Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr8
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: 19593398
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1222752 characters in sequence are not A, C, G, or T
File 25 of 50
Found at i:11262831 original size:8 final size:8
Alignment explanation
Indices: 11262808--11262854 Score: 62
Period size: 8 Copynumber: 6.1 Consensus size: 8
11262798 GAATCGGCTT
11262808 GGAAGAAA
1 GGAAGAAA
11262816 GG-AGAAA
1 GGAAGAAA
11262823 GGAAGAAA
1 GGAAGAAA
*
11262831 GGGAGAAA
1 GGAAGAAA
*
11262839 GAAAGAAA
1 GGAAGAAA
11262847 GG-AGAAA
1 GGAAGAAA
11262854 G
1 G
11262855 AAAAAAAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
7 13 0.38
8 21 0.62
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (8 bp):
GGAAGAAA
Found at i:11262855 original size:15 final size:15
Alignment explanation
Indices: 11262810--11262857 Score: 78
Period size: 15 Copynumber: 3.1 Consensus size: 15
11262800 ATCGGCTTGG
*
11262810 AAGAAAGGAGAAAGG
1 AAGAAAGGAGAAAGA
11262825 AAGAAAGGGAGAAAGA
1 AAGAAA-GGAGAAAGA
11262841 AAGAAAGGAGAAAGA
1 AAGAAAGGAGAAAGA
11262856 AA
1 AA
11262858 AAAAAGACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 17 0.55
16 14 0.45
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
AAGAAAGGAGAAAGA
Found at i:11264090 original size:26 final size:26
Alignment explanation
Indices: 11264061--11264124 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 26
11264051 TAGGTCGTTG
*
11264061 ATGGGCTATTAGACGTGGCTGGGGCC
1 ATGGTCTATTAGACGTGGCTGGGGCC
*
11264087 ATGGTCTATGATTATACGTGGCTGGGGCC
1 ATGGTC--T-ATTAGACGTGGCTGGGGCC
11264116 ATGGTCTAT
1 ATGGTCTAT
11264125 GATTATATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 7 0.21
27 1 0.03
28 1 0.03
29 24 0.73
ACGTcount: A:0.17, C:0.17, G:0.36, T:0.30
Consensus pattern (26 bp):
ATGGTCTATTAGACGTGGCTGGGGCC
Found at i:11264105 original size:29 final size:29
Alignment explanation
Indices: 11264068--11264137 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
11264058 TTGATGGGCT
*
11264068 ATTAGACGTGGCTGGGGCCATGGTCTATG
1 ATTATACGTGGCTGGGGCCATGGTCTATG
11264097 ATTATACGTGGCTGGGGCCATGGTCTATG
1 ATTATACGTGGCTGGGGCCATGGTCTATG
*
11264126 ATTATATGTGGC
1 ATTATACGTGGC
11264138 AAAGGCACAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.16, G:0.34, T:0.31
Consensus pattern (29 bp):
ATTATACGTGGCTGGGGCCATGGTCTATG
Found at i:11296308 original size:21 final size:21
Alignment explanation
Indices: 11296278--11296332 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
11296268 GGATATGTTT
11296278 ATGCAATTCATGACAAAAACTA
1 ATGC-ATTCATGACAAAAACTA
* * *
11296300 ATGCATTCATAACAAAAATTG
1 ATGCATTCATGACAAAAACTA
*
11296321 ATGCATTTATGA
1 ATGCATTCATGA
11296333 TAAGGACTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (21 bp):
ATGCATTCATGACAAAAACTA
Found at i:11297565 original size:15 final size:14
Alignment explanation
Indices: 11297545--11297576 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
11297535 CCTCTCTCCT
11297545 TTTTTCATTCTTTCA
1 TTTTTCATT-TTTCA
11297560 TTTTTCATTTTTCA
1 TTTTTCATTTTTCA
11297574 TTT
1 TTT
11297577 ATATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTCATTTTTCA
Found at i:11297567 original size:7 final size:7
Alignment explanation
Indices: 11297545--11297576 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
11297535 CCTCTCTCCT
11297545 TTTTTCA
1 TTTTTCA
11297552 TTCTTTCA
1 TT-TTTCA
11297560 TTTTTCA
1 TTTTTCA
11297567 TTTTTCA
1 TTTTTCA
11297574 TTT
1 TTT
11297577 ATATATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTTCA
Found at i:11298865 original size:3 final size:3
Alignment explanation
Indices: 11298859--11298888 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
11298849 CAACAACAAC
*
11298859 AAT AAT AAT AAT AAT ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11298889 TGAAATTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:11300663 original size:130 final size:129
Alignment explanation
Indices: 11300503--11300762 Score: 511
Period size: 130 Copynumber: 2.0 Consensus size: 129
11300493 TATTCCGCAC
11300503 GCGGAGAAATAATAAAAAAATAATAATATTTCTATCGAGGAAAAAATTTGCTAGATAAAAGGTAA
1 GCGGAGAAATAATAAAAAAATAATAATATTTCTATCGAGGAAAAAATTTGCTAGATAAAAGGTAA
11300568 TTCAGATGTGAATCAGGGCAAAATAAGATGTTTTGGAGCCCCAGAAGGCTAGTGAAAAATTTTA
66 TTCAGATGTGAATCAGGGCAAAATAAGATGTTTTGGAGCCCCAGAAGGCTAGTGAAAAATTTTA
11300632 GNCGGAGAAATAATAAAAAAATAATAATATTTCTATCGAGGAAAAAATTTGCTAGATAAAAGGTA
1 G-CGGAGAAATAATAAAAAAATAATAATATTTCTATCGAGGAAAAAATTTGCTAGATAAAAGGTA
11300697 ATTCAGATGTGAATCAGGGCAAAATAAGATGTTTTGGAGCCCCAGAAGGCTAGTGAAAAATTTTA
65 ATTCAGATGTGAATCAGGGCAAAATAAGATGTTTTGGAGCCCCAGAAGGCTAGTGAAAAATTTTA
11300762 G
1 G
11300763 AATAAAATAA
Statistics
Matches: 130, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
129 1 0.01
130 129 0.99
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.25
Consensus pattern (129 bp):
GCGGAGAAATAATAAAAAAATAATAATATTTCTATCGAGGAAAAAATTTGCTAGATAAAAGGTAA
TTCAGATGTGAATCAGGGCAAAATAAGATGTTTTGGAGCCCCAGAAGGCTAGTGAAAAATTTTA
Found at i:11311336 original size:22 final size:23
Alignment explanation
Indices: 11311298--11311341 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
11311288 TACCTGGAGA
* *
11311298 ACAAAATAAACCCAACATTAAAC
1 ACAAAATAAACCAAACAATAAAC
11311321 ACAAAA-AAACCAAACAATAAA
1 ACAAAATAAACCAAACAATAAA
11311342 TGAAAATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.68, C:0.23, G:0.00, T:0.09
Consensus pattern (23 bp):
ACAAAATAAACCAAACAATAAAC
Found at i:11313578 original size:11 final size:11
Alignment explanation
Indices: 11313562--11313590 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
11313552 AGATTTATCA
11313562 TTTCCATGCAT
1 TTTCCATGCAT
11313573 TTTCCAT-CAT
1 TTTCCATGCAT
11313583 TTTCCATG
1 TTTCCATG
11313591 GTTGAATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.17, C:0.28, G:0.07, T:0.48
Consensus pattern (11 bp):
TTTCCATGCAT
Found at i:11324994 original size:53 final size:53
Alignment explanation
Indices: 11324914--11325016 Score: 170
Period size: 53 Copynumber: 1.9 Consensus size: 53
11324904 AACCGAGGTG
** *
11324914 CAAAACATGGAGAGACAAAAGAGTAGGTAAAACCAGGGTCAAACAATACCTGA
1 CAAAACATAAAGAGACAAAAGAGTAGGTAAAACCAGGATCAAACAATACCTGA
*
11324967 CAAAACATAAAGAGACAAAAGAGTAGGTAGAACCAGGATCAAACAATACC
1 CAAAACATAAAGAGACAAAAGAGTAGGTAAAACCAGGATCAAACAATACC
11325017 CGAGCATTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.51, C:0.17, G:0.20, T:0.11
Consensus pattern (53 bp):
CAAAACATAAAGAGACAAAAGAGTAGGTAAAACCAGGATCAAACAATACCTGA
Found at i:11338246 original size:29 final size:28
Alignment explanation
Indices: 11338201--11338342 Score: 185
Period size: 29 Copynumber: 4.9 Consensus size: 28
11338191 GGCAGCTTTG
11338201 ACATGTTTGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
11338229 ACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATGTTT-GTCTTAATTTAGACAAGAAA
* *
11338258 ATATGTTTGCCTTAATTTAAGACAAGAAAA
1 ACATGTTTGTCTTAATTT-AGACAAG-AAA
* * *
11338288 ATATTTTTTGTCTTAATTTAGTCAAGAAA
1 ACA-TGTTTGTCTTAATTTAGACAAGAAA
* *
11338317 ACATATTTGTCTCAATTTAGACAAGA
1 ACATGTTTGTCTTAATTTAGACAAGA
11338343 TAAAATATTT
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
28 37 0.37
29 39 0.39
30 12 0.12
31 13 0.13
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAGAAA
Found at i:11338314 original size:59 final size:58
Alignment explanation
Indices: 11338201--11338375 Score: 226
Period size: 59 Copynumber: 3.0 Consensus size: 58
11338191 GGCAGCTTTG
* * *
11338201 ACATGTTTGTCTTAATTTAGACAAG-AAAACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
* * *
11338258 ATATGTTTGCCTTAATTTAAGACAAGAAAAATATTTTTTGTCTTAATTTAGTCAAGAAA
1 ACATGTTTGTCTTAATTT-AGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
* * *
11338317 ACATATTTGTCTCAATTTAGACAAGATAAAATATTTTTTTGTCTTAATTACAGACAAGA
1 ACATGTTTGTCTTAATTTAGACAAGA-AAAATA-TTTTTTGTCTTAATT-TAGACAAGA
11338376 GTTGTCTTAA
Statistics
Matches: 101, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
57 16 0.16
58 15 0.15
59 48 0.48
60 15 0.15
61 7 0.07
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (58 bp):
ACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
Found at i:11338350 original size:28 final size:28
Alignment explanation
Indices: 11338201--11338352 Score: 173
Period size: 28 Copynumber: 5.3 Consensus size: 28
11338191 GGCAGCTTTG
*
11338201 ACATGTTTGTCTTAATTTAGACAAGAAA
1 ACATATTTGTCTTAATTTAGACAAGAAA
*
11338229 ACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATATTT-GTCTTAATTTAGACAAGAAA
* * *
11338258 ATATGTTTGCCTTAATTTAAGACAAGAAA
1 ACATATTTGTCTTAATTT-AGACAAGAAA
*
11338287 A-ATATTTTTTGTCTTAATTTAGTCAAGAAA
1 ACATA---TTTGTCTTAATTTAGACAAGAAA
*
11338317 ACATATTTGTCTCAATTTAGACAAGATAA
1 ACATATTTGTCTTAATTTAGACAAGA-AA
11338346 A-ATATTT
1 ACATATTT
11338353 TTTTGTCTTA
Statistics
Matches: 110, Mismatches: 7, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
