Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1092
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: 788722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:221767 original size:21 final size:22
Alignment explanation
Indices: 221738--221790 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
221728 TAGCTAGATT
*
221738 TTTCCTTTTTCCTT-TTTTCTA
1 TTTCTTTTTTCCTTATTTTCTA
* *
221759 TTTCTTTTTTCTTTATTTTCTC
1 TTTCTTTTTTCCTTATTTTCTA
*
221781 TCTCTTTTTT
1 TTTCTTTTTT
221791 TTTTACTTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTCTTTTTTCCTTATTTTCTA
Found at i:223716 original size:14 final size:14
Alignment explanation
Indices: 223697--223724 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
223687 AAACATGAAA
223697 ATGAATATAATATT
1 ATGAATATAATATT
223711 ATGAATATAATATT
1 ATGAATATAATATT
223725 GTTGACCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
ATGAATATAATATT
Found at i:227038 original size:4 final size:4
Alignment explanation
Indices: 227029--227053 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
227019 AATGATGCTT
227029 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
227054 ATACTTCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:232067 original size:98 final size:99
Alignment explanation
Indices: 231942--232144 Score: 309
Period size: 98 Copynumber: 2.1 Consensus size: 99
231932 GGTGACAAAT
*
231942 AATTTTGATAAAGGAAGAGTTCAAATCTTGACAAATTTCGAAGAACGGGGTTGGAGTATCCCTTC
1 AATTTTGATAAAGGAAGAATTCAAATCTTGACAAATTTCGAAGAACGGGGTTGGAGTATCCCTTC
* * * *
232007 AAAAGGTCGAGGTTGGAGTATCTTCATGAA-CAA
66 AAAAGGTAGAGGTTAGAGTATCCTCATGAATAAA
* *
232040 AATTTTGATAAAGGAAGAATTCAAATCTTGACAAATTTCGAAGAGCGGGGTTGGAGTATCCCTTT
1 AATTTTGATAAAGGAAGAATTCAAATCTTGACAAATTTCGAAGAACGGGGTTGGAGTATCCCTTC
* * *
232105 GAAAGGTAGGGGTTAGAGTATCCTCGTGAATAAA
66 AAAAGGTAGAGGTTAGAGTATCCTCATGAATAAA
232139 AATTTT
1 AATTTT
232145 AATTTTTTAA
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
98 86 0.91
99 8 0.09
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (99 bp):
AATTTTGATAAAGGAAGAATTCAAATCTTGACAAATTTCGAAGAACGGGGTTGGAGTATCCCTTC
AAAAGGTAGAGGTTAGAGTATCCTCATGAATAAA
Found at i:234170 original size:20 final size:20
Alignment explanation
Indices: 234141--234193 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
234131 ACTGTCAAGA
234141 AAATGTATCGATATATTATT
1 AAATGTATCGATATATTATT
*
234161 AAATGCATCGATATATTATT
1 AAATGTATCGATATATTATT
234181 AAATGTATCGATA
1 AAATGTATCGATA
234194 CATGCTTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (20 bp):
AAATGTATCGATATATTATT
Found at i:234212 original size:22 final size:22
Alignment explanation
Indices: 234184--234240 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
234174 TATTATTAAA
234184 TGTATCGATACATGCTTAC-AAT
1 TGTATCGATACATGCTT-CTAAT
*
234206 TGTATCGATACAT--TTCTTAT
1 TGTATCGATACATGCTTCTAAT
234226 TGTATCGATACATGC
1 TGTATCGATACATGC
234241 AAGCAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 1 0.03
20 17 0.55
22 13 0.42
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (22 bp):
TGTATCGATACATGCTTCTAAT
Found at i:235154 original size:560 final size:563
Alignment explanation
Indices: 234206--235777 Score: 1989
Period size: 560 Copynumber: 2.7 Consensus size: 563
234196 TGCTTACAAT
*
234206 TGTATCGATACATT-TCTTATTGTATCGATACATGCAAGCAAATTTTGACATTTCGTGACTTTTT
1 TGTATCGATACATTAT-TTAATGTATCGATACATGCAAGCAAATTTTGACATTTCGTGACTTTTT
* *
234270 TTTCCTTTGCCAAATGAGTTTTTTGCATCATAATACCTCATTTTGTCCGGACTAATTTTTGACAA
65 TTTCCTTTGCCAAATGAGTTTTTTGCATCATAACACCTCATTTTGTCCGG-CCAATTTTTGACAA
* * *
234335 CTTGAGGCCTACCTAGTAGGTGGAGGATTAGAGATGTATGGGGAC-AAAGATCACCGGGCAAAAT
129 CTTGAGGCCTACCTAGTAGGTGAAGGATTGGAGATGTATGGGGACGAAATATCA-C---C--AA-
* * *
234399 GACGCTCGACGAAAAAGTACATTTAGGTTATCGAGACTTTTTGTCGAGCATGAAACCATTTCCCA
187 -ACGC-CTAC------GTACTTTTAGGTTATCGAGACTTTTTGTCGAGCACGAAACCATTTCCCA
*
234464 TCATCACTTATTGTGATAAAGTGTTCGGGAGGCAAAAAAGATGAAAAAGTCACATTTTTATTCAA
244 TCATCACTTATTGTGATAAAGTGTTCGGGAGGCAAAAAAGATGAAAAAGTCACATTTTTGTTCAA
** ** *
234529 ATGTATCGATACATTTCTAGAATGTATCGATACAACATCCCAACAATCAAACATTTTGAATTTCT
309 ATGTATCGATACATTTCTAGAATGTATCGATACAAGGTCCCAACGGTAAAACATTTTGAATTTCT
* *
234594 ACAATTTGTATCAATACAAATACTAAATGTATCGATACATAAGTTTTGTATTGATACAATGTATC
374 ACAATTTGTATCGATACAAATACTAAATGTATCGATACATAAGTTTTGTATCGATACAATGTATC
** * * *
234659 GATACAAAATTACGTTGCATACTACT-AAGAAAATGTATCGATATATTATTAAATGGATC-ACCT
439 GATACAAAATTACCCTACATACT-CTCAAGAAAATGTATCGATATATAATTAAATGGATCAACAT
* *
234722 GCTTACAATTGTATCAATAAATTTCTCATTGTATTGATAAATTCTGGGTTTTTAACCTAGA
503 GCTTACAATTGTATCAATAAATTTCTCATTGTATCGATAAATTCTGGGTTTTTAACCAAGA
* *
234783 TGTAACGATACATTATTTAATGTATCAATACATGCAAGCAAATTTTGACATTTCGTGACTTTTTT
1 TGTATCGATACATTATTTAATGTATCGATACATGCAAGCAAATTTTGACATTTCGTGACTTTTTT
* *
234848 TTCCTTTACTAAATGAGTTTTTTGCATCATAACACCTCATTTTGTCCGAGCCAATTTTTGACAAC
66 TTCCTTTGCCAAATGAGTTTTTTGCATCATAACACCTCATTTTGTCCG-GCCAATTTTTGACAAC
* * * *
234913 TAGAGGTCTACCTAGTAGGTGAAGGATTGGAGATGTATAGGGACGAAA-ATCACC-AA-GCAT-C
130 TTGAGGCCTACCTAGTAGGTGAAGGATTGGAGATGTATGGGGACGAAATATCACCAAACGCCTAC
* * *
234974 GTTACTTTTAGGTTATCGAGACTTTTCGTCCAGCACGAAACCATTTCCCATCATCCCTTATTGTG
195 G-TACTTTTAGGTTATCGAGACTTTTTGTCGAGCACGAAACCATTTCCCATCATCACTTATTGTG
* * *
235039 ATAAAGTGTTTGGGAGGCAAAAAAGATGAACAAGTCACATTTTTGTTCAAATGTATCGATA-AAT
259 ATAAAGTGTTCGGGAGGCAAAAAAGATGAAAAAGTCACATTTTTGTTCAAATGTATCGATACATT
* * *
235103 TCTAAAAATGTATCGATACAAGGTCCCAACGGTTAAACATTTTGAATTTCTATAATTT-TCATCG
324 TCT-AGAATGTATCGATACAAGGTCCCAACGGTAAAACATTTTGAATTTCTACAATTTGT-ATCG
* * *
235167 ATACAAACAGTAAATGTATCGATACATAAGTTTTGTATCGATACAATGTATCGATATAAAATTAC
387 ATACAAATACTAAATGTATCGATACATAAGTTTTGTATCGATACAATGTATCGATACAAAATTAC
* * * *
235232 CCTACATACTGTCAAGGAAATGTATTGATATATAATTAAATGTATCGATACATGCTTACAATTGT
452 CCTACATACTCTCAAGAAAATGTATCGATATATAATTAAATGGATC-A-ACATGCTTACAATTGT
* * * * *
235297 ATCAATATATTTCTCATTGTGTCGATATATTTTGGGTTTTTGACCAAGA
515 ATCAATAAATTTCTCATTGTATCGATAAATTCTGGGTTTTTAACCAAGA
* * *
235346 TGTATTGATACATTATTCAATGTATCGATACATGCAAGCAAATTTTGACATTTCATGACTTATTT
1 TGTATCGATACATTATTTAATGTATCGATACATGCAAGCAAATTTTGACATTTCGTGAC-T-TTT
* * * *
235411 TTTTCCTTTGCCAAATGAGTTTTTTGTATCATAACACCTCATTTTGTTCGGGTCAATTTTCGACA
64 TTTTCCTTTGCCAAATGAGTTTTTTGCATCATAACACCTCATTTTG-TCCGGCCAATTTTTGACA
* * * * *
235476 ACTTGAGGCCTACTTGGTAGGTGAAAGATTGGAGATGTATGGGGATGAAGATTGTTGAGCACCAA
128 ACTTGAGGCCTACCTAGTAGGTGAAGGATTGGAGATGTATGGGGACGAA-A----T-ATCACCAA
235541 CGACGCCTGACAAAAAAGTACTTTTAGGTTATC-AGGACTTTTTGTCGAGCACTGAAACCATTTC
187 --ACGCCT-AC------GTACTTTTAGGTTATCGA-GACTTTTTGTCGAGCAC-GAAACCATTTC
* * * *
235605 CCATCATCTCTTATTGTGATAAAGTGTTCAGGAGGTAAAAAAGATAAAAAAGTCACATTTTTGGT
241 CCATCATCACTTATTGTGATAAAGTGTTCGGGAGGCAAAAAAGATGAAAAAGTCACATTTTT-GT
* **
235670 TCAAATGTATCGATACATTTCTAGAATGTATTGATACAAGGTCCCAACGGTAAAACATTTCAAAT
305 TCAAATGTATCGATACATTTCTAGAATGTATCGATACAAGGTCCCAACGGTAAAACATTTTGAAT
*
235735 TTCTACAATTTGTATTGATACAAATAGC-AAATGTATCGATACA
370 TTCTACAATTTGTATCGATACAAATA-CTAAATGTATCGATACA
235778 AAATTACCCT
Statistics
Matches: 868, Mismatches: 89, Indels: 68
0.85 0.09 0.07
Matches are distributed among these distances:
559 8 0.01
560 263 0.30
563 111 0.13
564 1 0.00
565 101 0.12
566 4 0.00
567 2 0.00
568 1 0.00
570 1 0.00
572 5 0.01
573 2 0.00
575 1 0.00
576 4 0.00
577 162 0.19
578 6 0.01
582 1 0.00
583 30 0.03
584 68 0.08
585 91 0.10
586 6 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (563 bp):
TGTATCGATACATTATTTAATGTATCGATACATGCAAGCAAATTTTGACATTTCGTGACTTTTTT
TTCCTTTGCCAAATGAGTTTTTTGCATCATAACACCTCATTTTGTCCGGCCAATTTTTGACAACT
TGAGGCCTACCTAGTAGGTGAAGGATTGGAGATGTATGGGGACGAAATATCACCAAACGCCTACG
TACTTTTAGGTTATCGAGACTTTTTGTCGAGCACGAAACCATTTCCCATCATCACTTATTGTGAT
AAAGTGTTCGGGAGGCAAAAAAGATGAAAAAGTCACATTTTTGTTCAAATGTATCGATACATTTC
TAGAATGTATCGATACAAGGTCCCAACGGTAAAACATTTTGAATTTCTACAATTTGTATCGATAC
AAATACTAAATGTATCGATACATAAGTTTTGTATCGATACAATGTATCGATACAAAATTACCCTA
CATACTCTCAAGAAAATGTATCGATATATAATTAAATGGATCAACATGCTTACAATTGTATCAAT
AAATTTCTCATTGTATCGATAAATTCTGGGTTTTTAACCAAGA
Found at i:235827 original size:20 final size:20
Alignment explanation
Indices: 235802--235860 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
235792 ATTGTCAAGG
235802 AAATGTATCGATACATTATT
1 AAATGTATCGATACATTATT
* **
235822 AAATGTATCGAAACATGCTT
1 AAATGTATCGATACATTATT
*
235842 ACAATTGTATCTATACATT
1 A-AA-TGTATCGATACATT
235861 TCTCATTGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 18 0.58
21 2 0.06
22 11 0.35
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (20 bp):
AAATGTATCGATACATTATT
Found at i:240929 original size:21 final size:19
Alignment explanation
Indices: 240903--240958 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 19
240893 GTGCATTTGA
240903 ATGAAATGATGCATTAGTTAG
1 ATGAAA-GATGCATT-GTTAG
240924 ATGAAAGAATGCACTTGTTAG
1 ATGAAAG-ATGCA-TTGTTAG
240945 ATGTAAAGATGCAT
1 ATG-AAAGATGCAT
240959 ATTTATAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
20 2 0.06
21 24 0.75
22 6 0.19
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.30
Consensus pattern (19 bp):
ATGAAAGATGCATTGTTAG
Found at i:243017 original size:27 final size:27
Alignment explanation
Indices: 242979--243035 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
242969 TGATTGAAAA
*
242979 CCCTCGGAGGAATGGGGTTGGAGTGTC
1 CCCTCGGAGGAATGAGGTTGGAGTGTC
243006 CCCTCGGAGGAATGAGGTTGGAGTGTC
1 CCCTCGGAGGAATGAGGTTGGAGTGTC
243033 CCC
1 CCC
243036 GATGAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.16, C:0.23, G:0.40, T:0.21
Consensus pattern (27 bp):
CCCTCGGAGGAATGAGGTTGGAGTGTC
Found at i:244364 original size:20 final size:19
Alignment explanation
Indices: 244321--244364 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
244311 AAATATCATC
* *
244321 AATATTAATATAATAATTT
1 AATATTAATATAAAAATTA
*
244340 TATATTAACTATAAAAATTA
1 AATATTAA-TATAAAAATTA
244360 AATAT
1 AATAT
244365 GTAAAAATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AATATTAATATAAAAATTA
Found at i:247178 original size:56 final size:56
Alignment explanation
Indices: 247108--247240 Score: 176
Period size: 56 Copynumber: 2.4 Consensus size: 56
247098 TAAAGTAGAT
* *
247108 AGGTTATCTTAACAAGATAATGTCTGAAGTAGACATGTGTTAAGACAATATGCATA
1 AGGTTATCTTAACAAGACAATGTCTAAAGTAGACATGTGTTAAGACAATATGCATA
