATATATTGCATTGAA
1 TAAAAAATATATTGCATTGAA
*
1118728 TAAAAATTATATTGCATTGAA
1 TAAAAAATATATTGCATTGAA
1118749 T
1 T
1118750 CTTCAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (21 bp):
TAAAAAATATATTGCATTGAA
Found at i:1125577 original size:15 final size:14
Alignment explanation
Indices: 1125559--1125612 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1125549 TTATATTTAC
1125559 ACAAATATATATATT
1 ACAAATATATATA-T
*
1125574 ACAAATATATCTAT
1 ACAAATATATATAT
* *
1125588 ATAAATATATTTAT
1 ACAAATATATATAT
1125602 ATCTAAATATA
1 A-C-AAATATA
1125613 AGTTTCAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 14 0.42
15 12 0.36
16 7 0.21
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
ACAAATATATATAT
Found at i:1127674 original size:17 final size:17
Alignment explanation
Indices: 1127644--1127689 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
1127634 CAACATTTTT
1127644 AAAAGTATTT-TAAATTC
1 AAAA-TATTTATAAATTC
1127661 AAAATATTTATAAAATTC
1 AAAATATTTAT-AAATTC
*
1127679 TAAAT-TTTATA
1 AAAATATTTATA
1127690 TTTTTTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 6 0.23
17 10 0.38
18 10 0.38
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
AAAATATTTATAAATTC
Found at i:1127678 original size:18 final size:17
Alignment explanation
Indices: 1127655--1127689 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1127645 AAAGTATTTT
1127655 AAATTCAAAATATTTATA
1 AAATTCAAAAT-TTTATA
*
1127673 AAATTCTAAATTTTATA
1 AAATTCAAAATTTTATA
1127690 TTTTTTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTCAAAATTTTATA
Found at i:1128548 original size:18 final size:18
Alignment explanation
Indices: 1128513--1128550 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1128503 CGGTAAAGTA
*
1128513 TAAAAAACGAAATCTTAT
1 TAAAAAACGAAATATTAT
1128531 TAAAAAAC-AATATATTAT
1 TAAAAAACGAA-ATATTAT
1128549 TA
1 TA
1128551 TTATTGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.32
Consensus pattern (18 bp):
TAAAAAACGAAATATTAT
Found at i:1134315 original size:69 final size:69
Alignment explanation
Indices: 1134204--1134346 Score: 277
Period size: 69 Copynumber: 2.1 Consensus size: 69
1134194 TGAAAAATTA
1134204 GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAACG
1 GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAACG
1134269 GTTG
66 GTTG
*
1134273 GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAATG
1 GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAACG
1134338 GTTG
66 GTTG
1134342 GACCT
1 GACCT
1134347 TTCATACAAT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.34
Consensus pattern (69 bp):
GACCTCTCTTTCAATGACTTGTCTGGAAATATGTCTGCCCTTAAAAGTTTGGCATCCCTCCAACG
GTTG
Found at i:1147152 original size:91 final size:91
Alignment explanation
Indices: 1147018--1147202 Score: 370
Period size: 91 Copynumber: 2.0 Consensus size: 91
1147008 TAGATGACCT
1147018 TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCGGAGTTATTTCTGACTTA
1 TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCGGAGTTATTTCTGACTTA
1147083 ATCTGGAAAGTCTCTACTTATCTTTG
66 ATCTGGAAAGTCTCTACTTATCTTTG
1147109 TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCGGAGTTATTTCTGACTTA
1 TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCGGAGTTATTTCTGACTTA
1147174 ATCTGGAAAGTCTCTACTTATCTTTG
66 ATCTGGAAAGTCTCTACTTATCTTTG
1147200 TTT
1 TTT
1147203 GATGAAGATG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 94 1.00
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (91 bp):
TTTTAGCTTATAAGGATTTTGGTTCACAGGTCTTATTTTGTGGCATCGGAGTTATTTCTGACTTA
ATCTGGAAAGTCTCTACTTATCTTTG
Found at i:1147872 original size:3 final size:3
Alignment explanation