28 44 0.40
29 41 0.37
30 10 0.09
31 15 0.14
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.38
Consensus pattern (28 bp):
ACATATTTGTCTTAATTTAGACAAGAAA
Found at i:11341044 original size:20 final size:20
Alignment explanation
Indices: 11341021--11341396 Score: 284
Period size: 20 Copynumber: 18.3 Consensus size: 20
11341011 ATGCCTAGTG
*
11341021 ATATATATATATATACATAC
1 ATATATATATATATATATAC
*
11341041 ATATATATGTATATATATGTAC
1 ATATATA--TATATATATATAC
* * *
11341063 ATATATGTATGTATATGTAC
1 ATATATATATATATATATAC
* * *
11341083 ATATATGTATGTATATGTAC
1 ATATATATATATATATATAC
* * *
11341103 ATATATGTATGTATACATAC
1 ATATATATATATATATATAC
* * *
11341123 ATACATATGTACATATACATAC
1 AT--ATATATATATATATATAC
*
11341145 ATATACATACATATATATATAC
1 ATAT--ATATATATATATATAC
* *
11341167 ATATATGTACATATATATAC
1 ATATATATATATATATATAC
* *
11341187 ATACATATATATATACATATAT
1 AT--ATATATATATATATATAC
* *
11341209 ATATATGTATATACATATAC
1 ATATATATATATATATATAC
* * *
11341229 ATATATGTACATATACATAC
1 ATATATATATATATATATAC
* *
11341249 ATATGTATATACATATATGTAC
1 ATA--TATATATATATATATAC
* * *
11341271 ATATACATACATATATGTAC
1 ATATATATATATATATATAC
* *
11341291 ATATATATACATATATATAT
1 ATATATATATATATATATAC
* * * *
11341311 ATACATATGTATATACATAT
1 ATATATATATATATATATAC
* * *
11341331 ATATATGTATGTATATGTAC
1 ATATATATATATATATATAC
* *
11341351 ATATATGTATATGTATATAC
1 ATATATATATATATATATAC
* *
11341371 ATATATATATATGTATATAT
1 ATATATATATATATATATAC
11341391 ATATAT
1 ATATAT
11341397 GGCATTTGTG
Statistics
Matches: 299, Mismatches: 47, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
20 215 0.72
22 84 0.28
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (20 bp):
ATATATATATATATATATAC
Found at i:11341054 original size:10 final size:10
Alignment explanation
Indices: 11341021--11341396 Score: 239
Period size: 10 Copynumber: 37.6 Consensus size: 10
11341011 ATGCCTAGTG
11341021 ATATATATAT
1 ATATATATAT
* *
11341031 ATATACATAC
1 ATATATATAT
*
11341041 ATATATATGT
1 ATATATATAT
*
11341051 ATATATATGT
1 ATATATATAT
* *
11341061 ACATATATGT
1 ATATATATAT
* *
11341071 ATGTATATGT
1 ATATATATAT
* *
11341081 ACATATATGT
1 ATATATATAT
* *
11341091 ATGTATATGT
1 ATATATATAT
* *
11341101 ACATATATGT
1 ATATATATAT
* *
11341111 ATGTATACAT
1 ATATATATAT
* *
11341121 ACATACATAT
1 ATATATATAT
* * *
11341131 GTACATATAC
1 ATATATATAT
* *
11341141 ATACATATAC
1 ATATATATAT
*
11341151 ATACATATAT
1 ATATATATAT
*
11341161 ATATACATAT
1 ATATATATAT
* *
11341171 ATGTACATAT
1 ATATATATAT
* *
11341181 ATATACATAC
1 ATATATATAT
11341191 ATATATATAT
1 ATATATATAT
*
11341201 ACATATATAT
1 ATATATATAT
*
11341211 ATATGTATAT
1 ATATATATAT
* *
11341221 ACATATACAT
1 ATATATATAT
* *
11341231 ATATGTACAT
1 ATATATATAT
* *
11341241 ATACATACAT
1 ATATATATAT
* *
11341251 ATGTATATAC
1 ATATATATAT
* *
11341261 ATATATGTAC
1 ATATATATAT
* *
11341271 ATATACATAC
1 ATATATATAT
* *
11341281 ATATATGTAC
1 ATATATATAT
*
11341291 ATATATATAC
1 ATATATATAT
11341301 ATATATATAT
1 ATATATATAT
* *
11341311 ATACATATGT
1 ATATATATAT
*
11341321 ATATACATAT
1 ATATATATAT
*
11341331 ATATATGTAT
1 ATATATATAT
* * *
11341341 GTATATGTAC
1 ATATATATAT
*
11341351 ATATATGTAT
1 ATATATATAT
* *
11341361 ATGTATATAC
1 ATATATATAT
11341371 ATATATATAT
1 ATATATATAT
*
11341381 ATGTATATAT
1 ATATATATAT
11341391 ATATAT
1 ATATAT
11341397 GGCATTTGTG
Statistics
Matches: 290, Mismatches: 76, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 290 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (10 bp):
ATATATATAT
Found at i:11341067 original size:32 final size:32
Alignment explanation
Indices: 11341022--11341394 Score: 232
Period size: 32 Copynumber: 11.5 Consensus size: 32
11341012 TGCCTAGTGA
** *
11341022 TATATATATATATACATACATATATATGTATA
1 TATATATATATATATGTACATATATATATATA
* * * * *
11341054 TATATGTACATATATGT--ATGTATATGTACA
1 TATATATATATATATGTACATATATATATATA
* * * *
11341084 TATATGTATGTATATGTACATATATGTATGTA
1 TATATATATATATATGTACATATATATATATA
* * * * *
11341116 TACATACATACATATGTACATATACATACATA
1 TATATATATATATATGTACATATATATATATA
* * *
11341148 TACATACATATATATATACATATATGTACATATATA
1 TATATATATATATATGTACATATA--T--ATATATA
* * *
11341184 TACATACATATATATATACATATATATATATGTA
1 TATATATATATATATGTACATATATATATA--TA
* * *
11341218 TATACATATACATATATGTACATATACATACATA
1 TAT--ATATATATATATGTACATATATATATATA
* * * *
11341252 TGTATATACATATATGTACATATACATACATA
1 TATATATATATATATGTACATATATATATATA
* *
11341284 TATGTACATATATA--TACATATATATATATACA
1 TATATATATATATATGTACATATATATATAT--A
* * * * * * *
11341316 TATGTATATACATATATATATGTATGTATATG
1 TATATATATATATATGTACATATATATATATA
* * * *
11341348 TACATATATGTATATGTATATACATATATATA
1 TATATATATATATATGTACATATATATATATA
*
11341380 TATGTATATATATAT
1 TATATATATATATAT
11341395 ATGGCATTTG
Statistics
Matches: 270, Mismatches: 57, Indels: 28
0.76 0.16 0.08
Matches are distributed among these distances:
30 39 0.14
32 158 0.59
34 21 0.08
36 52 0.19
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.41
Consensus pattern (32 bp):
TATATATATATATATGTACATATATATATATA
Found at i:11345328 original size:20 final size:20
Alignment explanation
Indices: 11345283--11345328 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
11345273 GAAAAACGCG
11345283 ATTTTCCCTTTGAATTTTCT
1 ATTTTCCCTTTGAATTTTCT
* **
11345303 AGTTTCCCTTTGGTTTTTCT
1 ATTTTCCCTTTGAATTTTCT
*
11345323 CTTTTC
1 ATTTTC
11345329 TTCCTTTCCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.22, G:0.09, T:0.61
Consensus pattern (20 bp):
ATTTTCCCTTTGAATTTTCT
Found at i:11352886 original size:10 final size:10
Alignment explanation
Indices: 11352860--11352903 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
11352850 TTAATTTAAG
*
11352860 TTATTTTAGT
1 TTATTTTACT
11352870 TTAATTTTACT
1 TT-ATTTTACT
*
11352881 TTATTTTTCT
1 TTATTTTACT
*
11352891 TTAATTTACT
1 TTATTTTACT
11352901 TTA
1 TTA
11352904 AGAAGAGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (10 bp):
TTATTTTACT
Found at i:11352900 original size:20 final size:20
Alignment explanation
Indices: 11352850--11352903 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
11352840 TGTTGAGTAG
** *
11352850 TTAATTTAAGTTATTTTAGT
1 TTAATTTACTTTATTTTACT
*
11352870 TTAATTTTACTTTATTTTTCT
1 TTAA-TTTACTTTATTTTACT
11352891 TTAATTTACTTTA
1 TTAATTTACTTTA
11352904 AGAAGAGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.65
Consensus pattern (20 bp):
TTAATTTACTTTATTTTACT
Found at i:11356596 original size:20 final size:19
Alignment explanation
Indices: 11356567--11356607 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
11356557 AACCAAGCTT
11356567 TTTCTTCCTTTCTCCTTTC
1 TTTCTTCCTTTCTCCTTTC
11356586 TTTCTTTCCTTTCTCCTTTC
1 TTTC-TTCCTTTCTCCTTTC
11356606 TT
1 TT
11356608 CCAATTGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTCTTCCTTTCTCCTTTC
Found at i:11360706 original size:10 final size:10
Alignment explanation
Indices: 11360680--11360723 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
11360670 TTAATTTAAG
*
11360680 TTATTTTAGT
1 TTATTTTACT
11360690 TTAATTTTACT
1 TT-ATTTTACT
*
11360701 TTATTTTGCT
1 TTATTTTACT
*
11360711 TTAATTTACT
1 TTATTTTACT
11360721 TTA
1 TTA
11360724 AAAAGAGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.66
Consensus pattern (10 bp):
TTATTTTACT
Found at i:11360720 original size:20 final size:20
Alignment explanation
Indices: 11360670--11360723 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
11360660 TGTTGAGTAG
**
11360670 TTAATTTAAGTTATTTTAGT
1 TTAATTTACTTTATTTTAGT
11360690 TTAATTTTACTTTATTTT-GCT
1 TTAA-TTTACTTTATTTTAG-T
11360711 TTAATTTACTTTA
1 TTAATTTACTTTA
11360724 AAAAGAGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.63
Consensus pattern (20 bp):
TTAATTTACTTTATTTTAGT
Found at i:11364944 original size:20 final size:18
Alignment explanation
Indices: 11364918--11364966 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
11364908 CATATATTAG
11364918 TTTTAATTGTTAGTTTATTAA
1 TTTTAATTGTT--TTT-TTAA
11364939 -TTTAATT-TTTTTTTAA
1 TTTTAATTGTTTTTTTAA
11364955 TTTTAATTGTTT
1 TTTTAATTGTTT
11364967 AGATAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.15
17 10 0.38
18 3 0.12
19 2 0.08
20 7 0.27
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTTAATTGTTTTTTTAA
Found at i:11368810 original size:2 final size:2
Alignment explanation
Indices: 11368803--11368859 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
11368793 GCTTTAATAC
* * * * *
11368803 AT AT AT AT AT AT AT AT AT AT GT GT GT GT GT 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
* *
11368845 AT AT GT AT GT AT AT A
1 AT AT AT AT AT AT AT A
11368860 GACATTGACT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11368838 original size:22 final size:22
Alignment explanation
Indices: 11368810--11368859 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
11368800 TACATATATA
* * *
11368810 TATATATATATATGTGTGTGTG
1 TATATATATATATATATGTATG
11368832 TATATATATATATATATGTATG
