Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009259.1 Hibiscus syriacus cultivar Beakdansim tig00112910_pilon, whole genome shotgun sequence
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: 1149570
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:209203 original size:42 final size:42
Alignment explanation
Indices: 209112--209205 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 42
209102 TAAAGATCGT
* *
209112 ACCTCATCACGCCATGCACCATTATCTTCACGTAAAGTACCG
1 ACCTCATGACGCCATACACCATTATCTTCACGTAAAGTACCG
* *
209154 ACCTCATGACGCTATACACCATTGTCTTCACGTAAAGTACCG
1 ACCTCATGACGCCATACACCATTATCTTCACGTAAAGTACCG
209196 ACCTCATGAC
1 ACCTCATGAC
209206 ACAAAGCACT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.29, C:0.34, G:0.13, T:0.24
Consensus pattern (42 bp):
ACCTCATGACGCCATACACCATTATCTTCACGTAAAGTACCG
Found at i:210063 original size:23 final size:23
Alignment explanation
Indices: 210037--210105 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
210027 CACCACAGCT
* *
210037 CGTATAATTACACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
210060 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
210083 CGTAGAATTGTACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
210106 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:213949 original size:64 final size:64
Alignment explanation
Indices: 213862--214021 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 64
213852 TGTTTGAATG
* * * * *
213862 TGCACCGATGCAT-TGGTAATGCATCGATGCATCCCATTAATAGTGA-AACATCGAATGCAATCG
1 TGCACCGATGCATAAGG-AGTGCATCGATGCATCCCATCAATAAT-ACAACATCGAATACAATCG
*
213925 G
64 A
* * * **
213926 TGCATCGATGCATAAGGAGTGCATCGATGCATCTCATCAATAATACAACATCGAATACATTTTA
1 TGCACCGATGCATAAGGAGTGCATCGATGCATCCCATCAATAATACAACATCGAATACAATCGA
* *
213990 TGCACCGATGCATCAGTAGTGCATCGATGCAT
1 TGCACCGATGCATAAGGAGTGCATCGATGCAT
214022 ACCTTCATTA
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
63 1 0.01
64 77 0.96
65 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (64 bp):
TGCACCGATGCATAAGGAGTGCATCGATGCATCCCATCAATAATACAACATCGAATACAATCGA
Found at i:214715 original size:31 final size:31
Alignment explanation
Indices: 214677--214863 Score: 297
Period size: 31 Copynumber: 6.0 Consensus size: 31
214667 AGGGTTGAGG
214677 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
214708 GTTTACCTATGTTTTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
214739 GTTTACTTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
214770 ATTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
214801 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
214832 GTTTACCTA-GATTTTTCGGGATC-TATGGACT
1 GTTTACCTATG-TTCTTCGGGA-CATATGGACT
214863 G
1 G
214864 GTCCTTCGGG
Statistics
Matches: 145, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
30 1 0.01
31 144 0.99
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:218522 original size:64 final size:64
Alignment explanation
Indices: 218449--218625 Score: 205
Period size: 64 Copynumber: 2.8 Consensus size: 64
218439 TAAAATAAAT
* * ** *
218449 ACATCGAATGTAATTCGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGA-A
1 ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAAT-ACA
* * *
218513 ACATTGAATGCAA-TCAATGCATCGATGCATAAGGAGTGCATCGATGCATCTCAGCAATAATACA
1 ACATCGAATGCAATTC-ATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATACA
* * * * *
218577 ACATCGAATACATTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCAT
218626 ACCTTCATTA
Statistics
Matches: 95, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
63 3 0.03
64 91 0.96
65 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (64 bp):
ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATACA
Found at i:219306 original size:31 final size:31
Alignment explanation
Indices: 219268--219423 Score: 262
Period size: 31 Copynumber: 5.0 Consensus size: 31
219258 AGGGTTGAGG
219268 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
219299 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
219330 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
219361 GTTTACCTATATTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
219392 GTTTACCTA-GATTCTTCGGGATC-TATGGACT
1 GTTTACCTATG-TTCTTCGGGA-CATATGGACT
219423 G
1 G
219424 GTCCTTCGGG
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:221667 original size:22 final size:22
Alignment explanation
Indices: 221641--221693 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
221631 GAGATAGACA
*
221641 GATTTCGCCAGAGATGGGGATG
1 GATTTCGCCAGAGATGGGGACG
* *
221663 GATTTCGTCGGAGATGGGGACG
1 GATTTCGCCAGAGATGGGGACG
*
221685 GATGTCGCC
1 GATTTCGCC
221694 GTAGAGAGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.42, T:0.23
Consensus pattern (22 bp):
GATTTCGCCAGAGATGGGGACG
Found at i:221874 original size:20 final size:20
Alignment explanation
Indices: 221847--222003 Score: 170
Period size: 20 Copynumber: 7.8 Consensus size: 20
221837 TAAACGGGCT
221847 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
* *
221867 TAGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGCG
* * *
221887 TTGCAAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTCGCG
** *
221907 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGACTTTC-GCG
** *
221928 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGACTTTC-GCG
221949 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
* *
221969 TTGCAAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGCG
*
221989 TTGAGAATTTGACTT
1 TTGCGAATTTGACTT
222004 CTGTGTTGCG
Statistics
Matches: 117, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
20 78 0.67
21 39 0.33
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:221930 original size:21 final size:21
Alignment explanation
Indices: 221904--221960 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
221894 TTTGACTTTT
221904 GTGTTGCGAATTTGAAATTCA
1 GTGTTGCGAATTTGAAATTCA
221925 GTGTTGCGAATTTGAAATTCA
1 GTGTTGCGAATTTGAAATTCA
221946 GTGTTGCGAATTTGA
1 GTGTTGCGAATTTGA
221961 CTTTCGCGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (21 bp):
GTGTTGCGAATTTGAAATTCA
Found at i:222034 original size:20 final size:20
Alignment explanation
Indices: 222009--222054 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
221999 GACTTCTGTG
*
222009 TTGCGATTTACAAATTTGCA
1 TTGCGATTTACAAATTCGCA
* *
222029 TTGCGATTTACAGATTCGCG
1 TTGCGATTTACAAATTCGCA
222049 TTGCGA
1 TTGCGA
222055 ATTTTGGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACAAATTCGCA
Found at i:222954 original size:133 final size:139
Alignment explanation
Indices: 222785--223053 Score: 478
Period size: 133 Copynumber: 2.0 Consensus size: 139
222775 AGGGATGATG
222785 TTTATCCTTAGAGGTCTCAAGTTCAAGCACTAAAAATTCTAAGGATCTTTGAACTTTCATTATCA
1 TTTATCCTTAGAGGTCTCAAGTTCAAGCACTAAAAATTCTAAGGATCTTTGAACTTTCATTATCA
*
222850 AATATTTGAGAATCTTTAG-A-AGATA-TA-CTTATAATCACCCTAGATTA-TT-TATATATGTC
66 AATATTTGAGAATCTTTAGAACAAATATTACCTTATAATCACCCTAGATTATTTATATATATGTC
222909 ACACCCATT
131 ACACCCATT
*
222918 TTTATCCTTAGAGGTCTCAAGTTCAAGCACTGAAAATTCTAAGGATCTTTGAACTTTCATTATCA
1 TTTATCCTTAGAGGTCTCAAGTTCAAGCACTAAAAATTCTAAGGATCTTTGAACTTTCATTATCA
222983 AATATTTGAGAATCTTTAGAACAAATATTACCTTATAATCACCCTAGATTATTTATATATATGTC
66 AATATTTGAGAATCTTTAGAACAAATATTACCTTATAATCACCCTAGATTATTTATATATATGTC
223048 ACACCC
131 ACACCC
223054 CAACTTTTTA
Statistics
Matches: 128, Mismatches: 2, Indels: 6
0.94 0.01 0.04
Matches are distributed among these distances:
133 83 0.65
134 1 0.01
135 4 0.03
136 2 0.02
137 20 0.16
138 2 0.02
139 16 0.12
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (139 bp):
TTTATCCTTAGAGGTCTCAAGTTCAAGCACTAAAAATTCTAAGGATCTTTGAACTTTCATTATCA
AATATTTGAGAATCTTTAGAACAAATATTACCTTATAATCACCCTAGATTATTTATATATATGTC
ACACCCATT
Found at i:223400 original size:539 final size:539
Alignment explanation
Indices: 222369--223448 Score: 1505
Period size: 539 Copynumber: 2.0 Consensus size: 539
222359 GAGATGGTTC
*
222369 TTATCCTTAGAGGTATCAAGTTCAAGCACTAAAAATTTTAAGAGTCTTTGAACTTTCATTATCAA
1 TTATCCTTAGAGGTATCAAGTTCAAGCACTAAAAATTCTAAGAGTCTTTGAACTTTCATTATCAA
* * *
222434 ATAGTTGAGAATACTTAGAAGAGATGTTACCTTATAATCACCCTAGATTATTCACACACACACAC
66 ATAGTTGAGAATACTTAGAACAAATATTACCTTATAATCACCCTAGATTATT-------------
*
222499 ACACACATATATATCACACCCCAACTTTTTAGAGATTTAAATAAATAAATTATTAAATTAATAAT
118 --ACACATATATATCACACCCCAACTTTTTAGAGATTTAAATAAATAAATTAATAAATTAATAAT
* * * * *
222564 TTTAAAGGATCAAATTTAAAGATTCTGAAATATGAGACTTATTTTGTAAGCCCTAGTTAGTTCAG
181 TTTAAAGGATCAAATTTAAAGATTCTGAAACATAAGACTCATTCTGTAAGCCCTAGTTAGTTAAG
* *
222629 GGACTAGCCTTGTAATTTTACCCTTAACCAAAAATATCTGACAAAAAAGAATTTTATTTCCTTTT
246 GGACTAGCCTTATAATTTTACCCTTAACCAAAAATATCTGACAAAAAAGAATTTTATTTCCTCTT
* *
222694 GAATTTTCATATAGTATTTCAAATTTAGTGGTTTCAATATATGTTCTTTAACTACACAAACCAAA
311 AAATTTTCATATAGTATTTCAAATTTAGTGGTTTCAATATATATTCTTTAACTACACAAACCAAA
*
222759 CTACCTCATTAGTTAAAGGGATGATGTTTATCCTTAGAGGTCTCAAGTTCAAGCACTAAAAATTC
376 CTACCTCATAAGTTAAAGGGATGATGTTTATCCTTAGAGGTCTCAAGTTCAAGCACTAAAAATTC
*
222824 TAAGGATCTTTGAACTTTCATTATCAAATATTTGAGAATCTTTAG-A-AGATA-TA-CTTATAAT
441 TAAGGATCTTTGAACTTTCATTATCAAATAATTGAGAATCTTTAGAATAGATACTATCTTATAAT
* *
222885 CACCCTAGATTATTTATATATGTCACACCCATTT
506 CACCATAGATTATTCATATATGTCACACCCATTT
* *
222919 TTATCCTTAGAGGTCTCAAGTTCAAGCACTGAAAATTCTAAG-GATCTTTGAACTTTCATTATCA
1 TTATCCTTAGAGGTATCAAGTTCAAGCACTAAAAATTCTAAGAG-TCTTTGAACTTTCATTATCA
* * * *
222983 AATATTTGAGAAT-CTTTAGAACAAATATTACCTTATAATCACCCTAGATTATT-TATATATATG
65 AATAGTTGAGAATAC-TTAGAACAAATATTACCTTATAATCACCCTAGATTATTACACATATATA
* *
223046 TCACACCCCAACTTTTTAGAGATTTAAATAAATAAATTAATAAATTAATAATTTTGAATGATCAA
129 TCACACCCCAACTTTTTAGAGATTTAAATAAATAAATTAATAAATTAATAATTTTAAAGGATCAA
* *
223111 ATTTAAAGATTCTGAAACCTAAGAC-CGTTCTGTAAGCCCTAGTTAGTTTAAGGGACTAGCCTTA
194 ATTTAAAGATTCTGAAACATAAGACTCATTCTGTAAGCCCTAGTTAG-TTAAGGGACTAGCCTTA
* **
223175 TAGTTTTACCCTTAACCAAAAATATCATCTGACCAAAAACTAATTTTATTTCCTCTTAAATTTTC
258 TAATTTTACCCTTAACC-AAAA-AT-ATCTGA-CAAAAAAGAATTTTATTTCCTCTTAAATTTTC
* * * *
223240 ATGTAGTGTATTCAAATTTAGTGGTTTCAATATATATTCTTTAACTACACGAACCAAACTGCCTC
319 ATATAGTAT-TTCAAATTTAGTGGTTTCAATATATATTCTTTAACTACACAAACCAAACTACCTC
* * * *
223305 ATAAGTTAAATGGATGGT-TCTTATCCTTATAGGTCTTAAGTTCAAG-ACCTAAAAATTCTAAGG
383 ATAAGTTAAAGGGATGATGT-TTATCCTTAGAGGTCTCAAGTTCAAGCA-CTAAAAATTCTAAGG
*
223368 GTCTTTGAACTTTCATTATCAAATAATTGAGAATCTTTAGAATAGATACTATCTTATAATCACCA
446 ATCTTTGAACTTTCATTATCAAATAATTGAGAATCTTTAGAATAGATACTATCTTATAATCACCA
223433 TAGATTATTCATATAT
511 TAGATTATTCATATAT
223449 ATATGTCACA
Statistics
Matches: 476, Mismatches: 40, Indels: 35
