Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 51 of 54
Found at i:12072867 original size:17 final size:17
Alignment explanation
Indices: 12072845--12072883 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
12072835 GAGGTAACCC
*
12072845 ATTTTA-TTACTTTTTTT
1 ATTTTATTTA-TTTATTT
12072862 ATTTTATTTATTTATTT
1 ATTTTATTTATTTATTT
12072879 ATTTT
1 ATTTT
12072884 TATGTTTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (17 bp):
ATTTTATTTATTTATTT
Found at i:12074965 original size:14 final size:14
Alignment explanation
Indices: 12074911--12074977 Score: 64
Period size: 16 Copynumber: 4.6 Consensus size: 14
12074901 CTTCTATTAC
*
12074911 TTTATTTATTTTCTA
1 TTTATTTTTTTTC-A
*
12074926 ATTATTATTTTTTCA
1 TTTATT-TTTTTTCA
*
12074941 TTCAATATTTTTTT-A
1 TT-TAT-TTTTTTTCA
12074956 TTTATTTTTTTTCA
1 TTTATTTTTTTTCA
12074970 TTTATTTT
1 TTTATTTT
12074978 GATTAATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
13 7 0.16
14 11 0.26
15 10 0.23
16 14 0.33
17 1 0.02
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATTTTTTTTCA
Found at i:12075224 original size:23 final size:22
Alignment explanation
Indices: 12075198--12075243 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 22
12075188 ATCTTGTTGT
12075198 TCAACTAAAGTTGATCATCCCAA
1 TCAAC-AAAGTTGATCATCCCAA
*
12075221 T---CAAAGTTGATCATGCCAA
1 TCAACAAAGTTGATCATCCCAA
12075240 TCAA
1 TCAA
12075244 AATTATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 7
0.70 0.04 0.26
Matches are distributed among these distances:
19 17 0.89
20 1 0.05
23 1 0.05
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (22 bp):
TCAACAAAGTTGATCATCCCAA
Found at i:12075228 original size:19 final size:19
Alignment explanation
Indices: 12075204--12075244 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
12075194 TTGTTCAACT
12075204 AAAGTTGATCATCCCAATC
1 AAAGTTGATCATCCCAATC
*
12075223 AAAGTTGATCATGCCAATC
1 AAAGTTGATCATCCCAATC
12075242 AAA
1 AAA
12075245 ATTATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.24
Consensus pattern (19 bp):
AAAGTTGATCATCCCAATC
Found at i:12078215 original size:17 final size:17
Alignment explanation
Indices: 12078195--12078276 Score: 65
Period size: 17 Copynumber: 4.8 Consensus size: 17
12078185 TCATTTACCT
12078195 TACTATTTCTTTTATTG
1 TACTATTTCTTTTATTG
* **
12078212 TACTGTTTAATTTATTG
1 TACTATTTCTTTTATTG
* ** * *
12078229 TGCCGTATCTTTTGTTG
1 TACTATTTCTTTTATTG
*
12078246 TACTATATCTTTTATTG
1 TACTATTTCTTTTATTG
* *
12078263 TATTATTACTTTTA
1 TACTATTTCTTTTA
12078277 CTAATTGCAC
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 49 1.00
ACGTcount: A:0.20, C:0.11, G:0.10, T:0.60
Consensus pattern (17 bp):
TACTATTTCTTTTATTG
Found at i:12078336 original size:25 final size:25
Alignment explanation
Indices: 12078289--12078341 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
12078279 AATTGCACGT
* * *
12078289 CTAGAGTCAGGAATACACGAATGTA
1 CTAGAATCAGGAATACACAAATGCA
* *
12078314 CTAGAATCAGGAGTGCACAAATGCA
1 CTAGAATCAGGAATACACAAATGCA
12078339 CTA
1 CTA
12078342 ATAAGGAGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.19
Consensus pattern (25 bp):
CTAGAATCAGGAATACACAAATGCA
Found at i:12078361 original size:23 final size:23
Alignment explanation
Indices: 12078322--12078368 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
12078312 TACTAGAATC
*
12078322 AGGAGTGCACAAATGCACTAATA
1 AGGAGTACACAAATGCACTAATA
*
12078345 AGGAGTACA-AAACTGCACTGATA
1 AGGAGTACACAAA-TGCACTAATA
12078368 A
1 A
12078369 AGGACTGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (23 bp):
AGGAGTACACAAATGCACTAATA
Found at i:12078649 original size:29 final size:29
Alignment explanation
Indices: 12078597--12078655 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
12078587 ACCCAACCCA
* ** *
12078597 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCCAGCGACATTG
12078626 TAGGTCGCCATGCACTCCCAGCGACATTG
1 TAGGTCGCCATGCACTCCCAGCGACATTG
12078655 T
1 T
12078656 CTCCTCTTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.15, C:0.36, G:0.27, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACATTG
Found at i:12078719 original size:27 final size:27
Alignment explanation
Indices: 12078688--12078740 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
12078678 TATTTCTGCA
*
12078688 CGTCCCCTCTTGCTCCCCGCTGCATGT
1 CGTCCCCTCCTGCTCCCCGCTGCATGT
* *
12078715 CGTCCCCTCCTGTTCCCCGTTGCATG
1 CGTCCCCTCCTGCTCCCCGCTGCATG
12078741 CCGCTGCAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.04, C:0.47, G:0.19, T:0.30
Consensus pattern (27 bp):
CGTCCCCTCCTGCTCCCCGCTGCATGT
Found at i:12078973 original size:4 final size:4
Alignment explanation
Indices: 12078964--12079026 Score: 80
Period size: 4 Copynumber: 16.8 Consensus size: 4
12078954 ATTGCAGCCT
*
12078964 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG-- AGAA AGAA AGGA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
*
12079010 AGGA AG-A AG-A AGAA AGA
1 AGAA AGAA AGAA AGAA AGA
12079027 GAGATAACGC
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
2 2 0.04
3 6 0.11
4 47 0.85
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:12078974 original size:25 final size:26
Alignment explanation
Indices: 12078912--12078975 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
12078902 ACATAAAAGA
** *
12078912 AAGAAAGGGAGAAGAGATTGCAGTCG
1 AAGAAAGAAAGAAGAGATTGCAGTCC
* *
12078938 AAGAAAGGAAGAAGATATTGCAG-CC
1 AAGAAAGAAAGAAGAGATTGCAGTCC
*
12078963 TAGAAAGAAAGAA
1 AAGAAAGAAAGAA
12078976 AGAAAGAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 12 0.36
26 21 0.64
ACGTcount: A:0.50, C:0.08, G:0.31, T:0.11
Consensus pattern (26 bp):
AAGAAAGAAAGAAGAGATTGCAGTCC
Found at i:12081461 original size:23 final size:23
Alignment explanation
Indices: 12081401--12081464 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
12081391 CAGCTCATAT
*
12081401 AATTGCACC-TAAGAGCCACGTAG
1 AATTGCACCGT-AGTGCCACGTAG
* * *
12081424 AATTGCACTGGAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCACGTAG
12081447 AATTGCACCGTAGTGCCA
1 AATTGCACCGTAGTGCCA
12081465 TATAATAATG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.25, G:0.27, T:0.20
Consensus pattern (23 bp):
AATTGCACCGTAGTGCCACGTAG
Found at i:12081656 original size:103 final size:103
Alignment explanation
Indices: 12081480--12081697 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
12081470 TAATGTCCAT
* *
12081480 AAGGACCACATATCATTCCTTAAGAATCATATACATATGTCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
12081545 GACTTCACACATGTTCCAAAGAATACATATATGTCCTG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
12081583 AATGACCACATATCATTCTTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
12081648 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
12081686 AAGGACCACATA
1 AAGGACCACATA
12081698 GACCCTCTAC
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:12082210 original size:19 final size:20
Alignment explanation
Indices: 12082173--12082210 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12082163 TCTTTTTTTA
*
12082173 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
12082193 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
12082211 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:12082262 original size:21 final size:21
Alignment explanation
Indices: 12082238--12082280 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
12082228 TCATATTCGT
* *
12082238 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
12082259 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
12082280 T
1 T
12082281 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:12082677 original size:21 final size:21
Alignment explanation
Indices: 12082652--12082702 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
12082642 CTGATTATCA
12082652 CAACGCGATAATACGTGATCG
1 CAACGCGATAATACGTGATCG
*
12082673 CAACGTGATAATACGTGATCG
1 CAACGCGATAATACGTGATCG
12082694 CAACGCGAT
1 CAACGCGAT
12082703 TCTGACTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (21 bp):
CAACGCGATAATACGTGATCG
Found at i:12082718 original size:20 final size:20
Alignment explanation
Indices: 12082693--12082731 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
12082683 ATACGTGATC
12082693 GCAACGCGATTCTGACTATT
1 GCAACGCGATTCTGACTATT
12082713 GCAACGCGATTCTGACTAT
1 GCAACGCGATTCTGACTAT
12082732 CACATCACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (20 bp):
GCAACGCGATTCTGACTATT
Found at i:12084340 original size:20 final size:21
Alignment explanation
Indices: 12084315--12084375 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
12084305 TCTGAGAGAT
12084315 GGAGAT-AGACAGATTTCACC
1 GGAGATGAGACAGATTTCACC
* *
12084335 GGAGATGGGGACAGATTTCGCC
1 GGAGAT-GAGACAGATTTCACC
* *
12084357 GGAAATGGGGACAGATTTC
1 GGAGAT-GAGACAGATTTC
