Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003022.1 Hibiscus syriacus cultivar Beakdansim tig00006280_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: 62456
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6776 original size:22 final size:22
Alignment explanation
Indices: 6748--6804 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
6738 ATATCTACAT
*
6748 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCCC
*
6770 TCTTCAAAGACGATAGATTCCC
1 TCTTCAAAGATGATAGATTCCC
*
6792 TTTTCAAAGATGA
1 TCTTCAAAGATGA
6805 AGGTTTTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCCC
Found at i:8738 original size:31 final size:31
Alignment explanation
Indices: 8685--8791 Score: 94
Period size: 31 Copynumber: 3.4 Consensus size: 31
8675 GTTCTACGGA
*
8685 ACATATGGACAGAATTACCTATGTCTTTCGAG
1 ACATATGGACAGTA-TACCTATGTCTTTCGAG
***
8717 ACATATGGACAGTATACCTATGTTCTAAGGA-
1 ACATATGGACAGTATACCTATG-TCTTTCGAG
* *
8748 ACATATGGACAGT-TCACCTAGGTTTTTCG-G
1 ACATATGGACAGTAT-ACCTATGTCTTTCGAG
*
8778 AACCTATGGACAGT
1 -ACATATGGACAGT
8792 TGCCGAGGAT
Statistics
Matches: 61, Mismatches: 10, Indels: 9
0.76 0.12 0.11
Matches are distributed among these distances:
30 4 0.07
31 39 0.64
32 18 0.30
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (31 bp):
ACATATGGACAGTATACCTATGTCTTTCGAG
Found at i:8830 original size:30 final size:30
Alignment explanation
Indices: 8779--8850 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
8769 GTTTTTCGGA
* * * *
8779 ACCTATGGACAGTTGCCGAGGATCTTTATT
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
8809 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
8839 ACCTCTGGATAG
1 ACCTCTGGATAG
8851 GTCATGCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:13256 original size:11 final size:11
Alignment explanation
Indices: 13240--13275 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
13230 TATGCACCGA
13240 TGCATCAGTAG
1 TGCATCAGTAG
13251 TGCATC-G-A-
1 TGCATCAGTAG
13259 TGCATCAGTAG
1 TGCATCAGTAG
13270 TGCATC
1 TGCATC
13276 GATGCATACC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.27
9 2 0.09
10 2 0.09
11 12 0.55
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (11 bp):
TGCATCAGTAG
Found at i:13259 original size:19 final size:19
Alignment explanation
Indices: 13232--13282 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
13222 ATGCATTTTA
*
13232 TGCACCGATGCATCAGTAG
1 TGCATCGATGCATCAGTAG
13251 TGCATCGATGCATCAGTAG
1 TGCATCGATGCATCAGTAG
13270 TGCATCGATGCAT
1 TGCATCGATGCAT
13283 ACCTTCATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (19 bp):
TGCATCGATGCATCAGTAG
Found at i:14002 original size:31 final size:30
Alignment explanation
Indices: 13963--14056 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 30
13953 ATAGACATAA
13963 TTACCTATGTCTTTCGAGACATATGGACAG
1 TTACCTATGTCTTTCGAGACATATGGACAG
***
13993 TATACCTATGTTCTAAGGA-ACATATGGACAG
1 T-TACCTATG-TCTTTCGAGACATATGGACAG
* * *
14024 TTCACCTAGGTTTTTCG-GAACCTATGGACAG
1 TT-ACCTATGTCTTTCGAG-ACATATGGACAG
14055 TT
1 TT
14057 GCCGAGGATC
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
30 5 0.10
31 40 0.80
32 5 0.10
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (30 bp):
TTACCTATGTCTTTCGAGACATATGGACAG
Found at i:14094 original size:30 final size:30
Alignment explanation
Indices: 14043--14114 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
14033 GTTTTTCGGA
* * * *
14043 ACCTATGGACAGTTGCCGAGGATCTTTATT
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
14073 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
14103 ACCTCTGGATAG
1 ACCTCTGGATAG
14115 GTCCTGCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:15132 original size:113 final size:112
Alignment explanation
Indices: 14930--15490 Score: 694
Period size: 112 Copynumber: 4.9 Consensus size: 112
14920 GCAAAGATTC
* *
14930 GAATCCATCACTCAATGGATCAACATTTCC-TGAAGAGTTCATAATGAGAAGAGCTCATCTGAAG
1 GAATCCATCACTCAATGGATCAACATTACCATGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
14994 AAGGGAGAAGAAGTTCATAACGAGAAGAACTTGTTTAACCTTTTGCTT