0.86 0.07 0.06
Matches are distributed among these distances:
533 18 0.04
534 122 0.26
535 4 0.01
536 2 0.00
537 6 0.01
538 37 0.08
539 144 0.30
540 1 0.00
541 5 0.01
542 2 0.00
543 27 0.06
549 2 0.00
550 106 0.22
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (539 bp):
TTATCCTTAGAGGTATCAAGTTCAAGCACTAAAAATTCTAAGAGTCTTTGAACTTTCATTATCAA
ATAGTTGAGAATACTTAGAACAAATATTACCTTATAATCACCCTAGATTATTACACATATATATC
ACACCCCAACTTTTTAGAGATTTAAATAAATAAATTAATAAATTAATAATTTTAAAGGATCAAAT
TTAAAGATTCTGAAACATAAGACTCATTCTGTAAGCCCTAGTTAGTTAAGGGACTAGCCTTATAA
TTTTACCCTTAACCAAAAATATCTGACAAAAAAGAATTTTATTTCCTCTTAAATTTTCATATAGT
ATTTCAAATTTAGTGGTTTCAATATATATTCTTTAACTACACAAACCAAACTACCTCATAAGTTA
AAGGGATGATGTTTATCCTTAGAGGTCTCAAGTTCAAGCACTAAAAATTCTAAGGATCTTTGAAC
TTTCATTATCAAATAATTGAGAATCTTTAGAATAGATACTATCTTATAATCACCATAGATTATTC
ATATATGTCACACCCATTT
Found at i:226924 original size:20 final size:20
Alignment explanation
Indices: 226885--226924 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
226875 ATTAACTTGG
***
226885 TTATTAAAAATAATTTATTT
1 TTATTAAAAATAAACAATTT
226905 TTATTAAAAATAAACAATTT
1 TTATTAAAAATAAACAATTT
226925 ACAAATTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATTAAAAATAAACAATTT
Found at i:228386 original size:30 final size:30
Alignment explanation
Indices: 228352--228434 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
228342 GCCAAAACAT
*
228352 AAACTTAAATGGCTAAAACAATAAAAATAG
1 AAACTTAAAGGGCTAAAACAATAAAAATAG
*
228382 AAACTT-AAGGGTCTAAAATTAA-AAAAATAG
1 AAACTTAAAGGG-CTAAAA-CAATAAAAATAG
* *
228412 AAATTTAAAGGGCTCAAAGCAAT
1 AAACTTAAAGGGCT-AAAACAAT
228435 TAAACCAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
29 4 0.09
30 29 0.67
31 10 0.23
ACGTcount: A:0.55, C:0.10, G:0.13, T:0.22
Consensus pattern (30 bp):
AAACTTAAAGGGCTAAAACAATAAAAATAG
Found at i:230428 original size:134 final size:134
Alignment explanation
Indices: 230211--230569 Score: 522
Period size: 134 Copynumber: 2.7 Consensus size: 134
230201 GTTTGGGTCG
* * * ***
230211 TCTAAGGGTGACACGGTTCCTACGTGAT-AAGGAAATCTGGTCGAGGGATGACATTACTCATACG
1 TCTAAGGGTGACACGGCTCCTACGTGATGAA-GAGATCTGGTCGGGGGATGACACGGCTCATACG
* *
230275 TGATGAAGAGTTATGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGGCT
65 TGATGAAGAGTTATGGCCATCTTTAGGAAGGGAGATAACACGGTTCCTACGTGATGAGGACGGCT
230340 GGTTA
130 GGTTA
* * * *
230345 TCTAGGGGTGACACAGCTCATACGTGATGAAGAGATCTGGTCGGGGGATGACACGGCTCATACAT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGGATGACACGGCTCATACGT
* * *
230410 GATGAAGAGTTCTAGCCATCTTTAGGAAGGGAGATAACACGGTTCCTACGTGATGAGGACGGCTT
66 GATGAAGAGTTATGGCCATCTTTAGGAAGGGAGATAACACGGTTCCTACGTGATGAGGACGGCTG
230475 GTTA
131 GTTA
* * * *
230479 TCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGAGATGACACGGCTCATACGT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGGATGACACGGCTCATACGT
*
230544 GATGAAGAGTTTTGGCCATCTTTAGG
66 GATGAAGAGTTATGGCCATCTTTAGG
230570 GATAATGATT
Statistics
Matches: 200, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
134 198 0.99
135 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (134 bp):
TCTAAGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGGATGACACGGCTCATACGT
GATGAAGAGTTATGGCCATCTTTAGGAAGGGAGATAACACGGTTCCTACGTGATGAGGACGGCTG
GTTA
Found at i:230891 original size:30 final size:28
Alignment explanation
Indices: 230847--231079 Score: 94
Period size: 29 Copynumber: 7.8 Consensus size: 28
230837 CAAGAGAGAC
*
230847 AAAACTTTGTTTCAAAAGAAACAAACTCA
1 AAAATTTTGTTTCAAAAGAAAC-AACTCA
*
230876 AAAATTTTGGTTTCAAAAGAAACGACTCA
1 AAAATTTT-GTTTCAAAAGAAACAACTCA
* * *
230905 AAGATTTT-TTTCACGAAATTGTCTTAAGAGAA-AC-
1 AAAATTTTGTTTCA--AAA--G----AA-ACAACTCA
* * *
230939 AAAACTTTGGTTCAAAATAAACAACTCA
1 AAAATTTTGTTTCAAAAGAAACAACTCA
* *
230967 AAGATTTTTATTTCAAAAGAAACAACTCA
1 AA-AATTTTGTTTCAAAAGAAACAACTCA
* * * * *
230996 CAGATTTTTATTTCAAAATAGACAACTCA
1 -AAAATTTTGTTTCAAAAGAAACAACTCA
**
231025 AAGATAGGTTTTGTTTCAAGGGAAACAATCTCA
1 AA-A-A--TTTTGTTTCAAAAGAAACAA-CTCA
* * *
231058 AAGATGTTTGTTTTAAGAGAAA
1 AAAAT-TTTGTTTCAAAAGAAA
231080 TTGTCTTAAA
Statistics
Matches: 153, Mismatches: 30, Indels: 41
0.68 0.13 0.18
Matches are distributed among these distances:
26 3 0.02
27 8 0.05
28 3 0.02
29 69 0.45
30 29 0.19
31 2 0.01
32 15 0.10
33 9 0.06
34 6 0.04
35 7 0.05
36 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.30
Consensus pattern (28 bp):
AAAATTTTGTTTCAAAAGAAACAACTCA
Found at i:230982 original size:29 final size:29
Alignment explanation
Indices: 230949--231029 Score: 135
Period size: 29 Copynumber: 2.8 Consensus size: 29
230939 AAAACTTTGG
230949 TTCAAAATAAACAACTCAAAGATTTTTAT
1 TTCAAAATAAACAACTCAAAGATTTTTAT
* *
230978 TTCAAAAGAAACAACTCACAGATTTTTAT
1 TTCAAAATAAACAACTCAAAGATTTTTAT
*
231007 TTCAAAATAGACAACTCAAAGAT
1 TTCAAAATAAACAACTCAAAGAT
231030 AGGTTTTGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.30
Consensus pattern (29 bp):
TTCAAAATAAACAACTCAAAGATTTTTAT
Found at i:230995 original size:91 final size:93
Alignment explanation
Indices: 230791--231004 Score: 263
Period size: 91 Copynumber: 2.3 Consensus size: 93
230781 CTCAAAGATT
*
230791 TTTCAAAA-AGAACAAACTCAAAGATTTTTCTCAAGAAAAACTATCTCAAGAGAGACAAAACTTT
1 TTTCAAAAGA-AAC-AACTCAAAGATTTTTCTCAAG-AAAACTATCTCAAGAGAAACAAAACTTT
* *
230855 GTTTCAAAAGAAACAAACTCAAAAATTTTGG
63 GGTTCAAAAGAAACAAACTCAAAAATTTTGA
* * * * * *
230886 TTTCAAAAGAAACGACTCAAAGATTTTTTTCACG-AAATTGTCTTAAGAGAAACAAAACTTTGGT
1 TTTCAAAAGAAACAACTCAAAGATTTTTCTCAAGAAAACTATCTCAAGAGAAACAAAACTTTGGT
* * *
230950 TCAAAATAAAC-AACTCAAAGATTTTTA
66 TCAAAAGAAACAAACTCAAAAATTTTGA
*
230977 TTTCAAAAGAAACAACTCACAGATTTTT
1 TTTCAAAAGAAACAACTCAAAGATTTTT
231005 ATTTCAAAAT
Statistics
Matches: 104, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
91 39 0.38
92 35 0.34
94 18 0.17
95 11 0.11
96 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (93 bp):
TTTCAAAAGAAACAACTCAAAGATTTTTCTCAAGAAAACTATCTCAAGAGAAACAAAACTTTGGT
TCAAAAGAAACAAACTCAAAAATTTTGA
Found at i:231227 original size:64 final size:64
Alignment explanation
Indices: 231135--231266 Score: 194
Period size: 64 Copynumber: 2.1 Consensus size: 64
231125 AAGATTTTTC
* * * *
231135 TTCATAAGGAACTGTCTCAAAAGTGACAAAATTTTGTT-TCCAAAGAAACATACTCAATGATTCT
1 TTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTAT-CAAAGAAACATACTCAAAGATTCT
* *
231199 TTCAAAAGAAACTTTCTCAAAAGAGACAAAATTTTGTTATCAAAGAAACATACTCAAAGATTTT
1 TTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTATCAAAGAAACATACTCAAAGATTCT
231263 TTCA
1 TTCA
231267 TTTTGTTTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
64 60 0.98
65 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (64 bp):
TTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTATCAAAGAAACATACTCAAAGATTCT
Found at i:231270 original size:37 final size:37
Alignment explanation
Indices: 231229--231300 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
231219 AAGAGACAAA
*
231229 ATTTTGTTATCAA-AGAAACATACTCAAAGATTTTTTC
1 ATTTTGTT-TCAAGAGAAACAAACTCAAAGATTTTTTC
* *
231266 ATTTTGTTTTAAGTGAAACAAACTCAAAGATTTTT
1 ATTTTGTTTCAAGAGAAACAAACTCAAAGATTTTT
231301 CAAGAAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 3 0.10
37 28 0.90
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.42
Consensus pattern (37 bp):
ATTTTGTTTCAAGAGAAACAAACTCAAAGATTTTTTC
Found at i:231470 original size:36 final size:36
Alignment explanation
Indices: 231418--231533 Score: 137
Period size: 36 Copynumber: 3.3 Consensus size: 36
231408 AAATTCATAA
*
231418 TTTAGA-AAATTGTCTCAAGTGAGACAACATTTGAT
1 TTTAGAGAAATTGTCTCAAGCGAGACAACATTTGAT
* * * * * *
231453 TTTAGAGAAATTGTCTCAAACAACACAAAAATTGTT
1 TTTAGAGAAATTGTCTCAAGCGAGACAACATTTGAT
*
231489 TTTAGAGAAATTGTCTCAAGCGAGACAACGTTT-AT
1 TTTAGAGAAATTGTCTCAAGCGAGACAACATTTGAT
*
231524 TTTTGAGAAA
1 TTTAGAGAAA
231534 ACGATCTCAA
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
35 16 0.25
36 49 0.75
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (36 bp):
TTTAGAGAAATTGTCTCAAGCGAGACAACATTTGAT
Found at i:233209 original size:24 final size:24
Alignment explanation
Indices: 233168--233222 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
233158 TTTGTCTTTG
233168 TGCTTTTGTCTTCTTTTTAT-TCTT
1 TGCTTTTGTCTTCTTTTT-TCTCTT
*
233192 TGCTTTT-TCTTTTCTTTTTCTCTT
1 TGCTTTTGTCTTCT-TTTTTCTCTT
233216 TG-TTTTG
1 TGCTTTTG
233223 ATTCGATCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.02, C:0.16, G:0.09, T:0.73
Consensus pattern (24 bp):
TGCTTTTGTCTTCTTTTTTCTCTT
Found at i:238639 original size:3 final size:3
Alignment explanation
Indices: 238631--238682 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
238621 TGTAATTAAT
**
238631 TAA TAA TAA TAAA TAA CGA TAA TAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
238676 TAA -AA TA
1 TAA TAA TA
238683 GACCCGGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.83
4 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:238668 original size:14 final size:14
Alignment explanation
Indices: 238633--238682 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
238623 TAATTAATTA
*
238633 ATAATAATAAATAACG
1 ATAATAAT-AATAA-T
238649 ATAATAATAATAAT
1 ATAATAATAATAAT
238663 ATAATAATAATAAT
1 ATAATAATAATAAT
*
238677 AAAATA
1 ATAATA
238683 GACCCGGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 19 0.59
15 5 0.16
16 8 0.25
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:243010 original size:42 final size:42
Alignment explanation
Indices: 242953--243081 Score: 188
Period size: 42 Copynumber: 3.1 Consensus size: 42
242943 TGATGTTGAT
*
242953 TTTA-TTTAGACTTATTGAGACTTATTAGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
* * * * *
242994 TTTATTTTAAACTTATTGAGATTTAATGGTGTTAAGATGTTA
1 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
*
243036 TTTATTTTAGACTTATTGAGACTTAATAGTATTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
243078 TTTA
1 TTTA
243082 AAGGTGTAGC
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
41 4 0.05
42 71 0.95
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.51
Consensus pattern (42 bp):
TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
Found at i:244031 original size:21 final size:21
Alignment explanation
Indices: 243975--244032 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
243965 CATCTGACCT
* * * *
243975 GGCTACGGTGGCATATGATAT
1 GGCTGCGGTGCCATCTGATAC
* *
243996 GGCTGCAGTGTCATCTGATAC
1 GGCTGCGGTGCCATCTGATAC
244017 GGCTGCGGTGCCATCT
1 GGCTGCGGTGCCATCT
244033 AAAGTGGTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.28
Consensus pattern (21 bp):
GGCTGCGGTGCCATCTGATAC