* * * *
247164 AGGTTATCTTAACAAGACAATGTCTAAAGTAGACATGTTTTTAGACAATACGGATA
1 AGGTTATCTTAACAAGACAATGTCTAAAGTAGACATGTGTTAAGACAATATGCATA
* * * *
247220 AGTTTGTCATATCAAGACAAT
1 AGGTTATCTTAACAAGACAAT
247241 ATGGATAAAG
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 67 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (56 bp):
AGGTTATCTTAACAAGACAATGTCTAAAGTAGACATGTGTTAAGACAATATGCATA
Found at i:247257 original size:28 final size:28
Alignment explanation
Indices: 247206--247270 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
247196 ACATGTTTTT
* * *
247206 AGACAATACGGATAAGTTTGTCATATCA
1 AGACAATATGGATAAGTTTATCATAACA
*
247234 AGACAATATGGATAAAG-TTATCATAAGA
1 AGACAATATGGAT-AAGTTTATCATAACA
247262 AGACAATAT
1 AGACAATAT
247271 CTAAAATAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 29 0.91
29 3 0.09
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (28 bp):
AGACAATATGGATAAGTTTATCATAACA
Found at i:247303 original size:84 final size:84
Alignment explanation
Indices: 247149--247320 Score: 218
Period size: 84 Copynumber: 2.0 Consensus size: 84
247139 GACATGTGTT
* * * * * *
247149 AAGACAATATGCATAAGGTTATCTTAACAAGACAATGTCTAAAGTAGACATGTTTTTAGACAATA
1 AAGACAATATGCATAAAGTTATCATAACAAGACAATATCTAAAATAGACATGTGTTAAGACAATA
* *
247214 CGGATAAGTTTGTCATATC
66 CGGATAAGCTTATCATATC
* * * *
247233 AAGACAATATGGATAAAGTTATCATAAGAAGACAATATCTAAAATAGACATGTGTTAAGATAGTA
1 AAGACAATATGCATAAAGTTATCATAACAAGACAATATCTAAAATAGACATGTGTTAAGACAATA
* *
247298 TGGATAAGCTTATCTTATC
66 CGGATAAGCTTATCATATC
247317 AAGA
1 AAGA
247321 TAATGTCTAA
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
84 74 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (84 bp):
AAGACAATATGCATAAAGTTATCATAACAAGACAATATCTAAAATAGACATGTGTTAAGACAATA
CGGATAAGCTTATCATATC
Found at i:248473 original size:156 final size:156
Alignment explanation
Indices: 248286--248628 Score: 378
Period size: 156 Copynumber: 2.2 Consensus size: 156
248276 TCTTTAAACA
* ** * *
248286 CACACCTTTGG-CATAACAGCAACCCCATGACTATCTAGGACTTAGTTTCAGAAAAAATCACC-A
1 CACACC-TTGGACATAAAAGCAACCCGGTGACTATCAAGGACTTAATTTCAGAAAAAATCACCAA
*
248349 AAACGCCTTTAAGG-TATACCTTCT-ATC-TAAAAGTATCCCGGTAACCTTAAAAGACACAAAAA
65 AAAAGCC-TT-AGGATATACCTT-TGA-CATAAAAGTATCCCGGTAACCTTAAAAGACACAAAAA
*
248411 AGATAAGA-AAATGATGAACCTATCCTAAATG
126 AGATAA-ATAAAGGATGAACCTATCCTAAATG
* * *
248442 CACACCTTGGACATAAAAGCAACCCGGTGACTATCAAGGACTTAATTTTAGGAAAAATTACCAAA
1 CACACCTTGGACATAAAAGCAACCCGGTGACTATCAAGGACTTAATTTCAGAAAAAATCACCAAA
* * * ** * * * *
248507 AAATCCTTGGGATATACCTTTGACATGAAAGTATCTTGGTAACTTTGAAGGACACAAAAACGATA
66 AAAGCCTTAGGATATACCTTTGACATAAAAGTATCCCGGTAACCTTAAAAGACACAAAAAAGATA
248572 AATAAAGGATGAACCTATCCTAAATG
131 AATAAAGGATGAACCTATCCTAAATG
* * *
248598 --CACTTTTGACATAAAAGCAACTCGGTGACTA
1 CACACCTTGGACATAAAAGCAACCCGGTGACTA
248629 CTTTTGATAT
Statistics
Matches: 159, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
154 28 0.18
155 9 0.06
156 116 0.73
157 6 0.04
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.24
Consensus pattern (156 bp):
CACACCTTGGACATAAAAGCAACCCGGTGACTATCAAGGACTTAATTTCAGAAAAAATCACCAAA
AAAGCCTTAGGATATACCTTTGACATAAAAGTATCCCGGTAACCTTAAAAGACACAAAAAAGATA
AATAAAGGATGAACCTATCCTAAATG
Found at i:248854 original size:19 final size:19
Alignment explanation
Indices: 248832--248877 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
248822 TGAACCTATT
248832 GTAAAAGCACACCTTTGGC
1 GTAAAAGCACACCTTTGGC
248851 GTAAAAGCACACCTTTGGC
1 GTAAAAGCACACCTTTGGC
*
248870 ATAAAAGC
1 GTAAAAGC
248878 TACTCGAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (19 bp):
GTAAAAGCACACCTTTGGC
Found at i:249447 original size:20 final size:20
Alignment explanation
Indices: 249407--249460 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
249397 TTCTACAATT
249407 TGTATCGATACAATAAGTGAA
1 TGTATCGATAC-ATAAGTGAA
*
249428 TGTATCGATACATAATTGAA
1 TGTATCGATACATAAGTGAA
* *
249448 TATATCGACACAT
1 TGTATCGATACAT
249461 GTCTAAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:251380 original size:12 final size:13
Alignment explanation
Indices: 251344--251381 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
251334 ATACATTGTT
251344 CATTGTATCGATA
1 CATTGTATCGATA
*
251357 CATTGCATCGATA
1 CATTGTATCGATA
251370 CATT-TATCGATA
1 CATTGTATCGATA
251382 TGATCGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:253891 original size:50 final size:51
Alignment explanation
Indices: 253816--253934 Score: 186
Period size: 50 Copynumber: 2.4 Consensus size: 51
253806 TTATTTCCGA
* * * *
253816 GGGGATACTCTAACCTCGGTTTTATTTCTAAAACATC-AATTTTCATAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAAATTTTCAAAATC
253866 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAAATTTTCAAAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAAATTTTCAAAATC
*
253917 AGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
253935 TTATTTCTGA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
50 34 0.54
51 29 0.46
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.30
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAAATTTTCAAAATC
Found at i:253956 original size:28 final size:28
Alignment explanation
Indices: 253918--253989 Score: 135
Period size: 28 Copynumber: 2.6 Consensus size: 28
253908 TTCAAAATCA
253918 GGGATACTCCAACCCCGTTATTTCTGAG
1 GGGATACTCCAACCCCGTTATTTCTGAG
253946 GGGATACTCCAACCCCGTTATTTCTGAG
1 GGGATACTCCAACCCCGTTATTTCTGAG
*
253974 GGAATACTCCAACCCC
1 GGGATACTCCAACCCC
253990 AATTTTATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTCTGAG
Found at i:254048 original size:51 final size:51
Alignment explanation
Indices: 253993--254089 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
253983 CAACCCCAAT
*
253993 TTTATTTCCAAAATGC-T-GATTTCTCACAATCGGGGATACTCCAACCTCGGC
1 TTTATTT-CAAAA-GCATCGATTTCTCACAATCGAGGATACTCCAACCTCGGC
* * *
254044 TTTATTTCTAAAGCATCGATTTTTCACAATCGAGGATACTCTAACC
1 TTTATTTCAAAAGCATCGATTTCTCACAATCGAGGATACTCCAACC
254090 CCATTATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
49 2 0.05
50 5 0.12
51 33 0.82
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (51 bp):
TTTATTTCAAAAGCATCGATTTCTCACAATCGAGGATACTCCAACCTCGGC
Found at i:254097 original size:158 final size:157
Alignment explanation
Indices: 253788--254118 Score: 416
Period size: 158 Copynumber: 2.1 Consensus size: 157
253778 TTTTACAATC
* * * * ** *
253788 GGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCTAACCTCGGTTTTATTTCTAAAACATC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGAATACTCCAACCCCAATTTTATTTCCAAAACATC
* *
253853 AATTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAAATTTTCAAAATCA
66 AATTTTCACAATCGGGGATACTCCAACCCCGGCTTTATTTCCAAAACATCAAATTTTCAAAATCA
*
253918 GGGATACTCCAACCCCGTTATTTCTGA
131 GGGATACTCCAACCCCATTATTTCTGA
*
253945 GGGGATACTCCAACCCCGTTATTTCTGAGGGAATACTCCAACCCCAATTTTATTTCC-AAA-ATG
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGAATACTCCAACCCCAATTTTATTTCCAAAACAT-
* * * * * * *
254008 CTGATTTCTCACAATCGGGGATACTCCAACCTCGGCTTTATTTCTAAAGCATCGATTTTTCACAA
65 C-AATTT-TCACAATCGGGGATACTCCAACCCCGGCTTTATTTCCAAAACATCAAATTTTCAAAA
* *
254073 TC-GAGGATACTCTAACCCCATTATTTTTGA
128 TCAG-GGATACTCCAACCCCATTATTTCTGA
*
254103 GGAGATACTCCAACCC
1 GGGGATACTCCAACCC
254119 TAATTTTATT
Statistics
Matches: 149, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
155 2 0.01
156 4 0.03
157 54 0.36
158 89 0.60
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (157 bp):
GGGGATACTCCAACCCCGTTATTTCCGAGGGAATACTCCAACCCCAATTTTATTTCCAAAACATC
AATTTTCACAATCGGGGATACTCCAACCCCGGCTTTATTTCCAAAACATCAAATTTTCAAAATCA
GGGATACTCCAACCCCATTATTTCTGA
Found at i:260130 original size:13 final size:13
Alignment explanation
Indices: 260112--260136 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
260102 ACCAAGATCA
260112 TGTATCGATACAC
1 TGTATCGATACAC
260125 TGTATCGATACA
1 TGTATCGATACA
260137 AAGCAATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:260959 original size:35 final size:38
Alignment explanation
Indices: 260883--260959 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 38
260873 GCAAAATATC
* *
260883 TCTCCCCCTTTTACAAAATCTTATTTTATAAAACAATT
1 TCTCCCCCTTTTACAAAATCTTATTTTATAAAAAAAAT
260921 TCTCCCCCTTTT-C-AAAT-TTATTTTCA-AAAAAAAAT
1 TCTCCCCCTTTTACAAAATCTTATTTT-ATAAAAAAAAT
260956 TCTC
1 TCTC
260960 TCTCTTTTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
35 18 0.50
36 5 0.14
37 1 0.03
38 12 0.33
ACGTcount: A:0.34, C:0.25, G:0.00, T:0.42
Consensus pattern (38 bp):
TCTCCCCCTTTTACAAAATCTTATTTTATAAAAAAAAT
Found at i:261139 original size:16 final size:16
Alignment explanation
Indices: 261118--261153 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
261108 TTCATTAAGG
*
261118 AAAGTTAAGTACAAGC
1 AAAGTTAAGAACAAGC
*
261134 AAAGTTAAGAACATGC
1 AAAGTTAAGAACAAGC
261150 AAAG
1 AAAG
261154 AAATAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.11, G:0.19, T:0.17
Consensus pattern (16 bp):
AAAGTTAAGAACAAGC
Found at i:262255 original size:13 final size:13
Alignment explanation
Indices: 262237--262262 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
262227 CAATTTTTTG
262237 TGTATCGATACAT
1 TGTATCGATACAT
262250 TGTATCGATACAT
1 TGTATCGATACAT
262263 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:263727 original size:31 final size:29
Alignment explanation
Indices: 263682--263758 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 29
263672 TAACTGTTTT
263682 TGATGAAGATTTTGATGAAA-AATGAAAAGAAA
1 TGATGAA-A-TTTGATGAAATAA--AAAAGAAA
263714 TGATGTAAATTTGATGAAATTCAAAAAAGAAA
1 TGATG-AAATTTGATGAAA-T-AAAAAAGAAA
263746 TGATGAAATTTGA
1 TGATGAAATTTGA
263759 GATTGAATAC
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
31 18 0.44
32 19 0.46
33 2 0.05
34 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.19, T:0.29
Consensus pattern (29 bp):
TGATGAAATTTGATGAAATAAAAAAGAAA
Found at i:267828 original size:22 final size:21
Alignment explanation
Indices: 267776--267837 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
267766 ACCAACTTGC
* * *
267776 AATTCAATTATCTTCTTTTCT
1 AATTCACTTATTTTCTTTTTT
267797 AATTCACTTATTTTCTTTTTT
1 AATTCACTTATTTTCTTTTTT
*
267818 AATTCTTCTTA-TTTCTTTTT
1 AATTC-ACTTATTTTCTTTTT
267838 AAGCACATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 32 0.89