66 AA-GGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
*
15042 GAATCCATTACTCAATGGATCAACATTACCATGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATCCATCACTCAATGGATCAACATTACCATGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
** *
15107 AAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTTAACCTTTTGCTT
66 AAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
* * * *
15155 GAATCTATTACTCAATGGATTAACATTACCATGAAGAGTTCATAATGAGAAGAACTCATCTGAAA
1 GAATCCATCACTCAATGGATCAACATTACCATGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
15220 AAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
66 AAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
* * * * * * * *
15267 TAATTCATCACTCGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAATAACTCATCTGAAG
1 GAATCCATCACTCAATGGATCAACATTACCATGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
15332 AAGGAGAAGAAGTTCATAACGAGAAGAGCTCGTTCAACCTTTTGCTT
66 AAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
* * ** * * * *
15379 GATTCTATCACAGAAGGAGAT-AGATCATCATCAACATTTCCAGAAGTGTTCATAATGAGAAAAA
1 GAATCCATCACTCAATG-GATCA-A-CAT--T-ACCA--T---GAAGAGTTCATAATGAGAAGAA
* *
15443 CTCATCTGAAGAAGGAGAAGAAATTCATAATGAGAAGAATTTGTTCAA
55 CTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
15491 ACTTGCCTTA
Statistics
Matches: 392, Mismatches: 44, Indels: 16
0.87 0.10 0.04
Matches are distributed among these distances:
112 179 0.46
113 145 0.37
114 3 0.01
116 1 0.00
117 2 0.01
122 62 0.16
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (112 bp):
GAATCCATCACTCAATGGATCAACATTACCATGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
Found at i:15330 original size:225 final size:224
Alignment explanation
Indices: 14930--15509 Score: 718
Period size: 225 Copynumber: 2.5 Consensus size: 224
14920 GCAAAGATTC
* * * *
14930 GAATCCATCACTCAATGGATCAACATTTCC-TGAAGAGTTCATAATGAGAAGAGCTCATCTGAAG
1 GAATCTATCACTCAATGGATTAACATTACCATGAAGAGTTCATAATGAGAAGAACTCATCTGAA-
* * * * * *
14994 AAGGGAGAAGAAGTTCATAACGAGAAGAACTTGTTTAACCTTTTGCTTGAATCCATTACTCAATG
65 AAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATCACTCAATG
*
15059 GATCAACATTACCATGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
130 GATCAACATTACCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCA
* * * *
15124 TAATGAGAAGAGTTTGTTTAACCTTTTGCTT
194 TAACGAGAAGAGCTCGTTCAACCTTTTGCTT
*
15155 GAATCTATTACTCAATGGATTAACATTACCATGAAGAGTTCATAATGAGAAGAACTCATCTGAAA
1 GAATCTATCACTCAATGGATTAACATTACCATGAAGAGTTCATAATGAGAAGAACTCATCTGAAA
*
15220 AAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATCACTCGATGG
66 AAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATCACTCAATGG
* * * *
15285 ATTAACATTGCCAGGTAGAGTTCATAATGAGAATAACTCATCTGAAGAAGGAGAAGAAGTTCATA
131 ATCAACATTACCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATA
15350 ACGAGAAGAGCTCGTTCAACCTTTTGCTT
196 ACGAGAAGAGCTCGTTCAACCTTTTGCTT
* ** * * * *
15379 GATTCTATCACAGAA-GGAGATAGATCATCATCAACATTTCCAGAAGTGTTCATAATGAGAAAAA
1 GAATCTATCACTCAATGGA-TTA-A-CAT--T-ACCA--T---GAAGAGTTCATAATGAGAAGAA
* * * * *
15443 CTCATCTGAAGAAGGAGAAGAAATTCATAATGAGAAGAATTTGTTCAAAC--TTGCCTTAATTCA
55 CTCATCTGAAAAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCA
15506 TCAC
120 TCAC
15510 ATATGAAGCC
Statistics
Matches: 309, Mismatches: 34, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
223 3 0.01
224 52 0.17
225 132 0.43
226 35 0.11
228 1 0.00
229 3 0.01
231 1 0.00
232 16 0.05
234 66 0.21
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (224 bp):
GAATCTATCACTCAATGGATTAACATTACCATGAAGAGTTCATAATGAGAAGAACTCATCTGAAA
AAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTTAATTCATCACTCAATGG
ATCAACATTACCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATA
ACGAGAAGAGCTCGTTCAACCTTTTGCTT
Found at i:15917 original size:22 final size:21
Alignment explanation
Indices: 15875--15928 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
15865 TTATTTGTAT
*
15875 TATTATAATTATTATAATAAA
1 TATTATTATTATTATAATAAA
15896 TA-TATTTATTATTATTAATAAA
1 TATTA-TTATTATTA-TAATAAA
15918 TATTATTATTA
1 TATTATTATTA