Found at i:245741 original size:16 final size:16
Alignment explanation
Indices: 245720--245767 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
245710 TACAAAAAGT
*
245720 AATAAAAAATTAGTAC
1 AATAAAAAATTAGTAA
*
245736 AAT-AAAATTTAGTAA
1 AATAAAAAATTAGTAA
* *
245751 AATAATAAATTATTAA
1 AATAAAAAATTAGTAA
245767 A
1 A
245768 TAATTATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (16 bp):
AATAAAAAATTAGTAA
Found at i:250598 original size:21 final size:20
Alignment explanation
Indices: 250555--250604 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
250545 AAACACAACT
* *
250555 ATTCGCAACTCAATTTTCAA
1 ATTCGCAACGCAATTTCCAA
*
250575 ATTCGCAACGCGATTCTCCAA
1 ATTCGCAACGCAATT-TCCAA
*
250596 ATTTGCAAC
1 ATTCGCAAC
250605 ACGAATTTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.32, C:0.28, G:0.10, T:0.30
Consensus pattern (20 bp):
ATTCGCAACGCAATTTCCAA
Found at i:250644 original size:99 final size:98
Alignment explanation
Indices: 250474--250687 Score: 297
Period size: 99 Copynumber: 2.2 Consensus size: 98
250464 AAATAACCAA
* *
250474 CAAATTCGCAACGCGAACTCCAATTTCGCAACACAGTTTCCAAATTCGCAACGCTAATTACCGAT
1 CAAATTCGCAACGCGAACTCCAATTTCGCAACACAATTTCCAAATTCACAACGCTAATTACCGAT
250539 ATAGGTAAACACAACTATTCGCAACTCAATTTT
66 ATAGGTAAACACAACTATTCGCAACTCAATTTT
* ***
250572 CAAATTCGCAACGCGATTCTCCAAATTT-GCAACACGAATTT-CGTTTTCACAACGCTAATTACC
1 CAAATTCGCAACGCGA-ACTCC-AATTTCGCAACAC-AATTTCCAAATTCACAACGCTAATTACC
*
250635 GATATAGGTAAACACAACTATTCGCAACTCAGTTTT
63 GATATAGGTAAACACAACTATTCGCAACTCAATTTT
* **
250671 TAAATTCATAACGCGAA
1 CAAATTCGCAACGCGAA
250688 TTTCGTTTTC
Statistics
Matches: 102, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
98 16 0.16
99 77 0.75
100 9 0.09
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.27
Consensus pattern (98 bp):
CAAATTCGCAACGCGAACTCCAATTTCGCAACACAATTTCCAAATTCACAACGCTAATTACCGAT
ATAGGTAAACACAACTATTCGCAACTCAATTTT
Found at i:255123 original size:2 final size:2
Alignment explanation
Indices: 255116--255142 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
255106 TGACACCTGT
255116 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 T
255143 CTGTTGGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:256929 original size:36 final size:36
Alignment explanation
Indices: 256888--256963 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
256878 ATTTTCGGGA
*
256888 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
256924 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
256960 TTTT
1 TTTT
256964 TTGCTATAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:257405 original size:15 final size:15
Alignment explanation
Indices: 257385--257414 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
257375 TATCACAATC
257385 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
257400 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
257415 AGCACGTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:261906 original size:36 final size:36
Alignment explanation
Indices: 261865--261940 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
261855 ATTTTCGGGA
*
261865 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
261901 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
261937 TTTT
1 TTTT
261941 TTGCTATAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:263223 original size:14 final size:14
Alignment explanation
Indices: 263206--263232 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
263196 CTAACGAAGC
263206 AAATTTAAAATGTA
1 AAATTTAAAATGTA
263220 AAATTTAAAATGT
1 AAATTTAAAATGT
263233 CATAAACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (14 bp):
AAATTTAAAATGTA
Found at i:263786 original size:15 final size:17
Alignment explanation
Indices: 263766--263799 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
263756 TATACAACAG
263766 CATTAAAC-AAAT-AAA
1 CATTAAACGAAATGAAA
263781 CATTAAACGAAATGAAA
1 CATTAAACGAAATGAAA
263798 CA
1 CA
263800 AAACCCATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 4 0.24
17 5 0.29
ACGTcount: A:0.62, C:0.15, G:0.06, T:0.18
Consensus pattern (17 bp):
CATTAAACGAAATGAAA
Found at i:265505 original size:21 final size:21
Alignment explanation
Indices: 265480--265528 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
265470 TTTCACAAGA
* *
265480 AAAAGTTGGTTACGTCCCAGG
1 AAAAGTTAGTTACATCCCAGG
* *
265501 AAAAGCTAGTTGCATCCCAGG
1 AAAAGTTAGTTACATCCCAGG
265522 AAAAGTT
1 AAAAGTT
265529 CCAAAACTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.22
Consensus pattern (21 bp):
AAAAGTTAGTTACATCCCAGG
Found at i:266249 original size:37 final size:37
Alignment explanation
Indices: 266207--266303 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
266197 CCTTTTCGTC
* *
266207 CTACTAGGATTCAAACTCCTAAATATAGGATATAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
266244 TTACTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** *
266281 CTACTATTATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
266304 GATAAGATCC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.33
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:267098 original size:21 final size:21
Alignment explanation
Indices: 267074--267128 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 21
267064 ACTATTTAGT
267074 ATTTTATTATATTATACATAC
1 ATTTTATTATATTATACATAC
* * *
267095 A-TTT-TTATATTTTATATAT
1 ATTTTATTATATTATACATAC
*
267114 ATTTTATTATTTTAT
1 ATTTTATTATATTAT
267129 TTATACTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 13 0.48
20 6 0.22
21 8 0.30
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTATTATATTATACATAC
Found at i:267117 original size:19 final size:19
Alignment explanation
Indices: 267080--267159 Score: 58
Period size: 19 Copynumber: 4.1 Consensus size: 19
267070 TAGTATTTTA
* * *
267080 TTATATTATACATACATTT
1 TTATATTTTATATATATTT
267099 TTATATTTTATATATA-TT
1 TTATATTTTATATATATTT
267117 TTATTATTTTATTTATACTATTT
1 TTA-TATTTTA--TATA-TATTT
267140 ATT-TATTTTCAT-TATATTT
1 -TTATATTTT-ATATATATTT
267159 T
1 T
267160 AGTTTCTTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
18 6 0.12
19 25 0.49
20 2 0.04
21 5 0.10
22 8 0.16
23 3 0.06
24 2 0.04
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATATTTTATATATATTT
Found at i:267117 original size:66 final size:67
Alignment explanation
Indices: 267009--267157 Score: 146
Period size: 64 Copynumber: 2.2 Consensus size: 67
266999 GATTACTATT
* * *
267009 TTTTAGTTAATATTATATATATATATTTATTTTTCATTTA-TTTCTTA--TTATTATTACTATTT
1 TTTTA-TT-ATATTATACATACATATTTATTTTTCATTTATTTTATTATTTTATTA-TACTATTT
267071 A-GTA
63 ATGTA
*
267075 TTTTATTATATTATACATACATTTTTATATTTT-ATATATATTTTATTATTTTATTTATACTATT
1 TTTTATTATATTATACATACATATTTAT-TTTTCAT-T-TATTTTATTATTTTA-TTATACTATT
*
267139 TATTTA
62 TATGTA
267145 TTTTCATTATATT
1 TTTT-ATTATATT
267158 TTAGTTTCTT
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 7 0.10
67 6 0.09
69 12 0.17
70 9 0.13
71 8 0.12
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (67 bp):
TTTTATTATATTATACATACATATTTATTTTTCATTTATTTTATTATTTTATTATACTATTTATG
TA
Found at i:267118 original size:40 final size:41
Alignment explanation
Indices: 267073--267160 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 41
267063 TACTATTTAG
267073 TATTTTATTATATTATACATAC-ATTT-TTATATTTT-ATATA
1 TATTTTATTATATTATACATACTATTTATT-TATTTTCAT-TA
* **
267113 TATTTTATTATTTTATTTATACTATTTATTTATTTTCATTA
1 TATTTTATTATATTATACATACTATTTATTTATTTTCATTA
267154 TATTTTA
1 TATTTTA
267161 GTTTCTTTGC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
40 19 0.45
41 19 0.45
42 4 0.10
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.65
Consensus pattern (41 bp):
TATTTTATTATATTATACATACTATTTATTTATTTTCATTA
Found at i:267268 original size:20 final size:19
Alignment explanation
Indices: 267241--267297 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
267231 TTTTATCTTC
267241 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
* *
267260 ATTTCATTTTTTTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
267281 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
267298 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 12 0.39
20 14 0.45
21 5 0.16
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:268138 original size:20 final size:20
Alignment explanation
Indices: 268113--268158 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
268103 CTAAGGGTCT
*
268113 GGCAAGCCCAAGGGGGCACC
1 GGCAAGCCCAAGAGGGCACC
268133 GGCAAGCCCAAGAGGGCACC
1 GGCAAGCCCAAGAGGGCACC
268153 GGCAAG
1 GGCAAG
268159 GAGAACTCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.33, G:0.39, T:0.00
Consensus pattern (20 bp):
GGCAAGCCCAAGAGGGCACC
Found at i:271620 original size:24 final size:22
Alignment explanation
Indices: 271584--271658 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 22
271574 CAAAAAGGGA
*
271584 AAAAAACAAAAAAGAAAAGAAGC
1 AAAAAACAAAAAAAAAAAGAA-C
*
271607 AAAAAAGAAGAAAAAAAAAGAAC
1 AAAAAACAA-AAAAAAAAAGAAC
* * *
271630 AAAAATCAAAAAGAAAAAGGGAC
1 AAAAAACAAAAA-AAAAAAGAAC
271653 AAAAAA
1 AAAAAA
271659 GCACATGCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
22 3 0.07
23 29 0.67
24 11 0.26
ACGTcount: A:0.79, C:0.07, G:0.13, T:0.01
Consensus pattern (22 bp):
AAAAAACAAAAAAAAAAAGAAC
Found at i:272279 original size:22 final size:22
Alignment explanation
Indices: 272251--272305 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
272241 GCTACTCCAT
272251 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
272273 CAAACCTTTGAGCATCAAATGT
1 CAAACCTTTGAGCATCAAATGC
272295 CAAACCTTTGA
1 CAAACCTTTGA
272306 CCAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:273347 original size:106 final size:106
Alignment explanation
Indices: 273131--274611 Score: 2093
Period size: 106 Copynumber: 14.0 Consensus size: 106
273121 CTATCTTGCC
* * * * * * *
273131 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AATAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
273195 AATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
273236 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
273301 AATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
273342 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGATTGTCAATAAACAACTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
273407 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
273448 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* **
273513 AATTTCAGAGCCAATTTTAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
273554 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