12084376 GTCGAAGATG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 6 0.17
22 30 0.83
ACGTcount: A:0.30, C:0.16, G:0.34, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACAGATTTCACC
Found at i:12084349 original size:22 final size:22
Alignment explanation
Indices: 12084322--12084390 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
12084312 GATGGAGATA
*
12084322 GACAGATTTCACCGGAGATGGG
1 GACAGATTTCGCCGGAGATGGG
*
12084344 GACAGATTTCGCCGGAAATGGG
1 GACAGATTTCGCCGGAGATGGG
* *
12084366 GACAGATTTCGTCGAAGATGGG
1 GACAGATTTCGCCGGAGATGGG
12084388 GAC
1 GAC
12084391 GGATGTTACC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.28, C:0.17, G:0.36, T:0.19
Consensus pattern (22 bp):
GACAGATTTCGCCGGAGATGGG
Found at i:12084597 original size:20 final size:20
Alignment explanation
Indices: 12084574--12084697 Score: 135
Period size: 20 Copynumber: 6.1 Consensus size: 20
12084564 TCACAACGCA
* *
12084574 ATAGTCAGAATCACCTTGCG
1 ATAGTCAGAATCGCGTTGCG
12084594 ATAGTCAGAATCGCGTTGCG
1 ATAGTCAGAATCGCGTTGCG
**
12084614 ATTATGT-ATTATCGCGTTGCG
1 A-TA-GTCAGAATCGCGTTGCG
12084635 ATAGTCAGAATCGCGTTGCG
1 ATAGTCAGAATCGCGTTGCG
** *
12084655 ATTATGT-ATTATCGCGTTACG
1 A-TA-GTCAGAATCGCGTTGCG
12084676 ATAGTCAGAATCGCGTTGCG
1 ATAGTCAGAATCGCGTTGCG
12084696 AT
1 AT
12084698 TTACATATTT
Statistics
Matches: 86, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.05
20 49 0.57
21 29 0.34
22 4 0.05
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
ATAGTCAGAATCGCGTTGCG
Found at i:12084646 original size:41 final size:41
Alignment explanation
Indices: 12084589--12084698 Score: 211
Period size: 41 Copynumber: 2.7 Consensus size: 41
12084579 CAGAATCACC
12084589 TTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCG
1 TTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCG
12084630 TTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCG
1 TTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCG
*
12084671 TTACGATAGTCAGAATCGCGTTGCGATT
1 TTGCGATAGTCAGAATCGCGTTGCGATT
12084699 TACATATTTG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (41 bp):
TTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCG
Found at i:12084742 original size:21 final size:21
Alignment explanation
Indices: 12084712--12084758 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
12084702 ATATTTGCAT
* *
12084712 TGCGATTTTCTAAAATCGCAA
1 TGCGAATTTCAAAAATCGCAA
*
12084733 TGCGAATTTCAAAAATCTCAA
1 TGCGAATTTCAAAAATCGCAA
*
12084754 AGCGA
1 TGCGA
12084759 TAGTCAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (21 bp):
TGCGAATTTCAAAAATCGCAA
Found at i:12084837 original size:19 final size:19
Alignment explanation
Indices: 12084807--12084859 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
12084797 GATAATGGAG
*
12084807 ATCGCGTTGCGATTTAAAT
1 ATCGCATTGCGATTTAAAT
*
12084826 ATCTCATTGCGATTTAAAT
1 ATCGCATTGCGATTTAAAT
12084845 ATCGCATTGCGATTT
1 ATCGCATTGCGATTT
12084860 TATTGGTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (19 bp):
ATCGCATTGCGATTTAAAT
Found at i:12086419 original size:65 final size:60
Alignment explanation
Indices: 12086313--12086434 Score: 163
Period size: 65 Copynumber: 1.9 Consensus size: 60
12086303 TAATAATTTG
* * *
12086313 ATATTTAATGATTTAATTATAATATGATTTAGTCATGATTACTAATAATTATTTATTATAA
1 ATATTTAATGATTTAATTATAATATCATTTAGTAATGATTACTAATAA-TAATTATTATAA
*
12086374 ATATTTAATGATTTAGATTTGATACTAATCATTTAGTAATGATTACTAATAATAATTATTA
1 ATATTTAATGATTTA-A-TT-ATAAT-ATCATTTAGTAATGATTACTAATAATAATTATTA
12086435 GTTTGATAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
61 15 0.28
62 1 0.02
63 2 0.04
64 12 0.23
65 23 0.43
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (60 bp):
ATATTTAATGATTTAATTATAATATCATTTAGTAATGATTACTAATAATAATTATTATAA
Found at i:12087762 original size:28 final size:29
Alignment explanation
Indices: 12087658--12087767 Score: 132
Period size: 29 Copynumber: 3.8 Consensus size: 29
12087648 ATGCATAGCG
* *
12087658 CGCCCTGAGTGCATGGCAACCTCTCCTTGGT
1 CGCCCGGAGTGCATGGCGACCTCT--TTGGT
* **
12087689 CGCCCGAAGTGCATGATGACCTCTTTGGT
1 CGCCCGGAGTGCATGGCGACCTCTTTGGT
*
12087718 CGCCCGGAGTTCATGGCGACCTCTTTGGT
1 CGCCCGGAGTGCATGGCGACCTCTTTGGT
*
12087747 CG-TCGGAGTGCATGGCGACCT
1 CGCCCGGAGTGCATGGCGACCT
12087768 ACGACTTCAC
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
28 17 0.25
29 32 0.47
31 19 0.28
ACGTcount: A:0.14, C:0.31, G:0.30, T:0.25
Consensus pattern (29 bp):
CGCCCGGAGTGCATGGCGACCTCTTTGGT
Found at i:12088024 original size:29 final size:30
Alignment explanation
Indices: 12087981--12088063 Score: 114
Period size: 29 Copynumber: 2.8 Consensus size: 30
12087971 GTGAATTCGT
*
12087981 AGGTCGCCATGCACTCCGGGCGACCAA-TG
1 AGGTCGCCATGCACTCCGGGCGACCAAGAG
*
12088010 AGGTCGCCATACACTCCGGGCGACCAAGGAG
1 AGGTCGCCATGCACTCCGGGCGACCAA-GAG
* *
12088041 AGGTCGCTATGCACTCAGGGCGA
1 AGGTCGCCATGCACTCCGGGCGA
12088064 GCTATGCATG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 26 0.55
31 21 0.45
ACGTcount: A:0.23, C:0.31, G:0.33, T:0.13
Consensus pattern (30 bp):
AGGTCGCCATGCACTCCGGGCGACCAAGAG
Found at i:12088633 original size:21 final size:21
Alignment explanation
Indices: 12088604--12088647 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12088594 AATTTAGTTA
12088604 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* * *
12088625 ATTATTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
12088646 AT
1 AT
12088648 ATTATATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:12088648 original size:28 final size:28
Alignment explanation
Indices: 12088617--12088682 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
12088607 AGTTTGTTAG
*
12088617 TATAAATTATTATTTTGTTAGTTTAAGT
1 TATAAATTATTAGTTTGTTAGTTTAAGT
*
12088645 TAT-ATTATATTAGTTTGTTAGTTTAAGT
1 TATAAAT-TATTAGTTTGTTAGTTTAAGT
*
12088673 TATATATTAT
1 TATAAATTAT
12088683 ATTATATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.91
29 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (28 bp):
TATAAATTATTAGTTTGTTAGTTTAAGT
Found at i:12092228 original size:31 final size:30
Alignment explanation
Indices: 12092159--12092231 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
12092149 ACCCTTAAAC
*
12092159 AACTAATAAAATATTCTTTTATATAACTAA
1 AACTAATAAACTATTCTTTTATATAACTAA
12092189 AACTAATAAACTATT-TTTTATTATAA-TATA
1 AACTAATAAACTATTCTTTTA-TATAACTA-A
*
12092219 CTACTAATAAACT
1 -AACTAATAAACT
12092232 TACTAACTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
29 7 0.18
30 20 0.53
31 11 0.29
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (30 bp):
AACTAATAAACTATTCTTTTATATAACTAA
Found at i:12092576 original size:13 final size:13
Alignment explanation
Indices: 12092537--12092584 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
12092527 CTCACAAGAG
12092537 CCTTATCTCCCTTT
1 CCTT-TCTCCCTTT
* *
12092551 CTTCTTCTTCCTTT
1 CCT-TTCTCCCTTT
12092565 CCTTTCTCCCTTT
1 CCTTTCTCCCTTT
12092578 -CTTTCTC
1 CCTTTCTC
12092585 GGCTTCAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 7 0.24
13 9 0.31
14 12 0.41
15 1 0.03
ACGTcount: A:0.02, C:0.42, G:0.00, T:0.56
Consensus pattern (13 bp):
CCTTTCTCCCTTT
Found at i:12092583 original size:12 final size:12
Alignment explanation
Indices: 12092542--12092584 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
12092532 AAGAGCCTTA
12092542 TCTCCCTTTCTTCT
1 TCTCCCTTTC-T-T
*
12092556 TCTTCCTTTCCTT
1 TCTCCCTTT-CTT
12092569 TCTCCCTTTCTT
1 TCTCCCTTTCTT
12092581 TCTC
1 TCTC
12092585 GGCTTCAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 7 0.27
13 9 0.35
14 9 0.35
15 1 0.04
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (12 bp):
TCTCCCTTTCTT
Found at i:12092814 original size:25 final size:26
Alignment explanation
Indices: 12092786--12092843 Score: 93
Period size: 25 Copynumber: 2.3 Consensus size: 26
12092776 TCACGCTGCA
12092786 ATTGCAGCTATGATGGCTGCAGCGG-
1 ATTGCAGCTATGATGGCTGCAGCGGC
*
12092811 ATTGCAGCTATGATGGTTGCAGCGGC
1 ATTGCAGCTATGATGGCTGCAGCGGC
12092837 A-TGCAGC
1 ATTGCAGC
12092844 GGGGAGCAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (26 bp):
ATTGCAGCTATGATGGCTGCAGCGGC
Found at i:12092875 original size:27 final size:27
Alignment explanation
Indices: 12092837--12092888 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
12092827 TTGCAGCGGC
* *
12092837 ATGCAGCGGGGAGCAGGAGGGGACGGT
1 ATGCAACGGGGAGCAAGAGGGGACGGT
12092864 ATGCAACGGGGAGCAAGAGGGGACG
1 ATGCAACGGGGAGCAAGAGGGGACG
12092889 TGCAGAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.27, C:0.15, G:0.52, T:0.06
Consensus pattern (27 bp):
ATGCAACGGGGAGCAAGAGGGGACGGT
Found at i:12092954 original size:29 final size:29
Alignment explanation
Indices: 12092921--12093037 Score: 171
Period size: 29 Copynumber: 4.0 Consensus size: 29
12092911 GCAAGAGGAG
* *
12092921 ACAAGGTCGCTGGGAGTGCATGGCAACCT