15929 CAAAATAGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 2 0.07
21 10 0.34
22 15 0.52
23 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTATTATTATTATAATAAA
Found at i:17519 original size:2 final size:2
Alignment explanation
Indices: 17512--17565 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
17502 ATAAATATCT
17512 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17554 TA TA -A TA TA TA T
1 TA TA TA TA TA TA T
17566 TTTCTTAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18105 original size:2 final size:2
Alignment explanation
Indices: 18100--18143 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
18090 ATTTTTTATT
18100 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18142 TA
1 TA
18144 GTTTAAAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18169 original size:38 final size:38
Alignment explanation
Indices: 18127--18706 Score: 599
Period size: 38 Copynumber: 15.6 Consensus size: 38
18117 ATATATATAT
*
18127 ATATATATATATATATAG-TTTAAAAACATTTTT-AAA
1 ATATATATATATATATAGTTTTTAAAACATTTTTGAAA
* * *
18163 ACATATATA-ATATATAGTTTTGAAAACATGTTTGAAA
1 ATATATATATATATATAGTTTTTAAAACATTTTTGAAA
* * *
18200 ACATATATA-ATATATAGTTTTGAAAACATGTTTGAAA
1 ATATATATATATATATAGTTTTTAAAACATTTTTGAAA
* *
18237 ACATTTATATATTATATAGTTTTTAAAACA-TTTTGAAA
1 ATATATATATA-TATATAGTTTTTAAAACATTTTTGAAA
*
18275 ATAAATATA-ATATATAGTTTTTAAAACATTTTTTGAAA
1 ATATATATATATATATAGTTTTTAAAACA-TTTTTGAAA
18313 ATATATATAT-TATATAGTTTTTAAAACA-TTTTGAAA
1 ATATATATATATATATAGTTTTTAAAACATTTTTGAAA
*
18349 ATAAATATA-ATATATAGTTTTTAAAACAATTTTTGAAA
1 ATATATATATATATATAGTTTTTAAAAC-ATTTTTGAAA
18387 ATATATATAT-TATATAGTTTTTAAAACA-TTTTGAAA
1 ATATATATATATATATAGTTTTTAAAACATTTTTGAAA
* *
18423 ATAAATATA-ATATATAGTTTTTAAAATATTTTTGAAA
1 ATATATATATATATATAGTTTTTAAAACATTTTTGAAA
18460 ATATATATATTATATATAGTTTTT-AAACA-TTTTG---
1 ATATATATA-TATATATAGTTTTTAAAACATTTTTGAAA
*
18494 --A-A-A-ATATATATAGTTTTGAAAACA-TTTTGAAA
1 ATATATATATATATATAGTTTTTAAAACATTTTTGAAA
* *
18526 ACATTTATATATTATATAGTTTTTGAAAACCATTTTTG-AA
1 ATATATATATA-TATATAGTTTTT-AAAA-CATTTTTGAAA
18566 ATATATATA-ATATATAGTTTTTTAAAACATTTTTGAAA
1 ATATATATATATATATAG-TTTTTAAAACATTTTTGAAA
* *
18604 ATATATATAT-TATATAATTTTTTAAAAAAAACGTTTTTGAAA
1 ATATATATATATATAT-AGTTTTT----AAAACATTTTTGAAA
* * *
18646 A-ATACATATAATATAAAGTTTTTAAAATAACATTTTAGAAA
1 ATATATATAT-ATATATAGTTTTT--AA-AACATTTTTGAAA
*
18687 TTA-ATATAT-TATAT-GTTTTT
1 ATATATATATATATATAGTTTTT
18707 GAATTTTTTT
Statistics
Matches: 473, Mismatches: 31, Indels: 78
0.81 0.05 0.13
Matches are distributed among these distances:
28 13 0.03
29 11 0.02
30 1 0.00
31 1 0.00
32 1 0.00
34 1 0.00
35 8 0.02
36 106 0.22
37 83 0.18
38 134 0.28
39 45 0.10
40 15 0.03
41 28 0.06
42 22 0.05
43 4 0.01
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (38 bp):
ATATATATATATATATAGTTTTTAAAACATTTTTGAAA
Found at i:18198 original size:12 final size:12
Alignment explanation
Indices: 18181--18240 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
18171 AATATATAGT
18181 TTTGAAAACATG
1 TTTGAAAACATG
*
18193 TTTGAAAACATA
1 TTTGAAAACATG
* * *
18205 TAT-AATATATAG
1 TTTGAAAACAT-G
18217 TTTTGAAAACATG
1 -TTTGAAAACATG
18230 TTTGAAAACAT
1 TTTGAAAACAT
18241 TTATATATTA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
11 5 0.14
12 24 0.65
13 3 0.08
14 5 0.14
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.37
Consensus pattern (12 bp):
TTTGAAAACATG
Found at i:18347 original size:74 final size:73
Alignment explanation
Indices: 18131--18706 Score: 667
Period size: 74 Copynumber: 7.8 Consensus size: 73
18121 ATATATATAT
* * * *
18131 ATATATATATATAG-TTTAAAAACATTTTT-AAAACATATATAATATATAGTTTTGAAAACATGT
1 ATATA-ATATATAGTTTTTAAAACATTTTTGAAAATATATATATTATATAGTTTTTAAAACAT-T
* *
18194 TTGAAAACAT
64 TTGAAAATAA
* * *
18204 ATATAATATATAGTTTTGAAAACATGTTTGAAAACATTTATATATTATATAGTTTTTAAAACATT
1 ATATAATATATAGTTTTTAAAACATTTTTG-AAA-ATATATATATTATATAGTTTTTAAAACATT
18269 TTGAAAATAA
64 TTGAAAATAA
18279 ATATAATATATAGTTTTTAAAACATTTTTTGAAAATATATATATTATATAGTTTTTAAAACATTT
1 ATATAATATATAGTTTTTAAAACA-TTTTTGAAAATATATATATTATATAGTTTTTAAAACATTT