273619 AATTTCAGAGCTAATTTCAACTTTACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
273660 ACTCCAGACAAAGCAAGTTCAACTTCACAATGAAGGGACTGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
273725 AATTTCAGAGCCAGTTTCAACTTCACAACGAAGGTTATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
273766 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
273831 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
273872 ACTCCAGACAACGCAAGTTCAACTTCACGACTAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
273937 ATTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
273978 ACTCAAGACAACGCAAGTTCAATTTCACGACTAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
274043 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
274084 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
274149 AATTTTAGAGCCAATTTCAATTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
274190 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
274255 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
274296 ACTCAAGACAATGCAAGTTCAACTTCACAACGAAGGGACCGCTAGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** * * *
274361 AATTTCAGAGCCAATTTCAACTTTTCAACGAAGGATCTTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * * * * *
274402 AC-CCAAGGTAACACAAGCTCAACTTCACGATGAAGAGG-CGGCTGATTGTCAAC-AA-AA-TT-
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAG-GGACCGCTGGTTGTCAACAAACAACTTC
** *
274461 -TTATTT-AGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
64 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * * * * *
274502 ACTTGAGACAACACAAGTTCAACTTCACAACAAAGGGA-CGACTGGTTGTCAACAAACAATTTCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
** * *
274566 CGGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
274608 ACTC
1 ACTC
274612 AGAACAATGC
Statistics
Matches: 1232, Mismatches: 131, Indels: 25
0.89 0.09 0.02
Matches are distributed among these distances:
99 3 0.00
100 66 0.05
101 6 0.00
102 2 0.00
103 4 0.00
104 2 0.00
105 54 0.04
106 1093 0.89
107 2 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:275291 original size:37 final size:37
Alignment explanation
Indices: 275201--275305 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
275191 CTTTTTCGTC
*
275201 CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
275238 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
275275 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
275306 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:275776 original size:2 final size:2
Alignment explanation
Indices: 275769--275797 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
275759 TTTATATGTT
275769 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 T
275798 TTTAATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:275882 original size:21 final size:22
Alignment explanation
Indices: 275849--275896 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
275839 TTTTTTTTGC
*
275849 ATTATATTATATAT-TTCCTATT
1 ATTATATTATATATATT-ATATT
275871 ATTATA-TATATATATTATATT
1 ATTATATTATATATATTATATT
275892 ATTAT
1 ATTAT
275897 TATTTTTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTATATTATATATATTATATT
Found at i:275888 original size:13 final size:11
Alignment explanation
Indices: 275849--275899 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
275839 TTTTTTTTGC
275849 ATTATATTATAT
1 ATTATATTAT-T
**
275861 ATT-TCCTATT
1 ATTATATTATT
275871 ATTATATATATAT
1 ATTATAT-TAT-T
275884 ATTATATTATT
1 ATTATATTATT
275895 ATTAT
1 ATTAT
275900 TTTTATCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
10 4 0.12
11 11 0.34
12 9 0.28
13 8 0.25
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTATATTATT
Found at i:276109 original size:20 final size:19
Alignment explanation
Indices: 276084--276152 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 19
276074 ATATACATAC
276084 ATTTTTATATTTTTATATAT
1 ATTTTTATATTTTTAT-TAT
276104 ATTTTTAT-TATTTTATTTAT
1 ATTTTTATAT-TTTTA-TTAT
* *
276124 ACTGTTTATTTATTTTCATTAT
1 A-T-TTT-TATATTTTTATTAT
276146 ATTTTTA
1 ATTTTTA
276153 GTTTCTTTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
19 2 0.05
20 20 0.50
21 3 0.08
22 8 0.20
23 6 0.15
24 1 0.03
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (19 bp):
ATTTTTATATTTTTATTAT
Found at i:276136 original size:22 final size:20
Alignment explanation
Indices: 276094--276152 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 20
276084 ATTTTTATAT
*
276094 TTTTATATATATTTTTATTA
1 TTTTATATATATGTTTATTA
*
276114 TTTTATTTATACTGTTTATTTA
1 TTTTATATATA-TGTTTA-TTA
*
276136 TTTTCAT-TATATTTTTA
1 TTTT-ATATATATGTTTA
276153 GTTTCTTTGC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 10 0.30
21 10 0.30
22 11 0.33
23 2 0.06
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTATATATATGTTTATTA
Found at i:276249 original size:20 final size:19
Alignment explanation
Indices: 276224--276291 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
276214 TTTGTATATA
276224 TATTTTATATTCATTTATTT
1 TATTTT-TATTCATTTATTT
276244 TA-TTTTATTCAATTTCATTT
1 TATTTTTATTC-ATTT-ATTT
* *
276264 T-TTTTCATTCAATTATTT
1 TATTTTTATTCATTTATTT
*
276282 TATGTTTATT
1 TATTTTTATT
276292 ATTATTGGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
18 10 0.25
19 16 0.40
20 14 0.35
ACGTcount: A:0.24, C:0.07, G:0.01, T:0.68
Consensus pattern (19 bp):
TATTTTTATTCATTTATTT
Found at i:280157 original size:22 final size:22
Alignment explanation
Indices: 280117--280158 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
280107 ATCCATTTTT
*
280117 TTTTAATTTCGTTTTATTTTCA
1 TTTTAATTTCGTTTAATTTTCA
280139 TTTTAATTTC-TCTTAATTTT
1 TTTTAATTTCGT-TTAATTTT
280159 TAGACAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTAATTTCGTTTAATTTTCA
Found at i:282153 original size:34 final size:34
Alignment explanation
Indices: 282110--282181 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
282100 GGAGTATTCT
282110 TTTTCCCTCTCTTTGTTTGTTAATTTAATATACG
1 TTTTCCCTCTCTTTGTTTGTTAATTTAATATACG
282144 TTTTCCCTCTCTTTGTTTGTTAATTTAATATACG
1 TTTTCCCTCTCTTTGTTTGTTAATTTAATATACG
282178 TTTT
1 TTTT
282182 GGGACAAATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.17, C:0.17, G:0.08, T:0.58
Consensus pattern (34 bp):
TTTTCCCTCTCTTTGTTTGTTAATTTAATATACG
Found at i:284733 original size:14 final size:14
Alignment explanation
Indices: 284716--284764 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
284706 TATCTTTATC
284716 ATTATTTTATAATT
1 ATTATTTTATAATT
*
284730 ATTATTTT-TATTTT
1 ATTATTTTATA-ATT
*
284744 ATTATTTTATTATT
1 ATTATTTTATAATT
284758 A-TATTTT
1 ATTATTTT
284765 TATCCTTATC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 8 0.27
14 21 0.70
15 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTATTTTATAATT
Found at i:284735 original size:3 final size:3
Alignment explanation
Indices: 284711--284759 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
284701 CATTTTATCT
* * *
284711 TTA TCA TTA TT- TTA TAA TTA TTA TTT TTA TT- TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
284756 TTA T
1 TTA T
284760 ATTTTTATCC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 6 0.16
3 31 0.84
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:284773 original size:28 final size:28
Alignment explanation
Indices: 284716--284773 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
284706 TATCTTTATC
*
284716 ATTATTTTATAATTATTATTTTTATTTT
1 ATTATTTTATAATTATTATTTTTATCTT
*
284744 ATTATTTTATTATTA-TATTTTTATCCTT
1 ATTATTTTATAATTATTATTTTTAT-CTT
284772 AT
1 AT
284774 CCTTATCTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (28 bp):
ATTATTTTATAATTATTATTTTTATCTT
Found at i:288152 original size:29 final size:29
Alignment explanation
Indices: 288081--288267 Score: 254
Period size: 29 Copynumber: 6.6 Consensus size: 29
288071 ACTCGACCCA
* * **
288081 GTGATATTTTAGTAATTATTTT-GAAACC
1 GTGATATTTTGGTAATTATTTTAAAAAAG
*
288109 G-GATATTTTAGTAATTATTTTAAAAAAG
1 GTGATATTTTGGTAATTATTTTAAAAAAG
*
288137 GTGATATTTTGGTAATTATTTTGAAAAAG
1 GTGATATTTTGGTAATTATTTTAAAAAAG
*
288166 GTGATATTTTGGTAATTA-TTTAAAAAAA
1 GTGATATTTTGGTAATTATTTTAAAAAAG
*
288194 GTGATATTTTGGTAATTATTTTGAAAAAG
1 GTGATATTTTGGTAATTATTTTAAAAAAG
*
288223 GTGATATTTTGGTAATTATTTTAAAAAAT
1 GTGATATTTTGGTAATTATTTTAAAAAAG
* *
288252 GTGCTATTTTCGTAAT
1 GTGATATTTTGGTAAT
288268 AGTTGACTGT
Statistics
Matches: 143, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
27 20 0.14
28 31 0.22
29 92 0.64
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (29 bp):
GTGATATTTTGGTAATTATTTTAAAAAAG
Found at i:288209 original size:57 final size:58
Alignment explanation
Indices: 288080--288267 Score: 283
Period size: 57 Copynumber: 3.3 Consensus size: 58
288070 GACTCGACCC
* ** *
288080 AGTGATATTTTAGTAATTATTTTG-AAACCG-GATATTTTAGTAATTATTTTAAAAAA
1 AGTGATATTTTGGTAATTATTTTGAAAAAGGTGATATTTTGGTAATTATTTTAAAAAA
*
288136 GGTGATATTTTGGTAATTATTTTGAAAAAGGTGATATTTTGGTAATTA-TTTAAAAAA
1 AGTGATATTTTGGTAATTATTTTGAAAAAGGTGATATTTTGGTAATTATTTTAAAAAA
288193 AGTGATATTTTGGTAATTATTTTGAAAAAGGTGATATTTTGGTAATTATTTTAAAAAA
1 AGTGATATTTTGGTAATTATTTTGAAAAAGGTGATATTTTGGTAATTATTTTAAAAAA
* * *
288251 TGTGCTATTTTCGTAAT
1 AGTGATATTTTGGTAAT
288268 AGTTGACTGT
Statistics
Matches: 120, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
56 22 0.18
57 60 0.50
58 38 0.32
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.45
Consensus pattern (58 bp):
AGTGATATTTTGGTAATTATTTTGAAAAAGGTGATATTTTGGTAATTATTTTAAAAAA
Found at i:288225 original size:86 final size:85
Alignment explanation
Indices: 288081--288267 Score: 266
Period size: 86 Copynumber: 2.2 Consensus size: 85
288071 ACTCGACCCA
** **
288081 GTGATATTTTAGTAATTATTTTGAAACCGGATATTTTAGTAATTATTTTAAAAAAGGTGATATTT
1 GTGATATTTTAGTAATTATTTAAAAAAAGGATATTTTAGTAATTATTTTAAAAAAGGTGATATTT
*
288146 TGGTAATTATTTTGAAAAAG
66 TGGTAATTATTTTAAAAAAG
* * *
288166 GTGATATTTTGGTAATTATTTAAAAAAAGTGATATTTTGGTAATTATTTTGAAAAAGGTGATATT
1 GTGATATTTTAGTAATTATTTAAAAAAAG-GATATTTTAGTAATTATTTTAAAAAAGGTGATATT
*
288231 TTGGTAATTATTTTAAAAAAT
65 TTGGTAATTATTTTAAAAAAG
* *
288252 GTGCTATTTTCGTAAT
1 GTGATATTTTAGTAAT
288268 AGTTGACTGT
Statistics
Matches: 90, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
85 24 0.27
86 66 0.73
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (85 bp):
GTGATATTTTAGTAATTATTTAAAAAAAGGATATTTTAGTAATTATTTTAAAAAAGGTGATATTT
TGGTAATTATTTTAAAAAAG
Found at i:295445 original size:19 final size:19
Alignment explanation
Indices: 295418--295461 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
295408 GTTTGACCGA
*
295418 TCTGAACCGGATTGAAACGG
1 TCTG-ACCGGACTGAAACGG