1 TATATATATATATATATGTATG
11368854 TATATA
1 TATATA
11368860 GACATTGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (22 bp):
TATATATATATATATATGTATG
Found at i:11381452 original size:20 final size:20
Alignment explanation
Indices: 11381427--11381472 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
11381417 TTTTGACCCC
11381427 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
11381447 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
11381467 ATTTGA
1 ATTTGA
11381473 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:11381548 original size:28 final size:27
Alignment explanation
Indices: 11381517--11381569 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
11381507 TTTGGAGTAT
*
11381517 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
11381545 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
11381570 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:11381575 original size:28 final size:28
Alignment explanation
Indices: 11381517--11381575 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
11381507 TTTGGAGTAT
* *
11381517 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
11381545 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
11381573 AGG
1 AGG
11381576 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:11396640 original size:22 final size:21
Alignment explanation
Indices: 11396589--11396640 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
11396579 AAAACCCTAG
*
11396589 GTGAAAAAATTGAAGGAAAAA
1 GTGAAAAAATTCAAGGAAAAA
**
11396610 GTGTGAAAATTCAAGGAAACAA
1 GTGAAAAAATTCAAGGAAA-AA
11396632 GTGAAAAAA
1 GTGAAAAAA
11396641 GATAAGATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.58, C:0.04, G:0.23, T:0.15
Consensus pattern (21 bp):
GTGAAAAAATTCAAGGAAAAA
Found at i:11399821 original size:16 final size:15
Alignment explanation
Indices: 11399774--11399822 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 15
11399764 TAATATTTAT
*
11399774 TAAATATAATAA-AA
1 TAAATTTAATAATAA
*
11399788 TAAATTTAATATTAA
1 TAAATTTAATAATAA
*
11399803 TAAATTTTAATAATCA
1 TAAA-TTTAATAATAA
11399819 TAAA
1 TAAA
11399823 AATATTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 10 0.34
15 6 0.21
16 13 0.45
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAATTTAATAATAA
Found at i:11403863 original size:30 final size:30
Alignment explanation
Indices: 11403829--11403896 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
11403819 CTTGATTGAG
11403829 GATGAAGAAGATAACATGCAAAGAGATGAA
1 GATGAAGAAGATAACATGCAAAGAGATGAA
* * * *
11403859 GATGAAAAAGATGACATGGAAGGAGATGAA
1 GATGAAGAAGATAACATGCAAAGAGATGAA
*
11403889 AATGAAGA
1 GATGAAGA
11403897 TGACCATGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.53, C:0.04, G:0.29, T:0.13
Consensus pattern (30 bp):
GATGAAGAAGATAACATGCAAAGAGATGAA
Found at i:11403924 original size:18 final size:18
Alignment explanation
Indices: 11403892--11403926 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11403882 AGATGAAAAT
*
11403892 GAAGATGACCATGAAGAA
1 GAAGATGAACATGAAGAA
*
11403910 GAAGATGAACTTGAAGA
1 GAAGATGAACATGAAGA
11403927 CGACGCTTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.09, G:0.29, T:0.14
Consensus pattern (18 bp):
GAAGATGAACATGAAGAA
Found at i:11404645 original size:9 final size:9
Alignment explanation
Indices: 11404631--11404677 Score: 58
Period size: 9 Copynumber: 4.9 Consensus size: 9
11404621 GTATGTTGTC
11404631 TTGTTATAT
1 TTGTTATAT
11404640 TTGTTATAT
1 TTGTTATAT
*
11404649 TTGTTAATGAAA
1 TTGTT-AT--AT
11404661 TTGTTATAT
1 TTGTTATAT
11404670 TTGTTATA
1 TTGTTATA
11404678 AATTTATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 23 0.70
10 2 0.06
11 2 0.06
12 6 0.18
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.60
Consensus pattern (9 bp):
TTGTTATAT
Found at i:11406424 original size:15 final size:15
Alignment explanation
Indices: 11406404--11406433 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11406394 TTGGAAAATC
*
11406404 ATTTCCAATGGAATT
1 ATTTCCAACGGAATT
11406419 ATTTCCAACGGAATT
1 ATTTCCAACGGAATT
11406434 TTCCGTTGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (15 bp):
ATTTCCAACGGAATT
Found at i:11406455 original size:30 final size:26
Alignment explanation
Indices: 11406419--11406490 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 26
11406409 CAATGGAATT
11406419 ATTTCCAACGGAATTTTCCGTTGCAAAA
1 ATTTCCAACGGAATTTTCCGTTG--AAA
**
11406447 ACTATTCCAACGGAAAATTCCGTTGAAA
1 A-T-TTCCAACGGAATTTTCCGTTGAAA
11406475 ATTTCCAACGGAATTT
1 ATTTCCAACGGAATTT
11406491 CGTTGGGGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
26 12 0.32
27 1 0.03
28 5 0.13
29 1 0.03
30 19 0.50
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (26 bp):
ATTTCCAACGGAATTTTCCGTTGAAA
Found at i:11407218 original size:72 final size:74
Alignment explanation
Indices: 11407019--11407219 Score: 194
Period size: 74 Copynumber: 2.8 Consensus size: 74
11407009 GGACTGATGG
* * * * * * * *
11407019 AAATTATCCTTAAAG-ACAATGTATTGCACCTCAAACTTGTATCTGTTCCTTATTTCATACTTCG
1 AAATTATCCTTTAAGAACAGTGTATTACACTTCAGACTGGTTTCAGTTCCTTATTTCATACTTCG
*
11407083 AAGGGACAA
66 AAAGGACAA
* * * * * *
11407092 AAATTATCCTTTAAGGACAGTGTATTACACTTCAGACTTGTTTCAATTCTTTATTTCATATTTTG
1 AAATTATCCTTTAAGAACAGTGTATTACACTTCAGACTGGTTTCAGTTCCTTATTTCATACTTCG
*
11407157 AAAGG-CAT
66 AAAGGACAA
* * *
11407165 AAATTAT-CTTTAAGAATAGTGTATTACGTCTT-AGACTGGTTTTAGTTCCTTATTT
1 AAATTATCCTTTAAGAACAGTGTATTAC-ACTTCAGACTGGTTTCAGTTCCTTATTT
11407220 GCTTCACTTT
Statistics
Matches: 106, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
72 37 0.35
73 26 0.25
74 43 0.41
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (74 bp):
AAATTATCCTTTAAGAACAGTGTATTACACTTCAGACTGGTTTCAGTTCCTTATTTCATACTTCG
AAAGGACAA
Found at i:11407393 original size:127 final size:127
Alignment explanation
Indices: 11407208--11407502 Score: 527
Period size: 127 Copynumber: 2.3 Consensus size: 127
11407198 GACTGGTTTT
* *
11407208 AGTTCCTTATTTGCTTCACTTTTCGCTAACAAAGATATCATTTCTGGAGATATCCACTTTAATCC
1 AGTTCCTTA--TGCTTCACTTTTCACCAACAAAGATATCATTTCTGGAGATATCCACTTTAATCC
11407273 TTTTGCACTGCGAAAATGTGAAAATTATCATCAAGTATAATGTATCACGCATCAAACTTATTTC
64 TTTTGCACTGCGAAAATGTGAAAATTATCATCAAGTATAATGTATCACGCATCAAACTTATTTC
11407337 AGTTCCTTATGCTTCACTTTTCACCAACAAAGATATCATTTCTGGAGATATCCACTTTAATCCTT
1 AGTTCCTTATGCTTCACTTTTCACCAACAAAGATATCATTTCTGGAGATATCCACTTTAATCCTT
* *
11407402 TTGCACTGTGAAAATGTGAAAATTATCGTCAAGTATAATGTATCACGCATCAAACTTATTTC
66 TTGCACTGCGAAAATGTGAAAATTATCATCAAGTATAATGTATCACGCATCAAACTTATTTC
*
11407464 AGTTCCTTATGCTTCACTTTTCACCAACAAGGATATCAT
1 AGTTCCTTATGCTTCACTTTTCACCAACAAAGATATCAT
11407503 GCAAGTCCAA
Statistics
Matches: 161, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
127 152 0.94
129 9 0.06
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (127 bp):
AGTTCCTTATGCTTCACTTTTCACCAACAAAGATATCATTTCTGGAGATATCCACTTTAATCCTT
TTGCACTGCGAAAATGTGAAAATTATCATCAAGTATAATGTATCACGCATCAAACTTATTTC
Found at i:11409721 original size:2 final size:2
Alignment explanation
Indices: 11409714--11409750 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
11409704 CAGAAAAGAA
*
11409714 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11409751 AAGTAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11411092 original size:15 final size:15
Alignment explanation
Indices: 11411074--11411129 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
11411064 AATAAAAATA
11411074 AAAATATTTAACTTT
1 AAAATATTTAACTTT
*
11411089 AAAAATTTTTAAC-TT
1 -AAAATATTTAACTTT
*
11411104 AAAATA-TTAATATTT
1 AAAATATTTAA-CTTT
*
11411119 AAATTATTTAA
1 AAAATATTTAA
11411130 TACTATTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 4 0.12
14 5 0.15
15 9 0.27
16 15 0.45
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (15 bp):
AAAATATTTAACTTT
Found at i:11411093 original size:16 final size:15
Alignment explanation
Indices: 11411072--11411111 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
11411062 AAAATAAAAA
11411072 TAAAAATATTTAACTT
1 TAAAAATATTTAAC-T
*
11411088 TAAAAATTTTTAACT
1 TAAAAATATTTAACT
11411103 T-AAAATATT
1 TAAAAATATT
11411112 AATATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 7 0.32
15 2 0.09
16 13 0.59
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAAAATATTTAACT
Found at i:11414067 original size:73 final size:71
Alignment explanation
Indices: 11413933--11414140 Score: 203
Period size: 73 Copynumber: 2.9 Consensus size: 71
11413923 ACAGAATGAT
* * * *
11413933 CTTAGTTGACTAACTATGC-TCTTAGTCGACTAAGTCGTTTCTGTTTTCTG-A-TCCCAG-TTTC
1 CTTAGTTGACTAACT-TACTTCTTAGTCGATTAAGTTGTTTCTG-TCT-TGAAGT-CCAGATTTC
11413994 TAACAGTA-AGCA
62 TAACA--ACAG-A
*
11414006 CTTAGTTGACTAACTT-CTTTCTTAGTCGATTAAGTTGTTTCTGTCTTGAAGTCCAGATTTCTAG
1 CTTAGTTGACTAACTTAC-TTCTTAGTCGATTAAGTTGTTTCTGTCTTGAAGTCCAGATTTCTAA
11414070 CAACAGA
65 CAACAGA
* * * *