18344 TGAAAATAA
65 TGAAAATAA
18353 ATATAATATATAGTTTTTAAAACAATTTTTGAAAATATATATATTATATAGTTTTTAAAACATTT
1 ATATAATATATAGTTTTTAAAAC-ATTTTTGAAAATATATATATTATATAGTTTTTAAAACATTT
18418 TGAAAATAA
65 TGAAAATAA
*
18427 ATATAATATATAGTTTTTAAAATATTTTTGAAAATATATATATTATATATAGTTTTT-AAACATT
1 ATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATA-T-TATATAGTTTTTAAAACATT
18491 TTG-----AA
64 TTGAAAATAA
* *
18496 A-AT-ATATATAGTTTTGAAAACA-TTTTGAAAACATTTATATATTATATAGTTTTTGAAAACCA
1 ATATAATATATAGTTTTTAAAACATTTTTG-AAA-ATATATATATTATATAGTTTTT-AAAA-CA
*
18558 TTTTTG-AAATAT
62 -TTTTGAAAATAA
*
18570 ATATAATATATAGTTTTTTAAAACATTTTTGAAAATATATATATTATATAATTTTTTAAAAAAAA
1 ATATAATATATAG-TTTTTAAAACATTTTTGAAAATATATATATTATAT-AGTTTTT----AAAA
* *
18635 CGTTTTTGAAAAATAC
60 C-ATTTTG-AAAATAA
* * *
18651 ATATAATATAAAGTTTTTAAAATAACATTTTAGAAATTA-ATATATTATAT-GTTTTT
1 ATATAATATATAGTTTTT--AA-AACATTTTTGAAAATATATATATTATATAGTTTTT
18707 GAATTTTTTT
Statistics
Matches: 445, Mismatches: 26, Indels: 57
0.84 0.05 0.11
Matches are distributed among these distances:
66 17 0.04
67 21 0.05
68 13 0.03
69 5 0.01
70 5 0.01
72 8 0.02
73 37 0.08
74 146 0.33
75 53 0.12
76 52 0.12
77 19 0.04
78 5 0.01
79 6 0.01
80 14 0.03
81 17 0.04
82 13 0.03
83 14 0.03
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (73 bp):
ATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATATTATATAGTTTTTAAAACATTTT
GAAAATAA
Found at i:18501 original size:28 final size:29
Alignment explanation
Indices: 18470--18526 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
18460 ATATATATAT
*
18470 TATATATAGTTTT-TAAACATTTTGAAAA
1 TATATATAGTTTTGAAAACATTTTGAAAA
18498 TATATATAGTTTTGAAAACATTTTGAAAA
1 TATATATAGTTTTGAAAACATTTTGAAAA
18527 CATTTATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (29 bp):
TATATATAGTTTTGAAAACATTTTGAAAA
Found at i:18523 original size:11 final size:11
Alignment explanation
Indices: 18507--18531 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18497 ATATATATAG
18507 TTTTGAAAACA
1 TTTTGAAAACA
18518 TTTTGAAAACA
1 TTTTGAAAACA
18529 TTT
1 TTT
18532 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:18534 original size:29 final size:28
Alignment explanation
Indices: 18471--18534 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 28
18461 TATATATATT
* *
18471 ATATATAGTTTTTAAACATTTTGAAAAT
1 ATATATAGTTTTAAAACATTTTGAAAAC
18499 ATATATAGTTTTGAAAACATTTTGAAAAC
1 ATATATAGTTTT-AAAACATTTTGAAAAC
*
18528 ATTTATA
1 ATATATA
18535 TATTATATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 12 0.38
29 20 0.62
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (28 bp):
ATATATAGTTTTAAAACATTTTGAAAAC
Found at i:18542 original size:40 final size:39
Alignment explanation
Indices: 18498--18700 Score: 152
Period size: 41 Copynumber: 5.1 Consensus size: 39
18488 ATTTTGAAAA
18498 TATATATAG-TTTTGAAAACA-TTTTGAAAACATT-TATA-
1 TATATATAGTTTTTGAAAACATTTTTG-AAA-ATTATATAT
18535 TATTATATAGTTTTTGAAAACCATTTTTG-AAA-TATATAT
1 TA-TATATAGTTTTTGAAAA-CATTTTTGAAAATTATATAT
* *
18574 AATATATAGTTTTTTAAAACATTTTTGAAAATATATATAT
1 TATATATAGTTTTTGAAAACATTTTTGAAAAT-TATATAT
* * * * *
18614 TATATA-ATTTTTTAAAAAAAACGTTTTTGAAAAATACATAT
1 TATATATAGTTTTT---GAAAACATTTTTGAAAATTATATAT
* * * *
18655 AATATAAAGTTTTTAAAATAACATTTTAG-AAATTAATATAT
1 TATATATAGTTTTT-GAA-AACATTTTTGAAAATT-ATATAT
18696 TATAT
1 TATAT
18701 GTTTTTGAAT
Statistics
Matches: 136, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
37 11 0.08
38 31 0.23
39 18 0.13
40 22 0.16
41 33 0.24
42 21 0.15
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (39 bp):
TATATATAGTTTTTGAAAACATTTTTGAAAATTATATAT
Found at i:20233 original size:23 final size:23
Alignment explanation
Indices: 20189--20234 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
20179 TAATACTCTA
* *
20189 AATTTTTATTTTTATTTATTTTT
1 AATTATTATTATTATTTATTTTT
* *
20212 AATTATTATTATTCTTTTTTTTT
1 AATTATTATTATTATTTATTTTT
20235 TCTTTCACAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (23 bp):
AATTATTATTATTATTTATTTTT
Found at i:20556 original size:13 final size:13
Alignment explanation