295438 TCTGACCGGACTGAAACGG
1 TCTGACCGGACTGAAACGG
295457 TCTGA
1 TCTGA
295462 TCGGTCCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (19 bp):
TCTGACCGGACTGAAACGG
Found at i:295541 original size:25 final size:26
Alignment explanation
Indices: 295495--295582 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 26
295485 ACCCGACCTG
*
295495 TTGACAACCAAATATTTTAGTAATTATT
1 TTGA-AACCGAATA-TTTAGTAATTATT
295523 TTGAAACC-AATATTTAGTAATTATT
1 TTGAAACCGAATATTTAGTAATTATT
* *
295548 TTGAAACCGGTGATATTTGGGTAATTATT
1 TTGAAACC-G-AATATTT-AGTAATTATT
295577 TTGAAA
1 TTGAAA
295583 AAGGTGATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
25 21 0.39
26 4 0.07
27 4 0.07
28 10 0.19
29 15 0.28
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (26 bp):
TTGAAACCGAATATTTAGTAATTATT
Found at i:295573 original size:29 final size:29
Alignment explanation
Indices: 295539--295659 Score: 188
Period size: 29 Copynumber: 4.2 Consensus size: 29
295529 CCAATATTTA
** *
295539 GTAATTATTTTGAAACCGGTGATATTTGG
1 GTAATTATTTTGAAAAAGGTGATATTTTG
295568 GTAATTATTTTGAAAAAGGTGATATTTTG
1 GTAATTATTTTGAAAAAGGTGATATTTTG
295597 GTAATTATTTTGAAAAAGGTGATATTTTG
1 GTAATTATTTTGAAAAAGGTGATATTTTG
* * *
295626 GTAATTATTTTTAAAAAGGTGCTATTTTC
1 GTAATTATTTTGAAAAAGGTGATATTTTG
295655 GTAAT
1 GTAAT
295660 AGTTGACTAT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 86 1.00
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.45
Consensus pattern (29 bp):
GTAATTATTTTGAAAAAGGTGATATTTTG
Found at i:295595 original size:17 final size:17
Alignment explanation
Indices: 295573--295625 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
295563 TTTGGGTAAT
295573 TATTTTGAAAAAGGTGA
1 TATTTTGAAAAAGGTGA
**
295590 TATTTTG-GTAA--T--
1 TATTTTGAAAAAGGTGA
295602 TATTTTGAAAAAGGTGA
1 TATTTTGAAAAAGGTGA
295619 TATTTTG
1 TATTTTG
295626 GTAATTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 10
0.66 0.10 0.24
Matches are distributed among these distances:
12 7 0.26
13 2 0.07
14 1 0.04
15 1 0.04
16 2 0.07
17 14 0.52
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (17 bp):
TATTTTGAAAAAGGTGA
Found at i:295971 original size:21 final size:22
Alignment explanation
Indices: 295931--295971 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
295921 TCCGTTTGGT
295931 CAAATTCATACTCGAAAGCCTC
1 CAAATTCATACTCGAAAGCCTC
* *
295953 CAAATTGATAGTC-AAAGCC
1 CAAATTCATACTCGAAAGCC
295972 AAAAATGCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (22 bp):
CAAATTCATACTCGAAAGCCTC
Found at i:297475 original size:23 final size:23
Alignment explanation
Indices: 297441--297524 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 23
297431 TTTCGTAAGA
*
297441 GTACTTTATGTACTATGTCAAGT
1 GTACTTTGTGTACTATGTCAAGT
* *
297464 GTACTTTGTGTACTATGGCAAGA
1 GTACTTTGTGTACTATGTCAAGT
297487 GTACTTTGTGTACT-TGT--AGT
1 GTACTTTGTGTACTATGTCAAGT
* *
297507 CGTGCTTTGTTTACTATG
1 -GTACTTTGTGTACTATG
297525 GCACTTTGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.04
21 12 0.23
22 4 0.08
23 34 0.65
ACGTcount: A:0.20, C:0.13, G:0.23, T:0.44
Consensus pattern (23 bp):
GTACTTTGTGTACTATGTCAAGT
Found at i:298011 original size:2 final size:2
Alignment explanation
Indices: 298004--298030 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
297994 TTAAACGTTA
298004 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
298031 GTTGAAGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:299097 original size:15 final size:16
Alignment explanation
Indices: 299077--299106 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
299067 CTTTGACTTT
299077 AAGATATTTT-AATGA
1 AAGATATTTTCAATGA
299092 AAGATATTTTCAATG
1 AAGATATTTTCAATG
299107 GAAATTAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.40
Consensus pattern (16 bp):
AAGATATTTTCAATGA
Found at i:305032 original size:13 final size:12
Alignment explanation
Indices: 305016--305147 Score: 60
Period size: 13 Copynumber: 10.8 Consensus size: 12
305006 ATACTATTTC
305016 CATCACCATAAT
1 CATCACCATAAT
* *
305028 CCATCTTCCATTAT
1 -CATC-ACCATAAT
*
305042 CA-CGCC-TATAT
1 CATCACCATA-AT
*
305053 CATCACCATAGT
1 CATCACCATAAT
*
305065 CCATCACCATTAT
1 -CATCACCATAAT
*
305078 CA-CGCC-TATAT
1 CATCACCATA-AT
*
305089 CATCACCATAGT
1 CATCACCATAAT
*
305101 CCATCACCATTAT
1 -CATCACCATAAT
*
305114 CA-CGCC-TATAT
1 CATCACCATA-AT
*
305125 CATCACCATATT
1 CATCACCATAAT
305137 CCATCACCATA
1 -CATCACCATA
305148 TCACGCCTAT
Statistics
Matches: 88, Mismatches: 18, Indels: 26
0.67 0.14 0.20
Matches are distributed among these distances:
10 3 0.03
11 20 0.23
12 17 0.19
13 42 0.48
14 6 0.07
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (12 bp):
CATCACCATAAT
Found at i:305061 original size:23 final size:23
Alignment explanation
Indices: 305016--305150 Score: 75
Period size: 23 Copynumber: 5.6 Consensus size: 23
305006 ATACTATTTC
*
305016 CATCACCATAATCCATCTTCCATTAT
1 CATCACCAT-AT-CATC-ACCATTAT
*
305042 CA-CGCCTATATCATCACCA-TAGT
1 CATCACC-ATATCATCACCATTA-T
*
305065 CCATCACCAT-T-ATCACGCCTATAT
1 -CATCACCATATCATCAC-CAT-TAT
305089 CATCACCATAGTCCATCACCATTAT
1 CATCACCATA-T-CATCACCATTAT
*
305114 CA-CGCCTATATCATCACCA-TATT
1 CATCACC-ATATCATCACCATTA-T
305137 CCATCACCATATCA
1 -CATCACCATATCA
305151 CGCCTATATT
Statistics
Matches: 87, Mismatches: 7, Indels: 32
0.69 0.06 0.25
Matches are distributed among these distances:
22 9 0.10
23 24 0.28
24 21 0.24
25 22 0.25
26 6 0.07
27 5 0.06
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (23 bp):
CATCACCATATCATCACCATTAT
Found at i:305082 original size:36 final size:36
Alignment explanation
Indices: 305016--305164 Score: 246
Period size: 36 Copynumber: 4.1 Consensus size: 36
305006 ATACTATTTC
* *
305016 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAGTCCATC-ACCATTATCACGCCTATAT
305053 CATCACCATAGTCCATCACCATTATCACGCCTATAT
1 CATCACCATAGTCCATCACCATTATCACGCCTATAT
305089 CATCACCATAGTCCATCACCATTATCACGCCTATAT
1 CATCACCATAGTCCATCACCATTATCACGCCTATAT
*
305125 CATCACCATATTCCATCACCA-TATCACGCCTATAT
1 CATCACCATAGTCCATCACCATTATCACGCCTATAT
*
305160 TATCA
1 CATCA
305165 TCAACTTATA
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
35 18 0.17
36 74 0.69
37 16 0.15
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.30
Consensus pattern (36 bp):
CATCACCATAGTCCATCACCATTATCACGCCTATAT
Found at i:305632 original size:14 final size:15
Alignment explanation
Indices: 305598--305644 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
305588 AATTTGGAGT
305598 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
305613 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
305627 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
305644 G
1 G
305645 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:309528 original size:13 final size:12
Alignment explanation
Indices: 309512--309643 Score: 60
Period size: 13 Copynumber: 10.8 Consensus size: 12
309502 ATACTATTTC
309512 CATCACCATAAT
1 CATCACCATAAT
* *
309524 CCATCTTCCATTAT
1 -CATC-ACCATAAT
*
309538 CA-CGCC-TATAT
1 CATCACCATA-AT
*
309549 CATCACCATAGT
1 CATCACCATAAT
*
309561 CCATCACCATTAT
1 -CATCACCATAAT
*
309574 CA-CGCC-TATAT
1 CATCACCATA-AT
*
309585 CATCACCATAGT
1 CATCACCATAAT
*
309597 CCATCACCATTAT
1 -CATCACCATAAT
*
309610 CA-CGCC-TATAT
1 CATCACCATA-AT
*
309621 CATCACCATATT
1 CATCACCATAAT
309633 CCATCACCATA
1 -CATCACCATA
309644 TCACGCCTAT
Statistics
Matches: 88, Mismatches: 18, Indels: 26
0.67 0.14 0.20
Matches are distributed among these distances:
10 3 0.03
11 20 0.23
12 17 0.19
13 42 0.48
14 6 0.07
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (12 bp):
CATCACCATAAT
Found at i:309557 original size:23 final size:23
Alignment explanation
Indices: 309512--309646 Score: 75
Period size: 23 Copynumber: 5.6 Consensus size: 23
309502 ATACTATTTC
*
309512 CATCACCATAATCCATCTTCCATTAT
1 CATCACCAT-AT-CATC-ACCATTAT
*
309538 CA-CGCCTATATCATCACCA-TAGT
1 CATCACC-ATATCATCACCATTA-T
*
309561 CCATCACCAT-T-ATCACGCCTATAT
1 -CATCACCATATCATCAC-CAT-TAT
309585 CATCACCATAGTCCATCACCATTAT
1 CATCACCATA-T-CATCACCATTAT
*
309610 CA-CGCCTATATCATCACCA-TATT
1 CATCACC-ATATCATCACCATTA-T
309633 CCATCACCATATCA
1 -CATCACCATATCA
309647 CGCCTATATT
Statistics
Matches: 87, Mismatches: 7, Indels: 32
0.69 0.06 0.25
Matches are distributed among these distances:
22 9 0.10
23 24 0.28
24 21 0.24
25 22 0.25
26 6 0.07
27 5 0.06
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (23 bp):
CATCACCATATCATCACCATTAT
Found at i:309578 original size:36 final size:36
Alignment explanation
Indices: 309512--309663 Score: 252
Period size: 36 Copynumber: 4.2 Consensus size: 36
309502 ATACTATTTC
* *
309512 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAGTCCATC-ACCATTATCACGCCTATAT
309549 CATCACCATAGTCCATCACCATTATCACGCCTATAT
1 CATCACCATAGTCCATCACCATTATCACGCCTATAT
309585 CATCACCATAGTCCATCACCATTATCACGCCTATAT
1 CATCACCATAGTCCATCACCATTATCACGCCTATAT
*
309621 CATCACCATATTCCATCACCA-TATCACGCCTATAT
1 CATCACCATAGTCCATCACCATTATCACGCCTATAT
*
309656 TATCACCA
1 CATCACCA
309664 ACTTATAAAT
Statistics
Matches: 111, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
35 21 0.19
36 74 0.67
37 16 0.14
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
CATCACCATAGTCCATCACCATTATCACGCCTATAT
Found at i:315522 original size:72 final size:72
Alignment explanation
Indices: 315361--315637 Score: 306
Period size: 72 Copynumber: 3.8 Consensus size: 72
315351 AAATAAATAA
* * * * *
315361 GAAACTTGTTTTAAGAGAAGAGCA-CTCTAGTGAGATAAATTTTGTTTCGAGGGAAAACTGTCTC
1 GAAACTGGTTTTAAGA-AAAACCATCTCAAGTGAGATAAATTTTGTTTCAAGGG-AAACTGTCTC
* *
315425 AAGCGAGAC
64 CAGTGAGAC
** * * * *
315434 GAAGTTGGTTTTAAGAAAAACCATCTCGAGTTAGATAAATTTTATTTCAAGGGAAATTGTCTCCA
1 GAAACTGGTTTTAAGAAAAACCATCTCAAGTGAGATAAATTTTGTTTCAAGGGAAACTGTCTCCA
*
315499 GTGAGAT
66 GTGAGAC
*
315506 GAAACTGGTTTTAAGAACAAA-CATCTCAAGTGAGATAAAAATTTTTGTTTCAAAGGAAACTGTC
1 GAAACTGGTTTTAAGAA-AAACCATCTCAAGTGAGAT--AAA-TTTTGTTTCAAGGGAAACTGTC
315570 TCCAGTGAGAC
62 TCCAGTGAGAC
* * * * *
315581 GAAACTTGTTTTGATAGAAACAATCTCAAGTGAGATAAATTTTGTTTCAAGGGAAAC
1 GAAACTGGTTTTAAGAAAAACCATCTCAAGTGAGATAAATTTTGTTTCAAGGGAAAC
315638 ATGTTCAAAG
Statistics
Matches: 171, Mismatches: 27, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
72 65 0.38
73 44 0.26
74 6 0.04
75 56 0.33
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (72 bp):
GAAACTGGTTTTAAGAAAAACCATCTCAAGTGAGATAAATTTTGTTTCAAGGGAAACTGTCTCCA
GTGAGAC
Found at i:315638 original size:36 final size:36
Alignment explanation
Indices: 315389--315637 Score: 126
Period size: 36 Copynumber: 6.8 Consensus size: 36