1 ACAAGGTCGCTGGGAGGGCATGGCGACCT
*
12092950 ACAAGGTCGCTGGGAGGGCATTGCGACCT
1 ACAAGGTCGCTGGGAGGGCATGGCGACCT
* *
12092979 ACAAGGTCGCCGGGAGTGCATGGCGACCT
1 ACAAGGTCGCTGGGAGGGCATGGCGACCT
* *
12093008 ACAAGGTCGCTCGGAGGGCATGGAGACCT
1 ACAAGGTCGCTGGGAGGGCATGGCGACCT
12093037 A
1 A
12093038 TGGGTTGGGT
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 78 1.00
ACGTcount: A:0.23, C:0.25, G:0.37, T:0.15
Consensus pattern (29 bp):
ACAAGGTCGCTGGGAGGGCATGGCGACCT
Found at i:12092994 original size:58 final size:58
Alignment explanation
Indices: 12092921--12093037 Score: 189
Period size: 58 Copynumber: 2.0 Consensus size: 58
12092911 GCAAGAGGAG
* * * *
12092921 ACAAGGTCGCTGGGAGTGCATGGCAACCTACAAGGTCGCTGGGAGGGCATTGCGACCT
1 ACAAGGTCGCCGGGAGTGCATGGCAACCTACAAGGTCGCTCGGAGGGCATGGAGACCT
*
12092979 ACAAGGTCGCCGGGAGTGCATGGCGACCTACAAGGTCGCTCGGAGGGCATGGAGACCT
1 ACAAGGTCGCCGGGAGTGCATGGCAACCTACAAGGTCGCTCGGAGGGCATGGAGACCT
12093037 A
1 A
12093038 TGGGTTGGGT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.23, C:0.25, G:0.37, T:0.15
Consensus pattern (58 bp):
ACAAGGTCGCCGGGAGTGCATGGCAACCTACAAGGTCGCTCGGAGGGCATGGAGACCT
Found at i:12094290 original size:17 final size:19
Alignment explanation
Indices: 12094251--12094290 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
12094241 TTATTAATAG
12094251 AAAATATAAAGAAAAATTT
1 AAAATATAAAGAAAAATTT
*
12094270 -AAATAT-AAG-AGAATTT
1 AAAATATAAAGAAAAATTT
12094286 AAAAT
1 AAAAT
12094291 TTTTAAGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 6 0.32
17 7 0.37
18 6 0.32
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (19 bp):
AAAATATAAAGAAAAATTT
Found at i:12097431 original size:15 final size:15
Alignment explanation
Indices: 12097411--12097446 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12097401 GGCATCTGAC
*
12097411 GTGTTACAGGTCACG
1 GTGTTACAGGGCACG
*
12097426 GTGTTACAGGGGACG
1 GTGTTACAGGGCACG
12097441 GTGTTA
1 GTGTTA
12097447 TCTCTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.39, T:0.28
Consensus pattern (15 bp):
GTGTTACAGGGCACG
Found at i:12100236 original size:22 final size:19
Alignment explanation
Indices: 12100191--12100229 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
12100181 TTTACATAAC
12100191 TTAAAAAGAAGAAAAAAAA
1 TTAAAAAGAAGAAAAAAAA
12100210 TTAAAAAGAAGAAAAAAAA
1 TTAAAAAGAAGAAAAAAAA
12100229 T
1 T
12100230 ACATAAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (19 bp):
TTAAAAAGAAGAAAAAAAA
Found at i:12104218 original size:19 final size:20
Alignment explanation
Indices: 12104171--12104218 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
12104161 TAAATAAACA
*
12104171 TAAAATTATGATACTTAATT
1 TAAAATTAAGATACTTAATT
* * *
12104191 TTAATTTAAGA-ATTTAATT
1 TAAAATTAAGATACTTAATT
12104210 TAAAATTAA
1 TAAAATTAA
12104219 TTCAATCAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (20 bp):
TAAAATTAAGATACTTAATT
Found at i:12105257 original size:41 final size:42
Alignment explanation
Indices: 12105199--12105316 Score: 175
Period size: 41 Copynumber: 2.8 Consensus size: 42
12105189 AACTATACTT
12105199 CAACATTCTCCATGCTTCTCAACTTCGAAGAACTTCATTCTC
1 CAACATTCTCCATGCTTCTCAACTTCGAAGAACTTCATTCTC
* *
12105241 CAACATTC-GCATGCTTCTCAACTTCGAAGAACTTCATTCTT
1 CAACATTCTCCATGCTTCTCAACTTCGAAGAACTTCATTCTC
* * **
12105282 CATCATTCTCCGTGCTTCTCAACCGCGAAGAACTT
1 CAACATTCTCCATGCTTCTCAACTTCGAAGAACTT
12105317 TTAACATCTT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 38 0.56
42 30 0.44
ACGTcount: A:0.25, C:0.32, G:0.10, T:0.32
Consensus pattern (42 bp):
CAACATTCTCCATGCTTCTCAACTTCGAAGAACTTCATTCTC
Found at i:12109026 original size:24 final size:24
Alignment explanation
Indices: 12108999--12109110 Score: 163
Period size: 24 Copynumber: 4.7 Consensus size: 24
12108989 TTCTATTATA
*
12108999 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
12109023 ATACTTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
*
12109047 ATACTTGACCTGGATTCTGATCGA
1 ATACTTGACCTGGATTCTGATCGG
* *
12109071 ATACTTGACCTGGATTTTGA-CTTG
1 ATACTTGACCTGGATTCTGATC-GG
*
12109095 ATACTTGACCTCGATT
1 ATACTTGACCTGGATT
12109111 ATGTTTTGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
23 1 0.01
24 80 0.99
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:12122407 original size:17 final size:17
Alignment explanation
Indices: 12122387--12122421 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
12122377 GCACAATCTG
12122387 AAACAAGATGAACTGTA
1 AAACAAGATGAACTGTA
*
12122404 AAACAAGATGAATTGTA
1 AAACAAGATGAACTGTA
12122421 A
1 A
12122422 GTCTCTACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (17 bp):
AAACAAGATGAACTGTA
Found at i:12124100 original size:2 final size:2
Alignment explanation
Indices: 12124093--12124129 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12124083 ATAGTTAAAC
12124093 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12124130 GTCATTTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12125941 original size:15 final size:15
Alignment explanation
Indices: 12125848--12125942 Score: 64
Period size: 15 Copynumber: 6.0 Consensus size: 15
12125838 AATATTACAA
* * *
12125848 ATTATATGTAAGAAT
1 ATTATATATAATATT
*
12125863 ATTATATATATTATT
1 ATTATATATAATATT
*
12125878 ATTATTTATAATATTATT
1 ATTA--TAT-ATAATATT
* *
12125896 ATTTATTATATAAAAGT
1 A-TTA-TATATAATATT
*
12125913 ATTATATATTATATT
1 ATTATATATAATATT
*
12125928 ATTATAAATAATATT
1 ATTATATATAATATT
12125943 TAAATTTTGA
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
15 36 0.56
16 3 0.05
17 9 0.14
18 13 0.20
19 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATTATATATAATATT
Found at i:12129179 original size:2 final size:2
Alignment explanation
Indices: 12129172--12129207 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12129162 TAATTTTATG
12129172 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12129208 TGTTAATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12129470 original size:16 final size:14
Alignment explanation
Indices: 12129439--12129465 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12129429 TATAAATACC
12129439 ATTTAATTTTTTAT
1 ATTTAATTTTTTAT
12129453 ATTTAATTTTTTA
1 ATTTAATTTTTTA
12129466 GATATATTAT
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTAATTTTTTAT
Found at i:12134698 original size:22 final size:21
Alignment explanation
Indices: 12134635--12134699 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 21
12134625 AAAACCAAAA
*
12134635 CCCTCAGG-GGGTATCGATTC
1 CCCTAAGGAGGGTATCGATTC
* * *
12134655 CCCTAAGGGGGGAATCGGTTC
1 CCCTAAGGAGGGTATCGATTC
12134676 CCCTTCAA-GAGGGTATCGATTC
1 CCC-T-AAGGAGGGTATCGATTC
12134698 CC
1 CC
12134700 TCTGAACCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 7 0.19
21 13 0.36
22 14 0.39
23 2 0.06
ACGTcount: A:0.18, C:0.29, G:0.29, T:0.23
Consensus pattern (21 bp):
CCCTAAGGAGGGTATCGATTC
Found at i:12140170 original size:17 final size:17
Alignment explanation
Indices: 12140148--12140181 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12140138 CGGTACCCCC
12140148 TTGGGGGGGAATCGATT
1 TTGGGGGGGAATCGATT
12140165 TTGGGGGGGAATCGATT
1 TTGGGGGGGAATCGATT
12140182 CCCTCTGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.47, T:0.29
Consensus pattern (17 bp):
TTGGGGGGGAATCGATT
Found at i:12141548 original size:29 final size:29
Alignment explanation
Indices: 12141502--12141806 Score: 402
Period size: 29 Copynumber: 10.6 Consensus size: 29
12141492 CGACCCGACC
12141502 CAGTGATATTTTGGTAATTATTTTTAAAA
1 CAGTGATATTTTGGTAATTATTTTTAAAA
* * *
12141531 CGGTGATATTTCGATAATTATTTTTAAAA
1 CAGTGATATTTTGGTAATTATTTTTAAAA
* * *
12141560 TAGTAATATTTCGGTAATTATTTTTAAAA
1 CAGTGATATTTTGGTAATTATTTTTAAAA
12141589 C-GATGATATTTTGGTAATTATTTTT-AAA
1 CAG-TGATATTTTGGTAATTATTTTTAAAA
*
12141617 TAGTGATATTTTGGTAATTATTTTTAAAA
1 CAGTGATATTTTGGTAATTATTTTTAAAA
**
12141646 TGGTGATATTTTGGTAATTATTTTTAAAA
1 CAGTGATATTTTGGTAATTATTTTTAAAA
*
12141675 CAGTGATATTTTGGTAATTATTGTTAAAA
1 CAGTGATATTTTGGTAATTATTTTTAAAA
* * *
12141704 CAATTATATTTTGGTAATTATTGTTAAAA
1 CAGTGATATTTTGGTAATTATTTTTAAAA
* *
12141733 CAATTATATTTTGGTAATTATTTTT-AAA
1 CAGTGATATTTTGGTAATTATTTTTAAAA
*
12141761 -AGTGATATTTTTGTAATTATTTTTAAAA
1 CAGTGATATTTTGGTAATTATTTTTAAAA
* *
12141789 AATGTGATATTTTTGTAA
1 CA-GTGATATTTTGGTAA
12141807 ATGGTTTTAA
Statistics
Matches: 249, Mismatches: 21, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
27 21 0.08
28 32 0.13
29 181 0.73
30 15 0.06
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.50
Consensus pattern (29 bp):
CAGTGATATTTTGGTAATTATTTTTAAAA
Found at i:12141713 original size:115 final size:115
Alignment explanation
Indices: 12141502--12141806 Score: 434
Period size: 115 Copynumber: 2.6 Consensus size: 115
12141492 CGACCCGACC
* * * *
12141502 CAGTGATATTTTGGTAATTATTTTTAAAACGGTGATATTTCGATAATTATTTTTAAAATAGTAAT