Indices: 1147864--1147928 Score: 58
Period size: 3 Copynumber: 21.7 Consensus size: 3
1147854 TGACGAAGAG
* * ** * *
1147864 GAT GAT GAT GAC GAC GAT GAT GAT GGG GAT GAA GAT GAT GAT GAT GAC
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
1147912 GAT GAT GGT GAG GAT GA
1 GAT GAT GAT GAT GAT GA
1147929 AGAAGAGGAG
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.32, C:0.05, G:0.40, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:1147884 original size:15 final size:15
Alignment explanation
Indices: 1147864--1147918 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
1147854 TGACGAAGAG
*
1147864 GATGATGATGACGAC
1 GATGATGATGATGAC
*
1147879 GATGATGATGGGGATGAA
1 GATGATGAT---GATGAC
1147897 GATGATGATGATGAC
1 GATGATGATGATGAC
1147912 GATGATG
1 GATGATG
1147919 GTGAGGATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 21 0.62
18 13 0.38
ACGTcount: A:0.33, C:0.05, G:0.38, T:0.24
Consensus pattern (15 bp):
GATGATGATGATGAC
Found at i:1147945 original size:15 final size:15
Alignment explanation
Indices: 1147921--1147955 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1147911 CGATGATGGT
*
1147921 GAGGATGAAGAAGAG
1 GAGGACGAAGAAGAG
*
1147936 GAGGACGAAGAAGAT
1 GAGGACGAAGAAGAG
1147951 GAGGA
1 GAGGA
1147956 TGATGAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.46, T:0.06
Consensus pattern (15 bp):
GAGGACGAAGAAGAG
Found at i:1157323 original size:18 final size:18
Alignment explanation
Indices: 1157300--1157339 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1157290 TGCTAAAAAG
*
1157300 AAAAATT-CATAATTGATT
1 AAAAATTCCA-AAATGATT
1157318 AAAAATTCCAAAATGATT
1 AAAAATTCCAAAATGATT
1157336 AAAA
1 AAAA
1157340 TTAGCCCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAAATTCCAAAATGATT
Found at i:1170832 original size:15 final size:16
Alignment explanation
Indices: 1170805--1170834 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1170795 TACAAATATA
1170805 TAATAATTTAAAATAC
1 TAATAATTTAAAATAC
1170821 TAATAA-TTAAAATA
1 TAATAATTTAAAATA
1170835 TTCAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATAATTTAAAATAC
Found at i:1175638 original size:27 final size:27
Alignment explanation
Indices: 1175605--1175663 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
1175595 TTTTGGTTAA
*
1175605 AAATTAACCGAATTACCGAAATTAACC
1 AAATTAACCGAATTACCCAAATTAACC
*
1175632 AAATTAATCGAATTACCCAAATTAACC
1 AAATTAACCGAATTACCCAAATTAACC
*
1175659 GAATT
1 AAATT
1175664 GAATCACTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.25
Consensus pattern (27 bp):
AAATTAACCGAATTACCCAAATTAACC
Found at i:1175645 original size:18 final size:18
Alignment explanation
Indices: 1175606--1175663 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
1175596 TTTGGTTAAA
*
1175606 AATTAACCGAATT-ACCG
1 AATTAACCAAATTAACCG
*
1175623 AAATTAACCAAATTAATCG
1 -AATTAACCAAATTAACCG
*
1175642 AATTACCCAAATTAACCG
1 AATTAACCAAATTAACCG
1175660 AATT
1 AATT
1175664 GAATCACTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 32 0.91
19 3 0.09
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.26
Consensus pattern (18 bp):
AATTAACCAAATTAACCG
Found at i:1175663 original size:9 final size:9
Alignment explanation
Indices: 1175606--1175663 Score: 64
Period size: 9 Copynumber: 6.4 Consensus size: 9
1175596 TTTGGTTAAA
1175606 AATTAACCG
1 AATTAACCG
1175615 AATT-ACCG
1 AATTAACCG
*
1175623 AAATTAACCA
1 -AATTAACCG
*
1175633 AATTAATCG
1 AATTAACCG
* *
1175642 AATTACCCA
1 AATTAACCG
1175651 AATTAACCG
1 AATTAACCG
1175660 AATT
1 AATT
1175664 GAATCACTCC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
8 4 0.10
9 32 0.82
10 3 0.08