315379 AGAGCACTCT
* *
315389 AGTGAGATAAATTTTGTTTCGAGGGAAAACTGTCTCA
1 AGTGAGATAAATTTTGTTTCAAGGG-AAACTATCTCA
* ** * * * ** * *
315426 AGCGAGACGAAGTTGGTTTTAAGAAAAACCATCTCG
1 AGTGAGATAAATTTTGTTTCAAGGGAAACTATCTCA
* * * * *
315462 AGTTAGATAAATTTTATTTCAAGGGAAATTGTCTCC
1 AGTGAGATAAATTTTGTTTCAAGGGAAACTATCTCA
* * * **
315498 AGTGAGATGAAA-CTGGTTTTAAGAACAAAC-ATCTCA
1 AGTGAGAT-AAATTTTGTTTCAAG-GGAAACTATCTCA
* * *
315534 AGTGAGATAAAAATTTTTGTTTCAAAGGAAACTGTCTCC
1 AGTGAGAT--AAA-TTTTGTTTCAAGGGAAACTATCTCA
* * ** ** *
315573 AGTGAGACGAAA-CTTGTTTTGATAGAAACAATCTCA
1 AGTGAGA-TAAATTTTGTTTCAAGGGAAACTATCTCA
315609 AGTGAGATAAATTTTGTTTCAAGGGAAAC
1 AGTGAGATAAATTTTGTTTCAAGGGAAAC
315638 ATGTTCAAAG
Statistics
Matches: 144, Mismatches: 60, Indels: 17
0.65 0.27 0.08
Matches are distributed among these distances:
35 3 0.02
36 91 0.63
37 25 0.17
38 7 0.05
39 18 0.12
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (36 bp):
AGTGAGATAAATTTTGTTTCAAGGGAAACTATCTCA
Found at i:315700 original size:21 final size:21
Alignment explanation
Indices: 315675--315763 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 21
315665 AAACTGTCTC
315675 AGGGAGACAAAACTTGTTTCA
1 AGGGAGACAAAACTTGTTTCA
*
315696 AGGGAGACAAAATTTGTTTCA
1 AGGGAGACAAAACTTGTTTCA
*
315717 A--GAG---AAAC-TGTCTCA
1 AGGGAGACAAAACTTGTTTCA
*
315732 AGAGAGACAAAA-TTCGTTTCA
1 AGGGAGACAAAACTT-GTTTCA
*
315753 AGGGAAACAAA
1 AGGGAGACAAA
315764 TTCAAAGATT
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
15 7 0.13
16 3 0.05
17 3 0.05
19 3 0.05
20 4 0.07
21 35 0.64
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.21
Consensus pattern (21 bp):
AGGGAGACAAAACTTGTTTCA
Found at i:315846 original size:34 final size:36
Alignment explanation
Indices: 315778--315869 Score: 118
Period size: 34 Copynumber: 2.6 Consensus size: 36
315768 AAGATTTTGT
* *
315778 GTTTCAAGAGAAACT-GTCTCAAGAGAGAATAAATTC
1 GTTTCAAGGGAAA-TGGTCTCAAGAGAGAATAAATTA
315814 GTTTCAAGGGAAATGGTCTCAAGAGA-AA-AAATTA
1 GTTTCAAGGGAAATGGTCTCAAGAGAGAATAAATTA
* *
315848 ATTTCAAGGGAAATGTTCTCAA
1 GTTTCAAGGGAAATGGTCTCAA
315870 AGTTTATATT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
34 25 0.49
35 3 0.06
36 23 0.45
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (36 bp):
GTTTCAAGGGAAATGGTCTCAAGAGAGAATAAATTA
Found at i:315898 original size:166 final size:167
Alignment explanation
Indices: 315712--316103 Score: 630
Period size: 166 Copynumber: 2.4 Consensus size: 167
315702 ACAAAATTTG
* *
315712 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAAATTCAAAGATTTTG
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTG
* *
315777 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-ATAAATTCGTTTCAAGGGAAATGGTCTCAAGAGA-
66 TGTTTCAAGAGAAACTGTCTCAAGAGAGACA-AAATTCGTTTCAAGGG-AACGGTCTAAAGAGAG
*
315840 A-AAAATTAATTTCAAGGGAAATGTTCTCAAAGTTTATA
129 ACAAAATTAATTTCAAGGGAAACGTTCTCAAAGTTTATA
* *
315878 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTTT
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTG
315943 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAACGGTCTAAAGAGAGAC
66 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAACGGTCTAAAGAGAGAC
* *
316008 AAAATTCATTTCAAGGGAAACGTTCTCAAAGTTTATG
131 AAAATTAATTTCAAGGGAAACGTTCTCAAAGTTTATA
* *
316045 TTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAAC-AATCTCAAAG
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAAT-TCAAAG
316104 TTTATCAATT
Statistics
Matches: 210, Mismatches: 12, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
165 13 0.06
166 109 0.52
167 88 0.42
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (167 bp):
TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTG
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAACGGTCTAAAGAGAGAC
AAAATTAATTTCAAGGGAAACGTTCTCAAAGTTTATA
Found at i:315917 original size:99 final size:102
Alignment explanation
Indices: 315684--315926 Score: 300
Period size: 99 Copynumber: 2.4 Consensus size: 102
315674 CAGGGAGACA
* * **
315684 AAACTTGTTTCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGT
1 AAAC-TGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTAAT
* *
315749 TTCAAGGGAAACAAATTCAAAGATTTTGTGTTTCAAGAG
65 TTCAAGGGAAACAAATTCAAAGA-TTTATATTTCAAGAG
* *
315788 AAACTGTCTCAAGAGAGA-ATAAATTCGTTTCAAGGGAAA-TGGTCTCAAGAGA-A-AAAATTAA
1 AAACTGTCTCAAGGGAGACA-AAATTTGTTTCAAGGGAAACT-GTCTCAAGAGAGACAAAATTAA
***
315849 TTTCAAGGGAAA-TGTTCTCAAAG-TTTATATTTCAAGAG
64 TTTCAAGGGAAACAAAT-TCAAAGATTTATATTTCAAGAG
315887 AAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
1 AAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
315927 AGATTCAAAG
Statistics
Matches: 121, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
99 48 0.40
100 2 0.02
101 24 0.20
102 3 0.02
103 40 0.33
104 4 0.03
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.27
Consensus pattern (102 bp):
AAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTAATT
TCAAGGGAAACAAATTCAAAGATTTATATTTCAAGAG
Found at i:315972 original size:67 final size:65
Alignment explanation
Indices: 315814--315991 Score: 211
Period size: 67 Copynumber: 2.7 Consensus size: 65
315804 GAATAAATTC
* * * *
315814 GTTTCAAGGGAAA-TGGTCTCAAGAGA-A-AAAATTAATTTCAAGGGAAATGTTCTCAAAGTTTA
1 GTTTCAAGAGAAACT-GTCTCAAGAGAGACAAAATTAGTTTCAAGGGAAAAGATCTCAAAGTTTA
315876 T
65 T
* * *
315877 ATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGAT-TCAAAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAGGGAAA-AGATCTCAAAG--TT
*
315941 TTT
63 TAT
*
315944 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAA
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAGGGAA
315992 CGGTCTAAAG
Statistics
Matches: 98, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
63 21 0.21
64 2 0.02
65 24 0.24
66 2 0.02
67 49 0.50
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (65 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAGGGAAAAGATCTCAAAGTTTAT
Found at i:316006 original size:35 final size:35
Alignment explanation
Indices: 315944--316026 Score: 121
Period size: 35 Copynumber: 2.3 Consensus size: 35
315934 AAGATTTTTT
* * *
315944 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTC
1 GTTTCAAG-GGAACGGTCTAAAGAGAGACAAAATTC
315980 GTTTCAAGGGAACGGTCTAAAGAGAGACAAAATTC
1 GTTTCAAGGGAACGGTCTAAAGAGAGACAAAATTC
*
316015 ATTTCAAGGGAA
1 GTTTCAAGGGAA
316027 ACGTTCTCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 35 0.81
36 8 0.19
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (35 bp):
GTTTCAAGGGAACGGTCTAAAGAGAGACAAAATTC
Found at i:316076 original size:100 final size:102
Alignment explanation
Indices: 315878--316093 Score: 294
Period size: 100 Copynumber: 2.1 Consensus size: 102
315868 AAAGTTTATA
* * * ** *
315878 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTTT
1 TTTCAAGAGAAACGGTCTAAAGAGAGACAAAATTCATTTCAAGGGAAACAGATTCAAAGA-TTTA
315943 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCG
65 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCG
* *
315981 TTTCAAG-GGAACGGTCTAAAGAGAGACAAAATTCATTTCAAGGGAAAC-GTTCTCAAAG-TTTA
1 TTTCAAGAGAAACGGTCTAAAGAGAGACAAAATTCATTTCAAGGGAAACAGAT-TCAAAGATTTA
* * *
316043 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTG
65 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCG
316081 TTTCAAGAGAAAC
1 TTTCAAGAGAAAC
316094 AATCTCAAAG
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
100 45 0.45
101 6 0.06
102 41 0.41
103 7 0.07
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (102 bp):
TTTCAAGAGAAACGGTCTAAAGAGAGACAAAATTCATTTCAAGGGAAACAGATTCAAAGATTTAT
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCG
Found at i:317701 original size:2 final size:2
Alignment explanation
Indices: 317694--317724 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
317684 TTATTGTATT
317694 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
317725 GGGTATACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:319092 original size:149 final size:148
Alignment explanation
Indices: 318822--319112 Score: 386
Period size: 149 Copynumber: 2.0 Consensus size: 148
318812 CAAAGCTTCC
* * * *
318822 ACTTCATCTCCTACTTGCATAAGTCTTTTGAGCTGGTTCGTGATCTTCAACTGTTGGCTTCGATG
1 ACTTCATCTCCTACTTCCAGAAATCTTTCGAGCTGGTTCGTGATCTTCAACTGTTGGCTTCGA-G
** * *
318887 TCGAATTGTCTCGAGTCCAACTTGTTACCTCAGCAGGAAAATGTCTGGATCGTCTCCTTGGTAGA
65 TCGAATCATCTCGAGTCCAACTTGCTACCTCAGCAGGAAAATGCCTGGATCGTCTCCTTGGTAGA
318952 TAGACTCCCTCTGGCTCCT
130 TAGACTCCCTCTGGCTCCT
* * *
318971 ACTTCATCTCCTATTTCCAGAAATCTTTCGAGCTGGTTTGTGATCTTCAATTGTTGGCTTC-AGC
1 ACTTCATCTCCTACTTCCAGAAATCTTTCGAGCTGGTTCGTGATCTTCAACTGTTGGCTTCGAG-
* * * * * *
319035 ATCGAATCATCTTGAGTCCAACTTGCTACCTCAGTAGGCAGATGCCTGGCTTGTCTCCTTGGTAG
65 -TCGAATCATCTCGAGTCCAACTTGCTACCTCAGCAGGAAAATGCCTGGATCGTCTCCTTGGTAG
*
319100 GTAGACTCCCTCT
129 ATAGACTCCCTCT
319113 TGACTCTTCT
Statistics
Matches: 122, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
147 1 0.01
148 1 0.01
149 120 0.98
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (148 bp):
ACTTCATCTCCTACTTCCAGAAATCTTTCGAGCTGGTTCGTGATCTTCAACTGTTGGCTTCGAGT
CGAATCATCTCGAGTCCAACTTGCTACCTCAGCAGGAAAATGCCTGGATCGTCTCCTTGGTAGAT
AGACTCCCTCTGGCTCCT
Found at i:322171 original size:18 final size:17
Alignment explanation
Indices: 322136--322176 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
322126 TATTGATTGC
322136 TTTTTTTCTTTACTTTT
1 TTTTTTTCTTTACTTTT
*
322153 TCTTTTTTCTTTTTCTTTT
1 T-TTTTTTC-TTTACTTTT
322172 TTTTT
1 TTTTT
322177 ACTTGAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 11 0.52
19 9 0.43
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTTCTTTACTTTT
Found at i:322173 original size:13 final size:13
Alignment explanation
Indices: 322135--322173 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
322125 ATATTGATTG
*
322135 CTTTTT-TTCTTTA
1 CTTTTTCTT-TTTT
322148 CTTTTTCTTTTTT
1 CTTTTTCTTTTTT
322161 CTTTTTCTTTTTT
1 CTTTTTCTTTTTT
322174 TTTACTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 22 0.92
14 2 0.08
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (13 bp):
CTTTTTCTTTTTT
Found at i:329221 original size:39 final size:39
Alignment explanation
Indices: 329162--329357 Score: 214
Period size: 39 Copynumber: 5.0 Consensus size: 39
329152 CCTATACACC
* *
329162 CAGTAAGGACTTACCTTGTGCACAAAGCAGAGGAGCCTG
1 CAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTG
* * * * * * *
329201 CAGTAATGTCTTATCATGTGCACAAAGCAGATGAGCTTG
1 CAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTG
* * * *
329240 CAGTAAGGACTTACCCTAAGTACAAAGAAGATGAGCCTG
1 CAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTG
* * * *
329279 CAGTAAAGACTTACCTTGAGCACAAAGCCGAGGAACCTG
1 CAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTG
*
329318 CGGTAAGGACTTACCCTGAGCACAAAGTC-GAGGAGCCTG
1 CAGTAAGGACTTACCCTGAGCACAAAG-CAGAGGAGCCTG
329357 C
1 C
329358 GGAAAACGGT
Statistics
Matches: 129, Mismatches: 27, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
39 128 0.99
40 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.19
Consensus pattern (39 bp):
CAGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCCTG
Found at i:330159 original size:24 final size:24
Alignment explanation
Indices: 330127--330188 Score: 97
Period size: 24 Copynumber: 2.5 Consensus size: 24
330117 TAACTTCTTG
330127 GTCAAAGTCAACGGTCAACGATCA
1 GTCAAAGTCAACGGTCAACGATCA
* *
330151 GTCAAAGTCAACGGTCAACGGTCG
1 GTCAAAGTCAACGGTCAACGATCA
330175 GTCAAAAGTCAACG
1 GTC-AAAGTCAACG
330189 TTGGACTGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 25 0.71
25 10 0.29
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.16
Consensus pattern (24 bp):
GTCAAAGTCAACGGTCAACGATCA
Found at i:332275 original size:21 final size:21
Alignment explanation
Indices: 332249--332409 Score: 136
Period size: 21 Copynumber: 7.7 Consensus size: 21
332239 CATATTCGCA
332249 TTGCGATAGTCCAAGTTCTCG
1 TTGCGATAGTCCAAGTTCTCG
* *
332270 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCTCG
* *
332291 TTGCGATTTATTCCAA-AT-TCG
1 TTGCGA--TAGTCCAAGTTCTCG
*
332312 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCTCG
*
332333 TTGCGATTTATTCCAAG-T-TCG
1 TTGCGA--TAGTCCAAGTTCTCG
*
332354 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCTCG
* * *
332375 TTGCGCTTTATTCCAA-AT-TCG
1 TTGCG--ATAGTCCAAGTTCTCG
332396 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
332410 AATCGCAACG
Statistics
Matches: 111, Mismatches: 19, Indels: 22
0.73 0.12 0.14
Matches are distributed among these distances:
19 22 0.20
20 2 0.02
21 63 0.57
22 3 0.03
23 21 0.19
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCTCG
Found at i:332295 original size:42 final size:41
Alignment explanation
Indices: 332243--332409 Score: 228
Period size: 42 Copynumber: 4.0 Consensus size: 41
332233 GATTTACATA
* * *
332243 TTCGCATTGCGA-TAGTCCAAGTTCTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTATTCCAAG-T-TCGTTGCGATAGTCCAAG
*
332285 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAG
332327 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAG
* *
332369 TTCGCGTTGCGCTTTATTCCAAATTCGTTGCGATAGTCCAA
1 TTCGCGTTGCG-ATTATTCCAAGTTCGTTGCGATAGTCCAA
332410 AATCGCAACG
Statistics
Matches: 115, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
42 107 0.93
43 1 0.01
44 7 0.06
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (41 bp):
TTCGCGTTGCGATTATTCCAAGTTCGTTGCGATAGTCCAAG
Found at i:332377 original size:63 final size:63
Alignment explanation
Indices: 332242--332409 Score: 159
Period size: 63 Copynumber: 2.7 Consensus size: 63
332232 CGATTTACAT
* * * *
332242 ATTCGCATTGCGATAGTCCAAGTTCTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAA
1 ATTCGCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTC-CGTTGCGA-TTAGTCCAA
*
332307 ATT--CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT-CGTTGCGA-TAGTCCAA
1 ATTCGCGTTGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCCAAGTTCCGTTGCGATTAGTCCAA
* * * *
332368 GTTCGCGTTGCGCTTTATTCCAAATT--CGTTGCGATAGTCCAA
1 ATTCGCGTTGCG--ATAGTCCAAGTTCGCGTTGCGATAGTCCAA
332410 AATCGCAACG
Statistics
Matches: 87, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
61 16 0.18
63 50 0.57
65 21 0.24
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.35
Consensus pattern (63 bp):
ATTCGCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTCCGTTGCGATTAGTCCAA
Found at i:332440 original size:6 final size:6
Alignment explanation
Indices: 332429--332453 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
332419 GACTCGTATT
332429 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
332454 GACGGGACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:334427 original size:21 final size:21
Alignment explanation
Indices: 334387--334438 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
334377 AATGAGAAAA
*
334387 ATATATAGTTTAGACATTTTTT
1 ATATATA-TTAAGACATTTTTT
*
334409 ATATATATTAAGCCATTTTTT
1 ATATATATTAAGACATTTTTT
*
334430 ATACATATT
1 ATATATATT
334439 TGATTGGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.52
Consensus pattern (21 bp):
ATATATATTAAGACATTTTTT
Found at i:338773 original size:2 final size:2
Alignment explanation
Indices: 338766--338799 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
338756 ACATCAAGTA
338766 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
338800 TAATTGTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:343773 original size:21 final size:21
Alignment explanation
Indices: 343747--343788 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
343737 TTTTCTTATT
343747 TACATTAGCAT-ATATACATTG
1 TACATTA-CATGATATACATTG
*
343768 TACATTACATGGTATACATTG
1 TACATTACATGATATACATTG
343789 CATCTCAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (21 bp):
TACATTACATGATATACATTG
Found at i:344831 original size:2 final size:2
Alignment explanation
Indices: 344824--344855 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
344814 ATCCTTTCAA
344824 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
344856 CCTTGTTGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:345161 original size:11 final size:11
Alignment explanation
Indices: 345116--345185 Score: 58
Period size: 11 Copynumber: 6.7 Consensus size: 11
345106 TAACAAAAGG
*
345116 AAAAAAACA-A
1 AAAAAAAGAGA
* *
345126 AAAAAAAAAGT
1 AAAAAAAGAGA
*
345137 AAGAAAA-A-A
1 AAAAAAAGAGA
345146 AAAAAAAGAGA
1 AAAAAAAGAGA
*
345157 TAAAAAAGA-A
1 AAAAAAAGAGA
345167 AAAAAAAGAGA
1 AAAAAAAGAGA
*
345178 AAATAAAG
1 AAAAAAAG
345186 CCAAAAAAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
9 6 0.12
10 19 0.40
11 23 0.48
ACGTcount: A:0.83, C:0.01, G:0.11, T:0.04
Consensus pattern (11 bp):
AAAAAAAGAGA
Found at i:345161 original size:16 final size:17
Alignment explanation
Indices: 345124--345180 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
345114 GGAAAAAAAC
345124 AAAAAAAAAAAGTAAGAA
1 AAAAAAAAAAAG-AAGAA
345142 AAAAAAAAAAAG-AGATA
1 AAAAAAAAAAAGAAGA-A
*
345159 AAAAAGAAAAAAAAAGAGA
1 AAAAA-AAAAAAGAAGA-A
345178 AAA
1 AAA
345181 TAAAGCCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 3 0.09
17 6 0.18
18 18 0.53
19 7 0.21
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (17 bp):
AAAAAAAAAAAGAAGAA
Found at i:345185 original size:21 final size:20
Alignment explanation
Indices: 345110--345185 Score: 84
Period size: 21 Copynumber: 3.8 Consensus size: 20
345100 AATACATAAC
*
345110 AAAAG-GAAAAAAACAAAAA
1 AAAAGAGAAAAAAAGAAAAA
* *
345129 AAAAAAGTAAGAAAA-AAAAA
1 AAAAGAG-AAAAAAAGAAAAA
345149 AAAAGAGATAAAAAAGAAAAA
1 AAAAGAGA-AAAAAAGAAAAA
345170 AAAAGAGAAAATAAAG
1 AAAAGAGAAAA-AAAG
345186 CCAAAAAAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
19 5 0.10
20 20 0.42
21 23 0.48
ACGTcount: A:0.82, C:0.01, G:0.13, T:0.04
Consensus pattern (20 bp):
AAAAGAGAAAAAAAGAAAAA
Found at i:347273 original size:110 final size:110
Alignment explanation
Indices: 347114--347445 Score: 487
Period size: 110 Copynumber: 3.0 Consensus size: 110
347104 CCAAACAACA
* * *
347114 TGATGTTTTCAAAAGAATTTTTAAAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATT
1 TGATGTTTTCAAATGAGTTTTT--AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATGATT
347179 TCCAATGAATTTTTAAAATAAGCTAAGCCTAATTTTTAGGGGTTTCT
64 TCCAATGAATTTTTAAAATAAGCTAAGCCTAATTTTTAGGGGTTTCT
* *
347226 TGATGTTTTCAAATGAGTTTTTAGAAACTAGGCCTGATTTTCAGGGGTTTCTTGAAGATGATTTC
1 TGATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATGATTTC
* *
347291 CAATGAATTTTTAAAATAAGCTAAGCCTAAATTTTAAGGGGTTTTT
66 CAATGAATTTTTAAAATAAGCTAAGCCT-AATTTTTAGGGGTTTCT
*
347337 TGATGTTTTCAAATGAGTTTTTAGAAACTATGCCTGA-TTTCAGGGGTTTCTTGATGAT-ATTTC
1 TGATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATGATTTC
* * * *
347400 CAAAGAA-TTTT-AAAGAAGTTATG-CTAA-TTTTAGGGGTTTCT
66 CAATGAATTTTTAAAATAAGCTAAGCCTAATTTTTAGGGGTTTCT
347441 TGATG
1 TGATG
347446 ATAACTGAAA
Statistics
Matches: 204, Mismatches: 15, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
104 17 0.08
105 2 0.01
106 2 0.01
107 9 0.04
108 4 0.02
109 11 0.05
110 88 0.43
111 51 0.25
112 20 0.10
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.41
Consensus pattern (110 bp):
TGATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATGATTTC
CAATGAATTTTTAAAATAAGCTAAGCCTAATTTTTAGGGGTTTCT
Found at i:347789 original size:60 final size:59
Alignment explanation
Indices: 347633--347789 Score: 235
Period size: 59 Copynumber: 2.6 Consensus size: 59
347623 AGATGTTTTC
* * *
347633 AACATTTCCTTTGCTCGATTCACAACACTTCGAATCATCAAGTCCCCACCAGAGTGGTT
1 AACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAAGTACCCACCAGAGGGGTT
* *
347692 AACATTTCCTTTGCTCGTTTCACAACACTTCAAATCAGCAACG-ACCCACCAGAGGGGTT
1 AACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAA-GTACCCACCAGAGGGGTT
*
347751 AACATTTCCTATTGCTTGATTCACAACACTTCGAATCAG
1 AACATTTCCT-TTGCTCGATTCACAACACTTCGAATCAG
347790 TTTAAGTCAT
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
59 62 0.70
60 26 0.30
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (59 bp):
AACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAAGTACCCACCAGAGGGGTT
Found at i:347888 original size:41 final size:41
Alignment explanation
Indices: 347812--347898 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
347802 GGGAAATCAG
* *
347812 TAAGTCTTTCAAGCATGATACTTAAATCCTTCGGGTCATCTA
1 TAAGTCTTTCAAGCAAGATAC-TAAATCCTTCGGGTCATCCA
* *
347854 TAAGTCTTTCGAGCAAGATGA-TAACTCCTTCGGGTCATCCA
1 TAAGTCTTTCAAGCAAGAT-ACTAAATCCTTCGGGTCATCCA
347895 TAAG
1 TAAG
347899 ACCTTCGGGC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 22 0.55
42 17 0.43
43 1 0.03
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (41 bp):
TAAGTCTTTCAAGCAAGATACTAAATCCTTCGGGTCATCCA
Found at i:349463 original size:19 final size:19
Alignment explanation
Indices: 349436--349473 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
349426 TAGTCACTTT
*
349436 ACATTTTATTTTCATTTGC
1 ACATGTTATTTTCATTTGC
*
349455 ACATGTTATTTTTATTTGC
1 ACATGTTATTTTCATTTGC
349474 TTATATTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (19 bp):
ACATGTTATTTTCATTTGC
Found at i:349516 original size:33 final size:31
Alignment explanation
Indices: 349458--349518 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