Indices: 20538--20567 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
20528 CGAATCGGAT
20538 TTTTAAATTTAAA
1 TTTTAAATTTAAA
20551 TTTTAAATTTAAA
1 TTTTAAATTTAAA
20564 TTTT
1 TTTT
20568 CGCAACTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAATTTAAA
Found at i:31947 original size:14 final size:15
Alignment explanation
Indices: 31928--31965 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
31918 AATGAGAAGT
*
31928 AATCTCTGCAC-ATA
1 AATCTCTGCACTAAA
31942 AATCTCTGC-CTAAA
1 AATCTCTGCACTAAA
31956 AATCTCTGCA
1 AATCTCTGCA
31966 TATAGACAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 20 0.95
ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29
Consensus pattern (15 bp):
AATCTCTGCACTAAA
Found at i:32032 original size:48 final size:48
Alignment explanation
Indices: 31977--32073 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
31967 ATAGACAGAA
31977 ACGTAAGTCCT-GACAAAATTTAAAAAGAGGGAACATGAAGAGAAGGAT
1 ACGTAAGTCCTAG-CAAAATTTAAAAAGAGGGAACATGAAGAGAAGGAT
*
32025 ACGTAAGTCCTAGCTAAATTTAAAAAGAGGGAACATGAAGAGAAGGAT
1 ACGTAAGTCCTAGCAAAATTTAAAAAGAGGGAACATGAAGAGAAGGAT
32073 A
1 A
32074 TACGGAAGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 46 0.98
49 1 0.02
ACGTcount: A:0.47, C:0.10, G:0.25, T:0.18
Consensus pattern (48 bp):
ACGTAAGTCCTAGCAAAATTTAAAAAGAGGGAACATGAAGAGAAGGAT
Found at i:32087 original size:48 final size:47
Alignment explanation
Indices: 31992--32088 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 47
31982 AGTCCTGACA
*
31992 AAATTTAAAAAGAGGGAACATGAAGAGAAGGATACGTAAGTCCTAGCT
1 AAATTTAAAAAGAGGGAACATGAAGAGAAGGATACGGAAGT-CTAGCT
32040 AAATTTAAAAAGAGGGAACATGAAGAGAAGGATATACGGAAGT-TAGCT
1 AAATTTAAAAAGAGGGAACATGAAGAGAAGG--ATACGGAAGTCTAGCT
32088 A
1 A
32089 TAGCAAGCTA
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
48 37 0.80
50 9 0.20
ACGTcount: A:0.47, C:0.08, G:0.26, T:0.19
Consensus pattern (47 bp):
AAATTTAAAAAGAGGGAACATGAAGAGAAGGATACGGAAGTCTAGCT
Found at i:34269 original size:23 final size:23
Alignment explanation
Indices: 34229--34272 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
34219 ATAAATTATT
34229 ATTTATTATATTATTTTAAAATA
1 ATTTATTATATTATTTTAAAATA
*
34252 ATTTA-TATTTTATCTTTAAAA
1 ATTTATTATATTAT-TTTAAAA
34273 ATTTAATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTTATTATATTATTTTAAAATA
Found at i:36711 original size:7 final size:7
Alignment explanation
Indices: 36699--36740 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
36689 AAAACGATAA
36699 AATAAAT
1 AATAAAT
36706 AATAAA-
1 AATAAAT
*
36712 AACAAA-
1 AATAAAT
*
36718 AACAAAT
1 AATAAAT
36725 AATAAAT
1 AATAAAT
36732 AATAAAT
1 AATAAAT
36739 AA
1 AA
36741 AAAGGAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 11 0.34
7 21 0.66
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (7 bp):
AATAAAT
Found at i:36754 original size:26 final size:27
Alignment explanation
Indices: 36688--36754 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 27
36678 CAAACACCCA
*
36688 AAAAACGATAAAATAAATAATAAAAAC
1 AAAAACAATAAAATAAATAATAAAAAC
* *
36715 AAAAACAA-ATAATAAATAATAAATA-
1 AAAAACAATAAAATAAATAATAAAAAC
**
36740 AAAAGGAATAAAATA
1 AAAAACAATAAAATA
36755 CTATATGATA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 6 0.18
26 20 0.61
27 7 0.21
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.16
Consensus pattern (27 bp):
AAAAACAATAAAATAAATAATAAAAAC
Found at i:36846 original size:36 final size:35
Alignment explanation
Indices: 36783--36850 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 35
36773 TTTAAAACTT
* * * *
36783 TATATAATATATATTTCAAAGATATTTTCAAAATCA
1 TATATAATATAAATTTAAAAAACATTTT-AAAATCA
*
36819 TATATTATATAAATTTAAAAAACATTTTAAAA
1 TATATAATATAAATTTAAAAAACATTTTAAAA
36851 CTATATGTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 4 0.15
36 23 0.85
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.41
Consensus pattern (35 bp):
TATATAATATAAATTTAAAAAACATTTTAAAATCA
Found at i:36931 original size:100 final size:104
Alignment explanation
Indices: 36818--37008 Score: 300
Period size: 100 Copynumber: 1.9 Consensus size: 104