22 4 0.11
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCACTTATTTTCTTTTTT
Found at i:271426 original size:19 final size:19
Alignment explanation
Indices: 271398--271447 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
271388 AGCAATACAT
*
271398 TGTATTGATACAACACTTA
1 TGTATCGATACAACACTTA
271417 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
271436 TGTATCGATACA
1 TGTATCGATACA
271448 TTGTATCTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:274587 original size:52 final size:51
Alignment explanation
Indices: 274507--274625 Score: 202
Period size: 52 Copynumber: 2.3 Consensus size: 51
274497 AAAAGTTGCT
*
274507 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTACC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA-TTACC
* *
274559 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
274610 TGCATGTATCGATACA
1 TGCATGTATCGATACA
274626 AAGATCAGTG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
51 20 0.31
52 44 0.69
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (51 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
Found at i:274652 original size:13 final size:13
Alignment explanation
Indices: 274634--274658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
274624 CAAAGATCAG
274634 TGTATCGATACAA
1 TGTATCGATACAA
274647 TGTATCGATACA
1 TGTATCGATACA
274659 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:274736 original size:33 final size:33
Alignment explanation
Indices: 274699--274765 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
274689 AGTAGCTTAA
274699 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
274732 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
274765 A
1 A
274766 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:274739 original size:13 final size:13
Alignment explanation
Indices: 274721--274745 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
274711 CAAAAAAATA
274721 TGTATCGATACAT
1 TGTATCGATACAT
274734 TGTATCGATACA
1 TGTATCGATACA
274746 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:275700 original size:52 final size:52
Alignment explanation
Indices: 275562--275755 Score: 216
Period size: 52 Copynumber: 3.7 Consensus size: 52
275552 GAAAAGTGAT
* * * * **
275562 AAAGATGCCAATATG-TCGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCT-GATTCAAGGCCAGCTATATTGAACTTAAAGATG-G-A
* * *
275616 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGA
* * *
275669 AAAGGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGACTTAAAGGT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGA
275719 -AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
275756 GGCTTAGAAG
Statistics
Matches: 122, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
49 36 0.30
51 1 0.01
52 38 0.31
53 6 0.05
54 5 0.04
55 35 0.29
56 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGA
Found at i:275742 original size:49 final size:51
Alignment explanation
Indices: 275562--275766 Score: 209
Period size: 49 Copynumber: 3.9 Consensus size: 51
275552 GAAAAGTGAT
* * * * * *
275562 AAAGATGCCAATATG-TCGATTCACGGCCAACGATATTGGGCTTAAAGATGAG
1 AAAGGTGCCAATATGCT-GATTCAAGGCCAGCTATATTGGACTTAAAGGTG-G
* * * * *
275614 AAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 --AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGG
*
275668 AAAAGGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGACTTAAAGGT-G
1 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGG
*
275719 -AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAGAAGG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA-AAGG
275767 GTTGCCACCG
Statistics
Matches: 131, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
49 41 0.31
50 4 0.03
51 1 0.01
52 38 0.29
53 6 0.05
54 5 0.04
55 35 0.27
56 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.24
Consensus pattern (51 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGG
Found at i:275892 original size:30 final size:30
Alignment explanation
Indices: 275782--276234 Score: 384
Period size: 30 Copynumber: 15.5 Consensus size: 30
275772 CACCGACTTG
* * *
275782 TGTGGGCTTTGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
275812 TGTGGGC-TTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
275839 TGTGGGCTTTT--AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
**
275867 TGTGGGCTTTTGAAAAATATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* * *
275897 TGTGGGCTTTTGAACAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
275927 TGTGGGCTTTT--AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
** *
275955 TGTGGGCTTTTGAAAAATATGCCACTAACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* *
275985 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* *
276015 TGTGGGC---TGAAAA-GAGTGCTA-TAGAGT
1 TGTGGGCTTTTGAAAAGGA-TGCCACT-GACT
* ** * * *
276042 TGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTT----TTGAAAAGGA-TGCCACTGACT
* * *
276077 TGTGGACTTTGGAAAA-GATGCCACCGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
** * *
276106 TGTGGGCTTCGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
276136 TGTGGGC-TTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* *
276163 TGTGGGCTTTTGAAAA-AATGCCACCGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
**
276192 TGTGGGC-TTTGAAAAAAATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
276221 TGTGGACTTTTGAA
1 TGTGGGCTTTTGAA
276235 GGGTGATGAA
Statistics
Matches: 351, Mismatches: 49, Indels: 46
0.79 0.11 0.10
Matches are distributed among these distances:
26 2 0.01
27 60 0.17
28 67 0.19
29 63 0.18
30 131 0.37
31 5 0.01
34 5 0.01
35 18 0.05
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (30 bp):
TGTGGGCTTTTGAAAAGGATGCCACTGACT
Found at i:275948 original size:58 final size:59
Alignment explanation
Indices: 275766--276234 Score: 338
Period size: 58 Copynumber: 8.0 Consensus size: 59
275756 GGCTTAGAAG
* * * *
275766 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AA
1 GGTTGCCACTGAC-T-TGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAA
* *
275825 GGTTGCCACTGACTTGTGGGCTTTT--AAAGGTTGCCACTGACTTGTGGGCTTTTGAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAA
** *
275882 AATATGCCACTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTT-AAA
1 GGT-TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAA
***
275941 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTAACTTGTGGGCTTTTGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTG-AAA
* * * * * * **
276001 GGGTGCCACTAACTTGTGGGC---TGAAAAGAGTGCTA-TAGAGTTGTGAGCTTACAAAAGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTA-ACTTGTGGGCTT----TTG--AA
276062 A
59 A
* * * * * ** **
276063 GAG-TGCCACGGAGTTGTGGACTTTGGAAAA-GATGCCACCGACTTGTGGGCTTCGGAAAA
1 G-GTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTG-AAA
* * * *
276122 GGGTGCCACTGATTTGTGGGC-TTTG--AAGGTTGCCACTGACTTGTGGGCTTTTGAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAA
*** * *** * *
276178 AAATGCCACCGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGACTTTTGAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAA
276235 GGGTGATGAA
Statistics
Matches: 332, Mismatches: 56, Indels: 45
0.77 0.13 0.10
Matches are distributed among these distances:
55 22 0.07
56 31 0.09
57 54 0.16
58 101 0.30
59 36 0.11
60 48 0.14
61 1 0.00
62 19 0.06
63 1 0.00
64 14 0.04
65 5 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (59 bp):
GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAA
Found at i:275951 original size:88 final size:87
Alignment explanation
Indices: 275766--276234 Score: 387
Period size: 88 Copynumber: 5.3 Consensus size: 87
275756 GGCTTAGAAG
* * *** * *
275766 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGGTT
1 GGTTGCCACTGAC-T-TGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGT
*
275829 GCCACTGACTTGTGGGCTTTTAAA
64 GCCACTAACTTGTGGGCTTTTAAA
275853 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAACAGGGTG
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAA-AGGGTG
275918 CCACTAACTTGTGGGCTTTTAAA
65 CCACTAACTTGTGGGCTTTTAAA
*
275941 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTAACTTGTGGGCTTTTGAAAAGGGTG
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTG-AAAGGGTG
**
276006 CCACTAACTTGTGGGC-TGAAAA
65 CCACTAACTTGTGGGCTTTTAAA
* * * ** * * * * *
276028 GAG-TGCTA-TAGAGTTGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAA
1 G-GTTGCCACT-GACTTGTGGGCTT----TTGAAAAATA-TGCCACTGACTTGTGGGCTTTTGAA
* * ** **
276091 AAGATGCCACCGACTTGTGGGCTTCGGAAAA
59 AGGGTGCCACTAACTTGTGGGCTT--TTAAA
* * ** ***
276122 GGGTGCCACTGATTTGTGGGC-TTTG-AAGGT-TGCCACTGACTTGTGGGCTTTTGAAAAAATGC
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGTGC
** *
276184 CACCGACTTGTGGGCTTTGAAAA
66 CACTAACTTGTGGGCTTT-TAAA
*** *
276207 AAATGCCACTGACTTGTGGACTTTTGAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAA
276235 GGGTGATGAA
Statistics
Matches: 318, Mismatches: 45, Indels: 38
0.79 0.11 0.09
Matches are distributed among these distances:
85 52 0.16
86 54 0.17
87 34 0.11
88 107 0.34
89 3 0.01
91 27 0.08
92 19 0.06
93 2 0.01
94 19 0.06
95 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (87 bp):
GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGTGC
CACTAACTTGTGGGCTTTTAAA
Found at i:276108 original size:29 final size:29
Alignment explanation
Indices: 276059--276230 Score: 177
Period size: 29 Copynumber: 5.9 Consensus size: 29
276049 TTACAAAAGA
* * *
276059 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACTGACTTGTGGGCTTTGG
* *
276089 AAAAGATGCCACCGACTTGTGGGCTTCGG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
276118 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
1 AAAA-GATGCCACTGACTTGTGGGCTTTGG
* * *
276147 -AAGGTTGCCACTGACTTGTGGGCTTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* * *
276175 AAAAAATGCCACCGACTTGTGGGCTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
276204 AAAAAATGCCACTGACTTGTGGACTTT
1 AAAAGATGCCACTGACTTGTGGGCTTT
276231 TGAAGGGTGA
Statistics
Matches: 120, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
27 21 0.17
28 3 0.03
29 71 0.59
30 25 0.21
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGGCTTTGG
Found at i:276178 original size:86 final size:86