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:1175848 original size:18 final size:18
Alignment explanation
Indices: 1175809--1175851 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1175799 TATAATTGGG
*
1175809 TTGGGTTGGGTTGGGTAA
1 TTGGGTTGGGTTGGATAA
*
1175827 TTGGGTT-GGTGTGGATAC
1 TTGGGTTGGGT-TGGATAA
1175845 TTGGGTT
1 TTGGGTT
1175852 TGGATTGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.09, C:0.02, G:0.47, T:0.42
Consensus pattern (18 bp):
TTGGGTTGGGTTGGATAA
Found at i:1176190 original size:14 final size:14
Alignment explanation
Indices: 1176167--1176214 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
1176157 GTTACTGAAC
1176167 TATTTAAATTTTTT
1 TATTTAAATTTTTT
*
1176181 TATTTTAATTATTAATT
1 TATTTAAATT-TT--TT
*
1176198 TATTTAAATGTTTT
1 TATTTAAATTTTTT
1176212 TAT
1 TAT
1176215 GTAAGTCCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 14 0.50
15 2 0.07
16 2 0.07
17 10 0.36
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TATTTAAATTTTTT
Found at i:1182669 original size:16 final size:16
Alignment explanation
Indices: 1182637--1182669 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1182627 TATCATTATA
1182637 TGTTTAAATTTATAAT
1 TGTTTAAATTTATAAT
1182653 TGTTATAAATTTA-AAT
1 TGTT-TAAATTTATAAT
1182669 T
1 T
1182670 AAATTTTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
TGTTTAAATTTATAAT
Found at i:1191482 original size:46 final size:46
Alignment explanation
Indices: 1191374--1191529 Score: 255
Period size: 46 Copynumber: 3.5 Consensus size: 46
1191364 TACGTATGAT
* *
1191374 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
1191417 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGTTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1191463 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1191509 CACTTATCACTTTGTCACTTG
1 CACTTATCACTTTGTCACTTG
1191530 TCACTAATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
43 10 0.10
44 5 0.05
45 20 0.19
46 69 0.66
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:1192558 original size:11 final size:11
Alignment explanation
Indices: 1192542--1192599 Score: 68
Period size: 11 Copynumber: 5.4 Consensus size: 11
1192532 NNNNTTAAAA
1192542 TTTTAAAATAC
1 TTTTAAAATAC
1192553 TTTTAAAATAC
1 TTTTAAAATAC
1192564 TTTTATTAAA-A-
1 TTTTA--AAATAC
*
1192575 TTTTAAAAT-T
1 TTTTAAAATAC
1192585 TTTTAAAATAC
1 TTTTAAAATAC
1192596 TTTT
1 TTTT
1192600 TAATTTTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
9 3 0.07
10 9 0.22
11 25 0.61
12 1 0.02
13 3 0.07
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:1192578 original size:33 final size:32
Alignment explanation
Indices: 1192536--1192599 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
1192526 NNNNNNNNNN
1192536 TTAAAATTTTAAAATACTTTTAAAATACTTTTA
1 TTAAAATTTTAAAAT-CTTTTAAAATACTTTTA
*
1192569 TTAAAATTTTAAAATTTTTTAAAATACTTTT
1 TTAAAATTTTAAAATCTTTTAAAATACTTTT
1192600 TAATTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (32 bp):
TTAAAATTTTAAAATCTTTTAAAATACTTTTA
Found at i:1192600 original size:22 final size:21
Alignment explanation
Indices: 1192542--1192610 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 21
1192532 NNNNTTAAAA
1192542 TTTTAAAATACTTTTAAAATACT
1 TTTTAAAATACTTTTAAAAT--T
*
1192565 TTTATTAAA-A-TTTTAAAATT
1 TTT-TAAAATACTTTTAAAATT
*
1192585 TTTTAAAATACTTTT-TAATT
1 TTTTAAAATACTTTTAAAATT
1192605 TTTTAA
1 TTTTAA
1192611 TTTTAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
19 4 0.10
20 15 0.38
21 4 0.10
22 9 0.22
23 4 0.10
24 4 0.10
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTAAAATACTTTTAAAATT
Found at i:1192625 original size:36 final size:37
Alignment explanation