36808 TTTCAAAATC
*
36818 ATATATTATATAAATTTAAAAAACATTTTAAAACTATATGTTATAGTTTTCAAAAA-CGTTTT-A
1 ATATATTATATAAATTTAAAAAACATTTTAAAACTATATATTATAGTTTTCAAAAATCGTTTTAA
36881 AACTATAT-TATAT-GTTTCAAAAATGTTTTTTTTAACT
66 AACTATATATATATGGTTTCAAAAATGTTTTTTTTAACT
* ** *
36918 ATATATTATATAAATTTTAAAATGATTTTAAAACTATATATTATAGTTTTCAAAAATGGTTTTAA
1 ATATATTATATAAATTTAAAAAACATTTTAAAACTATATATTATAGTTTTCAAAAATCGTTTT-A
36983 AAACTATATATATATGGTTTCAAAAA
65 AAACTATATATATATGGTTTCAAAAA
37009 ATTCAAAAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
100 52 0.64
101 5 0.06
103 9 0.11
104 5 0.06
105 10 0.12
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.45
Consensus pattern (104 bp):
ATATATTATATAAATTTAAAAAACATTTTAAAACTATATATTATAGTTTTCAAAAATCGTTTTAA
AACTATATATATATGGTTTCAAAAATGTTTTTTTTAACT
Found at i:37023 original size:100 final size:97
Alignment explanation
Indices: 36785--37079 Score: 254
Period size: 100 Copynumber: 2.9 Consensus size: 97
36775 TAAAACTTTA
* * * * **
36785 TATAATATATATTTCAAAGATATTTTC-AAAATCATATATTATATAAATTTAAAAAACATTTTAA
1 TATATTATATGTTTCAAA-A-ATATTCAAAAAT-ATATATTATATAAATTTTAAAATGATTTTAA
*
36849 AACTATATGTTATAGTTTTCAAAAACGTTTTAAAC
63 AACTATATATTATAGTTTTCAAAAACGTTTTAAAC
* *** *
36884 TATATTATATGTTTCAAAAATGTTTTTTTTAACTATATATTATATAAATTTTAAAATGATTTTAA
1 TATATTATATGTTTCAAAAA---TATTCAAAAATATATATTATATAAATTTTAAAATGATTTTAA
*
36949 AACTATATATTATAGTTTTCAAAAATGGTTTTAAAAAC
63 AACTATATATTATAGTTTTCAAAAA-CGTTTT--AAAC
* *
36987 TATATATATATGGTTTCAAAAA-ATTCAAAAATTATATAATATATATATTTTCAAAAAATG-TTT
1 TATAT-TATAT-GTTTCAAAAATATTCAAAAA-TATATATTATATAAATTTT---AAAATGATTT
* *
37050 TCAAAAACCATATATTATATATTTTCAAAA
60 T--AAAACTATATATTATA-GTTTTCAAAA
37080 TGTTTTCTTT
Statistics
Matches: 161, Mismatches: 19, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
97 1 0.01
98 1 0.01
99 16 0.10
100 56 0.35
101 12 0.07
102 17 0.11
103 9 0.06
104 9 0.06
105 16 0.10
106 15 0.09
107 9 0.06
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (97 bp):
TATATTATATGTTTCAAAAATATTCAAAAATATATATTATATAAATTTTAAAATGATTTTAAAAC
TATATATTATAGTTTTCAAAAACGTTTTAAAC
Found at i:37086 original size:35 final size:35
Alignment explanation
Indices: 36766--37146 Score: 176
Period size: 35 Copynumber: 10.9 Consensus size: 35
36756 TATATGATAA
* *
36766 AAAATGTTTT--AAAACTTTATATAATATATATTTC
1 AAAATGTTTTCAAAAACTATATATTATATAT-TTTC
* * **
36800 AAAGATATTTTCAAAATC-ATATATTATATAAATTTAA
1 AAA-ATGTTTTCAAAAACTATATATTATAT--ATTTTC
** * *
36837 AAAACATTTT--AAAACTATATGTTATA-GTTTTC
1 AAAATGTTTTCAAAAACTATATATTATATATTTTC
* *
36869 AAAAACGTTTT---AAAC--TATATTATAT-GTTTC
1 -AAAATGTTTTCAAAAACTATATATTATATATTTTC
****
36899 AAAAATGTTTTTTTTAACTATATATTATATAAATTTT-
1 -AAAATGTTTTCAAAAACTATATATTATAT--ATTTTC
*
36936 AAAATGATTTT--AAAACTATATATTATA-GTTTTC
1 AAAATG-TTTTCAAAAACTATATATTATATATTTTC
**
36969 AAAAATGGTTTT-AAAAACTATATA-TATATGGTTTC
1 -AAAAT-GTTTTCAAAAACTATATATTATATATTTTC
** *
37004 AAAA--AATTCAAAAATTATATAATATATATATTTTC
1 AAAATGTTTTCAAAAACTATAT-AT-TATATATTTTC
*
37039 AAAAAATGTTTTCAAAAACCATATATTATATATTTTC
1 --AAAATGTTTTCAAAAACTATATATTATATATTTTC
*
37076 AAAATGTTTTCTTTTTAGAAAACCATATATTATATAGTTTTC
1 AAAATGTTTTC-----A-AAAACTATATATTATATA-TTTTC
* *
37118 AAAATGATTTC--AAACTATATAATATATAT
1 AAAATGTTTTCAAAAACTATATATTATATAT
37147 ATATATATAT
Statistics
Matches: 276, Mismatches: 34, Indels: 75
0.72 0.09 0.19
Matches are distributed among these distances:
30 22 0.08
31 2 0.01
32 21 0.08
33 14 0.05
34 39 0.14
35 76 0.28
36 21 0.08
37 28 0.10
38 7 0.03
39 12 0.04
40 1 0.00
41 18 0.07
42 15 0.05
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (35 bp):
AAAATGTTTTCAAAAACTATATATTATATATTTTC
Found at i:37144 original size:2 final size:2
Alignment explanation
Indices: 37133--37163 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
37123 GATTTCAAAC
37133 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37164 ATAAAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:37838 original size:84 final size:82
Alignment explanation
Indices: 37654--38451 Score: 667
Period size: 84 Copynumber: 9.7 Consensus size: 82
37644 GACAGTAGTG