1 CAGTGATATTTTGGTAATTATTTTTAAAA-GGTGATATTTTGGTAATTATTTTTAAAAAAGTGAT
* * * *
12141567 ATTTCGGTAATTATTTTTAAAACGATGATATTTTGGTAATTATT-TTTAAA
65 ATTTTGGTAATTATTGTTAAAACAATGATATTTTGGTAATTATTGTTAAAA
* *
12141617 TAGTGATATTTTGGTAATTATTTTTAAAATGGTGATATTTTGGTAATTATTTTTAAAACAGTGAT
1 CAGTGATATTTTGGTAATTATTTTTAAAA-GGTGATATTTTGGTAATTATTTTTAAAAAAGTGAT
*
12141682 ATTTTGGTAATTATTGTTAAAACAATTATATTTTGGTAATTATTGTTAAAA
65 ATTTTGGTAATTATTGTTAAAACAATGATATTTTGGTAATTATTGTTAAAA
* * *
12141733 CAATTATATTTTGGTAATTATTTTTAAAA-GTGATATTTTTGTAATTATTTTTAAAAAATGTGAT
1 CAGTGATATTTTGGTAATTATTTTTAAAAGGTGATATTTTGGTAATTATTTTTAAAAAA-GTGAT
*
12141797 ATTTTTGTAA
65 ATTTTGGTAA
12141807 ATGGTTTTAA
Statistics
Matches: 171, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
114 27 0.16
115 113 0.66
116 31 0.18
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.50
Consensus pattern (115 bp):
CAGTGATATTTTGGTAATTATTTTTAAAAGGTGATATTTTGGTAATTATTTTTAAAAAAGTGATA
TTTTGGTAATTATTGTTAAAACAATGATATTTTGGTAATTATTGTTAAAA
Found at i:12142916 original size:26 final size:26
Alignment explanation
Indices: 12142863--12142916 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
12142853 AGGATAACTC
* *
12142863 TTTTATGAGATTTATTGTAGTATAAT
1 TTTTATGAGATTTATAGTACTATAAT
*
12142889 TTTTATGAGATTTACTAG-ACTATGAT
1 TTTTATGAGATTTA-TAGTACTATAAT
12142915 TT
1 TT
12142917 GTTTAGTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.52
Consensus pattern (26 bp):
TTTTATGAGATTTATAGTACTATAAT
Found at i:12148935 original size:19 final size:19
Alignment explanation
Indices: 12148912--12148974 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
12148902 TTAACCGGCT
* *
12148912 TGACCGGTCTGAATCGGTT
1 TGACCGATCTGAATCGGTC
*
12148931 TGACCGATTTGAATCGGTC
1 TGACCGATCTGAATCGGTC
12148950 TGACCGATCTGAATCGGTC
1 TGACCGATCTGAATCGGTC
12148969 TGACCG
1 TGACCG
12148975 GTTCGAACCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.29
Consensus pattern (19 bp):
TGACCGATCTGAATCGGTC
Found at i:12148992 original size:38 final size:37
Alignment explanation
Indices: 12148904--12148992 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 37
12148894 TGATGTTATT
* * *
12148904 AACCGGCTTGACCGGTCTGAATCGGTTTGACCGATTTG
1 AACCGG-TTGACCGATCTGAATCGGTCTGACCGATTCG
* *
12148942 AATCGGTCTGACCGATCTGAATCGGTCTGACCGGTTCG
1 AACCGGT-TGACCGATCTGAATCGGTCTGACCGATTCG
12148980 AACCCGGTTGACC
1 AA-CCGGTTGACC
12148993 CGACCCGACC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
37 1 0.02
38 38 0.88
39 4 0.09
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.26
Consensus pattern (37 bp):
AACCGGTTGACCGATCTGAATCGGTCTGACCGATTCG
Found at i:12149269 original size:29 final size:29
Alignment explanation
Indices: 12149009--12149318 Score: 318
Period size: 29 Copynumber: 10.6 Consensus size: 29
12148999 GACCTGACCT
*
12149009 AGTGATAGTTTGGTAATTATTTTTAAAAC
1 AGTGATATTTTGGTAATTATTTTTAAAAC
* * *
12149038 GGTGATATTTCGATAATTATTTTTAAAAC
1 AGTGATATTTTGGTAATTATTTTTAAAAC
* * *
12149067 GGTGATATTTCGATAATTATTTTTAAAAC
1 AGTGATATTTTGGTAATTATTTTTAAAAC
* * *
12149096 ATTGATATTTCGGTAATTATTTTTAAAAT
1 AGTGATATTTTGGTAATTATTTTTAAAAC
*
12149125 AGTGATATTTTGGTTATTATTTTTAAAAC
1 AGTGATATTTTGGTAATTATTTTTAAAAC
*
12149154 GGTGATATTTTGGTAATTATTTTTAAAAC
1 AGTGATATTTTGGTAATTATTTTTAAAAC
** *
12149183 -GATGATATTTTGGTAATTATAGTTCAAAC
1 AG-TGATATTTTGGTAATTATTTTTAAAAC
* * *
12149212 AGAT-ACATTTTGGTAATTTTTTTTAAAAA
1 AG-TGATATTTTGGTAATTATTTTTAAAAC
** *
12149241 AGTGATATTTTTTTAATTATTTTTAAAAAA
1 AGTGATATTTTGGTAATTATTTTT-AAAAC
* * * *
12149271 AGGTGATATTTTTGTAAATAGTTTTAAAAAT
1 A-GTGATATTTTGGTAATTA-TTTTTAAAAC
* *
12149302 AGTGCTATTTTCGTAAT
1 AGTGATATTTTGGTAAT
12149319 AATTGTTGTG
Statistics
Matches: 241, Mismatches: 34, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
28 2 0.01
29 192 0.80
30 22 0.09
31 21 0.09
32 4 0.02
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (29 bp):
AGTGATATTTTGGTAATTATTTTTAAAAC
Found at i:12149271 original size:31 final size:31
Alignment explanation
Indices: 12149236--12149317 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 31
12149226 AATTTTTTTT
* * *
12149236 AAAAAAGTGATATTTTTTTAATTATTTTTAA
1 AAAAAAGTGATATTTTTGTAAATAGTTTTAA
*
12149267 AAAAAGGTGATATTTTTGTAAATAGTTTT-A
1 AAAAAAGTGATATTTTTGTAAATAGTTTTAA
* * *
12149297 AAAATAGTGCTATTTTCGTAA
1 AAAAAAGTGATATTTTTGTAA
12149318 TAATTGTTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 18 0.42
31 25 0.58
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45
Consensus pattern (31 bp):
AAAAAAGTGATATTTTTGTAAATAGTTTTAA
Found at i:12149319 original size:29 final size:28
Alignment explanation
Indices: 12149232--12149319 Score: 95
Period size: 30 Copynumber: 3.0 Consensus size: 28
12149222 TGGTAATTTT
* *
12149232 TTTTAAAAAAGTGATATTTTTTTAATTAT
1 TTTTAAAAAAGTGATATTTTTGTAA-TAG
12149261 TTTTAAAAAAAGGTGATATTTTTGTAAATAG
1 TTTT-AAAAAA-GTGATATTTTTGT-AATAG
* *
12149292 TTTTAAAAATAGTGCTATTTTCGTAATA
1 TTTTAAAAA-AGTGATATTTTTGTAATA
12149320 ATTGTTGTGG
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
29 8 0.16
30 22 0.43
31 19 0.37
32 2 0.04
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (28 bp):
TTTTAAAAAAGTGATATTTTTGTAATAG
Found at i:12149708 original size:142 final size:141
Alignment explanation
Indices: 12149524--12149813 Score: 526
Period size: 142 Copynumber: 2.0 Consensus size: 141
12149514 TAACCAAGAA
* *
12149524 TTTGAATTTTTGAAAAGTCATACTTTATGTTTTTCGACGTCCTGATTCCGATTCCGTAATTCGTT
1 TTTGAATTTTCGAAAAGTCATACTTTATGTTTTTCGACGTCCTGATTCCGATTCCGTAATCCGTT
12149589 TGGTCAAATTCAGAATCGAAAGCCTCCAAATTGATAGTCAAACCCGAAAAATGCTTATGTACTTA
66 TGGTCAAATTCAGAATCGAAAGCCTCCAAATTGATAGTCAAACCCGAAAAATGCTTATGTACTTA
12149654 AGAGTTTTAGC
131 AGAGTTTTAGC
* *
12149665 TTTTGAATTTTCGAAAAGTCATACTTTATGTTTTTCGATGTCCTGATTCCGATTTCGTAATCCGT
1 -TTTGAATTTTCGAAAAGTCATACTTTATGTTTTTCGACGTCCTGATTCCGATTCCGTAATCCGT
*
12149730 TTGGTCAAATTCAGAATCGAAAGCCTCCAAATTGATAGTCAAACCTGAAAAATGCTTATGTACTT
65 TTGGTCAAATTCAGAATCGAAAGCCTCCAAATTGATAGTCAAACCCGAAAAATGCTTATGTACTT
12149795 AAGAGTTTTAGC
130 AAGAGTTTTAGC
12149807 TTTGAAT
1 TTTGAAT
12149814 GATTGAGTAA
Statistics
Matches: 143, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
141 7 0.05
142 136 0.95
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (141 bp):
TTTGAATTTTCGAAAAGTCATACTTTATGTTTTTCGACGTCCTGATTCCGATTCCGTAATCCGTT
TGGTCAAATTCAGAATCGAAAGCCTCCAAATTGATAGTCAAACCCGAAAAATGCTTATGTACTTA
AGAGTTTTAGC
Found at i:12157450 original size:27 final size:27
Alignment explanation
Indices: 12157420--12157473 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
12157410 TTTTTTTCAT
12157420 AAAAATACATATGTTTAACAAAAGCAAAA
1 AAAAAT-CATAT-TTTAACAAAAGCAAAA
* *
12157449 AAAAATTATATTTTAACAAATGCAA
1 AAAAATCATATTTTAACAAAAGCAA
12157474 GCTTGTGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 13 0.57
28 4 0.17
29 6 0.26
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (27 bp):
AAAAATCATATTTTAACAAAAGCAAAA
Found at i:12157954 original size:24 final size:25
Alignment explanation
Indices: 12157904--12157954 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
12157894 CGGTTTCAGT
12157904 TTTTTTCGGTTATCGATTTTTTAGATC
1 TTTTTTCGGTTAT--ATTTTTTAGATC
*
12157931 TTTTTTCGGTTAT-TTTTTTGGATC
1 TTTTTTCGGTTATATTTTTTAGATC
12157955 GGATTGGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 10 0.43
27 13 0.57
ACGTcount: A:0.12, C:0.10, G:0.16, T:0.63
Consensus pattern (25 bp):
TTTTTTCGGTTATATTTTTTAGATC
Found at i:12159278 original size:18 final size:18
Alignment explanation
Indices: 12159255--12159289 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12159245 TTTATACAAC
12159255 GAGATTTAGAGAGAACGT
1 GAGATTTAGAGAGAACGT
* *
12159273 GAGATTTTGGGAGAACG
1 GAGATTTAGAGAGAACG
12159290 CGGATCGACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.37, T:0.23
Consensus pattern (18 bp):
GAGATTTAGAGAGAACGT
Found at i:12159915 original size:53 final size:53
Alignment explanation
Indices: 12159835--12159940 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
12159825 AAATTCTGAG
*
12159835 TTCGCACGTGTCTGCATGTAAATTAAACCATTATTGACTGATACACAAACTTT
1 TTCGCACGTGTCTGCATGCAAATTAAACCATTATTGACTGATACACAAACTTT
*
12159888 TTCGCACGTGTCTGCATGCAAATTAAACCATTGTTGACTGATACACAAACTTT
1 TTCGCACGTGTCTGCATGCAAATTAAACCATTATTGACTGATACACAAACTTT
12159941 CTCCAGGAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (53 bp):
TTCGCACGTGTCTGCATGCAAATTAAACCATTATTGACTGATACACAAACTTT
Found at i:12162169 original size:22 final size:22
Alignment explanation
Indices: 12162142--12162183 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
12162132 TGAAAAGGAT
12162142 AATTAGTGTCACAAACAAAATA
1 AATTAGTGTCACAAACAAAATA
12162164 AATTAGTGTCACAAACAAAA
1 AATTAGTGTCACAAACAAAA
12162184 GAGAAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (22 bp):