Alignment explanation
Indices: 276066--276236 Score: 227
Period size: 86 Copynumber: 2.0 Consensus size: 86
276056 AGAAAAAGAG
* * ***
276066 TGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCAC
1 TGCCACGGACTTGTGGACTTTGGAAAAAATGCCACCGACTTGTGGGCTT-GGAAAAAAATGCCAC
* *
276131 TGATTTGTGGGC-TTTGAAGGT
65 TGACTTGTGGACTTTTGAAGGT
* * * *
276152 TGCCACTGACTTGTGGGCTTTTGAAAAAATGCCACCGACTTGTGGGCTTTGAAAAAAATGCCACT
1 TGCCACGGACTTGTGGACTTTGGAAAAAATGCCACCGACTTGTGGGCTTGGAAAAAAATGCCACT
276217 GACTTGTGGACTTTTGAAGG
66 GACTTGTGGACTTTTGAAGG
276237 GTGATGAATG
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
85 21 0.29
86 52 0.71
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.28
Consensus pattern (86 bp):
TGCCACGGACTTGTGGACTTTGGAAAAAATGCCACCGACTTGTGGGCTTGGAAAAAAATGCCACT
GACTTGTGGACTTTTGAAGGT
Found at i:277677 original size:1 final size:1
Alignment explanation
Indices: 277673--277779 Score: 70
Period size: 1 Copynumber: 107.0 Consensus size: 1
277663 CCGGACCCCC
* * * * * ** * * *
277673 TTTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTTTTTTCCTTTTGTTTTTTTCTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** ** **
277738 TTTTTTTGGTTTTTCATTTTTTTTCGTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
277780 GGAGGACGCC
Statistics
Matches: 80, Mismatches: 26, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 80 1.00
ACGTcount: A:0.02, C:0.05, G:0.08, T:0.85
Consensus pattern (1 bp):
T
Found at i:277702 original size:11 final size:10
Alignment explanation
Indices: 277673--277779 Score: 78
Period size: 10 Copynumber: 10.5 Consensus size: 10
277663 CCGGACCCCC
277673 TTTTTTTGTT
1 TTTTTTTGTT
*
277683 TTTGTTTGTT
1 TTTTTTTGTT
277693 TTTTTATTG--
1 TTTTT-TTGTT
277702 TTTTTTT-TT
1 TTTTTTTGTT
**
277711 TCCTTTTGTT
1 TTTTTTTGTT
*
277721 TTTTTCTGTT
1 TTTTTTTGTT
*
277731 TTTTTTTTTT
1 TTTTTTTGTT
*
277741 TTTTGGTTTTTCAT
1 TTTT--TTTGT--T
277755 TTTTTTTCGTT
1 TTTTTTT-GTT
277766 TTTTTTT-TT
1 TTTTTTTGTT
277775 TTTTT
1 TTTTT
277780 GGAGGACGCC
Statistics
Matches: 78, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
8 2 0.03
9 17 0.22
10 34 0.44
11 11 0.14
12 8 0.10
13 1 0.01
14 5 0.06
ACGTcount: A:0.02, C:0.05, G:0.08, T:0.85
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:277767 original size:27 final size:26
Alignment explanation
Indices: 277673--277778 Score: 99
Period size: 27 Copynumber: 3.9 Consensus size: 26
277663 CCGGACCCCC
*
277673 TTTTTTTGTTTTTGTTTGTTTTTTTAT
1 TTTTTTTGTTTTT-TTTGTTTTTTCAT
277700 TGTTTTTT-TTTTCCTTTTGTTTTTTTC-T
1 T-TTTTTTGTTTT--TTTTG-TTTTTTCAT
* *
277728 GTTTTTTTTTTTTTTTTGGTTTTTCAT
1 -TTTTTTTGTTTTTTTTGTTTTTTCAT
*
277755 TTTTTTTCGTTTTTTTTTTTTTTT
1 TTTTTTT-GTTTTTTTTGTTTTTT
277779 TGGAGGACGC
Statistics
Matches: 66, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
26 13 0.20
27 24 0.36
28 17 0.26
29 12 0.18
ACGTcount: A:0.02, C:0.05, G:0.08, T:0.85
Consensus pattern (26 bp):
TTTTTTTGTTTTTTTTGTTTTTTCAT
Found at i:287482 original size:10 final size:10
Alignment explanation
Indices: 287467--287493 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
287457 ATGTATCAAG
287467 CAAAAACAAA
1 CAAAAACAAA
287477 CAAAAACAAA
1 CAAAAACAAA
287487 CAAAAAC
1 CAAAAAC
287494 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:291705 original size:52 final size:51
Alignment explanation
Indices: 291625--291743 Score: 193
Period size: 52 Copynumber: 2.3 Consensus size: 51
291615 AAAAGTTGCT
* *
291625 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGTAAATTTACC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA-TTACC
* *
291677 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
291728 TGCATGTATCGATACA
1 TGCATGTATCGATACA
291744 AAGATCAGTG
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
51 20 0.32
52 43 0.68
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (51 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
Found at i:291770 original size:13 final size:13
Alignment explanation
Indices: 291752--291776 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
291742 CAAAGATCAG
291752 TGTATCGATACAA
1 TGTATCGATACAA
291765 TGTATCGATACA
1 TGTATCGATACA
291777 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:291856 original size:13 final size:13
Alignment explanation
Indices: 291838--291894 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
291828 ACAAAAAATA
291838 TGTATCGATACAT
1 TGTATCGATACAT
291851 TGTATCGATACAACATTT
1 TGTATCGAT---ACA--T
291869 ATGTATCGATACAT
1 -TGTATCGATACAT
291883 TGTATCGATACA
1 TGTATCGATACA
291895 CATTTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:291858 original size:32 final size:32
Alignment explanation
Indices: 291817--291913 Score: 149
Period size: 32 Copynumber: 3.0 Consensus size: 32
291807 AGTAGCTTAA
**
291817 ATTGTATCGATACAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAATTTATGTATCGATAC
*
291849 ATTGTATCGATACAACATTTATGTATCGATAC
1 ATTGTATCGATACAAAATTTATGTATCGATAC
* *
291881 ATTGTATCGATACACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAATTTATGTATCGATAC
291913 A
1 A
291914 AATCGTTGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.36
Consensus pattern (32 bp):
ATTGTATCGATACAAAATTTATGTATCGATAC
Found at i:291875 original size:19 final size:18
Alignment explanation
Indices: 291851--291913 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
291841 ATCGATACAT
291851 TGTATCGATACAACATTTA
1 TGTATCGATAC-ACATTTA
291870 TGTATCGAT--ACA--T-
1 TGTATCGATACACATTTA
291883 TGTATCGATACACATTTTA
1 TGTATCGATACACA-TTTA
291902 TGTATCGATACA
1 TGTATCGATACA
291914 AATCGTTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
15 3 0.08
16 3 0.08
18 1 0.03
19 21 0.55
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (18 bp):
TGTATCGATACACATTTA
Found at i:294434 original size:20 final size:22
Alignment explanation
Indices: 294411--294452 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
294401 AAAGCAATAA
294411 GTATCGATAC-TTCT-GGGTTT
1 GTATCGATACTTTCTAGGGTTT
*
294431 GTATTGATACTTTCTAGGGTTT
1 GTATCGATACTTTCTAGGGTTT
294453 TGACCTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 4 0.21
22 6 0.32
ACGTcount: A:0.17, C:0.12, G:0.24, T:0.48
Consensus pattern (22 bp):
GTATCGATACTTTCTAGGGTTT
Found at i:296052 original size:46 final size:46
Alignment explanation
Indices: 295985--296132 Score: 269
Period size: 46 Copynumber: 3.2 Consensus size: 46
295975 TGAAGCTTGA
*
295985 GTTTAAACTTGTGATGCCCATCTCACCCTTTCTCTTGGTTATGGAC
1 GTTTAAACTTGTGATGCCCATCTCACCCTTTCTCTTGGTTATGGAT
*
296031 GTTTAAACTTGTGATGCCCATCTCACCCTTTCTGTTGGTTATGGAT
1 GTTTAAACTTGTGATGCCCATCTCACCCTTTCTCTTGGTTATGGAT
296077 GTTTAAACTTGTGATGCCCATCTCACCCTTTCTCTTGGTTATGGAT
1 GTTTAAACTTGTGATGCCCATCTCACCCTTTCTCTTGGTTATGGAT
*
296123 GTTTGAACTT
1 GTTTAAACTT
296133 CCATAGCCCG
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 98 1.00
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (46 bp):
GTTTAAACTTGTGATGCCCATCTCACCCTTTCTCTTGGTTATGGAT
Found at i:297971 original size:13 final size:13
Alignment explanation
Indices: 297953--297979 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
297943 ATTCATCATA
297953 TATCGATACAATG
1 TATCGATACAATG
297966 TATCGATACAATG
1 TATCGATACAATG
297979 T
1 T
297980 GCCATGTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:297990 original size:33 final size:32
Alignment explanation
Indices: 297928--297996 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
297918 CCGTTTGAAG
297928 CAATGCATCGATACAATTCATCATATATCGATA
1 CAATGCATCGATACAATTCA-CATATATCGATA
* *
297961 CAATGTATCGATACAATGTGC-CATGTATCGATA
1 CAATGCATCGATACAAT-T-CACATATATCGATA
297994 CAA
1 CAA
297997 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (32 bp):
CAATGCATCGATACAATTCACATATATCGATA
Found at i:298069 original size:19 final size:19
Alignment explanation
Indices: 298025--298097 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
298015 TTGCCAGTTT
* **
298025 CATGTGTCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
298045 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
298064 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
298085 -ATGTATCGATACA
1 CATGTATCGATACA
298098 TCTAGGTGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 18 0.38
20 28 0.60
21 1 0.02
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:300499 original size:13 final size:13
Alignment explanation
Indices: 300481--300510 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
300471 ACAATTCATC
*
300481 ATGTATTGATACA
1 ATGTATCGATACA
300494 ATGTATCGATACA
1 ATGTATCGATACA
300507 ATGT
1 ATGT
300511 GCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:300517 original size:33 final size:32
Alignment explanation
Indices: 300459--300527 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
300449 TCGTTTAAAG
*
300459 CAATATATCGATACAATTCATCATGTATTGATA
1 CAATATATCGATACAATTCA-CATGTATCGATA
*
300492 CAATGTATCGATACAATGTGC-CATGTATCGATA
1 CAATATATCGATACAAT-T-CACATGTATCGATA
300525 CAA
1 CAA
300528 ATAGTGGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (32 bp):
CAATATATCGATACAATTCACATGTATCGATA
Found at i:303993 original size:13 final size:13
Alignment explanation
Indices: 303975--304001 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
303965 ACATACTGCT
303975 TTGTATCGATACA
1 TTGTATCGATACA
303988 TTGTATCGATACA
1 TTGTATCGATACA
304001 T
1 T
304002 GCTTATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:303998 original size:33 final size:32
Alignment explanation
Indices: 303956--304020 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
303946 CACTCCTAAA
303956 TGTATCGATACATACTGCT-TTGTATCGATACAT
1 TGTATCGATACATACT--TATTGTATCGATACAT
*
303989 TGTATCGATACATGCTTATTGTATCGATACAT
1 TGTATCGATACATACTTATTGTATCGATACAT
304021 GGATAATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 1 0.03
32 14 0.47
33 15 0.50
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATACTTATTGTATCGATACAT
Found at i:304031 original size:20 final size:20
Alignment explanation
Indices: 303982--304041 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
303972 GCTTTGTATC
303982 GATACATTGTATCGATACAT-
1 GATA-ATTGTATCGATACATG
* *
304002 GCTTATTGTATCGATACATG
1 GATAATTGTATCGATACATG
304022 GATAATTGTATCGATACATG
1 GATAATTGTATCGATACATG