349448 CATTTGCACA
*
349458 TGTTATTTTTATTTGCTTATATTATGATCGT
1 TGTTATTTTTATTTGATTATATTATGATCGT
* *
349489 TGTTATATTTTATTTTATTTTAGTTATGAT
1 TGTTAT-TTTTATTTGATTATA-TTATGAT
349519 ATGTTTCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 6 0.24
32 12 0.48
33 7 0.28
ACGTcount: A:0.21, C:0.03, G:0.11, T:0.64
Consensus pattern (31 bp):
TGTTATTTTTATTTGATTATATTATGATCGT
Found at i:350013 original size:18 final size:15
Alignment explanation
Indices: 349987--350024 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
349977 GTCTGTTAAT
*
349987 TTATTATTTTA-AT-
1 TTATTATTTTATTTA
350000 TTATTATTTTATTTA
1 TTATTATTTTATTTA
350015 TTATTATTTT
1 TTATTATTTT
350025 TACCCTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.50
14 1 0.05
15 10 0.45
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTATTTTATTTA
Found at i:350015 original size:12 final size:13
Alignment explanation
Indices: 349982--350019 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
349972 TTTCAGTCTG
349982 TTAATTTATTATT
1 TTAATTTATTATT
349995 TTAATTTATTATT
1 TTAATTTATTATT
350008 TT-ATTTATTATT
1 TTAATTTATTATT
350020 ATTTTTACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTAATTTATTATT
Found at i:355823 original size:24 final size:24
Alignment explanation
Indices: 355796--355851 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
355786 AGAGCACATT
355796 CTTTGGAATACCAAATGTTCCAAC
1 CTTTGGAATACCAAATGTTCCAAC
355820 CTTTGGAATACCAAATGTTCCAAC
1 CTTTGGAATACCAAATGTTCCAAC
355844 CTTTGGAA
1 CTTTGGAA
355852 CTTCAATGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.30
Consensus pattern (24 bp):
CTTTGGAATACCAAATGTTCCAAC
Found at i:359746 original size:21 final size:21
Alignment explanation
Indices: 359720--359777 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
359710 ATTTACCTTG
**
359720 ATTGCGGTTGTCGCGGACGCT
1 ATTGCGGCCGTCGCGGACGCT
359741 ATTGCGGCCGTCGCGGACGCT
1 ATTGCGGCCGTCGCGGACGCT
*
359762 ATTACGGCCGTCGCGG
1 ATTGCGGCCGTCGCGG
359778 GTTACTCGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.10, C:0.29, G:0.38, T:0.22
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGACGCT
Found at i:362577 original size:194 final size:192
Alignment explanation
Indices: 362150--362668 Score: 604
Period size: 194 Copynumber: 2.7 Consensus size: 192
362140 ACAAAACCGT
* * * * * * *
362150 TTGAAATATGACAAAA-TCGATTTCAATTTGACACAATCAGTTAAGAGATATCAAAATTGTTGGA
1 TTGAAATTTGACAAAACTGGA-TTCAATTTGACAAAACCGGTAAAGAGATA-CAGAATTGTT-GA
* * * * *
362214 ATTTGTATCGATAATTTTATAAGTACATGTACAAAAGTATCGGTACTTTGGGAAATT-AAAAGAA
63 A--AGTATCGAT-ATTTTATAAGTATATGTACCATAGTATCGGTACTTTAGG-AATTGAAAAGAA
* *
362278 TTGCAATAATAGTGCCTATAAAGTATCAATACCTTAGACACATGTATAGATACATGACAATATAA
124 TTGCAATAATAGCGCCTAAAAAGTATCAATACCTTAGACACATGTATAGATACATGACAATATAA
*
362343 CATG
189 CAAG
* *
362347 TTGAAATTTGACAAAACAGGTTTCAATTTGACAAAACCGGTAAAGAGATACCAGAATTGTTGAAA
1 TTGAAATTTGACAAAACTGGATTCAATTTGACAAAACCGGTAAAGAGATA-CAGAATTGTTGAAA
* * * *
362412 GTATCGATATTATTATAAGTATATGTACCATAGTATTGGTATTTTAGGAATTGAAAGGAATTGCG
65 GTATCGATATT-TTATAAGTATATGTACCATAGTATCGGTACTTTAGGAATTGAAAAGAATTGCA
* * * *
362477 ATAATAGCGCCTAAAAAGTATCAAT-CCTTAGACACATGTTTCGTTATATGACAATATAACAAG
129 ATAATAGCGCCTAAAAAGTATCAATACCTTAGACACATGTATAGATACATGACAATATAACAAG
* * *
362540 TTGAAATTTGACAAAACTGGATTCAATTTTGACAAAACCGATAAAGCGCTACAGGAATTGTTGAA
1 TTGAAATTTGACAAAACTGGATTCAA-TTTGACAAAACCGGTAAAGAGATACA-GAATTGTTGAA
* **
362605 ATTATCGATA-CGT-T---TATATGTACCATAGTATCGGTACTTTAGGAATTGAAAAGAATTGCA
64 AGTATCGATATTTTATAAGTATATGTACCATAGTATCGGTACTTTAGGAATTGAAAAGAATTGCA
362665 ATAA
129 ATAA
362669 GAAAAATGTC
Statistics
Matches: 279, Mismatches: 38, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
188 46 0.16
191 1 0.00
192 1 0.00
193 66 0.24
194 112 0.40
196 3 0.01
197 49 0.18
198 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (192 bp):
TTGAAATTTGACAAAACTGGATTCAATTTGACAAAACCGGTAAAGAGATACAGAATTGTTGAAAG
TATCGATATTTTATAAGTATATGTACCATAGTATCGGTACTTTAGGAATTGAAAAGAATTGCAAT
AATAGCGCCTAAAAAGTATCAATACCTTAGACACATGTATAGATACATGACAATATAACAAG
Found at i:363816 original size:3 final size:3
Alignment explanation
Indices: 363808--363873 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
363798 ATATTACGGG
* * * *
363808 TTA TTA TTA ATA TTTA ATA ATA ATA TTA TTA TT- TATA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
363854 TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
363874 GTTTTTTACA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 1 0.02
3 52 0.93
4 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:372493 original size:257 final size:256
Alignment explanation
Indices: 372031--372944 Score: 906
Period size: 257 Copynumber: 3.7 Consensus size: 256
372021 ATTAAGTTAT
* * * * * *
372031 TTTG-AAAATGAAAAAGTGATTTCCAAAGTTTCTCATTTA-AATCTTTTCTGGAAATGAAAGTTT
1 TTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTAT-TTTT-AGAAAATGAAATTTT
* * * * * *
372094 TGAAAAGTAAGAAAGCGATTTTCAATGTTTTTTACCCAGTAAATTATCTCCAAAATTAATAAGTC
64 TGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAATAAGTA
*
372159 CTTCGAGCCATCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCATTTATAAGTCTTT
129 CTTCGAGCCATCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTT
* * ** * * *
372224 CAAGCGAGATGATAAGTCTTTTGGGCCATTCGTAAGACCT-TCGAGTATGAAGCTTTCACATGAA
194 CAAGCAAGATGATAAGTCATTCAGGCCATCCATAAGACCTCT-GAGTAGGAAG-TTTCACATGAA
* *
372288 TTTGAAAAATGAGAAAGCGGTTTCCAAAGTTTCTCCTTTAGTATTTTTAGAAAATGAAATTTTTG
1 TTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAAATGAAATTTTTG
* * * * * **
372353 AAAAGTAAGAAAGTGATTTCCAAAATTTCTTACCTAATAAACTATTTCCCAAATTTTTAAGTACT
66 AAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAATAAGTACT
* * * * * *
372418 TCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTTGGGTCATCTGTAAGTCTTTCG
131 TCGAGCCATCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCA
* * *
372483 AGCAAGATGATAAGTCATTCATGCCATCCATAAGACCTCTGGGTAGGATGTTTCACATGAA
196 AGCAAGATGATAAGTCATTCAGGCCATCCATAAGACCTCTGAGTAGGAAGTTTCACATGAA
* * * *
372544 TTTGAAAAATGGGGAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATTTTTT
1 TTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAAATGAAATTTTTG
*
372609 AAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTT-CAAAA--ATTAA-TA--
66 AAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAATAAGTACT
* * *
372668 ---AG---TC----A----TTCGGGCATGATGATTAAATTCTTCGGGTCATCTATAAGTCTTTCG
131 TCGAGCCATCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCA
* * * * *
372719 AGCGATATAATAAGTCCTTCAGG-----C--AAGA----T--GT------TTTCACATGAT
196 AGCAAGATGATAAGTCATTCAGGCCATCCATAAGACCTCTGAGTAGGAAGTTTCACATGAA
*
372761 TTTCGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAATTTTT
1 TTT-GAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAAATGAAATTTTT
** * * *
372826 GAAAAGTAAGAAAACGGTTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAGTAAGTCC
65 GAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAATAAGTAC
* * * * * *
372891 TTTGGGCCA-CCGTGAAGTCTTTCGAGCATGATTATTAAATCCTTCGGGTTATCT
130 TTCGAGCCATCAGT-AAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCT
372945 GTCGGTCTCA
Statistics
Matches: 557, Mismatches: 75, Indels: 69
0.79 0.11 0.10
Matches are distributed among these distances:
217 13 0.02
218 103 0.18
219 5 0.01
221 4 0.01
222 1 0.00
223 2 0.00
225 1 0.00
227 1 0.00
229 5 0.01
231 1 0.00
234 1 0.00
236 59 0.11
238 30 0.05
240 1 0.00
244 2 0.00
247 1 0.00
252 2 0.00
253 4 0.01
255 4 0.01
256 113 0.20
257 166 0.30
258 36 0.06
259 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (256 bp):
TTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTTAGAAAATGAAATTTTTG
AAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAATAAGTACT
TCGAGCCATCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCA
AGCAAGATGATAAGTCATTCAGGCCATCCATAAGACCTCTGAGTAGGAAGTTTCACATGAA
Found at i:375670 original size:20 final size:19
Alignment explanation
Indices: 375645--375695 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
375635 GAAATCCCTT
**
375645 TGAAAATACATGATTTTTAA
1 TGAAAATACATG-TCGTTAA
*
375665 TGAAAATACAAGTCGTTAA
1 TGAAAATACATGTCGTTAA
375684 TGAAAATACATG
1 TGAAAATACATG
375696 CTCTTGGCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (19 bp):
TGAAAATACATGTCGTTAA
Found at i:378499 original size:37 final size:37
Alignment explanation
Indices: 378409--378513 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
378399 TCTTTTCGTC
* *
378409 CTACTAGGATTCAAACTCATAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
378446 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
378483 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
378514 CCACAAGCAT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:378974 original size:2 final size:2
Alignment explanation
Indices: 378961--378997 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
378951 CTTTATTATT
*
378961 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
378998 TTAATTATAT
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:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:379264 original size:19 final size:18
Alignment explanation
Indices: 379242--379277 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
379232 ATTTTTCATT
*
379242 TATTTATTATTATTATTAC
1 TATTTAGTATT-TTATTAC
379261 TATTTAGTATTTTATTA
1 TATTTAGTATTTTATTA
379278 TAATATACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
TATTTAGTATTTTATTAC
Found at i:383838 original size:14 final size:13
Alignment explanation
Indices: 383798--383851 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
383788 AAAAGGGCAA
*
383798 AAAAGAAAAGAAGC
1 AAAA-AAAAGAAAC
383812 AAAAAAGAAGAAAAC
1 AAAAAA-AAG-AAAC
*
383827 AAAAAAAAGAAAG
1 AAAAAAAAGAAAC
*
383840 AACAAAAAGAAA
1 AAAAAAAAGAAA
383852 AGAGAAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 16 0.46
14 10 0.29
15 9 0.26
ACGTcount: A:0.80, C:0.06, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAC
Found at i:383853 original size:14 final size:15
Alignment explanation
Indices: 383795--383854 Score: 70
Period size: 15 Copynumber: 3.9 Consensus size: 15
383785 ACAAAAAGGG
383795 CAAAAAAGAAAAGAA
1 CAAAAAAGAAAAGAA
383810 GCAAAAAAGAAGAA-AA
1 -CAAAAAAGAA-AAGAA
*
383826 CAAAAAAAAGAAAGAA
1 CAAAAAAGA-AAAGAA
383842 C-AAAAAGAAAAGA
1 CAAAAAAGAAAAGA
383855 GAAAAAGGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
14 5 0.13
15 16 0.41
16 16 0.41
17 2 0.05
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (15 bp):
CAAAAAAGAAAAGAA
Done.