AATTAGTGTCACAAACAAAATA
Found at i:12164789 original size:15 final size:15
Alignment explanation
Indices: 12164769--12164807 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
12164759 TCCTTATTGA
12164769 TCGGCGGTGAAGCAT
1 TCGGCGGTGAAGCAT
12164784 TCGGCGGTGAAGCAT
1 TCGGCGGTGAAGCAT
12164799 TCGGCGGTG
1 TCGGCGGTG
12164808 GTCCATTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.15, C:0.21, G:0.44, T:0.21
Consensus pattern (15 bp):
TCGGCGGTGAAGCAT
Found at i:12165556 original size:127 final size:126
Alignment explanation
Indices: 12165252--12165716 Score: 734
Period size: 127 Copynumber: 3.7 Consensus size: 126
12165242 ATCTGTTAAA
* *
12165252 GTGATGACAC-AGCTAATCTGTTCATGAGTCTTGGCCATCTAAGGGTGATAACAAGGTTCCTACG
1 GTGATGACACTA-CTCATCTGTTCATGAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCTACG
* * * *
12165316 TGATGAGGACGGCTGGTTATCTGAGTTGACACAACTCATACATAATGAAGAGATCTAGTCAG
65 TGATGAGGACGGCTGGTTATCTGAGTTGACACAACTCTTACATAATGAGGAGATCTGGTCAT
*
12165378 GTGATGACACTACTCATCTATTCATGAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCTACGT
1 GTGATGACACTACTCATCTGTTCATGAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCTACGT
*
12165443 GATGAGGACGGCTGGTTATCGGAGTTGACACAACTCCTTACATAATGAGGAGATCTGGTCAT
66 GATGAGGACGGCTGGTTATCTGAGTTGACACAACT-CTTACATAATGAGGAGATCTGGTCAT
* * *
12165505 GTGATGACACTGCTCATTTGTTCATGAGTCTTGGCCATCTAAGGGTGATAACACAGTTCCTACGT
1 GTGATGACACTACTCATCTGTTCATGAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCTACGT
* * * *
12165570 GATAAGGACGGCTGGTTATCTAAGTTGACAGAGCTTCTTACATAATGAGGAGATCTGGTCAT
66 GATGAGGACGGCTGGTTATCTGAGTTGACACAAC-TCTTACATAATGAGGAGATCTGGTCAT
* * *
12165632 ATGATGACACTACTCATTTGTTCATGAGTTTTGGCCATCTAAGGGTGATAACACGGTTCCTACGT
1 GTGATGACACTACTCATCTGTTCATGAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCTACGT
12165697 GATGAGGACGGCTGGTTATC
66 GATGAGGACGGCTGGTTATC
12165717 AATGCTCATA
Statistics
Matches: 314, Mismatches: 22, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
126 94 0.30
127 219 0.70
128 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (126 bp):
GTGATGACACTACTCATCTGTTCATGAGTCTTGGCCATCTAAGGGTGATAACACGGTTCCTACGT
GATGAGGACGGCTGGTTATCTGAGTTGACACAACTCTTACATAATGAGGAGATCTGGTCAT
Found at i:12166737 original size:10 final size:10
Alignment explanation
Indices: 12166722--12166755 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
12166712 TTGAGCCCTC
12166722 CTTTCTTTTT
1 CTTTCTTTTT
12166732 CTTTCTTTTT
1 CTTTCTTTTT
12166742 CTTTTCTTTTT
1 C-TTTCTTTTT
12166753 CTT
1 CTT
12166756 CTTCTTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:12166747 original size:11 final size:11
Alignment explanation
Indices: 12166723--12166761 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
12166713 TGAGCCCTCC
12166723 TTTCTTTTTC-
1 TTTCTTTTTCT
12166733 TTTCTTTTTCT
1 TTTCTTTTTCT
12166744 TTTCTTTTTCT
1 TTTCTTTTTCT
12166755 TCTTCTT
1 T-TTCTT
12166762 CAAGTGTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.37
11 12 0.44
12 5 0.19
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:12173654 original size:29 final size:30
Alignment explanation
Indices: 12173608--12173680 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
12173598 TTTAAATTTG
* * *
12173608 GATGCATGTTATTGGTAATGCT-TTA-TAAT
1 GATGCATTTTATTAGTAATG-TGTTACAAAT
*
12173637 GATGCATTTTGTTAGTAATGTGTTACAAAT
1 GATGCATTTTATTAGTAATGTGTTACAAAT
12173667 GATGCATTTTATTA
1 GATGCATTTTATTA
12173681 TGCATAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.03
29 20 0.54
30 16 0.43
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.45
Consensus pattern (30 bp):
GATGCATTTTATTAGTAATGTGTTACAAAT
Found at i:12173712 original size:13 final size:13
Alignment explanation
Indices: 12173694--12173720 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12173684 ATAATAAATG
12173694 ATGCAAATGCAAA
1 ATGCAAATGCAAA
12173707 ATGCAAATGCAAA
1 ATGCAAATGCAAA
12173720 A
1 A
12173721 GACATCGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (13 bp):
ATGCAAATGCAAA
Found at i:12180169 original size:3 final size:3
Alignment explanation
Indices: 12180161--12180188 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12180151 ACCCGAATGA
12180161 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12180189 TCTCAAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12182125 original size:20 final size:21
Alignment explanation
Indices: 12182100--12182140 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12182090 GAATATCCGG
*
12182100 ATCTG-ATTTTTTTTTTGGAT
1 ATCTGAATTTTTTTTTCGGAT
12182120 ATCTGAATTTTTTTTTCGGAT
1 ATCTGAATTTTTTTTTCGGAT
12182141 CGAATACGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.17, C:0.07, G:0.15, T:0.61
Consensus pattern (21 bp):
ATCTGAATTTTTTTTTCGGAT
Found at i:12182193 original size:16 final size:17
Alignment explanation
Indices: 12182162--12182197 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
12182152 CATTATTTTA
12182162 GATATCTGAAATTTTCG
1 GATATCTGAAATTTTCG
12182179 GATATCTGAAA-TTTCG
1 GATATCTGAAATTTTCG
12182195 GAT
1 GAT
12182198 TGGATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (17 bp):
GATATCTGAAATTTTCG
Found at i:12186586 original size:108 final size:108
Alignment explanation
Indices: 12186397--12186591 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 108
12186387 TTCTTTATAA
**
12186397 GCTTATCCTGAATTTCCTGCACAAGCTGCGGCAAATTAGGATCGGTCGCCTTCCTCACAGCCACA
1 GCTTATCCTGAATTTCCTGCACAAGCTGCGGCAAATTAGGATCAATCGCCTTCCTCACAGCCACA
12186462 TGATTCCCACTCCTTTCATTTTGCCTCCTATGGTTGACGGGCC
66 TGATTCCCACTCCTTTCATTTTGCCTCCTATGGTTGACGGGCC
* * * * *
12186505 GCTTATCCTGTATTTCCTGCACAAGCTGCGGCGAATTAGGATCAATCTCCTTCCTCACCGTCACA
1 GCTTATCCTGAATTTCCTGCACAAGCTGCGGCAAATTAGGATCAATCGCCTTCCTCACAGCCACA
* *
12186570 TGATTCTCACTCCTTTCCTTTT
66 TGATTCCCACTCCTTTCATTTT
12186592 CCCTATCTCT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 78 1.00
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.32
Consensus pattern (108 bp):
GCTTATCCTGAATTTCCTGCACAAGCTGCGGCAAATTAGGATCAATCGCCTTCCTCACAGCCACA
TGATTCCCACTCCTTTCATTTTGCCTCCTATGGTTGACGGGCC
Found at i:12190190 original size:46 final size:46
Alignment explanation
Indices: 12190104--12190191 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
12190094 AAATAGTACC
*
12190104 AATAATAAATAATATAATAATATTATTAAATATACCAATAAATAGT
1 AATAATAAATAATATAATAATATTACTAAATATACCAATAAATAGT
* *
12190150 AATAAT-AATAA-ATAATAATATATACTATATAATACTAATAAA
1 AATAATAAATAATATAATAATAT-TACTAAAT-ATACCAATAAA
12190192 AAAATACGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 10 0.27
45 11 0.30
46 16 0.43
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (46 bp):
AATAATAAATAATATAATAATATTACTAAATATACCAATAAATAGT
Found at i:12190934 original size:2 final size:2
Alignment explanation
Indices: 12190929--12190989 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
12190919 ACCATAAATA
12190929 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12190971 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
12190990 AGTTAAGGTG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12199691 original size:12 final size:13
Alignment explanation
Indices: 12199669--12199702 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
12199659 TAAGATTTTC
12199669 TTTGAAAATCATT
1 TTTGAAAATCATT
12199682 TTTG-AAATCATT
1 TTTGAAAATCATT
*
12199694 TTTTAAAAT
1 TTTGAAAAT
12199703 TTCTCCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (13 bp):
TTTGAAAATCATT
Found at i:12199727 original size:17 final size:17
Alignment explanation
Indices: 12199705--12199747 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
12199695 TTTAAAATTT
12199705 CTCCCCCTTACTTTATC
1 CTCCCCCTTACTTTATC
*
12199722 CTCCCCCTTACTTTATT
1 CTCCCCCTTACTTTATC
12199739 CTCCCCCTT
1 CTCCCCCTT
12199748 TTTGTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.09, C:0.49, G:0.00, T:0.42
Consensus pattern (17 bp):
CTCCCCCTTACTTTATC
Found at i:12200858 original size:15 final size:15
Alignment explanation
Indices: 12200838--12200867 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12200828 CAATCTTTTT
12200838 TTCGTTATCTAAACC
1 TTCGTTATCTAAACC
12200853 TTCGTTATCTAAACC
1 TTCGTTATCTAAACC
12200868 AAAAATATTA
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:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (15 bp):
TTCGTTATCTAAACC
Found at i:12201457 original size:13 final size:12
Alignment explanation
Indices: 12201423--12201461 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
12201413 ATCCTAATGG
12201423 ACAATTTTTGAAA
1 ACAA-TTTTGAAA
*
12201436 ACTATTTTGAAA
1 ACAATTTTGAAA
12201448 ACAATGTTTGAAA
1 ACAAT-TTTGAAA
12201461 A
1 A
12201462 ATCATAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (12 bp):
ACAATTTTGAAA
Found at i:12202003 original size:21 final size:20