304042 AAACTGGCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 15 0.43
20 20 0.57
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (20 bp):
GATAATTGTATCGATACATG
Found at i:312189 original size:19 final size:22
Alignment explanation
Indices: 312145--312194 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 22
312135 TTATTTGACA
312145 AAGGGGGAGAAATTCTTTGATT
1 AAGGGGGAGAAATTCTTTGATT
*
312167 AAGGGGGAG-AATT-TTT-TTT
1 AAGGGGGAGAAATTCTTTGATT
312186 AAGGGGGAG
1 AAGGGGGAG
312195 TAAAACGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.41
20 3 0.11
21 4 0.15
22 9 0.33
ACGTcount: A:0.30, C:0.02, G:0.38, T:0.30
Consensus pattern (22 bp):
AAGGGGGAGAAATTCTTTGATT
Found at i:312764 original size:19 final size:19
Alignment explanation
Indices: 312721--312792 Score: 90
Period size: 20 Copynumber: 3.7 Consensus size: 19
312711 CACTCCCTGA
* *
312721 TGTATCGATACATACTGCTT
1 TGTATCGATACATGCT-CAT
312741 TGTATCGATACATGCTCAT
1 TGTATCGATACATGCTCAT
**
312760 TGTATCGATACATGGACAAT
1 TGTATCGATACATGCTC-AT
312780 TGTATCGATACAT
1 TGTATCGATACAT
312793 CAAACTAGCA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
19 17 0.36
20 30 0.64
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATGCTCAT
Found at i:312852 original size:20 final size:20
Alignment explanation
Indices: 312823--312920 Score: 71
Period size: 20 Copynumber: 5.6 Consensus size: 20
312813 TATCACTATT
312823 TGTATCGATACATGGAATAA
1 TGTATCGATACATGGAATAA
*
312843 TGTATTGATAC-------AA
1 TGTATCGATACATGGAATAA
312856 TGTATCGATACATGGAATAA
1 TGTATCGATACATGGAATAA
*
312876 TGTATTGATAC-------AA
1 TGTATCGATACATGGAATAA
312889 TGTATCGATACATGGAATAA
1 TGTATCGATACATGGAATAA
*
312909 TGTATTGATACA
1 TGTATCGATACA
312921 ATGTATCGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 28
0.64 0.05 0.30
Matches are distributed among these distances:
13 24 0.41
20 35 0.59
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATGGAATAA
Found at i:312859 original size:13 final size:13
Alignment explanation
Indices: 312841--312933 Score: 57
Period size: 13 Copynumber: 8.1 Consensus size: 13
312831 TACATGGAAT
*
312841 AATGTATTGATAC
1 AATGTATCGATAC
312854 AATGTATCGATAC
1 AATGTATCGATAC
*
312867 -ATG----GA-AT
1 AATGTATCGATAC
*
312874 AATGTATTGATAC
1 AATGTATCGATAC
312887 AATGTATCGATAC
1 AATGTATCGATAC
*
312900 -ATG----GA-AT
1 AATGTATCGATAC
*
312907 AATGTATTGATAC
1 AATGTATCGATAC
312920 AATGTATCGATAC
1 AATGTATCGATAC
312933 A
1 A
312934 TTATGAAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 24
0.66 0.08 0.26
Matches are distributed among these distances:
7 2 0.03
8 10 0.16
12 10 0.16
13 39 0.64
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:312865 original size:33 final size:33
Alignment explanation
Indices: 312823--312934 Score: 224
Period size: 33 Copynumber: 3.4 Consensus size: 33
312813 TATCACTATT
312823 TGTATCGATACATGGAATAATGTATTGATACAA
1 TGTATCGATACATGGAATAATGTATTGATACAA
312856 TGTATCGATACATGGAATAATGTATTGATACAA
1 TGTATCGATACATGGAATAATGTATTGATACAA
312889 TGTATCGATACATGGAATAATGTATTGATACAA
1 TGTATCGATACATGGAATAATGTATTGATACAA
312922 TGTATCGATACAT
1 TGTATCGATACAT
312935 TATGAAATTG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGGAATAATGTATTGATACAA
Found at i:317646 original size:3 final size:3
Alignment explanation
Indices: 317638--317671 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
317628 TCCGAGTCAC
*
317638 CAT CAT CAT CAT CAT CAT CAT CAT CAT CTT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
317672 GTCTTTGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:319347 original size:13 final size:13
Alignment explanation
Indices: 319329--319355 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
319319 TGCCAGTTTC
319329 ATGTATCGATACA
1 ATGTATCGATACA
319342 ATGTATCGATACA
1 ATGTATCGATACA
319355 A
1 A
319356 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:320118 original size:20 final size:21
Alignment explanation
Indices: 320090--320149 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
320080 CTGTTGGGCT
320090 AATTGTATCGATACAATTCTGG
1 AATTGTATCGATAC-ATTCTGG
*
320112 -A-TGTATCGATACACTCTGG
1 AATTGTATCGATACATTCTGG
320131 AATTGTATCGATACATTCT
1 AATTGTATCGATACATTCT
320150 TATGTATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 6 0.18
20 12 0.35
21 16 0.47
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (21 bp):
AATTGTATCGATACATTCTGG
Found at i:320251 original size:33 final size:33
Alignment explanation
Indices: 320214--320280 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
320204 ACTTTATCAT
*
320214 AATGTATCGATGCATTACAACT-TGTATCGATAC
1 AATGTATCGATACATTACAA-TGTGTATCGATAC
* *
320247 AATGTATCGATACATTGCAATGTTTATCGATAC
1 AATGTATCGATACATTACAATGTGTATCGATAC
320280 A
1 A
320281 TCTGCATGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (33 bp):
AATGTATCGATACATTACAATGTGTATCGATAC
Found at i:320254 original size:13 final size:13
Alignment explanation
Indices: 320236--320260 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
320226 CATTACAACT
320236 TGTATCGATACAA
1 TGTATCGATACAA
320249 TGTATCGATACA
1 TGTATCGATACA
320261 TTGCAATGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:320276 original size:20 final size:20
Alignment explanation
Indices: 320249--320300 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
320239 ATCGATACAA
320249 TGTATCGATACAT-TGCAATG
1 TGTATCGATACATCTGC-ATG
*
320269 TTTATCGATACATCTGCATG
1 TGTATCGATACATCTGCATG
320289 TGTATCGATACA
1 TGTATCGATACA
320301 AATAAGGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATCTGCATG
Found at i:320426 original size:22 final size:21
Alignment explanation
Indices: 320387--320445 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 21
320377 GTGTATTTAC
**
320387 TTGAAAAACATTACTTCTTCGT
1 TTGAAAAACATTTTTTCTT-GT
320409 TTGAAAAACATTTTTTCTTGT
1 TTGAAAAACATTTTTTCTTGT
* **
320430 CTCTAAAACATTTTTT
1 TTGAAAAACATTTTTT
320446 ATACTTGAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
TTGAAAAACATTTTTTCTTGT
Found at i:328767 original size:20 final size:20
Alignment explanation
Indices: 328738--328811 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
328728 TTAGGCTAAT
328738 TGTATCGATACAATTCTAGA
1 TGTATCGATACAATTCTAGA
*
328758 TGTATTGATACAATTCTAGA
1 TGTATCGATACAATTCTAGA
* *
328778 TATATCGATAC-ATTCCTATATA
1 TGTATCGATACAATT-C--TAGA
328800 TGTATCGATACA
1 TGTATCGATACA
328812 TTTGAAGAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.07
20 29 0.64
22 13 0.29
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (20 bp):
TGTATCGATACAATTCTAGA
Found at i:329492 original size:79 final size:79
Alignment explanation
Indices: 329395--329547 Score: 193
Period size: 79 Copynumber: 1.9 Consensus size: 79
329385 CTCTAAGGAC
* * * * * **
329395 ACTCTAACCCCACCATCTCTG-AGGGAATATTCTAA-CTCTGTTTTTACTTCCAAAATGTTGAAT
1 ACTCCAACACCACCATCTCTGAAGGG-ATACTCCAACCTC-ATTTTTACTTCCAAAACATTGAAT
329458 TTTTCATCTTTGGGGT
64 TTTTCATCTTTGGGGT
* *
329474 ACTCCAACACCACTATCTCTGAAGGGATACTCCAACCTCATTTTTACTTCCACAACATTGAATTT
1 ACTCCAACACCACCATCTCTGAAGGGATACTCCAACCTCATTTTTACTTCCAAAACATTGAATTT
329539 TTCATCTTT
66 TTCATCTTT
329548 AGGAATAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
79 56 0.89
80 7 0.11
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.37
Consensus pattern (79 bp):
ACTCCAACACCACCATCTCTGAAGGGATACTCCAACCTCATTTTTACTTCCAAAACATTGAATTT
TTCATCTTTGGGGT
Found at i:329674 original size:131 final size:132
Alignment explanation
Indices: 329435--329674 Score: 299
Period size: 131 Copynumber: 1.8 Consensus size: 132
329425 TCTAACTCTG
* ** * * ** *
329435 TTTTTACTTCCAAAATGTTGAATTTTTCATCTTTGGGGTACTCCAACACCACTATCTCTGAAGGG
1 TTTTTACTTCCAAAATATTGAATAGTTCATCTTTGGGATACTCCAACACCACTACCTCCAAAAGG
** *
329500 ATACTCCAACCTCATTTTTACTTCCACAACATTGAATTTTTCATCTTTAGGAATAATTCACCCCA
66 ATACTCCAACCTCATTTTTACTTCCACAACATCAAATTCTTCATCTTTAGGAATAATTCACCCCA
329565 TT
131 TT
* *
329567 TTTTTACTTCCATAATATTGAA-AGTTCATCTTTAGGGATACTCCAAC-CC-TTACCTCCAAAAG
1 TTTTTACTTCCAAAATATTGAATAGTTCATCTTT-GGGATACTCCAACACCACTACCTCCAAAAG
*
329629 GATACTCCAATCC-CATTTTTTACTTCCACAATATCAAATTCTTCAT
65 GATACTCCAA-CCTCA-TTTTTACTTCCACAACATCAAATTCTTCAT
329675 ATCCGAGGAT
Statistics
Matches: 91, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
130 20 0.22
131 39 0.43
132 32 0.35
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (132 bp):
TTTTTACTTCCAAAATATTGAATAGTTCATCTTTGGGATACTCCAACACCACTACCTCCAAAAGG
ATACTCCAACCTCATTTTTACTTCCACAACATCAAATTCTTCATCTTTAGGAATAATTCACCCCA
TT
Found at i:332433 original size:22 final size:23
Alignment explanation
Indices: 332382--332436 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
332372 AAAAATAGCG
*
332382 AAATGCAGAACACACAAACAGCA
1 AAATGAAGAACACACAAACAGCA
* *
332405 AAATGAAGAACACACGAGCAGC-
1 AAATGAAGAACACACAAACAGCA
332427 AAATGAAGAA
1 AAATGAAGAA
332437 ACGTGACAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.56, C:0.20, G:0.18, T:0.05
Consensus pattern (23 bp):
AAATGAAGAACACACAAACAGCA
Found at i:332851 original size:22 final size:24
Alignment explanation
Indices: 332826--332875 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 24
332816 AAGTGAGGAG
332826 AGAAGAAACAGAAAGC-AAAG-AA
1 AGAAGAAACAGAAAGCAAAAGCAA
*
332848 AGAAGAAACAGCAAGCAAAAGCAA
1 AGAAGAAACAGAAAGCAAAAGCAA
332872 AGAA
1 AGAA
332876 AAAAGCTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 15 0.60
23 4 0.16
24 6 0.24
ACGTcount: A:0.66, C:0.12, G:0.22, T:0.00
Consensus pattern (24 bp):
AGAAGAAACAGAAAGCAAAAGCAA
Found at i:334463 original size:156 final size:156
Alignment explanation
Indices: 334200--335034 Score: 856
Period size: 156 Copynumber: 5.3 Consensus size: 156
334190 TTAAGGTTGT
* * * * * ***
334200 CGGGATACTTTTACATTGAAGGTAT-ACCTATGAGGGCATTTTCATAATTTTTCAAAACCGAGTC
1 CGGGATACTTTCACGTCGAAGGTATCCCCTA-G-GGGTATTTTCATAATTTTTTTGAACCGAGTC
* * * * * * * *
334264 CTGGGTTATCACCAAGTCCGTTTTTATGTCGAAGGTGGGTATTTAGGATACGTTTAGCCCTTTTA
64 CTAGGTTATAACCGAGTCCGCTTTTATGCCGAAGATGGGTATTTAGGATAGGTTCAGCCCTTTTA
* *
334329 CAGTCCTTTTTAAGTCCTTTAAGGGTAC
129 TAGTCCTTTTTAAGTCCTTTAGGGGTAC
* * * ** **
334357 CGGGATACTTTCACGTTGAAGGTATCCCCTTGGGGTATTTTTATAATTTTTTTGAATTGAGTTTT
1 CGGGATACTTTCACGTCGAAGGTATCCCCTAGGGGTATTTTCATAATTTTTTTGAACCGAG-TCC
* * * *