11414077 CTTATGGTCGACTAGCTTACTTCTTGGTCGATTAAGTTGGTTCTGTCTTGAAGTCCAGATTTCT
1 CTTA--GTTGACTAACTTACTTCTTAGTCGATTAAGTTGTTTCTGTCTTGAAGTCCAGATTTCT
11414141 GGTAATAGAC
Statistics
Matches: 118, Mismatches: 8, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
71 9 0.08
72 10 0.08
73 98 0.83
74 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (71 bp):
CTTAGTTGACTAACTTACTTCTTAGTCGATTAAGTTGTTTCTGTCTTGAAGTCCAGATTTCTAAC
AACAGA
Found at i:11414161 original size:73 final size:73
Alignment explanation
Indices: 11414024--11414163 Score: 201
Period size: 73 Copynumber: 1.9 Consensus size: 73
11414014 ACTAACTTCT
* **
11414024 TTCTTAGTCGATTAAGTTGTTTCTGTCTTGAAGTCCAGATTTCTAGCAACAGACTTATGGTCGAC
1 TTCTTAGTCGATTAAGTTGGTTCTGTCTTGAAGTCCAGATTTCTAGCAACAGACTTATAATCGAC
11414089 TAGCTTAC
66 TAGCTTAC
* * * *
11414097 TTCTTGGTCGATTAAGTTGGTTCTGTCTTGAAGTCCAGATTTCTGGTAATAGACTCT-TAATCGA
1 TTCTTAGTCGATTAAGTTGGTTCTGTCTTGAAGTCCAGATTTCTAGCAACAGACT-TATAATCGA
11414161 CTA
65 CTA
11414164 ACCCATTTCT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
73 58 0.98
74 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (73 bp):
TTCTTAGTCGATTAAGTTGGTTCTGTCTTGAAGTCCAGATTTCTAGCAACAGACTTATAATCGAC
TAGCTTAC
Found at i:11414174 original size:73 final size:73
Alignment explanation
Indices: 11414023--11414186 Score: 195
Period size: 73 Copynumber: 2.2 Consensus size: 73
11414013 GACTAACTTC
* * **
11414023 TTTCTTAGTCGATTAAGTTGTTTCTGTCTTGAAGTCCAGATTTCTAGCAACAGACTTATGGTCGA
1 TTTCTTGGTCGATTAAGTTGGTTCTGTCTTGAAGTCCAGATTTCTAGCAACAGACTTATAATCGA
* **
11414088 CTAGCTTA
66 CTAACCCA
* * * *
11414096 CTTCTTGGTCGATTAAGTTGGTTCTGTCTTGAAGTCCAGATTTCTGGTAATAGACTCT-TAATCG
1 TTTCTTGGTCGATTAAGTTGGTTCTGTCTTGAAGTCCAGATTTCTAGCAACAGACT-TATAATCG
11414160 ACTAACCCA
65 ACTAACCCA
* *
11414169 TTTCTTGGTTGACTAAGT
1 TTTCTTGGTCGATTAAGT
11414187 CTTTTCTGTT
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
73 75 0.99
74 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.40
Consensus pattern (73 bp):
TTTCTTGGTCGATTAAGTTGGTTCTGTCTTGAAGTCCAGATTTCTAGCAACAGACTTATAATCGA
CTAACCCA
Found at i:11422938 original size:10 final size:10
Alignment explanation
Indices: 11422923--11422972 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
11422913 CTAGATCTCC
11422923 CTTTTTTTTT
1 CTTTTTTTTT
*
11422933 CTTTTTTGTT
1 CTTTTTTTTT
*
11422943 C-ATTTTTTT
1 CTTTTTTTTT
*
11422952 CTTTCTTTTT
1 CTTTTTTTTT
11422962 CTTGTTTTTTT
1 CTT-TTTTTTT
11422973 TCCTTGCTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
9 7 0.22
10 19 0.59
11 6 0.19
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.82
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:11426243 original size:23 final size:21
Alignment explanation
Indices: 11426204--11426247 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
11426194 AATTGTGAAA
11426204 TTTACAAGCTTTCACCAAGCT
1 TTTACAAGCTTTCACCAAGCT
*
11426225 TTTACAATGGCTTTTACCAAGCT
1 TTTACAA--GCTTTCACCAAGCT
11426248 CAGCCAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
23 13 0.65
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.36
Consensus pattern (21 bp):
TTTACAAGCTTTCACCAAGCT
Found at i:11439673 original size:22 final size:23
Alignment explanation
Indices: 11439648--11439697 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
11439638 AACCTAATTG
11439648 TAGAAGAAACGATACCTTAAA-A
1 TAGAAGAAACGATACCTTAAAGA
* * *
11439670 TAGAAGAATCGATTCTTTAAAGA
1 TAGAAGAAACGATACCTTAAAGA
11439693 TAGAA
1 TAGAA
11439698 AGCTACAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.50, C:0.10, G:0.16, T:0.24
Consensus pattern (23 bp):
TAGAAGAAACGATACCTTAAAGA
Found at i:11440294 original size:35 final size:34
Alignment explanation
Indices: 11440245--11440332 Score: 95
Period size: 35 Copynumber: 2.6 Consensus size: 34
11440235 GTCTTGATAG
*
11440245 AGGTTATGCTTGATCTTGTAAAAGACATGTTGTAA
1 AGGTTATGCCTGATCTTGTAAAAGACATGTTGT-A
* * ** *
11440280 AGGTCATGCCTGATCCTACAAAAGGCATGTTGTA
1 AGGTTATGCCTGATCTTGTAAAAGACATGTTGTA
* *
11440314 AGGTTACGCCTGACCTTGT
1 AGGTTATGCCTGATCTTGT
11440333 TGAAAAGGCA
Statistics
Matches: 41, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
34 14 0.34
35 27 0.66
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (34 bp):
AGGTTATGCCTGATCTTGTAAAAGACATGTTGTA
Found at i:11444401 original size:119 final size:119
Alignment explanation
Indices: 11444190--11444419 Score: 408
Period size: 119 Copynumber: 1.9 Consensus size: 119
11444180 GACGATTATA
*
11444190 ATGATGTAGTCTAAATATTCTTTATGGCCTATGAGCATAAAAATAAATGTTTTAATTAGTCTTTT
1 ATGATGTAGTCTAAATATTCTTTATGGCCTATGAGCACAAAAATAAATGTTTTAATTAGTCTTTT
*
11444255 AACACTTAAAACCAATAAATCATGTCATGTTATTTCAGAGTGTCTTCTTCTATT
66 AACACTTAAAACAAATAAATCATGTCATGTTATTTCAGAGTGTCTTCTTCTATT
* *
11444309 ATGATGCT-GTCTAAATCTTCTTTATGGCCTATGAGCACAAAAATAAGTGTTTTAATTAGTCTTT
1 ATGATG-TAGTCTAAATATTCTTTATGGCCTATGAGCACAAAAATAAATGTTTTAATTAGTCTTT
11444373 TAACACTTAAAACAAATAAATCATGTCATGTTATTTCAGAGTGTCTT
65 TAACACTTAAAACAAATAAATCATGTCATGTTATTTCAGAGTGTCTT
11444420 TAGAGTAACA
Statistics
Matches: 106, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
119 105 0.99
120 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (119 bp):
ATGATGTAGTCTAAATATTCTTTATGGCCTATGAGCACAAAAATAAATGTTTTAATTAGTCTTTT
AACACTTAAAACAAATAAATCATGTCATGTTATTTCAGAGTGTCTTCTTCTATT
Found at i:11448342 original size:21 final size:21
Alignment explanation
Indices: 11448304--11448352 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
11448294 TTCTCCTTCA
* *
11448304 ATAAAAAAATTCTAATATTTT
1 ATAAAAATATTCTAATATTAT
* *
11448325 ATAAAAATATTTTTATATTAT
1 ATAAAAATATTCTAATATTAT
11448346 -TAAAAAT
1 ATAAAAAT
11448353 TGCATTACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAAAAATATTCTAATATTAT
Found at i:11449210 original size:21 final size:23
Alignment explanation
Indices: 11449182--11449230 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
11449172 TAATGCAATC
*
11449182 TTTA-ATAATA-T-AAAAATAAT
1 TTTATATAATATTCAAAAAAAAT
11449202 TTTATATAATATTCAAAAAAAAT
1 TTTATATAATATTCAAAAAAAAT
11449225 TTTATA
1 TTTATA
11449231 AAAAGGGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.16
21 6 0.24
22 1 0.04
23 14 0.56
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTATATAATATTCAAAAAAAAT
Found at i:11451197 original size:28 final size:27
Alignment explanation
Indices: 11451031--11451267 Score: 264
Period size: 27 Copynumber: 8.7 Consensus size: 27
11451021 TTAAAAAAAA
* * *
11451031 AACAATTATAATTTTTAACATGGCGTGT
1 AACAACTAT-ATTTTCAACATGACGTGT
* *
11451059 AACAACTAAATCTTCAACATGACGTGT
1 AACAACTATATTTTCAACATGACGTGT
11451086 AACAACTATATTTTCAACATGACGTGT
1 AACAACTATATTTTCAACATGACGTGT
*
11451113 AACAACTATATTTTCAACATGATGTGT
1 AACAACTATATTTTCAACATGACGTGT
*
11451140 AACAACTAAATTTTCAACAT-AGCGTGT
1 AACAACTATATTTTCAACATGA-CGTGT
** *
11451167 AACAACTATATTTTTCAATGTGACGTAT
1 AACAACTATA-TTTTCAACATGACGTGT
* *
11451195 AACAACTATATTTTTCAATATGATGTGT
1 AACAACTATA-TTTTCAACATGACGTGT
* * *
11451223 AACAACTAAAATTTCAACATG--GTATT
1 AACAACTATATTTTCAACATGACGT-GT
*
11451249 AACAACTACATTTTCAACA
1 AACAACTATATTTTCAACA
11451268 CAATTTTTTG
Statistics
Matches: 182, Mismatches: 23, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
25 2 0.01
26 19 0.10
27 107 0.59
28 53 0.29
29 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.34
Consensus pattern (27 bp):
AACAACTATATTTTCAACATGACGTGT
Found at i:11452229 original size:21 final size:21
Alignment explanation
Indices: 11452205--11452263 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
11452195 AGAATTGAAG
*
11452205 AACATTTATCGAT-GAATGTTC
1 AACATCTATCGATAG-ATGTTC
*
11452226 AACATCTGTCGATAGATGTTC
1 AACATCTATCGATAGATGTTC
*
11452247 AACATCTATCAATAGAT
1 AACATCTATCGATAGAT
11452264 CGAGTTTATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 32 0.97
22 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (21 bp):
AACATCTATCGATAGATGTTC
Found at i:11453192 original size:15 final size:15
Alignment explanation
Indices: 11453163--11453249 Score: 62
Period size: 15 Copynumber: 6.1 Consensus size: 15
11453153 GCTTAGAATT
11453163 TAATTAA-AATATTAA
1 TAATTAATAAT-TTAA
11453178 TAATTAATAATTTAA
1 TAATTAATAATTTAA
11453193 -ATATTAAT-ATTT--
1 TA-ATTAATAATTTAA
*
11453205 T-ATTTATAATTTAA
1 TAATTAATAATTTAA
* *
11453219 TCATTAATATTTTAA
1 TAATTAATAATTTAA
*
11453234 AATATTAAT-ATTTAA
1 TA-ATTAATAATTTAA
11453249 T
1 T
11453250 TTAATTTAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
11 5 0.09
12 4 0.07
14 6 0.11
15 33 0.58
16 9 0.16
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (15 bp):
TAATTAATAATTTAA
Found at i:11453200 original size:34 final size:34
Alignment explanation
Indices: 11453141--11453264 Score: 82
Period size: 34 Copynumber: 3.7 Consensus size: 34
11453131 TTAGATTTTT
**
11453141 TTAAT-ATTAATAGCTTAGAAT-TTAATTAAAATA
1 TTAATAATTAATAATTTA-AATATTAATTAAAATA
***
11453174 TTAATAATTAATAATTTAAATATTAA-TATTTTA
1 TTAATAATTAATAATTTAAATATTAATTAAAATA