Indices: 1192573--1192644 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 37
1192563 CTTTTATTAA
*
1192573 AATTTTAAAATTTTTTAAAATACT-TTTTAATTTTTT
1 AATTTTAAAATATTTTAAAATACTATTTTAATTTTTT
**
1192609 AATTTTAAAATATTTTAAAATTTTATTTTAATTTTT
1 AATTTTAAAATATTTTAAAATACTATTTTAATTTTT
1192645 AAAATAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 21 0.66
37 11 0.34
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (37 bp):
AATTTTAAAATATTTTAAAATACTATTTTAATTTTTT
Found at i:1194973 original size:45 final size:45
Alignment explanation
Indices: 1194909--1194996 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
1194899 ACAGAAACTT
* *
1194909 GGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCC
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
1194954 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1194997 TCAGTTCACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
Found at i:1195065 original size:51 final size:50
Alignment explanation
Indices: 1195007--1195193 Score: 214
Period size: 51 Copynumber: 3.7 Consensus size: 50
1194997 TCAGTTCACA
* * *
1195007 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCAATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATCTAGTACACG
* * * * * *
1195058 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCTTGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATCTAGTACACG
* * * * *
1195109 TAGTAGCCTGCACATAGTACTACATATGCGACC-TATCATTCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TCTAGTACACG
1195159 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1195194 CACTTTCACT
Statistics
Matches: 111, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
49 2 0.02
50 39 0.35
51 68 0.61
52 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATCTAGTACACG
Found at i:1195181 original size:101 final size:101
Alignment explanation
Indices: 1195005--1195189 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
1194995 GTTCAGTTCA
*
1195005 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCAATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCAATACACGTAGTAGCCTGCA
1195070 CATAGTACTACACACGTGATCGAAACTATCTTGTACG
65 CATAGTACTACACACGTGATCGAAACTATCTTGTACG
* * ***
1195107 CATAGTAGCCTGCACATAGTACTACATATGCGACC-TATCATTCTGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCAATACACGTAGTAGCCTGCA
1195171 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
1195190 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 4 0.05
101 39 0.51
102 33 0.43
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCAATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCTTGTACG
Found at i:1206433 original size:15 final size:15
Alignment explanation
Indices: 1206413--1206443 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1206403 AATATTTTTT
*
1206413 AAATAAATTATAAAA
1 AAATAAATAATAAAA
1206428 AAATAAATAATAAAA
1 AAATAAATAATAAAA
1206443 A
1 A
1206444 CTCCAAATAT
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAATAATAAAA
Found at i:1208357 original size:16 final size:16
Alignment explanation
Indices: 1208338--1208368 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1208328 TTATAAATGA
1208338 TTAAATATATATATTT
1 TTAAATATATATATTT
1208354 TTAAATATATATATT
1 TTAAATATATATATT
1208369 AATTTTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAAATATATATATTT
Found at i:1237858 original size:30 final size:31
Alignment explanation
Indices: 1237801--1237875 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 31
1237791 TTACAATTTG
1237801 GTCACTGAACTATTCAAAAATTTTTATTTAA
1 GTCACTGAACTATTCAAAAATTTTTATTTAA
*
1237832 GTCACTAAACTATTCAAAAA-TTTTATTTAA
1 GTCACTGAACTATTCAAAAATTTTTATTTAA
*