334422 TA-GTTATCACCGAATCCACTTTTATACCGAAGATGGGTATTTAGGATAGGTTCAGCCCTTTTAT
65 TAGGTTATAACCGAGTCCGCTTTTATGCCGAAGATGGGTATTTAGGATAGGTTCAGCCCTTTTAT
* *
334486 AGTCCCTTTTTAAGTCTTTTCGGGGTAC
130 AGT-CCTTTTTAAGTCCTTTAGGGGTAC
* * *
334514 CTAGGATACTTTCACGTCAAAGGTATCCCCTAGAGGTATTTTCATAATTTTTTTGAACCGAGTCC
1 C-GGGATACTTTCACGTCGAAGGTATCCCCTAGGGGTATTTTCATAATTTTTTTGAACCGAGTCC
* * * * *
334579 TAGGTTATAAACGAGTCCGTTTTTATGTCGAATGA-GGGTATTTATGATAAGTTCAGCCCTTTTA
65 TAGGTTATAACCGAGTCCGCTTTTATGCCGAA-GATGGGTATTTAGGATAGGTTCAGCCCTTTTA
* * * *
334643 TAGTCTTTTTTAAGTTCTTCAGGGGTAT
129 TAGTCCTTTTTAAGTCCTTTAGGGGTAC
* * ** * * ** **
334671 CAGGATACTTTCACATTAAAGGTATCCCCTAAGGGTATTTTCTTAATTTTTCAGAATAGAGTCCT
1 CGGGATACTTTCACGTCGAAGGTATCCCCTAGGGGTATTTTCATAATTTTTTTGAACCGAGTCCT
* * * * *
334736 AAGTTATAATCGAGTCCGTTTTTATGCCGAATG-TGGGTATTTAGAATAGGTTCAACCCTTTTAT
66 AGGTTATAACCGAGTCCGCTTTTATGCCGAA-GATGGGTATTTAGGATAGGTTCAGCCCTTTTAT
*
334800 AATCCTTTTTAAGTCCTTT-GAGGGTAC
130 AGTCCTTTTTAAGTCCTTTAG-GGGTAC
* * * * * *** *
334827 CGGGATACTTTCACGTCGAAGGTATCACCTAGGCGCATTTTCGTAAATTTTCAAAACCAAGTCCT
1 CGGGATACTTTCACGTCGAAGGTATCCCCTAGGGGTATTTTCATAATTTTTTTGAACCGAGTCCT
* * *
334892 AGGTTATAACCGAGTCCGCTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCATTTTATA
66 AGGTTATAACCGAGTCCGCTTTTATGCCGAAGATGGGTATTTAGGATAGGTTCAGCCCTTTTATA
*
334957 GTCCTTTTTAAGTCCTTTAGGGGTAT
131 GTCCTTTTTAAGTCCTTTAGGGGTAC
** * *
334983 CGGG-TAC-TTCTACGTCGAAGGTATCCTTTAGGGGCATTTTCGTAATTTTTTT
1 CGGGATACTTTC-ACGTCGAAGGTATCCCCTAGGGGTATTTTCATAATTTTTTT
335035 AAACTTAGCC
Statistics
Matches: 565, Mismatches: 102, Indels: 24
0.82 0.15 0.03
Matches are distributed among these distances:
154 3 0.01
155 39 0.07
156 342 0.61
157 71 0.13
158 108 0.19
159 2 0.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.38
Consensus pattern (156 bp):
CGGGATACTTTCACGTCGAAGGTATCCCCTAGGGGTATTTTCATAATTTTTTTGAACCGAGTCCT
AGGTTATAACCGAGTCCGCTTTTATGCCGAAGATGGGTATTTAGGATAGGTTCAGCCCTTTTATA
GTCCTTTTTAAGTCCTTTAGGGGTAC
Found at i:334775 original size:314 final size:311
Alignment explanation
Indices: 334218--334991 Score: 955
Period size: 314 Copynumber: 2.5 Consensus size: 311
334208 TTTTACATTG
* * * *
334218 AAGGTAT-ACCTATGAGGGCATTTTCATAATTTTTCAAAACCGAGTCCTGGGTTATCACCAAGTC
1 AAGGTATCACCTA-G-GCGCATTTTCATAATTTTTCAAAACCGAGTCCTAGGTTATAACCGAGTC
* * *
334282 CGTTTTTATGTCGAAGGTGGGTATTTAGGATACGTTTAGCCCTTTTACAGTCCTTTTTAAGTCCT
64 CGTTTTTATGTCGAAGGTGGGTATTTAGGATAAGTTCAGCCCTTTTATAGTCCTTTTTAAGTCCT
* * * * ** **
334347 TTAAGGGTACCGGGATACTTTCACGTTGAAGGTATCCCCTTGGGGTATTTTTATAATTTTTTTGA
129 TTAGGGGTATC-GGATACTTTCACATTAAAGGTATCCCCTAAGGGTATTTTTATAATTTTTCAGA
* ** * * * *
334412 ATTGAGTTTTTAGTTATCACCGAATCCACTTTTATACCGAAGATGGGTATTTAGGATAGGTTCAG
193 ATAGAGTCCTAAGTTATAACCGAATCCACTTTTATACCGAAGATGGGTATTTAGAATAGGTTCAA
* *
334477 CCCTTTTATAGTCCCTTTTTAAGTCTTTTCG-GGGTACCTAGGATACTTTCACGTCA
258 CCCTTTTATAAT-CCTTTTTAAGTCCTTT-GAGGGTACC-AGGATACTTTCACGTCA
* * *** *
334533 AAGGTATCCCCTAGAG-GTATTTTCATAATTTTTTTGAACCGAGTCCTAGGTTATAAACGAGTCC
1 AAGGTATCACCTAG-GCGCATTTTCATAATTTTTCAAAACCGAGTCCTAGGTTATAACCGAGTCC
* * * * *
334597 GTTTTTATGTCGAATGAGGGTATTTATGATAAGTTCAGCCCTTTTATAGTCTTTTTTAAGTTCTT
65 GTTTTTATGTCGAAGGTGGGTATTTAGGATAAGTTCAGCCCTTTTATAGTCCTTTTTAAGTCCTT
*
334662 CAGGGGTATCAGGATACTTTCACATTAAAGGTATCCCCTAAGGGTATTTTCT-TAATTTTTCAGA
130 TAGGGGTATC-GGATACTTTCACATTAAAGGTATCCCCTAAGGGTATTTT-TATAATTTTTCAGA
* * ** *
334726 ATAGAGTCCTAAGTTATAATCGAGTCCGTTTTTATGCCGAATG-TGGGTATTTAGAATAGGTTCA
193 ATAGAGTCCTAAGTTATAACCGAATCCACTTTTATACCGAA-GATGGGTATTTAGAATAGGTTCA
* *
334790 ACCCTTTTATAATCCTTTTTAAGTCCTTTGAGGGTACCGGGATACTTTCACGTCG
257 ACCCTTTTATAATCCTTTTTAAGTCCTTTGAGGGTACCAGGATACTTTCACGTCA
* * *
334845 AAGGTATCACCTAGGCGCATTTTCGTAAATTTTCAAAACCAAGTCCTAGGTTATAACCGAGTCCG
1 AAGGTATCACCTAGGCGCATTTTCATAATTTTTCAAAACCGAGTCCTAGGTTATAACCGAGTCCG
* * * * *
334910 CTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCATTTTATAGTCCTTTTTAAGTCCTTT
66 TTTTTATGTCGAAGGTGGGTATTTAGGATAAGTTCAGCCCTTTTATAGTCCTTTTTAAGTCCTTT
*
334975 AGGGGTATCGGGTACTT
131 AGGGGTATCGGATACTT
334992 CTACGTCGAA
Statistics
Matches: 390, Mismatches: 64, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
311 8 0.02
312 133 0.34
313 22 0.06
314 211 0.54
315 12 0.03
316 4 0.01
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.38
Consensus pattern (311 bp):
AAGGTATCACCTAGGCGCATTTTCATAATTTTTCAAAACCGAGTCCTAGGTTATAACCGAGTCCG
TTTTTATGTCGAAGGTGGGTATTTAGGATAAGTTCAGCCCTTTTATAGTCCTTTTTAAGTCCTTT
AGGGGTATCGGATACTTTCACATTAAAGGTATCCCCTAAGGGTATTTTTATAATTTTTCAGAATA
GAGTCCTAAGTTATAACCGAATCCACTTTTATACCGAAGATGGGTATTTAGAATAGGTTCAACCC
TTTTATAATCCTTTTTAAGTCCTTTGAGGGTACCAGGATACTTTCACGTCA
Found at i:337280 original size:20 final size:20
Alignment explanation
Indices: 337241--337280 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
337231 CCCTATTTAT
*
337241 TTATTTATTTATTTTGATTA
1 TTATTTATTAATTTTGATTA
337261 TTATTTATCTAATTTT-ATTA
1 TTATTTAT-TAATTTTGATTA
337281 AAAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TTATTTATTAATTTTGATTA
Found at i:338352 original size:18 final size:18
Alignment explanation
Indices: 338302--338341 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
338292 TTTAATGACT
*
338302 TTTTTACATTT-TATTTTA
1 TTTTT-CATTTATTTTTTA
338320 TTTTTCATTTATTTTTTA
1 TTTTTCATTTATTTTTTA
338338 TTTT
1 TTTT
338342 GATTTGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTCATTTATTTTTTA
Found at i:340943 original size:22 final size:22
Alignment explanation
Indices: 340917--340962 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
340907 TTTAATTTTC
340917 TTTTATCTTTATTTTTAAATAT
1 TTTTATCTTTATTTTTAAATAT
340939 TTTTATCTTTATTTTTAAATAT
1 TTTTATCTTTATTTTTAAATAT
340961 TT
1 TT
340963 GGTTAACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTATCTTTATTTTTAAATAT
Found at i:341241 original size:45 final size:45
Alignment explanation
Indices: 341177--341262 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
341167 TTTAAATATT
*
341177 TAGTTGCTTTAAATTTAAATAAATTAATAAAAACTACATATCTAA
1 TAGTTGATTTAAATTTAAATAAATTAATAAAAACTACATATCTAA
* **
341222 TAGTTGATTTGAATTTAAATAAATTAATAAAATTTACATAT
1 TAGTTGATTTAAATTTAAATAAATTAATAAAAACTACATAT
341263 TTAAATAGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.41
Consensus pattern (45 bp):
TAGTTGATTTAAATTTAAATAAATTAATAAAAACTACATATCTAA
Found at i:341395 original size:22 final size:22
Alignment explanation
Indices: 341370--341415 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
341360 TAGGAAAGTT
*
341370 TAGTGATTTGAAAGTATACTAG
1 TAGTAATTTGAAAGTATACTAG
*
341392 TAGTAATTTTAAAGTATACTAG
1 TAGTAATTTGAAAGTATACTAG
341414 TA
1 TA
341416 TCATGTGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.39
Consensus pattern (22 bp):
TAGTAATTTGAAAGTATACTAG
Found at i:341706 original size:2 final size:2
Alignment explanation
Indices: 341699--341757 Score: 55
Period size: 2 Copynumber: 27.5 Consensus size: 2
341689 TTCACATTTT
* * *
341699 TA TA TA TA GA TGA TA TA TGA TA GA TGA TA TA TG TGA TA TA TA TA
1 TA TA TA TA TA T-A TA TA T-A TA TA T-A TA TA TA T-A TA TA TA TA
341743 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
341758 GAATCAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 40 0.85
3 7 0.15
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (2 bp):
TA
Found at i:344473 original size:2 final size:2
Alignment explanation
Indices: 344466--344540 Score: 87
Period size: 2 Copynumber: 35.5 Consensus size: 2
344456 TCTTTGAATC
*
344466 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
* *
344509 AT AT AT CAT CT AT CAT AT AT CAT CT AT AT AT A
1 AT AT AT -AT AT AT -AT AT AT -AT AT AT AT AT A
344541 AAAATGTGAA
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
2 56 0.89
3 7 0.11
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:344802 original size:26 final size:25
Alignment explanation
Indices: 344747--344806 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
344737 AATTGACAAA
*
344747 ATTATCTTATTTAAATATATAATTTT
1 ATTAT-TTATTTAAATATATAATTTG
*
344773 ATTATTTATTTAAATTTA-AATTAATG
1 ATTATTTATTTAAATATATAATT--TG
344799 ATTATTTA
1 ATTATTTA
344807 AAAGTAGAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 4 0.13
25 12 0.40
26 14 0.47
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTATTTATTTAAATATATAATTTG
Found at i:344851 original size:22 final size:22
Alignment explanation
Indices: 344825--344870 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
344815 GTCCACATGA
344825 TACTAGTATACTTTAAAATTAC
1 TACTAGTATACTTTAAAATTAC
*
344847 TACTAGTATACTTTCAAATTAC
1 TACTAGTATACTTTAAAATTAC
344869 TA
1 TA
344871 AACTTTCCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.04, T:0.41
Consensus pattern (22 bp):
TACTAGTATACTTTAAAATTAC
Found at i:345061 original size:45 final size:45
Alignment explanation
Indices: 344973--345062 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
344963 CTTTCCCTAT
**
344973 TTAAATATGTAATTTTTATTAATTTATTTAAATTCAACTCAACTA
1 TTAAATATGTAATTTTTATTAATTTATTTAAATTCAAAGCAACTA
* *
345018 TTAAATATGTAGTTTTTATTAATTTATTTAAATTTAAAGCAACTA
1 TTAAATATGTAATTTTTATTAATTTATTTAAATTCAAAGCAACTA
345063 AATATTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (45 bp):
TTAAATATGTAATTTTTATTAATTTATTTAAATTCAAAGCAACTA
Found at i:345305 original size:22 final size:22
Alignment explanation
Indices: 345277--345322 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
345267 TAAGTTAACC
345277 AAATATTTAAAAATAAAGATAA
1 AAATATTTAAAAATAAAGATAA
345299 AAATATTTAAAAATAAAGATAA
1 AAATATTTAAAAATAAAGATAA
345321 AA
1 AA
345323 GAAAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (22 bp):
AAATATTTAAAAATAAAGATAA
Found at i:348199 original size:13 final size:13
Alignment explanation
Indices: 348181--348206 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
348171 ACATTTTGGG
348181 ATGTATCGATACA
1 ATGTATCGATACA
348194 ATGTATCGATACA
1 ATGTATCGATACA
348207 TATTGTGTGT
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:348201 original size:33 final size:32
Alignment explanation
Indices: 348159--348226 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
348149 CGTTACAAGC
*
348159 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGG-TGTATCGATA
*
348192 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGGGTGTATCGATA
348224 CAA
1 CAA
348227 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCGATA
Found at i:356845 original size:33 final size:32
Alignment explanation
Indices: 356799--356866 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
356789 CATTACAAGC
*
356799 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGG-TGTATCGATA
* * *
356832 CAATGTATTGATACATATTGTGTGTATTGATA
1 CAATGTATCGATACATATTGGGTGTATCGATA
356864 CAA
1 CAA
356867 ACAGTTAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 12 0.39
33 19 0.61
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.38
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCGATA
Found at i:359209 original size:21 final size:22
Alignment explanation
Indices: 359178--359245 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 22
359168 CATTTTACTG
* *
359178 GAAAAGAAAGAAAGAAAAAAAC
1 GAAAGGAAAGAAAGAAAAAAAA
*
359200 G-ATGGAAAGAAAGGAGAAAAAAA
1 GAAAGGAAAGAAA-GA-AAAAAAA
359223 GAAAAAGGAAAGAAAGAAAAAAA
1 G--AAAGGAAAGAAAGAAAAAAA
359246 GGGAAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 9 0.24
22 3 0.08
23 7 0.19
24 6 0.16
25 2 0.05
26 10 0.27
ACGTcount: A:0.74, C:0.01, G:0.24, T:0.01
Consensus pattern (22 bp):
GAAAGGAAAGAAAGAAAAAAAA
Found at i:359229 original size:17 final size:16
Alignment explanation
Indices: 359209--359254 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
359199 CGATGGAAAG
359209 AAAGGAGAAAAAAAGAA
1 AAAGGAGAAAAAAA-AA
359226 AAAGGA-AAGAAAGAAAA
1 AAAGGAGAA-AAA-AAAA
359243 AAAGG-GAAAAAA
1 AAAGGAGAAAAAA
359255 TTTATATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
15 1 0.04
16 5 0.19
17 18 0.69
18 2 0.08
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAGGAGAAAAAAAAA
Found at i:360159 original size:16 final size:16
Alignment explanation
Indices: 360138--360171 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
360128 AGAAAGATGG
360138 AAAGAAAAAAAAGAAA
1 AAAGAAAAAAAAGAAA
**
360154 AAAGAAAAGCAAGAAA
1 AAAGAAAAAAAAGAAA
360170 AA
1 AA
360172 GAGAGAGAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAAGAAA
Found at i:360267 original size:8 final size:9
Alignment explanation
Indices: 360244--360298 Score: 51
Period size: 10 Copynumber: 6.0 Consensus size: 9
360234 GGTTTAAAGA
*
360244 ATTATAAAT
1 ATTATATAT
360253 -TTATATAAT
1 ATTATAT-AT
360262 ATTATATAT
1 ATTATATAT
360271 ATATATATAT
1 AT-TATATAT
360281 ATT-TATAT
1 ATTATATAT
*
360289 GTTACTATAT
1 ATTA-TATAT
360299 TCATGTCATA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 12 0.31
9 7 0.18
10 20 0.51
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (9 bp):
ATTATATAT
Found at i:360339 original size:21 final size:21
Alignment explanation
Indices: 360313--360357 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
360303 GTCATATTCA
360313 TTTTTATATTATATTTTAATT
1 TTTTTATATTATATTTTAATT
*
360334 TTTTTATATTATATTTTTATT
1 TTTTTATATTATATTTTAATT
360355 TTT
1 TTT
360358 CGTATATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTATATTATATTTTAATT
Found at i:361287 original size:16 final size:17
Alignment explanation
Indices: 361256--361298 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
361246 TTATTTTTAA
361256 AATAATTTTA-TTAATT
1 AATAATTTTATTTAATT
361272 -ATAATTTTATTTAATT
1 AATAATTTTATTTAATT
*
361288 AAAAATTTTAT
1 AATAATTTTAT
361299 AACTATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 9 0.38
16 6 0.25
17 9 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATAATTTTATTTAATT
Found at i:361957 original size:22 final size:22
Alignment explanation
Indices: 361932--362025 Score: 70
Period size: 22 Copynumber: 4.4 Consensus size: 22
361922 AATATAATAG
*
361932 TAGTAAAATATTAATAACGTAA
1 TAGTAAAATATTAATAACATAA
* * * *
361954 TAGTATACTATCAATAACATAT
1 TAGTAAAATATTAATAACATAA
* *
361976 TAATAAATTATTAATAACAT-A
1 TAGTAAAATATTAATAACATAA
* *
361997 TAG-AAAATGATTGATAA-ATAT
1 TAGTAAAAT-ATTAATAACATAA
362018 TAG-AAAAT
1 TAGTAAAAT
362026 GAATGATAAT
Statistics
Matches: 56, Mismatches: 14, Indels: 5
0.75 0.19 0.07
Matches are distributed among these distances:
20 6 0.11
21 17 0.30
22 33 0.59
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.34
Consensus pattern (22 bp):
TAGTAAAATATTAATAACATAA
Found at i:362013 original size:21 final size:22
Alignment explanation
Indices: 361967--362034 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 22
361957 TATACTATCA
* *
361967 ATAACATATTA-ATAAATTATTA
1 ATAACATATTAGA-AAATGATTG
361989 ATAACATA-TAGAAAATGATTG
1 ATAACATATTAGAAAATGATTG
*
362010 ATAA-ATATTAGAAAATGAATG
1 ATAACATATTAGAAAATGATTG
362031 ATAA
1 ATAA
362035 TATAGTACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
20 3 0.07
21 29 0.71
22 9 0.22
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.32
Consensus pattern (22 bp):
ATAACATATTAGAAAATGATTG
Found at i:362203 original size:29 final size:30
Alignment explanation
Indices: 362171--362228 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
362161 ATTTATAATT
362171 TTTTAA-TAAAAGATA-AATAATTTTTATAC
1 TTTTAATTAAAA-ATATAATAATTTTTATAC
* *
362200 TTTTAATTAAAAATATCATATTTTTTATA
1 TTTTAATTAAAAATATAATAATTTTTATA
362229 AAACCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (30 bp):
TTTTAATTAAAAATATAATAATTTTTATAC
Found at i:362467 original size:18 final size:19
Alignment explanation
Indices: 362436--362484 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
362426 ACATGCTCAC
*
362436 TAATTTTCTATTTAT-TCTT
1 TAATTTT-TATTTATATATT
362455 TAATTTTTATTTATATATT
1 TAATTTTTATTTATATATT
*
362474 TTATTTTTATT
1 TAATTTTTATT
362485 ATTACTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (19 bp):
TAATTTTTATTTATATATT
Found at i:363525 original size:22 final size:22
Alignment explanation
Indices: 363465--363525 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
363455 TTTAAATAAG
363465 ATAGTAAATGATTGATA-AATA
1 ATAGTAAATGATTGATAGAATA
* * * *
363486 GTAATAAATGATTAATAGTATA
1 ATAGTAAATGATTGATAGAATA
*
363508 ATAGTAAATTATTGATAG
1 ATAGTAAATGATTGATAG
363526 CATAGCAATA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 14 0.45
22 17 0.55
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (22 bp):
ATAGTAAATGATTGATAGAATA
Found at i:371680 original size:16 final size:15
Alignment explanation
Indices: 371617--371681 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 15
371607 AATTTATTTT
371617 TAAAATTTTTATAATA
1 TAAAATTTTTA-AATA
*
371633 -AAAA-TTATAATATA
1 TAAAATTTTTAA-ATA
371647 TTAAAATTTATATAAATA
1 -TAAAATTT-T-TAAATA
371665 TAAAATATTTTAAATA
1 TAAAAT-TTTTAAATA
371681 T
1 T
371682 GATTATAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
13 1 0.03
14 7 0.17
15 4 0.10
16 11 0.28
17 9 0.22
18 5 0.12
19 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAAATTTTTAAATA
Found at i:373565 original size:11 final size:11
Alignment explanation
Indices: 373549--373575 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
373539 ATTAGTATTA
373549 TAAAAATAGAG
1 TAAAAATAGAG
373560 TAAAAATAGAG
1 TAAAAATAGAG
373571 TAAAA
1 TAAAA
373576 GATACTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.19
Consensus pattern (11 bp):
TAAAAATAGAG
Found at i:375096 original size:35 final size:34
Alignment explanation
Indices: 375046--375278 Score: 148
Period size: 35 Copynumber: 6.4 Consensus size: 34
375036 AAAATAAATG
* *
375046 TATATATATAATAAATAATTAAAATTTATTAAAAA
1 TATATTTATATTAAATAA-TAAAATTTATTAAAAA
* * * *
375081 TATATTTATATTAAATAATAAAGTATACATAAAAT
1 TATATTTATATTAAATAATAAAATTTA-TTAAAAA
*
375116 TATATTTATATTTAATAATAATTAAAAATTA-TAAAAA
1 TATATTTATA-TT-A-AATAA-TAAAATTTATTAAAAA
* * *
375153 TTATATTTATATTAAATAATAAAATATAAATAAAAT
1 -TATATTTATATTAAATAATAAAAT-TTATTAAAAA
** * *
375189 TATATTTATGTAGAATAATAATTAAAAATTATT-AAAT
1 TATATTTA--TATTA-AATAA-TAAAATTTATTAAAAA
*
375226 TCTATTTATATTAAA-AATAAATATTTATATTAAATAA
1 TATATTTATATTAAATAATAAA-A-TT-TATTAAA-AA
*
375263 TAAATTATATATTAAA
1 TATATT-TATATTAAA
375279 AGCTAAAAAT
Statistics
Matches: 155, Mismatches: 25, Indels: 33
0.73 0.12 0.15
Matches are distributed among these distances:
32 4 0.03
33 3 0.02
34 15 0.10
35 53 0.34
36 10 0.06
37 27 0.17
38 32 0.21
39 11 0.07
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (34 bp):
TATATTTATATTAAATAATAAAATTTATTAAAAA
Found at i:375136 original size:38 final size:34
Alignment explanation
Indices: 375075--375249 Score: 165
Period size: 35 Copynumber: 4.9 Consensus size: 34
375065 TAAAATTTAT
* *
375075 TAAAAATATATTTATATTAAATAATAAAGTATACA
1 TAAAATTATATTTATATTAAATAATAAA-TATAAA
* * *
375110 TAAAATTATATTTATATTTAATAATAATTAAAAATTA
1 TAAAATTATATTTATATTAAATAATAAAT-ATAA--A
375147 TAAAAATTATATTTATATTAAATAATAAAATATAAA
1 T-AAAATTATATTTATATTAAATAAT-AAATATAAA
* * *
375183 TAAAATTATATTTAT-GTAGAATAATAATTAAAAA
1 TAAAATTATATTTATATTA-AATAATAAATATAAA
*
375217 TTATTAAATTCTATTTATATTAAA-AATAAATAT
1 -TA--AAATTATATTTATATTAAATAATAAATAT
375250 TTATATTAAA
Statistics
Matches: 115, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
34 10 0.09
35 49 0.43
36 9 0.08
37 16 0.14
38 28 0.24
39 3 0.03
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (34 bp):
TAAAATTATATTTATATTAAATAATAAATATAAA
Found at i:375157 original size:32 final size:35
Alignment explanation
Indices: 375037--375246 Score: 164
Period size: 35 Copynumber: 5.9 Consensus size: 35
375027 TATTTAATTA
* *
375037 AAAT-AAATGTATATATATAATAAATAATTAAAAT-T
1 AAATAAAAT-TATATTTATATTAAATAA-TAAAATAT
* * * *
375072 TATTAAAAATATATTTATATTAAATAATAAAGTAT
1 AAATAAAATTATATTTATATTAAATAATAAAATAT
*
375107 ACATAAAATTATATTTATATTTAATAATAATTAAAA-AT
1 AAATAAAATTATATTTATA-TT-A-AATAA-TAAAATAT
*
375145 -TATAAAAATTATATTTATATTAAATAATAAAATAT
1 AAAT-AAAATTATATTTATATTAAATAATAAAATAT
* * *
375180 AAATAAAATTATATTTAT-GTAGAATAAT-AATTAA
1 AAATAAAATTATATTTATATTA-AATAATAAAATAT
*
375214 AAATTATTAAATTCTATTTATATTAAA-AATAAA
1 AAA-TA--AAATTATATTTATATTAAATAATAAA
375247 TATTTATATT
Statistics
Matches: 142, Mismatches: 18, Indels: 28
0.76 0.10 0.15
Matches are distributed among these distances:
34 19 0.13
35 63 0.44
36 11 0.08
37 21 0.15
38 24 0.17
39 4 0.03
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (35 bp):
AAATAAAATTATATTTATATTAAATAATAAAATAT
Found at i:375164 original size:73 final size:73
Alignment explanation
Indices: 375048--375246 Score: 287
Period size: 73 Copynumber: 2.7 Consensus size: 73