* *
11453207 TTTATAATTTAATCA-TT-AATATT--TTAAAATA
1 TTAATAA-TTAATAATTTAAATATTAATTAAAATA
* *
11453238 TTAATATTTAATTTAATTTAATTATTA
1 TTAATAATTAA--TAATTTAAATATTA
11453265 TTATGATTAA
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
30 4 0.06
31 9 0.13
32 8 0.12
33 22 0.32
34 25 0.37
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (34 bp):
TTAATAATTAATAATTTAAATATTAATTAAAATA
Found at i:11453239 original size:64 final size:61
Alignment explanation
Indices: 11453166--11453319 Score: 157
Period size: 64 Copynumber: 2.4 Consensus size: 61
11453156 TAGAATTTAA
*
11453166 TTAAAATATTAATAATTAATAATTTAAATATTAATAT-TTTATTTATAATTTAATCATTAATATT
1 TTAAAATATTAATAATTAATAATTTAAATATTAATATATTAATTT-TAATTTAAT--TTAAT-TT
* * * * * *
11453230 TTAAAATATTAATATTTAATTTAATTTAATTATTATTATGATTAATTTTTATTTTATTTTATTT
1 TTAAAATATTAATAATTAA--TAATTTAAATATTAATAT-ATTAATTTTAATTTAATTTAATTT
* *
11453294 TTTAAATATTAATAATTGATAATTTA
1 TTAAAATATTAATAATTAATAATTTA
11453320 TTTAAAATAT
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
62 7 0.09
64 36 0.47
65 4 0.05
66 16 0.21
67 7 0.09
68 6 0.08
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (61 bp):
TTAAAATATTAATAATTAATAATTTAAATATTAATATATTAATTTTAATTTAATTTAATTT
Found at i:11453252 original size:42 final size:40
Alignment explanation
Indices: 11453160--11453401 Score: 137
Period size: 41 Copynumber: 6.1 Consensus size: 40
11453150 ATAGCTTAGA
*
11453160 ATTTAATTAAAATATTAATAATTAATAATTTAAATATTAAT
1 ATTTAATTATAAT-TTAATAATTAATAATTTAAATATTAAT
* * *
11453201 ATTTTATTTATAATTTAATCATTAATATTTTAAAATATTAAT
1 A-TTTAATTATAATTTAATAATTAATAATTT-AAATATTAAT
* * * *
11453243 ATTTAATT-TAATTTAATTATT-ATTATGATT-AATTTTTAT
1 ATTTAATTATAATTTAATAATTAATAAT--TTAAATATTAAT
* ** * *
11453282 -TTTATTTTATTTTTTAA-ATATTAATAATTGATA-ATT--T
1 ATTTA-ATTATAATTTAATA-ATTAATAATTTAAATATTAAT
* * **
11453319 ATTTAA-AAT-A-TTAATAATTGACCATTTAAATATTAAT
1 ATTTAATTATAATTTAATAATTAATAATTTAAATATTAAT
* * * *
11453356 ATTTTATTTATAATTTAGTCATTAATATTTTAAAATATTAAT
1 A-TTTAATTATAATTTAATAATTAATAATTT-AAATATTAAT
11453398 ATTT
1 ATTT
11453402 TATNNNNNNN
Statistics
Matches: 148, Mismatches: 34, Indels: 38
0.67 0.15 0.17
Matches are distributed among these distances:
34 13 0.09
35 4 0.03
36 2 0.01
37 3 0.02
38 12 0.08
39 17 0.11
40 23 0.16
41 42 0.28
42 32 0.22
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (40 bp):
ATTTAATTATAATTTAATAATTAATAATTTAAATATTAAT
Found at i:11453304 original size:155 final size:156
Alignment explanation
Indices: 11453121--11453401 Score: 449
Period size: 155 Copynumber: 1.8 Consensus size: 156
11453111 TATATGACTA
* *
11453121 TTTATTTTTATTAGATTTTTTTAATATTAATAGCTT-AGAATTTAATTAAAATATTAATAATTAA
1 TTTATTTTTATTAGATTTTTTAAATATTAATA-ATTGAGAATTTAATTAAAATATTAATAATTAA
*
11453185 TAATTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTTTAAAATATTAATATTTAAT
65 CAATTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTTTAAAATATTAATATTTAAT
11453250 TTAATTTAATTATTATTATGATTAATT
130 TTAATTTAATTATTATTATGATTAATT
** * * *
11453277 TTTA-TTTTATTTTATTTTTTAAATATTAATAATTGATAATTTATTTAAAATATTAATAATTGAC
1 TTTATTTTTATTAGATTTTTTAAATATTAATAATTGAGAATTTAATTAAAATATTAATAATTAAC
* *
11453341 CATTTAAATATTAATATTTTATTTATAATTTAGTCATTAATATTTTAAAATATTAATATTT
66 AATTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTTTAAAATATTAATATTT
11453402 TATNNNNNNN
Statistics
Matches: 114, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
154 2 0.02
155 108 0.95
156 4 0.04
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (156 bp):
TTTATTTTTATTAGATTTTTTAAATATTAATAATTGAGAATTTAATTAAAATATTAATAATTAAC
AATTTAAATATTAATATTTTATTTATAATTTAATCATTAATATTTTAAAATATTAATATTTAATT
TAATTTAATTATTATTATGATTAATT
Found at i:11453330 original size:27 final size:25
Alignment explanation
Indices: 11453290--11453339 Score: 82
Period size: 27 Copynumber: 1.9 Consensus size: 25
11453280 ATTTTATTTT
11453290 ATTTTTTAAATATTAATAATTGATA
1 ATTTTTTAAATATTAATAATTGATA
11453315 ATTTATTTAAAATATTAATAATTGA
1 ATTT-TTT-AAATATTAATAATTGA
11453340 CCATTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 4 0.17
26 3 0.13
27 16 0.70
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (25 bp):
ATTTTTTAAATATTAATAATTGATA
Found at i:11453345 original size:27 final size:26
Alignment explanation
Indices: 11453290--11453346 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
11453280 ATTTTATTTT
*
11453290 ATTT-TTTAAATATTAATAATTGATA
1 ATTTATTTAAATATTAATAATTGACA
*
11453315 ATTTATTTAAAATATTAATAATTGACC
1 ATTTATTT-AAATATTAATAATTGACA
11453342 ATTTA
1 ATTTA
11453347 AATATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 4 0.14
26 3 0.11
27 21 0.75
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (26 bp):
ATTTATTTAAATATTAATAATTGACA
Found at i:11453714 original size:48 final size:42
Alignment explanation
Indices: 11453693--11453793 Score: 177
Period size: 41 Copynumber: 2.4 Consensus size: 42
11453683 ATTGTAATTT
11453693 AAATATTAATATTTTATTTATAATTTAATTTTTAATATTTTA
1 AAATATTAATATTTTATTTATAATTTAATTTTTAATATTTTA
* *
11453735 AAATATTAATATTTTATTTATAATTTAA-TATCAATATTTTA
1 AAATATTAATATTTTATTTATAATTTAATTTTTAATATTTTA
11453776 AAATATTAATATTTTATT
1 AAATATTAATATTTTATT
11453794 AAAAGTTAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
41 29 0.51
42 28 0.49
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (42 bp):
AAATATTAATATTTTATTTATAATTTAATTTTTAATATTTTA
Found at i:11453735 original size:8 final size:8
Alignment explanation
Indices: 11453716--11453791 Score: 50
Period size: 8 Copynumber: 9.5 Consensus size: 8
11453706 TTATTTATAA
11453716 TTTAAT-T
1 TTTAATAT
11453723 TTTAATAT
1 TTTAATAT
*
11453731 TTTAAAAT
1 TTTAATAT
*
11453739 ATTAATAT
1 TTTAATAT
*
11453747 TTTATTTATAA
1 TTTA---ATAT
11453758 TTTAATA-
1 TTTAATAT
*
11453765 -TCAATAT
1 TTTAATAT
*
11453772 TTTAAAAT
1 TTTAATAT
*
11453780 ATTAATAT
1 TTTAATAT
11453788 TTTA
1 TTTA
11453792 TTAAAAGTTA
Statistics
Matches: 52, Mismatches: 11, Indels: 11
0.70 0.15 0.15
Matches are distributed among these distances:
6 5 0.10
7 6 0.12
8 34 0.65
11 7 0.13
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (8 bp):
TTTAATAT
Found at i:11453786 original size:16 final size:15
Alignment explanation
Indices: 11453690--11453791 Score: 78
Period size: 16 Copynumber: 7.3 Consensus size: 15
11453680 ATAATTGTAA
11453690 TTTAAATATTAATAT
1 TTTAAATATTAATAT
*
11453705 TTT--AT-TT-ATAA
1 TTTAAATATTAATAT
* *
11453716 TTTAATTTTTAATAT
1 TTTAAATATTAATAT
11453731 TTTAAAATATTAATAT
1 TTT-AAATATTAATAT
*
11453747 TTT--AT-TT-ATAA
1 TTTAAATATTAATAT
*
11453758 TTT-AATATCAATAT
1 TTTAAATATTAATAT
11453772 TTTAAAATATTAATAT
1 TTT-AAATATTAATAT
11453788 TTTA
1 TTTA
11453792 TTAAAAGTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
11 12 0.18
12 6 0.09
13 6 0.09
14 8 0.12
15 10 0.15
16 26 0.38
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAAATATTAATAT
Found at i:11454793 original size:64 final size:64
Alignment explanation
Indices: 11454681--11454844 Score: 220
Period size: 64 Copynumber: 2.6 Consensus size: 64
11454671 TTTCTAGCAT
* * * *
11454681 TTCCACATGGTGTGAGGCAACATTCCACACGTGGTGAATGAGTCTAGTATGATGGATGATGGCA
1 TTCCACACGGTGTGAGGTAATATTCCACACGTGGTGAATGAGTATAGTATGATGGATGATGGCA
** * * *
11454745 TTTTACACGGTGTGAGGTAATATTCCACATGTGGTGAATGCGTATAGTATGATGGATGATGGCG
1 TTCCACACGGTGTGAGGTAATATTCCACACGTGGTGAATGAGTATAGTATGATGGATGATGGCA
* * *
11454809 TTCCACATGGTGTGATGTAATATTACACACGTGGTG
1 TTCCACACGGTGTGAGGTAATATTCCACACGTGGTG
11454845 CTAAGGACCA
Statistics
Matches: 85, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
64 85 1.00
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (64 bp):
TTCCACACGGTGTGAGGTAATATTCCACACGTGGTGAATGAGTATAGTATGATGGATGATGGCA
Found at i:11455192 original size:29 final size:29
Alignment explanation
Indices: 11455160--11455215 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
11455150 GGGTTAGATA
* *
11455160 GATTGATAAATGATTACTTGAGTTATATG
1 GATTGAGAAATGATTACTAGAGTTATATG
*
11455189 GATTGGGAAATGATTACTAGAGTTATA
1 GATTGAGAAATGATTACTAGAGTTATA
11455216 GATGGGAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.38
Consensus pattern (29 bp):
GATTGAGAAATGATTACTAGAGTTATATG
Found at i:11460019 original size:54 final size:54
Alignment explanation
Indices: 11459854--11460019 Score: 242
Period size: 54 Copynumber: 3.1 Consensus size: 54
11459844 TCCTTATGTG
* *
11459854 CATCTCACCCAGCTCATGTGCATCCGACCACATCATGCACATAGTCGGACATCC
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGTCGGACATCC
* * * * **
11459908 CATATCGCCCAGCTCATGTGCATCCCACCACATTGTGCACATAGCCAAACATCC
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGTCGGACATCC
* *
11459962 CATCTCACCTAGCTCATGTGCATCCCACCACATCGTGCAAATAGTCGGACATCC
1 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGTCGGACATCC
11460016 CATC
1 CATC
11460020 CATCTCCCTC
Statistics
Matches: 96, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.27, C:0.39, G:0.14, T:0.21