Alignment explanation
Indices: 12201933--12202009 Score: 75
Period size: 23 Copynumber: 3.6 Consensus size: 20
12201923 AACCCGATAG
**
12201933 GTGTATCGATACAC-TCTTGA
1 GTGTATCGATACACAT-TCAA
12201953 GTGTATCGATACACATTCAA
1 GTGTATCGATACACATTCAA
*
12201973 GGAATGTATCGGTACACATTCATA
1 -G--TGTATCGATACACATTCA-A
12201997 GTGTATCGATACA
1 GTGTATCGATACA
12202010 TAGCGAGGGG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
20 16 0.33
21 13 0.27
23 18 0.38
24 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (20 bp):
GTGTATCGATACACATTCAA
Found at i:12204658 original size:10 final size:9
Alignment explanation
Indices: 12204623--12204721 Score: 90
Period size: 10 Copynumber: 10.3 Consensus size: 9
12204613 GCTGCTGGAA
*
12204623 ACCGGTTTA
1 ACCGGTTTG
*
12204632 ACCGGTTTTCA
1 ACCGG-TTT-G
12204643 ACCGGTTCTG
1 ACCGGTT-TG
12204653 ACCGGTTTG
1 ACCGGTTTG
*
12204662 ACCGGTTTCA
1 ACCGGTTT-G
*
12204672 ACCGGTTCG
1 ACCGGTTTG
12204681 AACCGGTTTG
1 -ACCGGTTTG
*
12204691 ACCGGTCTG
1 ACCGGTTTG
12204700 AACCGGTTTG
1 -ACCGGTTTG
*
12204710 ACCGGTCTG
1 ACCGGTTTG
12204719 ACC
1 ACC
12204722 CGACCCGACC
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
9 34 0.45
10 35 0.46
11 7 0.09
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:12204667 original size:19 final size:19
Alignment explanation
Indices: 12204624--12204721 Score: 87
Period size: 19 Copynumber: 5.1 Consensus size: 19
12204614 CTGCTGGAAA
* * *
12204624 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
12204644 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
12204663 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
12204683 CCGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
12204702 CCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
12204720 CC
1 CC
12204722 CGACCCGACC
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
18 6 0.09
19 40 0.58
20 15 0.22
21 8 0.12
ACGTcount: A:0.15, C:0.29, G:0.28, T:0.29
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:12204685 original size:29 final size:28
Alignment explanation
Indices: 12204623--12204721 Score: 126
Period size: 29 Copynumber: 3.4 Consensus size: 28
12204613 GCTGCTGGAA
*
12204623 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
12204653 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * *
12204681 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
*
12204710 ACCGGTCTGACC
1 ACCGGTTTGACC
12204722 CGACCCGACC
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
28 12 0.19
29 38 0.60
30 13 0.21
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.28
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:12204728 original size:5 final size:5
Alignment explanation
Indices: 12204718--12204775 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
12204708 TGACCGGTCT
* *
12204718 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
12204767 GACCC GACC
1 GACCC GACC
12204776 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:12204744 original size:22 final size:22
Alignment explanation
Indices: 12204718--12204782 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
12204708 TGACCGGTCT
12204718 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
12204740 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
12204762 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
12204783 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:12211995 original size:19 final size:19
Alignment explanation
Indices: 12211970--12212104 Score: 186
Period size: 19 Copynumber: 7.1 Consensus size: 19
12211960 ACCGGTTTTC
*
12211970 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTCTG
*
12211990 -ACCGGTTTCAACCGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
12212009 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
*
12212028 AACCGGTTTGACCGGTCCG
1 AACCGGTTTGACCGGTCTG
12212047 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
12212066 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
12212085 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
12212104 A
1 A
12212105 CCCGACCCGA
Statistics
Matches: 107, Mismatches: 4, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
18 2 0.02
19 97 0.91
20 8 0.07
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.26
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:12212013 original size:29 final size:28
Alignment explanation
Indices: 12211951--12212106 Score: 147
Period size: 29 Copynumber: 5.4 Consensus size: 28
12211941 GCTGCTGGAA
*
12211951 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
12211981 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
*
12212009 AACCGGTTTGACCGG-TTCGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTC-AACCGGTTCG
** *
12212038 ACCGGTCCGAACCGGTTT-GACCGG-TCTG
1 ACCGGTTTG-ACCGGTTTCAACCGGTTC-G
* * *
12212066 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
*
12212095 ACCGGTCTGACC
1 ACCGGTTTGACC
12212107 CGACCCGACC
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
27 1 0.01
28 35 0.33
29 54 0.51
30 16 0.15
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.27
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:12212101 original size:38 final size:38
Alignment explanation
Indices: 12211950--12212104 Score: 190
Period size: 38 Copynumber: 4.0 Consensus size: 38
12211940 GGCTGCTGGA
* * *
12211950 AACCGGTTTAACCGGTTTTCAACCGGTTCTGACCGGTTTG
1 AACCGGTTTAACCGG-TCTGAACCGGTT-TGACCGGTCTG
12211990 -ACCGGTTTCAACCGGT-TCGAACCGGTTTGACCGGT-TCG
1 AACCGGTTT-AACCGGTCT-GAACCGGTTTGACCGGTCT-G
* *
12212028 AACCGGTTTGACCGGTCCGAACCGGTTTGACCGGTCTG
1 AACCGGTTTAACCGGTCTGAACCGGTTTGACCGGTCTG
*
12212066 AACCGGTTTGACCGGTCTGAACCGGTTTGACCGGTCTG
1 AACCGGTTTAACCGGTCTGAACCGGTTTGACCGGTCTG
12212104 A
1 A
12212105 CCCGACCCGA
Statistics
Matches: 105, Mismatches: 4, Indels: 14
0.85 0.03 0.11
Matches are distributed among these distances:
37 1 0.01
38 72 0.69
39 26 0.25
40 6 0.06
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (38 bp):
AACCGGTTTAACCGGTCTGAACCGGTTTGACCGGTCTG
Found at i:12212113 original size:5 final size:5
Alignment explanation
Indices: 12212103--12212160 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
12212093 TGACCGGTCT
* *
12212103 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
12212152 GACCC GACC
1 GACCC GACC
12212161 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:12212117 original size:38 final size:38
Alignment explanation
Indices: 12212000--12212117 Score: 121
Period size: 38 Copynumber: 3.1 Consensus size: 38
12211990 ACCGGTTTCA
* ****
12212000 ACCGGTTCGAACCGGTTTGACCGGT-TCGAACCGGTTTG
1 ACCGGTCCGAACCGGTTTGACCGGTCT-GAACCGACCCG
****
12212038 ACCGGTCCGAACCGGTTTGACCGGTCTGAACCGGTTTG
1 ACCGGTCCGAACCGGTTTGACCGGTCTGAACCGACCCG
* *
12212076 ACCGGTCTGAACCGGTTTGACCGGTCTGACCCGACCCG
1 ACCGGTCCGAACCGGTTTGACCGGTCTGAACCGACCCG
12212114 ACCG
1 ACCG
12212118 TTGACCCGAC
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
38 71 0.99
39 1 0.01
ACGTcount: A:0.16, C:0.31, G:0.31, T:0.22
Consensus pattern (38 bp):
ACCGGTCCGAACCGGTTTGACCGGTCTGAACCGACCCG
Found at i:12212129 original size:22 final size:22
Alignment explanation
Indices: 12212103--12212167 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
12212093 TGACCGGTCT
12212103 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
12212125 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
12212147 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
12212168 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:12212169 original size:7 final size:7
Alignment explanation
Indices: 12212157--12212187 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
12212147 GACCCGACCC
12212157 GACCGTT
1 GACCGTT
12212164 GACCGTT
1 GACCGTT
12212171 GACCGTT
1 GACCGTT
12212178 GACCGTT
1 GACCGTT
12212185 GAC
1 GAC
12212188 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:12218409 original size:27 final size:27
Alignment explanation
Indices: 12218371--12218428 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
12218361 ATTAAATGAT
12218371 TCTGATTTTGTTATCTTGCGTGTTGTC
1 TCTGATTTTGTTATCTTGCGTGTTGTC
12218398 TCTGATTTTGTTATCTTGCGTGTTGTC
1 TCTGATTTTGTTATCTTGCGTGTTGTC
12218425 TCTG
1 TCTG
12218429 CAGGTGGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.07, C:0.16, G:0.22, T:0.55
Consensus pattern (27 bp):
TCTGATTTTGTTATCTTGCGTGTTGTC
Found at i:12218811 original size:3 final size:3
Alignment explanation
Indices: 12218803--12218832 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12218793 TAATATGGAT
12218803 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12218833 TATGTATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12222008 original size:19 final size:20
Alignment explanation
Indices: 12221961--12222016 Score: 73