1237862 GTCATTGAACTATT
1 GTCACTGAACTATT
1237876 AAGTTTTTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 22 0.54
31 19 0.46
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (31 bp):
GTCACTGAACTATTCAAAAATTTTTATTTAA
Found at i:1244312 original size:25 final size:25
Alignment explanation
Indices: 1244283--1244334 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1244273 AAAATTGGTA
*
1244283 AGACATTTTCCATT-TTTCTCTAAGC
1 AGACATTTTCCATTCTCT-TCTAAGC
1244308 AGACATTTTCCATTCTCTTCTAAGC
1 AGACATTTTCCATTCTCTTCTAAGC
1244333 AG
1 AG
1244335 CAGACATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (25 bp):
AGACATTTTCCATTCTCTTCTAAGC
Found at i:1249531 original size:8 final size:10
Alignment explanation
Indices: 1249511--1249541 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
1249501 AAAAACAATT
1249511 TATTAATATA
1 TATTAATATA
1249521 TATTAATATA
1 TATTAATATA
1249531 TATTAATATA
1 TATTAATATA
1249541 T
1 T
1249542 GTAAAAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TATTAATATA
Found at i:1249596 original size:32 final size:33
Alignment explanation
Indices: 1249560--1249644 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
1249550 AACTTTTCCG
* * *
1249560 GAAAATATTTT-CAGGAAATCTGCCAAACAGCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
1249592 GAAAATATTTTACA-CAGATTTACCAAACACCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
1249624 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTACAGCAAATC
1249645 ATTTTACAGA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
32 37 0.88
33 5 0.12
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCTACCAAACACCA
Found at i:1249643 original size:14 final size:15
Alignment explanation
Indices: 1249621--1249697 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
1249611 TTACCAAACA
1249621 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
1249635 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
1249650 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
1249670 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
1249684 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
1249698 ACTGCCAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:1249662 original size:20 final size:20
Alignment explanation
Indices: 1249637--1249676 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1249627 AATATTTTCC
*
1249637 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
1249657 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
1249677 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:1249682 original size:34 final size:35
Alignment explanation
Indices: 1249625--1249691 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
1249615 CAAACACCAG
*
1249625 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
1249660 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
1249692 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:1249698 original size:14 final size:14
Alignment explanation
Indices: 1249660--1249699 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1249650 ACAGAAAAGT
*
1249660 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
1249674 AAATCATTTTACGG
1 AAAACATTTTACAG
1249688 AAAACATTTTAC
1 AAAACATTTTAC
1249700 TGCCAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:1264842 original size:47 final size:47
Alignment explanation
Indices: 1264789--1264882 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
1264779 AAACTGAGCA
*
1264789 GAAGTATTAATGGATAGATTTGCAAAATAGCTAACAATGAATGCACT
1 GAAGTATTAATGGATAGATCTGCAAAATAGCTAACAATGAATGCACT
1264836 GAAGTATTAATGGATAGATCTGCAAAATAGCTAACAATGAATGCACT
1 GAAGTATTAATGGATAGATCTGCAAAATAGCTAACAATGAATGCACT