375038 AATAAATGTA
* * *
375048 TATATATAATAAATAATTAAAATTTATTAAAAA-TATATTTATATTAAATAATAAAGTATACATA
1 TATATATAAT-AATAATTAAAAATTA-TAAAAATTATATTTATATTAAATAATAAAATATAAATA
375112 AAATTATATT
64 AAATTATATT
*
375122 TATATTTAATAATAATTAAAAATTATAAAAATTATATTTATATTAAATAATAAAATATAAATAAA
1 TATATATAATAATAATTAAAAATTATAAAAATTATATTTATATTAAATAATAAAATATAAATAAA
375187 ATTATATT
66 ATTATATT
* * * *
375195 TATGTAGAATAATAATTAAAAATTAT-TAAATTCTATTTATATTAAA-AATAAA
1 TATATATAATAATAATTAAAAATTATAAAAATTATATTTATATTAAATAATAAA
375247 TATTTATATT
Statistics
Matches: 115, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
71 6 0.05
72 24 0.21
73 76 0.66
74 9 0.08
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (73 bp):
TATATATAATAATAATTAAAAATTATAAAAATTATATTTATATTAAATAATAAAATATAAATAAA
ATTATATT
Found at i:375250 original size:19 final size:19
Alignment explanation
Indices: 375228--375279 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
375218 TATTAAATTC
375228 TATTTATATTAAAAATAAA
1 TATTTATATTAAAAATAAA
375247 TATTTATATTAAATAATAAA
1 TATTTATATTAAA-AATAAA
*
375267 T-TATATATTAAAA
1 TATTTATATTAAAA
375280 GCTAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 1 0.03
19 23 0.74
20 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TATTTATATTAAAAATAAA
Found at i:375290 original size:21 final size:19
Alignment explanation
Indices: 375232--375293 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
375222 AAATTCTATT
*
375232 TATATTAAAAATAAATATT-
1 TATATT-AAAATAAAAATTA
375251 TATATT-AAATAATAAATTA
1 TATATTAAAATAA-AAATTA
375270 TATATTAAAAGCTAAAAATTA
1 TATATTAAAA--TAAAAATTA
375291 TAT
1 TAT
375294 TTATATTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
17 6 0.16
18 4 0.11
19 12 0.32
20 3 0.08
21 9 0.24
22 3 0.08
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TATATTAAAATAAAAATTA
Found at i:375292 original size:38 final size:37
Alignment explanation
Indices: 375232--375315 Score: 91
Period size: 38 Copynumber: 2.3 Consensus size: 37
375222 AAATTCTATT
* *
375232 TATATTAAAAATAAATATTTATATTAAATAATAAATTA
1 TATATTAAAAATAAATAATTATATT-AATAATAAATAA
* * *
375270 TATATTAAAAGCTAAA-AATTATATTTATATTAAATAA
1 TATATTAAAA-ATAAATAATTATATTAATAATAAATAA
375307 T-TATTAAAA
1 TATATTAAAA
375316 TATTATTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
36 8 0.20
37 10 0.25
38 18 0.45
39 4 0.10
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (37 bp):
TATATTAAAAATAAATAATTATATTAATAATAAATAA
Found at i:387251 original size:13 final size:13
Alignment explanation
Indices: 387222--387250 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
387212 GGAAATTTGC
387222 AAAATATTTGAGA
1 AAAATATTTGAGA
387235 AAAATATTT-AGA
1 AAAATATTTGAGA
387247 AAAA
1 AAAA
387251 ACATAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (13 bp):
AAAATATTTGAGA
Found at i:391361 original size:18 final size:21
Alignment explanation
Indices: 391314--391361 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
391304 AAAAAAAAAA
*
391314 AAGAAAAGAGAAAGTGAGCCT
1 AAGAAAAAAGAAAGTGAGCCT
*
391335 AAGAGAAAAGAAAGTG-G-C-
1 AAGAAAAAAGAAAGTGAGCCT
391353 AAGAAAAAA
1 AAGAAAAAA
391362 AATGAGAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 8 0.33
19 1 0.04
20 1 0.04
21 14 0.58
ACGTcount: A:0.60, C:0.06, G:0.27, T:0.06
Consensus pattern (21 bp):
AAGAAAAAAGAAAGTGAGCCT
Found at i:398248 original size:20 final size:20
Alignment explanation
Indices: 398182--398258 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
398172 ATTTACCTGC
* *
398182 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTTATTA
* ** *
398202 ATGTATCGATAGAAATAGTAA
1 ATGTATCGATACATTTA-TTA
*
398223 ATGTATCGATACATTTATTT
1 ATGTATCGATACATTTATTA
**
398243 ATGTATTAATACATTT
1 ATGTATCGATACATTT
398259 CCTTTCCAGA
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTATTA
Found at i:399108 original size:107 final size:108
Alignment explanation
Indices: 398911--399152 Score: 274
Period size: 107 Copynumber: 2.2 Consensus size: 108
398901 TGTAGATATG
* * * *
398911 CTAATTCACA-GCCAATGATATCGAGCTTGAAGATGAAGAGAAAGATAAATGTGCCAAAAAGCTG
1 CTAATTCA-AGGCCAATGACATTGGGCTTGAAGATGAAGAGAAAGATAAAGGTGCCAAAAAGCTG
* *
398975 AGTCAAGGCCAACGATATTGGGCTT-AAAAAAGGTGCCAATGTC
65 AGTCAAGGCCAACGATATTGGACTTAAAAAAAAGTGCCAATGTC
* * * * * *
399018 CTGATTTAAGGCCAATGACATTGGGCTTTAAGATG-AGAAGAATGATAAAGGTGCCAATATGCTG
1 CTAATTCAAGGCCAATGACATTGGGCTTGAAGATGAAG-AGAAAGATAAAGGTGCCAAAAAGCTG
* * *
399082 ATTCAAGGCCTACGATATTGGACTTAAGAAAAAAAAGTGCCAATGTG
65 AGTCAAGGCCAACGATATTGGACTT---AAAAAAAAGTGCCAATGTC
*
399129 CTAATTCACGGCCAATGACATTGG
1 CTAATTCAAGGCCAATGACATTGG
399153 ACTTAGAAAG
Statistics
Matches: 111, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
106 3 0.03
107 71 0.64
111 37 0.33
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (108 bp):
CTAATTCAAGGCCAATGACATTGGGCTTGAAGATGAAGAGAAAGATAAAGGTGCCAAAAAGCTGA
GTCAAGGCCAACGATATTGGACTTAAAAAAAAGTGCCAATGTC
Found at i:399321 original size:33 final size:32
Alignment explanation
Indices: 399232--399658 Score: 267
Period size: 33 Copynumber: 13.3 Consensus size: 32
399222 GATGCCACTA
* * *
399232 ACTTGTGTGGGCTTTTGAG-AGGGTTACCACCA
1 ACTTGTGTGGGC-TTGGAGAAGGGTTGCCACCG
* * * * * *
399264 ACTTATGTAGGCTT-TAGAATGGTTGCCGCTG
1 ACTTGTGTGGGCTTGGAGAAGGGTTGCCACCG
* *
399295 ACTTGTGTGGGCTTGGGAGAAGGGTTGCGATCG
1 ACTTGTGTGGGCTT-GGAGAAGGGTTGCCACCG
* * * *
399328 ACTTATGTGGGCTT-TAGAAGGGTTGTCACTG
1 ACTTGTGTGGGCTTGGAGAAGGGTTGCCACCG
* * * *
399359 ACTTGTGTGGGTTTTGCAAAAAGGTTGCCACCG
1 ACTTGTGTGGG-CTTGGAGAAGGGTTGCCACCG
** *
399392 ACTTGTGTGGGCTTTTAGAAAAGG-TGCCACCG
1 ACTTGTGTGGGCTTGGAG-AAGGGTTGCCACCG
399424 ACTTGTGTGGGCTTTGGAGAAGGGTTGCCACCG
1 ACTTGTGTGGGC-TTGGAGAAGGGTTGCCACCG
* * * **
399457 ACTTATGTGGGCTTTAGAAAAGGG-TGCCATTG
1 ACTTGTGTGGGC-TTGGAGAAGGGTTGCCACCG
* * * * *
399489 ACTTATGCGAGATTCGGAGAAGGGTTACCACCG
1 ACTTGTGTGGGCTT-GGAGAAGGGTTGCCACCG
* * ** * *
399522 ACTTGTGTGAGTTTTTAGAAAAGG-TGCCACCA
1 ACTTGTGTGGGCTTGGAG-AAGGGTTGCCACCG
* * **
399554 ACTTGTGTAGGCTTTGGAGAATGGTTGCCACTA
1 ACTTGTGTGGGC-TTGGAGAAGGGTTGCCACCG
* * **
399587 ACTTGTGTGGGTTTTGA-AAGGTGTTGCCACTA
1 ACTTGTGTGGGCTTGGAGAAGG-GTTGCCACCG
* * *
399619 ACTTGTGTAGGCTT-TAGAGGGGTTGCCACCG
1 ACTTGTGTGGGCTTGGAGAAGGGTTGCCACCG
399650 ACTTGTGTG
1 ACTTGTGTG
399659 AGGTTTAGAA
Statistics
Matches: 305, Mismatches: 75, Indels: 31
0.74 0.18 0.08
Matches are distributed among these distances:
30 2 0.01
31 66 0.22
32 111 0.36
33 126 0.41
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (32 bp):
ACTTGTGTGGGCTTGGAGAAGGGTTGCCACCG
Found at i:399450 original size:65 final size:64
Alignment explanation
Indices: 399209--399668 Score: 414
Period size: 65 Copynumber: 7.2 Consensus size: 64
399199 CCAACGATAT
* * * * * * *
399209 TGGGC-TTAGAAGAGATGCCACTAACTTGTGTGGGCTTTTGAG-AGGGTTACCACCAACTTATG
1 TGGGCTTTAGAAAAGGTGCCACTGACTTGTGTGGGCTTTGGAGAAGGGTTGCCACCGACTTGTG
* * * * * * *
399271 TAGGCTTTAG-AATGGTTGCCGCTGACTTGTGTGGGCTTGGGAGAAGGGTTGCGATCGACTTATG
1 TGGGCTTTAGAAAAGG-TGCCACTGACTTGTGTGGGCTTTGGAGAAGGGTTGCCACCGACTTGTG
* * * * * *
399335 TGGGCTTTAG-AAGGGTTGTCACTGACTTGTGTGGGTTTTGCAAAAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAAAGG-TGCCACTGACTTGTGTGGGCTTTGGAGAAGGGTTGCCACCGACTTGTG
* *
399399 TGGGCTTTTAGAAAAGGTGCCACCGACTTGTGTGGGCTTTGGAGAAGGGTTGCCACCGACTTATG
1 TGGGC-TTTAGAAAAGGTGCCACTGACTTGTGTGGGCTTTGGAGAAGGGTTGCCACCGACTTGTG
* * * * * * *
399464 TGGGCTTTAGAAAAGGGTGCCATTGACTTATGCGAGATTCGGAGAAGGGTTACCACCGACTTGTG
1 TGGGCTTTAGAAAA-GGTGCCACTGACTTGTGTGGGCTTTGGAGAAGGGTTGCCACCGACTTGTG
** ** * * **
399529 TGAGTTTTTAGAAAAGGTGCCACCAACTTGTGTAGGCTTTGGAGAATGGTTGCCACTAACTTGTG
1 TG-GGCTTTAGAAAAGGTGCCACTGACTTGTGTGGGCTTTGGAGAAGGGTTGCCACCGACTTGTG
* * * * *
399594 TGGG-TTTTGAAAGGTGTTGCCACTAACTTGTGTAGGCTTT--AGAGGGGTTGCCACCGACTTGT
1 TGGGCTTTAGAAAAG-G-TGCCACTGACTTGTGTGGGCTTTGGAGAAGGGTTGCCACCGACTTGT
399656 G
64 G
399657 TGAGG-TTTAGAA
1 TG-GGCTTTAGAA
399669 GGGTAAAGGT
Statistics
Matches: 323, Mismatches: 65, Indels: 18
0.80 0.16 0.04
Matches are distributed among these distances:
62 6 0.02
63 56 0.17
64 92 0.28
65 155 0.48
66 14 0.04
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.30
Consensus pattern (64 bp):
TGGGCTTTAGAAAAGGTGCCACTGACTTGTGTGGGCTTTGGAGAAGGGTTGCCACCGACTTGTG
Found at i:399760 original size:32 final size:31
Alignment explanation
Indices: 399673--399978 Score: 178
Period size: 32 Copynumber: 9.8 Consensus size: 31
399663 TTAGAAGGGT
* * * *
399673 AAAGGTACCATAGAGCTGTGGACTTAAAAAA
1 AAAGGTGCCATGGAGTTGTGGACTTAAAAGA
** *
399704 AAAGGCACCACGGAGTTGTGGACTTAGAAAGA
1 AAAGGTGCCATGGAGTTGTGGACTTA-AAAGA
* *
399736 TAAGGTGCCATGGAGTTGTAGACTT---A-A
1 AAAGGTGCCATGGAGTTGTGGACTTAAAAGA
* ***
399763 AATGGTGCCACAAAGTTGTGGACTTAAAAGAGA
1 AAAGGTGCCATGGAGTTGTGGACTT-AAA-AGA
* ***
399796 AAAAGTGCCACAAAGTTGTGGACTTAAAAG-
1 AAAGGTGCCATGGAGTTGTGGACTTAAAAGA
* *
399826 ---GGTGCCACTGAAGTTATGGACTTAAAAGGGA
1 AAAGGTGCCA-TGGAGTTGTGGACTTAAAA--GA
* *
399857 AAAGGTACCATGGAGTTGTGGACTTAGAAAAA
1 AAAGGTGCCATGGAGTTGTGGACTTA-AAAGA
* *
399889 AAAGGTACCATGGAGTTCTGGACTTAGAAAGA
1 AAAGGTGCCATGGAGTTGTGGACTTA-AAAGA
* * ** * * *
399921 AAATGTGCTACAGTGTTATAGACTTAAAAGGGA
1 AAAGGTGCCATGGAGTTGTGGACTTAAAA--GA
* *
399954 AAAGGTGCCATGGAGTCGTGAACTT
1 AAAGGTGCCATGGAGTTGTGGACTT
399979 CGAGTAGAGA
Statistics
Matches: 213, Mismatches: 45, Indels: 32
0.73 0.16 0.11
Matches are distributed among these distances:
27 26 0.12
28 17 0.08
30 1 0.00
31 27 0.13
32 77 0.36
33 56 0.26
34 9 0.04
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (31 bp):
AAAGGTGCCATGGAGTTGTGGACTTAAAAGA
Found at i:399769 original size:27 final size:27
Alignment explanation
Indices: 399749--399852 Score: 82
Period size: 33 Copynumber: 3.6 Consensus size: 27
399739 GGTGCCATGG
399749 AGTTGTAGACTTAAAATGGTGCCACAA
1 AGTTGTAGACTTAAAATGGTGCCACAA
* *
399776 AGTTGTGGACTTAAAAGAGAAAAAGTGCCACAA
1 AGTTGTAGACTTAAAA-TG-----GTGCCACAA
* * *
399809 AGTTGTGGACTTAAAAGGGTGCCACTGA
1 AGTTGTAGACTTAAAATGGTGCCAC-AA
* *
399837 AGTTATGGACTTAAAA
1 AGTTGTAGACTTAAAA
399853 GGGAAAAGGT
Statistics
Matches: 65, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
27 22 0.34
28 17 0.26
32 1 0.02
33 25 0.38
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.24
Consensus pattern (27 bp):
AGTTGTAGACTTAAAATGGTGCCACAA
Done.