Period size: 18 Copynumber: 3.0 Consensus size: 20
12221951 ATCCATTCTC
*
12221961 TTTTATAAAAGTTTTAA-AT
1 TTTTATAATAGTTTTAATAT
12221980 TTTTAT-ATA-TTTTAATAT
1 TTTTATAATAGTTTTAATAT
*
12221998 TTTTATAATATTTTTAATA
1 TTTTATAATAGTTTTAATA
12222017 ATTTATTTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 6 0.18
18 10 0.30
19 9 0.27
20 8 0.24
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTTATAATAGTTTTAATAT
Found at i:12222021 original size:19 final size:18
Alignment explanation
Indices: 12221972--12222022 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
12221962 TTTATAAAAG
*
12221972 TTTTAA-ATTTTTATATA
1 TTTTAATATATTTATATA
*
12221989 TTTTAATATTTTTATAATA
1 TTTTAATATATTTAT-ATA
12222008 TTTTTAATA-ATTTAT
1 -TTTTAATATATTTAT
12222023 TTCGTCTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 6 0.20
18 8 0.27
19 8 0.27
20 8 0.27
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTAATATATTTATATA
Found at i:12222394 original size:32 final size:34
Alignment explanation
Indices: 12222347--12222420 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
12222337 CCCGAACCCG
* *
12222347 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAA
*
12222381 AAAATATTATATATATAATTAATATAAAATATAA
1 AAAATATTATATATATAATTAATATAAAAAATAA
12222415 AAAATA
1 AAAATA
12222421 AAAAATATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAA
Found at i:12222440 original size:34 final size:35
Alignment explanation
Indices: 12222369--12222449 Score: 83
Period size: 41 Copynumber: 2.1 Consensus size: 35
12222359 ATATAATTAA
12222369 TATAAAAAATATAAAATATTATATATATAATTAATATAAAA
1 TATAAAAAATATAAAA-A-TAT-TATAT-A-T-ATATAAAA
*
12222410 TATAAAAAATA-AAAAATATTATATATATATATATA
1 TATAAAAAATATAAAAATATTATATATATATA-AAA
12222445 TATAA
1 TATAA
12222450 TCGGGGCGGG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
34 5 0.13
35 8 0.21
36 1 0.03
37 5 0.13
38 3 0.08
39 1 0.03
40 4 0.11
41 11 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (35 bp):
TATAAAAAATATAAAAATATTATATATATATAAAA
Found at i:12225642 original size:25 final size:25
Alignment explanation
Indices: 12225613--12225668 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
12225603 AATCAAGAAG
12225613 TGACATATTATAATGTTATCAACAT
1 TGACATATTATAATGTTATCAACAT
*
12225638 TGACATATTATAATGTTATGAACAT
1 TGACATATTATAATGTTATCAACAT
12225663 TGACAT
1 TGACAT
12225669 TTCTGTACGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (25 bp):
TGACATATTATAATGTTATCAACAT
Found at i:12238501 original size:15 final size:15
Alignment explanation
Indices: 12238451--12238507 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
12238441 TCAAATAAGT
*
12238451 ATATATTAAAATAAA
1 ATATATTAAATTAAA
*
12238466 ATATAATACTAATTAAA
1 ATATATTA--AATTAAA
12238483 ATATATATAAATT-AA
1 ATATAT-TAAATTAAA
12238498 ATATATTAAA
1 ATATATTAAA
12238508 AAATAAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 4 0.11
15 15 0.42
16 4 0.11
17 11 0.31
18 2 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATATTAAATTAAA
Found at i:12238503 original size:17 final size:16
Alignment explanation
Indices: 12238450--12238507 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
12238440 ATCAAATAAG
*
12238450 TATATATTAAAATAAAA
1 TATATA-TAAATTAAAA
12238467 TATA-ATACTAATTAAAA
1 TATATATA--AATTAAAA
12238484 TATATATAAATT-AAA
1 TATATATAAATTAAAA
12238499 TATAT-TAAA
1 TATATATAAA
12238508 AAATAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
14 4 0.11
15 10 0.27
16 5 0.14
17 15 0.41
18 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
TATATATAAATTAAAA
Found at i:12238561 original size:30 final size:31
Alignment explanation
Indices: 12238490--12238562 Score: 78
Period size: 32 Copynumber: 2.4 Consensus size: 31
12238480 AAAATATATA
12238490 TAAATTAAATATATTAAAAAATAAAATAAAAT
1 TAAATTAAATATATTAAAAAAT-AAATAAAAT
* * *
12238522 TAAACTAAATATA-TAAAAAGT-AATAAACT
1 TAAATTAAATATATTAAAAAATAAATAAAAT
*
12238551 TGTAATTAAATA
1 T-AAATTAAATA
12238563 AAGTATTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 8 0.23
30 8 0.23
31 7 0.20
32 12 0.34
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (31 bp):
TAAATTAAATATATTAAAAAATAAATAAAAT
Found at i:12239051 original size:71 final size:71
Alignment explanation
Indices: 12238935--12239078 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
12238925 CCCTAAACGC
12238935 CTGGCCCGAAGGGCCAGGCTTCCTCATTTGCTTCTTTCTCAGCTTCTCTCTAAAATGAGAGAATT
1 CTGGCCCGAAGGGCCAGGCTTCCTCATTTGCTTCTTTCTCAGCTTCTCTCTAAAATGAGAGAATT
12239000 TAAATT
66 TAAATT
12239006 CTGGCCCGAAGGGCCAGGCTTCCTCATTTGCTTCTTTCTCAGCTTCTCTCTAAAATGAGAGAATT
1 CTGGCCCGAAGGGCCAGGCTTCCTCATTTGCTTCTTTCTCAGCTTCTCTCTAAAATGAGAGAATT
12239071 TAAATT
66 TAAATT
12239077 CT
1 CT
12239079 CTCGCTTCTC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (71 bp):
CTGGCCCGAAGGGCCAGGCTTCCTCATTTGCTTCTTTCTCAGCTTCTCTCTAAAATGAGAGAATT
TAAATT
Found at i:12239805 original size:26 final size:26
Alignment explanation
Indices: 12239775--12239829 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
12239765 TCTGGTTGGT
* *
12239775 CTGGGCCGGTTCTGGTTTGTTTGTAA
1 CTGGGCCGGTCCAGGTTTGTTTGTAA
*
12239801 CTGGGCCGGTCCAGTTTTGTTTGTAA
1 CTGGGCCGGTCCAGGTTTGTTTGTAA
12239827 CTG
1 CTG
12239830 TTTGTAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.09, C:0.18, G:0.33, T:0.40
Consensus pattern (26 bp):
CTGGGCCGGTCCAGGTTTGTTTGTAA
Found at i:12239893 original size:21 final size:21
Alignment explanation
Indices: 12239841--12239901 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
12239831 TTGTAAATAA
* *
12239841 TAATTATAAT-ATAATATAATT
1 TAATTTTAATAATAATA-ATTT
* *
12239862 TAATATAAATAATAATAATTT
1 TAATTTTAATAATAATAATTT
12239883 TAATTTTAATAATAATAAT
1 TAATTTTAATAATAATAAT
12239902 AAAAACAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 27 0.82
22 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATTTTAATAATAATAATTT
Found at i:12240823 original size:378 final size:379
Alignment explanation
Indices: 12240060--12240846 Score: 1447
Period size: 378 Copynumber: 2.1 Consensus size: 379
12240050 AGAGGTCTTA
* * *
12240060 AAAACATCATGCACTGCATGACTTACAGATGACCCCAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 AAAACATCATGCACTGAAGGACTTACAGATGACCCCAAGGCTTTGAAAACATCAAAAAGCTCCCG
*
12240125 AAAGCTTTTTGGAAACATCATGCACTGCAGGACTTAAAGATGACCCTAAGGCTTTGAAAACATCA
66 AAAGCTTTTTGGAAACATCATGCACTGAAGGACTTAAAGATGACCCTAAGGCTTTGAAAACATCA
12240190 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTT
131 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTT
12240255 TGAAAACATCAAAAGATCCGAAGGCTTTTTGGAAATATCATGCACTGAAGGACTTACAGATGACC
196 TGAAAACATCAAAAGATCCGAAGGCTTTTTGGAAATATCATGCACTGAAGGACTTACAGATGACC
*
12240320 CTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACT
261 CTAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACT
12240385 TACAAATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
326 TACAAATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
*
12240439 -AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 AAAACATCATGCACTGAAGGACTTACAGATGACCCCAAGGCTTTGAAAACATCAAAAAGCTCCCG
* *
12240503 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
66 AAAGCTTTTTGGAAACATCATGCACTGAAGGACTTAAAGATGACCCTAAGGCTTTGAAAACATCA
12240568 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTT
131 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTT
12240633 TGAAAACATCAAAAAGATCCCGAAGGCTTTTTGG-AA-A-CATGCACTGAAGGACTTACAGATGA
196 TGAAAACATC-AAAAGAT-CCGAAGGCTTTTTGGAAATATCATGCACTGAAGGACTTACAGATGA
12240695 CCCTAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
259 CCCTAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGA
*
12240760 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
324 CTTACAAATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
12240816 AAAACATCATGCACTGAAGGACTTACAGATG
1 AAAACATCATGCACTGAAGGACTTACAGATG
12240847 TGGGAAATAG
Statistics
Matches: 396, Mismatches: 9, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
377 144 0.36
378 228 0.58
379 9 0.02
380 15 0.04
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (379 bp):
AAAACATCATGCACTGAAGGACTTACAGATGACCCCAAGGCTTTGAAAACATCAAAAAGCTCCCG
AAAGCTTTTTGGAAACATCATGCACTGAAGGACTTAAAGATGACCCTAAGGCTTTGAAAACATCA
AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTT
TGAAAACATCAAAAGATCCGAAGGCTTTTTGGAAATATCATGCACTGAAGGACTTACAGATGACC
CTAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACT
TACAAATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
Found at i:12240872 original size:76 final size:76
Alignment explanation
Indices: 12240061--12240846 Score: 1420
Period size: 76 Copynumber: 10.4 Consensus size: 76
12240051 GAGGTCTTAA
* * * *
12240061 AAACATCATGCACTGCATGACTTACAGATGACCCCAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