1264883 TACTTTCTCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.27
Consensus pattern (47 bp):
GAAGTATTAATGGATAGATCTGCAAAATAGCTAACAATGAATGCACT
Found at i:1290571 original size:6 final size:6
Alignment explanation
Indices: 1290560--1290597 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
1290550 TTAAAATAGT
*
1290560 TTAGGG TTAGGG TTACGG TTAGGG TTAGGG TTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TT
1290598 TTGTTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.16, C:0.03, G:0.45, T:0.37
Consensus pattern (6 bp):
TTAGGG
Found at i:1290712 original size:34 final size:35
Alignment explanation
Indices: 1290648--1290764 Score: 134
Period size: 34 Copynumber: 3.4 Consensus size: 35
1290638 TTTTAAAAAA
* * *
1290648 TAAATTAGGGTTT-GGAGTTTTTTTAAAAATTAAT
1 TAAATTAGGGTTTATGAGTGTTTTAAAAAATTAAT
* *
1290682 TAAGTTAGGTTTTATG-G-GTTTTAAATAAATTAAT
1 TAAATTAGGGTTTATGAGTGTTTTAAA-AAATTAAT
* *
1290716 TAAATTAGGGTTTA-GAGTTTTTTTAAAAATTAAT
1 TAAATTAGGGTTTATGAGTGTTTTAAAAAATTAAT
1290750 TAAATTAGGGTTTAT
1 TAAATTAGGGTTTAT
1290765 TTTTAAAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
33 7 0.10
34 55 0.80
35 7 0.10
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (35 bp):
TAAATTAGGGTTTATGAGTGTTTTAAAAAATTAAT
Found at i:1291156 original size:125 final size:124
Alignment explanation
Indices: 1290856--1291228 Score: 507
Period size: 124 Copynumber: 3.0 Consensus size: 124
1290846 GTAGTTTCAA
* * *
1290856 AAAAATTAATTTTGAGAAGACAGTTCTGAAAAAATGGTGTCAAAAACGCTTTAAGCAAGATGCAC
1 AAAAA-TAATTTTGAGAAGACGGTTCTGAACAAATGGTGTCAAAAACGCTTCAAGCAAGATGCAC
** * *
1290921 TGTCAGCAAAAATATTGAAAAAAGCTCTCATATGGACGCTCTTTTTTTACATTAGTTCTTG
65 TGTCAGCAAAAATA-TGAAAAAAGCTCTCACGTGGACGCTCTTTTTATACAGTAGTTCTTG
* * * *
1290982 -GAAATAATTTTGAGAAGACGGTTTTGAACAAATGGTGTCAAAAATGCTTCAAGCAAGATGTACT
1 AAAAATAATTTTGAGAAGACGGTTCTGAACAAATGGTGTCAAAAACGCTTCAAGCAAGATGCACT
*
1291046 GTCAGCAAAAATACTGAAAAAAAGCTCTCACGTGG-CACTCTTTTTATACAGTAGTTCTTG
66 GTCAGCAAAAATA-TG-AAAAAAGCTCTCACGTGGACGCTCTTTTTATACAGTAGTTCTTG
* * * *
1291106 AAAAATAATTTTCAGAAGATGGTTCTGAACAAATGGCGTCAAAAACGCTTCAAGCAGGATGCACT
1 AAAAATAATTTTGAGAAGACGGTTCTGAACAAATGGTGTCAAAAACGCTTCAAGCAAGATGCACT
* * * *
1291171 GTTAGCAAAATTGATGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAGTAGTTCT
66 GTCAGCAAAAAT-ATGAAAAAAGCTCTCACGTGGACGCTCTTTTTATACAGTAGTTCT
1291229 GGTTTGGCCT
Statistics
Matches: 217, Mismatches: 26, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
124 108 0.50
125 108 0.50
126 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (124 bp):
AAAAATAATTTTGAGAAGACGGTTCTGAACAAATGGTGTCAAAAACGCTTCAAGCAAGATGCACT
GTCAGCAAAAATATGAAAAAAGCTCTCACGTGGACGCTCTTTTTATACAGTAGTTCTTG
Found at i:1294253 original size:26 final size:26
Alignment explanation
Indices: 1294219--1294274 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
1294209 TAGTTTGTAC
1294219 AAAT-ATATTAAAACAATTTA-TATTA
1 AAATAATATTAAAACAATTTACTA-TA
*
1294244 AAATAATATTAAAATAATTTACTATA
1 AAATAATATTAAAACAATTTACTATA
1294270 AAATA
1 AAATA
1294275 TTAAAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 4 0.14
26 22 0.79
27 2 0.07
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (26 bp):
AAATAATATTAAAACAATTTACTATA
Found at i:1294727 original size:18 final size:18
Alignment explanation
Indices: 1294701--1294743 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1294691 GACTGAGAAA
* *
1294701 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
1294719 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
1294737 AGGATAC
1 AGGATAC
1294744 GCACCTAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Done.