Consensus pattern (54 bp):
CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGTCGGACATCC
Found at i:11461398 original size:14 final size:14
Alignment explanation
Indices: 11461381--11461415 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
11461371 TTTAGTGAAT
11461381 TGAAATATTAGAAA
1 TGAAATATTAGAAA
11461395 TGAAATATTAGAAA
1 TGAAATATTAGAAA
11461409 TGAAATA
1 TGAAATA
11461416 GAGCAATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (14 bp):
TGAAATATTAGAAA
Found at i:11463996 original size:19 final size:20
Alignment explanation
Indices: 11463969--11464014 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
11463959 AGGAAACAAG
*
11463969 ATAAAATTTTTA-AAATAAA
1 ATAATATTTTTATAAATAAA
*
11463988 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATAAATAAA
11464007 ATAATATT
1 ATAATATT
11464015 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATAAATAAA
Found at i:11475737 original size:20 final size:20
Alignment explanation
Indices: 11475712--11475751 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11475702 CTTCCTAGTT
*
11475712 GCTATCTATCGATCGATCTG
1 GCTATCTATCGATAGATCTG
*
11475732 GCTATCTATGGATAGATCTG
1 GCTATCTATCGATAGATCTG
11475752 CTCAACTATC
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:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
GCTATCTATCGATAGATCTG
Found at i:11479216 original size:4 final size:4
Alignment explanation
Indices: 11479207--11479237 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
11479197 ACACAAACAT
11479207 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
11479238 GACACACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:11487914 original size:18 final size:19
Alignment explanation
Indices: 11487891--11487930 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
11487881 CAAGTGGAGA
11487891 ATTTTA-AAATAAAATAAT
1 ATTTTATAAATAAAATAAT
* *
11487909 ATTTTATTAATAAAATATT
1 ATTTTATAAATAAAATAAT
11487928 ATT
1 ATT
11487931 AAAATAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTTATAAATAAAATAAT
Found at i:11488805 original size:12 final size:11
Alignment explanation
Indices: 11488764--11488806 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
11488754 GAGCTCCACC
*
11488764 AAAGAGGAAGA
1 AAAGAGAAAGA
* *
11488775 AAAGGGACAGA
1 AAAGAGAAAGA
11488786 AAAGAGAAAGA
1 AAAGAGAAAGA
11488797 AAGAGAGAAA
1 AA-AGAGAAA
11488807 ATGGAGGAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 19 0.73
12 7 0.27
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (11 bp):
AAAGAGAAAGA
Found at i:11493488 original size:28 final size:28
Alignment explanation
Indices: 11493448--11493515 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
11493438 GTTGTTAGAT
*
11493448 GTGGTTAGGCCACGATCTGTGATTATAC
1 GTGGCTAGGCCACGATCTGTGATTATAC
*
11493476 GTGGCTAGGCCACGATCTGTGATTATAT
1 GTGGCTAGGCCACGATCTGTGATTATAC
*
11493504 GTGGCAAGGCCA
1 GTGGCTAGGCCA
11493516 GGGGTTGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (28 bp):
GTGGCTAGGCCACGATCTGTGATTATAC
Found at i:11498984 original size:34 final size:37
Alignment explanation
Indices: 11498941--11499029 Score: 121
Period size: 34 Copynumber: 2.5 Consensus size: 37
11498931 CTTACTCAGC
11498941 TCATGTGCACTCCCTACACGCACAAGAC-A-A-ATCA
1 TCATGTGCACTCCCTACACGCACAAGACAATATATCA
* ***
11498975 TCATGTGCACTCCCTACATGCACACTTCAATATATCA
1 TCATGTGCACTCCCTACACGCACAAGACAATATATCA
11499012 TCATGTGCACTCCCTACA
1 TCATGTGCACTCCCTACA
11499030 TGCATATATC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
34 24 0.50
35 1 0.02
36 1 0.02
37 22 0.46
ACGTcount: A:0.30, C:0.35, G:0.10, T:0.25
Consensus pattern (37 bp):
TCATGTGCACTCCCTACACGCACAAGACAATATATCA
Found at i:11499021 original size:37 final size:34
Alignment explanation
Indices: 11498941--11499033 Score: 123
Period size: 37 Copynumber: 2.6 Consensus size: 34
11498931 CTTACTCAGC
*
11498941 TCATGTGCACTCCCTACACGCACAAGACAAATCA
1 TCATGTGCACTCCCTACATGCACAAGACAAATCA
***
11498975 TCATGTGCACTCCCTACATGCACACTTCAATATATCA
1 TCATGTGCACTCCCTACATGCACAAGAC-A-A-ATCA
11499012 TCATGTGCACTCCCTACATGCA
1 TCATGTGCACTCCCTACATGCA
11499034 TATATCAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
34 24 0.46
35 1 0.02
36 1 0.02
37 26 0.50
ACGTcount: A:0.30, C:0.34, G:0.11, T:0.25
Consensus pattern (34 bp):
TCATGTGCACTCCCTACATGCACAAGACAAATCA
Found at i:11499042 original size:37 final size:38
Alignment explanation
Indices: 11498971--11499049 Score: 126
Period size: 37 Copynumber: 2.1 Consensus size: 38
11498961 CACAAGACAA
11498971 ATCATCATGTGCACTCCCTACATGCACACTTCAATAT-
1 ATCATCATGTGCACTCCCTACATGCACACTTCAATATC
*
11499008 ATCATCATGTGCACTCCCTACATGCATA-TATCAATATC
1 ATCATCATGTGCACTCCCTACATGCACACT-TCAATATC
11499046 ATCA
1 ATCA
11499050 CACGCACTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
36 1 0.03
37 34 0.87
38 4 0.10
ACGTcount: A:0.32, C:0.30, G:0.08, T:0.30
Consensus pattern (38 bp):
ATCATCATGTGCACTCCCTACATGCACACTTCAATATC
Found at i:11499057 original size:35 final size:36
Alignment explanation
Indices: 11498971--11499058 Score: 92
Period size: 37 Copynumber: 2.4 Consensus size: 36
11498961 CACAAGACAA
*
11498971 ATCATCATGTGCACTCCCTACATGCACACTTCAATAT
1 ATCATCA-GCGCACTCCCTACATGCACACTTCAATAT
* *
11499008 ATCATCATGTGCACTCCCTACATGCATA-TATCAATAT
1 ATCATCA-GCGCACTCCCTACATGCACACT-TCAATAT
11499045 CATCA-CA-CGCACTC
1 -ATCATCAGCGCACTC
11499059 TCGCCCACAT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
35 6 0.13
36 1 0.02
37 36 0.77
38 4 0.09
ACGTcount: A:0.31, C:0.33, G:0.08, T:0.28
Consensus pattern (36 bp):
ATCATCAGCGCACTCCCTACATGCACACTTCAATAT
Found at i:11500254 original size:20 final size:20
Alignment explanation
Indices: 11500194--11500254 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
11500184 TGGCAAGGTA
* *
11500194 AAAATGGC-ATGGAAGCATG
1 AAAATGGCGTTGGGAGCATG
* * **
11500213 AAAATGGCGTTAGGTGGGTG
1 AAAATGGCGTTGGGAGCATG
11500233 AAAATGGCGTTGGGAGCATG
1 AAAATGGCGTTGGGAGCATG
11500253 AA
1 AA
11500255 GGTGGAGGAG
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
19 8 0.26
20 23 0.74
ACGTcount: A:0.34, C:0.08, G:0.38, T:0.20
Consensus pattern (20 bp):
AAAATGGCGTTGGGAGCATG
Found at i:11509075 original size:2 final size:2
Alignment explanation
Indices: 11509068--11509100 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11509058 TTCAAATCTT
11509068 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 T
11509101 NCTCCACTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11509158 original size:2 final size:2
Alignment explanation
Indices: 11509151--11509175 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11509141 TAATACTTAT
11509151 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 T
11509176 CTTTGACAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11510047 original size:30 final size:30
Alignment explanation
Indices: 11510013--11510080 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 30
11510003 TCATAAAAGC
11510013 TTATTTGATT-CAAAATAAAAATATAAAAAT
1 TTATTT-ATTACAAAATAAAAATATAAAAAT
* *
11510043 TTATTTATTATAAAATAAAAATATAAGAAT
1 TTATTTATTACAAAATAAAAATATAAAAAT
11510073 TTGATTTA
1 TT-ATTTA
11510081 ATATATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 3 0.09
30 26 0.76
31 5 0.15
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.41
Consensus pattern (30 bp):
TTATTTATTACAAAATAAAAATATAAAAAT
Found at i:11510094 original size:31 final size:30
Alignment explanation
Indices: 11510024--11510085 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
11510014 TATTTGATTC
*
11510024 AAAATAAAAATATAAAAATTTATTTATTAT
1 AAAATAAAAATATAAAAATTTATTTAATAT
*
11510054 AAAATAAAAATATAAGAATTTGATTTAATAT
1 AAAATAAAAATATAAAAATTT-ATTTAATAT
11510085 A
1 A
11510086 TTTAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 20 0.69
31 9 0.31
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAATAAAAATATAAAAATTTATTTAATAT
Found at i:11511568 original size:4 final size:4
Alignment explanation
Indices: 11511559--11511612 Score: 65
Period size: 4 Copynumber: 13.5 Consensus size: 4
11511549 GCTCTGTATT
* * *
11511559 TACA TACA TACA CT-CA CACA CACA TACA TACA TACA TACA TATA TACA
1 TACA TACA TACA -TACA TACA TACA TACA TACA TACA TACA TACA TACA
11511607 TACA TA
1 TACA TA
11511613 TATATATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
4 43 0.98
5 1 0.02
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (4 bp):
TACA
Found at i:11511613 original size:12 final size:12
Alignment explanation
Indices: 11511580--11511628 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
11511570 ACTCACACAC
*
11511580 ACATACATACAT
1 ACATACATATAT
11511592 ACATACATATAT
1 ACATACATATAT
11511604 ACATACATATAT
1 ACATACATATAT
* *
11511616 ATATATATATAT
1 ACATACATATAT
11511628 A
1 A
11511629 TTAACAAGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (12 bp):
ACATACATATAT
Found at i:11517257 original size:36 final size:36
Alignment explanation