12240126 AAGCTTTTTGG
66 AGGCTTTTTGG
* *
12240137 AAACATCATGCACTGCAGGACTTAAAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
12240202 AGGCTTTTTGG
66 AGGCTTTTTGG
*
12240213 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGAT-CCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
12240276 AGGCTTTTTGG
66 AGGCTTTTTGG
*
12240287 AAATATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
12240352 AGGCTTTTTGG
66 AGGCTTTTTGG
*
12240363 AAACATCATGCACTGAAGGACTTACAAATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
12240428 AGGCTTTTTGG
66 AGGCTTTTTGG
12240439 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
12240504 AGGCTTTTTGG
66 AGGCTTTTTGG
12240515 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
12240580 AGGCTTTTTGG
66 AGGCTTTTTGG
*
12240591 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
12240656 AGGCTTTTTGG
66 AGGCTTTTTGG
*
12240667 -AA-A-CATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
12240729 AGGCTTTTTGG
66 AGGCTTTTTGG
12240740 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
12240805 AGGCTTTTTGG
66 AGGCTTTTTGG
12240816 AAAACATCATGCACTGAAGGACTTACAGATG
1 -AAACATCATGCACTGAAGGACTTACAGATG
12240847 TGGGAAATAG
Statistics
Matches: 689, Mismatches: 15, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
73 70 0.10
74 69 0.10
75 15 0.02
76 505 0.73
77 30 0.04
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:12241558 original size:22 final size:22
Alignment explanation
Indices: 12241531--12241573 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
12241521 TTTGTTTTTG
12241531 AAAAGAGAATCTATCATCTTTA
1 AAAAGAGAATCTATCATCTTTA
12241553 AAAAGAGAATCTATCATCTTT
1 AAAAGAGAATCTATCATCTTT
12241574 GAAGAGTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (22 bp):
AAAAGAGAATCTATCATCTTTA
Found at i:12243136 original size:29 final size:29
Alignment explanation
Indices: 12243094--12243153 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
12243084 CTGATTCTGT
12243094 TTGAAAAGGGTATTCAGCATGCCCCAATA
1 TTGAAAAGGGTATTCAGCATGCCCCAATA
12243123 TTGAAAAGGGTATTCAGCATGCCCCAATA
1 TTGAAAAGGGTATTCAGCATGCCCCAATA
12243152 TT
1 TT
12243154 TGCTTCTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (29 bp):
TTGAAAAGGGTATTCAGCATGCCCCAATA
Found at i:12250777 original size:22 final size:18
Alignment explanation
Indices: 12250734--12250805 Score: 56
Period size: 18 Copynumber: 3.7 Consensus size: 18
12250724 ACAGAAAAAT
* *
12250734 AAATAATAAAATACT-TGC
1 AAATAAT-AAATATTATGA
12250752 AAATAATGAAATATTAATAAGA
1 AAATAAT-AAATATT-AT--GA
*
12250774 AAATATATAAATACTATGA
1 AAATA-ATAAATATTATGA
12250793 AAATAATAAATAT
1 AAATAATAAATAT
12250806 ATAAAAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
18 20 0.45
19 7 0.16
20 1 0.02
21 2 0.05
22 12 0.27
23 2 0.05
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29
Consensus pattern (18 bp):
AAATAATAAATATTATGA
Found at i:12250804 original size:18 final size:19
Alignment explanation
Indices: 12250734--12250802 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 19
12250724 ACAGAAAAAT
*
12250734 AAATAATAAAATACT-TGC
1 AAATAATAAAATACTATGA
* *
12250752 AAATAATGAAATATTAATAAGA
1 AAATAAT-AAA-A-TACTATGA
12250774 AAAT-ATATAAATACTATGA
1 AAATAATA-AAATACTATGA
12250793 AAATAATAAA
1 AAATAATAAA
12250803 TATATAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
18 7 0.17
19 15 0.38
20 6 0.15
21 7 0.17
22 5 0.12
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (19 bp):
AAATAATAAAATACTATGA
Found at i:12250813 original size:18 final size:19
Alignment explanation
Indices: 12250752--12250814 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 19
12250742 AAATACTTGC
*
12250752 AAATAATGAAATATTAATAAGA
1 AAATAAT-AAATACT-ATAA-A
*
12250774 AAATATATAAATACTAT-GA
1 AAATA-ATAAATACTATAAA
12250793 AAATAATAAATA-TATAAA
1 AAATAATAAATACTATAAA
12250811 AAAT
1 AAAT
12250815 TTGAAAAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 3 0.08
18 12 0.33
19 6 0.17
21 2 0.06
22 11 0.31
23 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (19 bp):
AAATAATAAATACTATAAA
Found at i:12251572 original size:20 final size:22
Alignment explanation
Indices: 12251547--12251588 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
12251537 AAAATTAATC
12251547 AAATAATATA-T-ATTAAAATA
1 AAATAATATACTAATTAAAATA
12251567 AAATAATATACTAATTAAAATA
1 AAATAATATACTAATTAAAATA
12251589 TTATAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.50
21 1 0.05
22 9 0.45
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATAATATACTAATTAAAATA
Found at i:12251600 original size:16 final size:16
Alignment explanation
Indices: 12251560--12251611 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
12251550 TAATATATAT
*
12251560 TAAAA-TAAAATAATA
1 TAAAATTAAAATATTA
*
12251575 TACTAATTAAAATATTA
1 TA-AAATTAAAATATTA
12251592 TAAAATTAAAAATATT-
1 TAAAATT-AAAATATTA
12251608 TAAA
1 TAAA
12251612 CAATAATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 2 0.06
16 10 0.32
17 19 0.61
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAAATTAAAATATTA
Found at i:12252819 original size:26 final size:26
Alignment explanation
Indices: 12252789--12252843 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
12252779 TCTGGTTGGT
* *
12252789 CTGGGCCGGTTCTGGTTTGTTTGTAA
1 CTGGGCCGGTCCAGGTTTGTTTGTAA
* *
12252815 CTGGGCTGGTCCAGTTTTGTTTGTAA
1 CTGGGCCGGTCCAGGTTTGTTTGTAA
12252841 CTG
1 CTG
12252844 TTTGTAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.09, C:0.16, G:0.33, T:0.42
Consensus pattern (26 bp):
CTGGGCCGGTCCAGGTTTGTTTGTAA
Found at i:12252858 original size:3 final size:3
Alignment explanation
Indices: 12252850--12252917 Score: 50
Period size: 3 Copynumber: 22.7 Consensus size: 3
12252840 ACTGTTTGTA
* *
12252850 AAT AAT AAT TAT AAT -AT AAT AAT AAT ATTT AAT -AT AAAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT -AAT AAT AAT
** **
12252895 AAT TTT AAT TTT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
12252918 AAACAAAAAT
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
2 4 0.08
3 41 0.84
4 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
AAT
Found at i:12252916 original size:27 final size:27
Alignment explanation
Indices: 12252852--12252917 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
12252842 TGTTTGTAAA
*
12252852 TAATAATTATAATATAATAATAATATT
1 TAATAATAATAATATAATAATAATATT
**
12252879 TAAT-ATAAATAATAATAATTTTAAT-TT
1 TAATAAT-AATAAT-ATAATAATAATATT
12252906 TAATAATAATAA
1 TAATAATAATAA
12252918 AAACAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 2 0.06
27 20 0.61
28 11 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TAATAATAATAATATAATAATAATATT
Found at i:12254312 original size:21 final size:20
Alignment explanation
Indices: 12254285--12254334 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
12254275 TTTTGTTATG
*
12254285 ATTTTTTTAACCCCAAATTT
1 ATTTTTTTAACCCCAAATGT
12254305 ATTTTTTTAACCCCAAATGT
1 ATTTTTTTAACCCCAAATGT
12254325 ATTTTTTTAA
1 ATTTTTTTAA
12254335 TTATAGTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.16, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTTTTTTAACCCCAAATGT
Found at i:12260697 original size:19 final size:19
Alignment explanation
Indices: 12260660--12260707 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
12260650 CTAAATCATT
12260660 TTTTCAAAATTTCATTTTTA
1 TTTTCAAAA-TTCATTTTTA
*
12260680 TTTTCAAAA-TCAATTTTTG
1 TTTTCAAAATTC-ATTTTTA
*
12260699 CTTTCAAAA
1 TTTTCAAAA
12260708 CCAAATCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 14 0.56
20 9 0.36
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTTCAAAATTCATTTTTA
Found at i:12263387 original size:20 final size:20
Alignment explanation
Indices: 12263364--12263406 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12263354 ATTCCACCAT
**
12263364 ATGCAACTATATTCTCCTAA
1 ATGCAACTATATGATCCTAA
*
12263384 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
12263404 ATG
1 ATG
12263407 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:12264597 original size:83 final size:83
Alignment explanation
Indices: 12264498--12264663 Score: 332
Period size: 83 Copynumber: 2.0 Consensus size: 83
12264488 GATTGGAGCA
12264498 CTAGTATAGACCAAAATTCTCCACACATATAACAATTCCACCTTTAAAATATTTTGCCTTGGCAT
1 CTAGTATAGACCAAAATTCTCCACACATATAACAATTCCACCTTTAAAATATTTTGCCTTGGCAT
12264563 TTTGTTCTCTTTTCGCTC
66 TTTGTTCTCTTTTCGCTC
12264581 CTAGTATAGACCAAAATTCTCCACACATATAACAATTCCACCTTTAAAATATTTTGCCTTGGCAT
1 CTAGTATAGACCAAAATTCTCCACACATATAACAATTCCACCTTTAAAATATTTTGCCTTGGCAT
12264646 TTTGTTCTCTTTTCGCTC
66 TTTGTTCTCTTTTCGCTC
12264664 TTTTTTACTG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.39
Consensus pattern (83 bp):
CTAGTATAGACCAAAATTCTCCACACATATAACAATTCCACCTTTAAAATATTTTGCCTTGGCAT
TTTGTTCTCTTTTCGCTC
Done.