Indices: 11517217--11517310 Score: 109
Period size: 36 Copynumber: 2.5 Consensus size: 36
11517207 TTAAAATAAA
11517217 AATATTTAATATTTTAATTACAAATTATAAAAA-ATT
1 AATATTTAATATTTTAATTA-AAATTATAAAAATATT
* * *
11517253 AATATTTAAAATTTAAAATTTAAAATTTTAAAAATTATT
1 AATATTTAATATTT-TAA-TTAAAATTATAAAAA-TATT
11517292 AATATTTTAATATTTTAAT
1 AATA-TTTAATATTTTAAT
11517311 CATATAATGT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
36 13 0.27
37 13 0.27
38 4 0.08
39 9 0.19
40 9 0.19
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (36 bp):
AATATTTAATATTTTAATTAAAATTATAAAAATATT
Found at i:11517261 original size:7 final size:7
Alignment explanation
Indices: 11517246--11517285 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
11517236 ACAAATTATA
*
11517246 AAAAATT
1 AAAATTT
*
11517253 AATATTT
1 AAAATTT
11517260 AAAATTT
1 AAAATTT
11517267 AAAATTT
1 AAAATTT
11517274 AAAATTTT
1 AAAA-TTT
11517282 AAAA
1 AAAA
11517286 ATTATTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAAATTT
Found at i:11517276 original size:29 final size:30
Alignment explanation
Indices: 11517204--11517277 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 30
11517194 CCCTTATAAG
*
11517204 AATTTAAAA--TAAAAATATTTAATATTTT
1 AATTTAAAATTTAAAAATATTTAATATTTA
11517232 AA-TTACAAATTATAAAAA-A-TTAATATTTAA
1 AATTTA-AAATT-TAAAAATATTTAATATTT-A
11517262 AATTTAAAATTTAAAA
1 AATTTAAAATTTAAAA
11517278 TTTTAAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
27 3 0.08
28 5 0.13
29 14 0.36
30 8 0.21
31 9 0.23
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (30 bp):
AATTTAAAATTTAAAAATATTTAATATTTA
Found at i:11517284 original size:8 final size:8
Alignment explanation
Indices: 11517257--11517309 Score: 56
Period size: 8 Copynumber: 6.6 Consensus size: 8
11517247 AAAATTAATA
11517257 TTTAAAA-
1 TTTAAAAT
11517264 TTTAAAA-
1 TTTAAAAT
11517271 TTTAAAAT
1 TTTAAAAT
11517279 TTTAAAAAT
1 TTT-AAAAT
*
11517288 TATTAATAT
1 T-TTAAAAT
*
11517297 TTTAATAT
1 TTTAAAAT
11517305 TTTAA
1 TTTAA
11517310 TCATATAATG
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
7 14 0.33
8 15 0.36
9 11 0.26
10 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
TTTAAAAT
Found at i:11517327 original size:39 final size:39
Alignment explanation
Indices: 11517284--11517400 Score: 107
Period size: 39 Copynumber: 2.9 Consensus size: 39
11517274 AAAATTTTAA
*
11517284 AAATTATTAATATTTTAATATTTT--AATCATATAATGTTT
1 AAATTATTAA-ATTTTAATATTTTAAAATTAT-TAATGTTT
*
11517323 AAATTATAAATAAAATATTAATATTTTAAAATTATTAATGTTT
1 AAATTAT---T-AAATTTTAATATTTTAAAATTATTAATGTTT
* *
11517366 AACTTA-CAAATTATTAATATTTTAAAATT-TTAATG
1 AAATTATTAAATT-TTAATATTTTAAAATTATTAATG
11517401 AGAATATAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
38 10 0.15
39 23 0.35
42 13 0.20
43 15 0.23
44 5 0.08
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (39 bp):
AAATTATTAAATTTTAATATTTTAAAATTATTAATGTTT
Found at i:11517853 original size:30 final size:30
Alignment explanation
Indices: 11517784--11517853 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
11517774 CTTTAACATA
11517784 CTACCTTTTCTTGAGGAAGTATAACCTTTCT
1 CTACCTTTTCTTGA-GAAGTATAACCTTTCT
* * *
11517815 CAATCTTTTCTATGA-AGGTATAACCTTTCT
1 CTACCTTTTCT-TGAGAAGTATAACCTTTCT
11517845 CTACCTTTT
1 CTACCTTTT
11517854 ACAATACAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 21 0.64
31 9 0.27
32 3 0.09
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (30 bp):
CTACCTTTTCTTGAGAAGTATAACCTTTCT
Found at i:11517916 original size:47 final size:47
Alignment explanation
Indices: 11517847--11517940 Score: 109
Period size: 47 Copynumber: 2.0 Consensus size: 47
11517837 ACCTTTCTCT
*
11517847 ACCTTTTACAATACAAGAATAACCTTACACTGCCTTTTACAATGGAG
1 ACCTTTTACAATACAAGAATAACCTTACACTACCTTTTACAATGGAG
* * * * * *
11517894 ACCTTTTACAATGA-AGGTATAACTTTACATTACCTTTTGCGATGGAG
1 ACCTTTTACAAT-ACAAGAATAACCTTACACTACCTTTTACAATGGAG
11517941 GTATAACTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
47 38 0.97
48 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (47 bp):
ACCTTTTACAATACAAGAATAACCTTACACTACCTTTTACAATGGAG
Found at i:11517930 original size:31 final size:31
Alignment explanation
Indices: 11517894--11517953 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
11517884 TACAATGGAG
11517894 ACCTTTTACAATGAAGGTATAACTTTACATT
1 ACCTTTTACAATGAAGGTATAACTTTACATT
* * *
11517925 ACCTTTTGCGATGGAGGTATAACTTTACA
1 ACCTTTTACAATGAAGGTATAACTTTACA
11517954 ATAGTAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (31 bp):
ACCTTTTACAATGAAGGTATAACTTTACATT
Found at i:11520890 original size:27 final size:27
Alignment explanation
Indices: 11520839--11520890 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
11520829 TCCTGGTGGT
*
11520839 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTGACCCTGA
*
11520866 GGTGGTAAAATTACCATTTT-ACCCT
1 GGTGG-AAAATTACAATTTTGACCCT
11520891 TATACACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTGA
Found at i:11520966 original size:20 final size:20
Alignment explanation
Indices: 11520943--11520981 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
11520933 ACCTCAAACC
11520943 ATACTCCAATAAGTCAAATT
1 ATACTCCAATAAGTCAAATT
11520963 ATACTCCAATAAGTCAAAT
1 ATACTCCAATAAGTCAAAT
11520982 GGGGCCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.21, G:0.05, T:0.28
Consensus pattern (20 bp):
ATACTCCAATAAGTCAAATT
Found at i:11521940 original size:24 final size:24
Alignment explanation
Indices: 11521904--11521949 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
11521894 GTAACTATCT
* **
11521904 AACAAGGAGGAAGCCTATTGGTGA
1 AACAAGGAAGAAGAATATTGGTGA
11521928 AACAAGGAAGAAGAATATTGGT
1 AACAAGGAAGAAGAATATTGGT
11521950 TGACCAAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.09, G:0.30, T:0.17
Consensus pattern (24 bp):
AACAAGGAAGAAGAATATTGGTGA
Found at i:11523575 original size:40 final size:40
Alignment explanation
Indices: 11523529--11523732 Score: 228
Period size: 40 Copynumber: 5.0 Consensus size: 40
11523519 AAAGATCTTA
* *
11523529 AACATAAACTTAAATAGCTAAAAACAAATATCCATACAAC
1 AACATAAACTTAAATAACTAAAAACAAATATCCAAACAAC
* * * * *
11523569 GACATAAACTTAGATAACTATATACAAATATCCAAATAAC
1 AACATAAACTTAAATAACTAAAAACAAATATCCAAACAAC
* * *
11523609 AACATAAACTTAAATAACTAAACACAAAGATCCAAACAAAT
1 AACATAAACTTAAATAACTAAAAACAAATATCCAAAC-AAC
* * * *
11523650 AACATAAATTTAAATAACCAAACACATATATCCAAACAACAAC
1 AACATAAACTTAAATAACTAAAAACAAATATCC--A-AACAAC
* *
11523693 AACATAAACTTCAATAACTAAAAATAAATATCCAAACAAC
1 AACATAAACTTAAATAACTAAAAACAAATATCCAAACAAC
11523733 TAGTGTATAT
Statistics
Matches: 135, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
40 70 0.52
41 32 0.24
43 30 0.22
44 3 0.02
ACGTcount: A:0.58, C:0.20, G:0.02, T:0.20
Consensus pattern (40 bp):
AACATAAACTTAAATAACTAAAAACAAATATCCAAACAAC
Found at i:11523726 original size:84 final size:81
Alignment explanation
Indices: 11523529--11523731 Score: 237
Period size: 84 Copynumber: 2.5 Consensus size: 81
11523519 AAAGATCTTA
* * * * * * *
11523529 AACATAAACTTAAATAGCTAAAAACAAATATCCATAC-AACGACATAAACTTAGATAACTATATA
1 AACATAAACTTAAATAACTAAAAACAAATATCCAAACAAACAACATAAACTTAAATAACCAAACA
*
11523593 CAAATATCCAAATAAC
66 CAAATATCCAAACAAC
* * * *
11523609 AACATAAACTTAAATAACTAAACACAAAGATCCAAACAAATAACATAAATTTAAATAACCAAACA
1 AACATAAACTTAAATAACTAAAAACAAATATCCAAACAAACAACATAAACTTAAATAACCAAACA
*
11523674 CATATATCCAAACAACAAC
66 CAAATATCC--A-AACAAC
* *
11523693 AACATAAACTTCAATAACTAAAAATAAATATCCAAACAA
1 AACATAAACTTAAATAACTAAAAACAAATATCCAAACAA
11523732 CTAGTGTATA
Statistics
Matches: 102, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
80 33 0.32
81 28 0.27
83 1 0.01
84 40 0.39
ACGTcount: A:0.58, C:0.20, G:0.02, T:0.20
Consensus pattern (81 bp):
AACATAAACTTAAATAACTAAAAACAAATATCCAAACAAACAACATAAACTTAAATAACCAAACA
CAAATATCCAAACAAC
Found at i:11523863 original size:15 final size:17
Alignment explanation
Indices: 11523843--11523875 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
11523833 ATTACAATTA
11523843 ATAA-TTTTATAA-GTT
1 ATAATTTTTATAATGTT
11523858 ATAATTTTTATAATGTT
1 ATAATTTTTATAATGTT
11523875 A
1 A
11523876 ACACAAAATA
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:11527853 original size:42 final size:42
Alignment explanation
Indices: 11527790--11527912 Score: 158
Period size: 42 Copynumber: 2.9 Consensus size: 42
11527780 ATGATAATTA
*
11527790 TGACCCAGCCATGTGCGGTGTAGGATTGCACATGAGCTGTGC
1 TGACCCAGCCATGTGCGGTGTAGGAGTGCACATGAGCTGTGC
*
11527832 TGACCCAGCCATGTGCTGTGTAGGAGTGCACATGAGCTGTGC
1 TGACCCAGCCATGTGCGGTGTAGGAGTGCACATGAGCTGTGC
* ** * * *
11527874 TAACCTGGCTATGTGCGGTGT-GGTAATGCACATAAGCTG
1 TGACCCAGCCATGTGCGGTGTAGG-AGTGCACATGAGCTG
11527913 AGACAGAGTT
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 2 0.03
42 69 0.97
ACGTcount: A:0.20, C:0.22, G:0.33, T:0.25
Consensus pattern (42 bp):
TGACCCAGCCATGTGCGGTGTAGGAGTGCACATGAGCTGTGC
Found at i:11534447 original size:46 final size:46
Alignment explanation
Indices: 11534380--11534470 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
11534370 TTCAACAGAG
*
11534380 AGTGCAATTTATGGGTAATAGATAGCAGAATAACCCCTACTCCAAT
1 AGTGCAATTTATGGGTAATAGATAGCAGAATAACCCCCACTCCAAT
11534426 AGTGCAATTTATGGGTAATAGATAGCAGAATAACCCCCACTCCAA
1 AGTGCAATTTATGGGTAATAGATAGCAGAATAACCCCCACTCCAA
11534471 CACTAACAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (46 bp):
AGTGCAATTTATGGGTAATAGATAGCAGAATAACCCCCACTCCAAT
Found at i:11547728 original size:17 final size:17
Alignment explanation
Indices: 11547708--11547744 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
11547698 TTTTATTAAG
* *
11547708 GCACATATTTAGGGGGA
1 GCACATATTCAGGAGGA
11547725 GCACATATTCAGGAGGA
1 GCACATATTCAGGAGGA
11547742 GCA
1 GCA
11547745 ATCCCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.19
Consensus pattern (17 bp):
GCACATATTCAGGAGGA
Found at i:11550154 original size:18 final size:18
Alignment explanation
Indices: 11550131--11550165 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11550121 TAGGTAGGCT
*
11550131 AAGCAGCCTAAGCAAGCC
1 AAGCAGCCCAAGCAAGCC
11550149 AAGCAGCCCAAGCAAGC
1 AAGCAGCCCAAGCAAGC
11550166 TAGGCAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.34, G:0.23, T:0.03
Consensus pattern (18 bp):
AAGCAGCCCAAGCAAGCC
Found at i:11550278 original size:21 final size:20
Alignment explanation
Indices: 11550231--11550278 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
11550221 TGAACTTTTG
* *
11550231 GATTTGATTATATACATTTA
1 GATTAGATTATATACATTAA
*
11550251 GATTTAGATTATATTAGATTAA
1 GA-TTAGATTATA-TACATTAA
11550273 GATTAG
1 GATTAG
11550279 GATTTGGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 13 0.57
22 8 0.35
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.46
Consensus pattern (20 bp):
GATTAGATTATATACATTAA
Found at i:11550800 original size:22 final size:22
Alignment explanation
Indices: 11550770--11550814 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
11550760 ACAATATTTT
* *
11550770 AATTATATTTTTGAAATTTAAA
1 AATTATATTGTTGAAATATAAA
* *
11550792 AATTTTATTGTTGATATATAAA
1 AATTATATTGTTGAAATATAAA
11550814 A
1 A
11550815 TAATATTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (22 bp):
AATTATATTGTTGAAATATAAA
Found at i:11552557 original size:13 final size:13
Alignment explanation
Indices: 11552539--11552564 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11552529 GCCACATCAA
11552539 CATCATATCACAT
1 CATCATATCACAT
11552552 CATCATATCACAT
1 CATCATATCACAT
11552565 TATTATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (13 bp):
CATCATATCACAT
Found at i:11552672 original size:30 final size:30
Alignment explanation
Indices: 11552653--11552761 Score: 98
Period size: 30 Copynumber: 3.7 Consensus size: 30
11552643 AATCATTAAT
11552653 TATAAAAATTTATTTAAATTAAAACAAAAG
1 TATAAAAATTTATTTAAATTAAAACAAAAG
* * * *
11552683 TATAAAAATTTATTTGAATCAAAATAAAAA
1 TATAAAAATTTATTTAAATTAAAACAAAAG
* * * *
11552713 TATAAGAATTTGA-TTGAATATAATACAATA-
1 TATAAAAATTT-ATTTAAAT-TAAAACAAAAG
*
11552743 -ATAAAATTTTATTTAAATT
1 TATAAAAATTTATTTAAATT
11552762 TTTTTTAAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
28 2 0.03
29 13 0.20
30 42 0.66
31 7 0.11
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (30 bp):
TATAAAAATTTATTTAAATTAAAACAAAAG
Found at i:11554156 original size:2 final size:2
Alignment explanation
Indices: 11554151--11554188 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11554141 ACACACACAC
11554151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11554189 TAACAAGGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11561730 original size:14 final size:12
Alignment explanation
Indices: 11561703--11561728 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11561693 CCTCTTGTGA
11561703 TTAAATATATTT
1 TTAAATATATTT
11561715 TTAAATATATTT
1 TTAAATATATTT
11561727 TT
1 TT
11561729 TTCTACTTGG
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTAAATATATTT
Found at i:11567306 original size:2 final size:2
Alignment explanation
Indices: 11567299--11567328 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11567289 CATACACAAC
11567299 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
11567329 NNNNNNNNNN
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:11571971 original size:15 final size:15
Alignment explanation
Indices: 11571921--11571971 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
11571911 TTCTTAAAAC
*
11571921 AACTTTAAAACTAAA
1 AACTTTAAAACCAAA
11571936 AACTTTAAAATCC-AA
1 AACTTTAAAA-CCAAA
*
11571951 AGCTTTAAAACCAAA
1 AACTTTAAAACCAAA
*
11571966 ATCTTT
1 AACTTT
11571972 GATCTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 2 0.06
15 28 0.90
16 1 0.03
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.29
Consensus pattern (15 bp):
AACTTTAAAACCAAA
Found at i:11577849 original size:17 final size:17
Alignment explanation
Indices: 11577827--11577862 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
11577817 AAATATGAAT
11577827 TTATAAAATAAATGGAA
1 TTATAAAATAAATGGAA
*
11577844 TTATAAAATAAATTGAA
1 TTATAAAATAAATGGAA
11577861 TT
1 TT
11577863 TTTTATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (17 bp):
TTATAAAATAAATGGAA
Found at i:11579906 original size:28 final size:27
Alignment explanation
Indices: 11579867--11579920 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
11579857 GTGTCCTGGT
**
11579867 GGTGGAAAATTACTGTTTTGCCCCTAA
1 GGTGGAAAATTACCATTTTGCCCCTAA
11579894 GGTGGCAAAATTACCATTTTGCCCCTA
1 GGTGG-AAAATTACCATTTTGCCCCTA
11579921 TGCTCTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (27 bp):
GGTGGAAAATTACCATTTTGCCCCTAA
Found at i:11597811 original size:21 final size:22
Alignment explanation
Indices: 11597786--11597826 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
11597776 CCTAGGTGGA
11597786 AAAATTCAAGGAAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
11597807 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
11597827 AAAAAATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.54, C:0.07, G:0.22, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:11597832 original size:22 final size:21
Alignment explanation
Indices: 11597785--11597833 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
11597775 CCCTAGGTGG
*
11597785 AAAAATTCAAGGAAAAAGTGT
1 AAAAATTCAAGGAAAAAGTGA
*
11597806 GAAAATTCAAGGAAACAAGTGA
1 AAAAATTCAAGGAAA-AAGTGA
11597828 AAAAAT
1 AAAAAT
11597834 GTAAGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.59, C:0.06, G:0.18, T:0.16
Consensus pattern (21 bp):
AAAAATTCAAGGAAAAAGTGA
Found at i:11607561 original size:22 final size:22
Alignment explanation
Indices: 11607536--11607586 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
11607526 ATAATTTTAA
* *
11607536 TTAATT-TAATAATTTTATATAT
1 TTAATTATAATAAATTAATA-AT
*
11607558 TTAATTATATTAAATTAATAAT
1 TTAATTATAATAAATTAATAAT
11607580 TTAATTA
1 TTAATTA
11607587 CCAATAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTAATTATAATAAATTAATAAT
Found at i:11607579 original size:17 final size:17
Alignment explanation
Indices: 11607520--11607586 Score: 68
Period size: 18 Copynumber: 4.1 Consensus size: 17
11607510 TGGGCTAAAA
11607520 AAATTAATAATTTTAATT
1 AAATTAATAATTTT-ATT
*
11607538 AATTTAATAATTTTA-T
1 AAATTAATAATTTTATT
* *
11607554 ATATT--TAATTATATT
1 AAATTAATAATTTTATT
*
11607569 AAATTAATAATTTAATT
1 AAATTAATAATTTTATT
11607586 A
1 A
11607587 CCAATAATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
14 7 0.18
15 5 0.13
16 4 0.10
17 10 0.26
18 13 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AAATTAATAATTTTATT
Found at i:11613707 original size:20 final size:20
Alignment explanation
Indices: 11613684--11613721 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11613674 AAATCTAAAC
*
11613684 TTAAAAAATTATTATTTTTA
1 TTAAAAAATTAATATTTTTA
11613704 TTAAAAAATTAATATTTT
1 TTAAAAAATTAATATTTT
11613722 GACTATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAAAAAATTAATATTTTTA
Found at i:11613766 original size:19 final size:20
Alignment explanation
Indices: 11613726--11613778 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
11613716 TATTTTGACT
11613726 ATAATAATATTAAATTATAA
1 ATAATAATATTAAATTATAA
*
11613746 ATAA-AATA-TAAATTTTAAA
1 ATAATAATATTAAATTAT-AA
* *
11613765 ATATTAATTTTAAA
1 ATAATAATATTAAA
11613779 ATTTTTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 7 0.26
19 9 0.33
20 7 0.26
21 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAATAATATTAAATTATAA
Found at i:11613779 original size:14 final size:14
Alignment explanation
Indices: 11613747--11613780 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
11613737 AAATTATAAA
11613747 TAAAATATAAATTT
1 TAAAATATAAATTT
*
11613761 TAAAATATTAATTT
1 TAAAATATAAATTT
11613775 TAAAAT
1 TAAAAT
11613781 TTTTAAGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAAATATAAATTT
Done.