* * * * * *
37654 AATGATGTGTCATGGAGCTGA-TCGTAGTCGAACTCGAATGTCTTTGTAACAGATAACCCTTCTC
1 AATGATGTGCCTTGGAGCTGAGT-GTAGTCGAACTCAAAGGTCTTTGTAGCAGATAACCCTTCTA
* * *
37718 GCCTTGAGTTATGCTGTA
65 GACTTAAGTTATGCTGCA
* *
37736 AATGATGCGCCGTT-GAGCTGAGTGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGACAACCCTTC
1 AATGATGTGCC-TTGGAGCTGAGTGTAGTCGAACTCAAAGGTC-TTTG-TAGCAGATAACCCTTC
* *
37800 TAGACTTAAGTTGTGTTGCA
63 TAGACTTAAGTTATGCTGCA
* * * * *
37820 AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCT
1 AATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCAAAGGTCTTT-G-TAGCAGATAACCCTTCT
*
37885 CGACTTAAGTTATGCTGCA
64 AGACTTAAGTTATGCTGCA
* * * *** * * *
37904 AATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTG--GTAGATAGCCCTTCTC
1 AATGATGTG-CCTTGGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTGTAGCAGATAACCCTTCTA
* *
37967 GACTTAAGCTATGTTGCA
65 GACTTAAGTTATGCTGCA
* *
37985 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA-CAGATAACCCTCC
1 AATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCAAAGGTC-TTT-GT-AGCAGATAACCCTTC
* * *
38049 TAGCCTTGAGTTATGCTGTA
63 TAGACTTAAGTTATGCTGCA
* * * *** * *
38069 AATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTG--GCAGATAGCCCTTCTC
1 AATGATGTG-CCTTGGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTGTAGCAGATAACCCTTCTA
* *
38132 GACTTAAGCTATGCTGCG
65 GACTTAAGTTATGCTGCA
* * *
38150 AATGATATGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCT
1 AATGATGTGCC-TTGGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTG-TAGCAGATAACCCTTCT
* * *
38214 AGCCTTGAGTTATGCTGTA
64 AGACTTAAGTTATGCTGCA
* * * * **** *
38233 AATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTGGGGGTCTTTG--GCAGATAGCCC-T-T-
1 AATGATGTG-CCTTGGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTGTAGCAGATAACCCTTCTA
* *
38293 --CTTAAGCTATTCTGCA
65 GACTTAAGTTATGCTGCA
* *
38309 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTA
1 AATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTG-TAGCAGATAACCCTTCTA
* * *
38374 GCCTTGAGTTATGCTGTA
65 GACTTAAGTTATGCTGCA
* * * * * * *
38392 AATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTG--GCAGATAGCCCTT
1 AATGATGTG-CCTTGGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTGTAGCAGATAACCCTT
38452 GAGCTAAACT
Statistics
Matches: 567, Mismatches: 120, Indels: 59
0.76 0.16 0.08
Matches are distributed among these distances:
75 30 0.05
76 19 0.03
78 9 0.02
79 2 0.00
80 56 0.10
81 95 0.17
82 34 0.06
83 67 0.12
84 199 0.35
85 56 0.10
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (82 bp):
AATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCAAAGGTCTTTGTAGCAGATAACCCTTCTAG
ACTTAAGTTATGCTGCA
Found at i:37998 original size:165 final size:163
Alignment explanation
Indices: 37654--38451 Score: 1054
Period size: 165 Copynumber: 4.9 Consensus size: 163
37644 GACAGTAGTG
* * * * * *
37654 AATGATGTGTCATGGAGCTGATCGTAGTCGAACTCGAATGTCTTTGTAACAGATAACCCTTCTCG
1 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGTAACAGATAACCCTTCTAG
* * * ***
37719 CCTTGAGTTATGCTGTAAATGATGCGCCGTTG-AGCTGAGTGTAGTCGAACTCAAAGGTCTTTTG
66 CCTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTG
* * * * *
37783 TTAGCAGACAACCCTTCTAGACTTAAGTTGTGTTGCA
130 ---GCAGATAGCCCTTCTCGACTTAAGCTATGTTGCA
* * ** *
37820 AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCT
1 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT-G-TAACAGATAACCCTTCT
* * * * *
37885 CGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
64 AGCCTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
*
37950 GGTAGATAGCCCTTCTCGACTTAAGCTATGTTGCA
129 GGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCA
* *
37985 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTCCT
1 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTT-GTAACAGATAACCCTTCT
*
38050 AGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
64 AGCCTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
* *
38115 GGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCG
129 GGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCA
*
38150 AATGATATGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCT
1 AATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTG-TAACAGATAACCCTTCT
* * *
38214 AGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTGGGGGTCTTT
64 AGCCTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
38279 GGCAGATAGCCC-T-T---CTTAAGCTAT-TCTGCA
129 GGCAGATAGCCCTTCTCGACTTAAGCTATGT-TGCA
38309 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTA
1 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTG-TAACAGATAACCCTTCTA
* * ***
38374 GCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTG
65 GCCTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTG
38439 GCAGATAGCCCTT
130 GCAGATAGCCCTT
38452 GAGCTAAACT
Statistics
Matches: 574, Mismatches: 49, Indels: 24
0.89 0.08 0.04
Matches are distributed among these distances:
158 2 0.00
159 148 0.26
160 1 0.00
162 1 0.00
163 2 0.00
164 91 0.16
165 212 0.37
166 47 0.08
167 1 0.00
168 46 0.08
169 23 0.04
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (163 bp):
AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGTAACAGATAACCCTTCTAG
CCTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
CAGATAGCCCTTCTCGACTTAAGCTATGTTGCA
Found at i:41857 original size:18 final size:19
Alignment explanation
Indices: 41816--41860 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
41806 AGTTAATGTG
41816 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
41835 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
41853 AATGCAAA
1 AATGCAAA
41861 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:45099 original size:7 final size:7
Alignment explanation
Indices: 45087--45128 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
45077 AAAACGATAA
45087 AATAAAT
1 AATAAAT
45094 AATAAA-
1 AATAAAT
*
45100 AACAAA-
1 AATAAAT
*
45106 AACAAAT
1 AATAAAT
45113 AATAAAT
1 AATAAAT
45120 AATAAAT
1 AATAAAT
45127 AA
1 AA
45129 AAAGGAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 11 0.34
7 21 0.66
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (7 bp):
AATAAAT
Found at i:45142 original size:26 final size:27
Alignment explanation
Indices: 45076--45142 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 27
45066 CAAACACCCA
*
45076 AAAAACGATAAAATAAATAATAAAAAC
1 AAAAACAATAAAATAAATAATAAAAAC
* *
45103 AAAAACAA-ATAATAAATAATAAATA-
1 AAAAACAATAAAATAAATAATAAAAAC
**
45128 AAAAGGAATAAAATA
1 AAAAACAATAAAATA
45143 CTATATGATA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 6 0.18
26 20 0.61
27 7 0.21
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.16
Consensus pattern (27 bp):
AAAAACAATAAAATAAATAATAAAAAC
Found at i:45287 original size:30 final size:33
Alignment explanation
Indices: 45224--45297 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 33
45214 TATAAATTTA
45224 AAAAACGTTTTAAAACTATATGTTATAGTTTTC
1 AAAAACGTTTTAAAACTATATGTTATAGTTTTC
45257 AAAAACGTTTT-AAACTATA--TTATA-TGTTTC
1 AAAAACGTTTTAAAACTATATGTTATAGT-TTTC
*
45287 AAAAATGTTTT
1 AAAAACGTTTT
45298 TTTTAACTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 1 0.03
30 19 0.49
32 8 0.21
33 11 0.28
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (33 bp):
AAAAACGTTTTAAAACTATATGTTATAGTTTTC
Found at i:45314 original size:35 final size:35
Alignment explanation
Indices: 45153--45480 Score: 189
Period size: 35 Copynumber: 9.3 Consensus size: 35
45143 CTATATGATA
*
45153 AAAAATG-TTTTAAAACTTTATATAATATATA-TTTC
1 AAAAATGTTTTTAAAAC--TATATATTATATAGTTTC
* * * * *
45188 AAAGATATTTTCAAAA-TCATATATTATATAAATTTA
1 AAAAATGTTTTTAAAACT-ATATATTATAT-AGTTTC
* *
45224 AAAAACG-TTTTAAAACTATAT-GT-TATAGTTTTC
1 AAAAATGTTTTTAAAACTATATATTATATAG-TTTC
*
45257 AAAAACG-TTTT-AAAC--TATATTATAT-GTTTC
1 AAAAATGTTTTTAAAACTATATATTATATAGTTTC
** *
45287 AAAAATGTTTTTTTTAACTATATATTATATAAATTT-
1 AAAAATG-TTTTTAAAACTATATATTATAT-AGTTTC
* *
45323 TAAAATGATTTTAAAACTATATATTATATAAGTTTTC
1 AAAAATGTTTTTAAAACTATATATTATAT-AG-TTTC
* *
45360 AAAAATGGTTTTAAAAACTATATAATATATATGGTTTC
1 AAAAAT-GTTTTTAAAACTATAT-AT-TATATAGTTTC
** ** * *
45398 AAAAA-AATTCAAAAATTATATAATATATATGTTTTC
1 AAAAATGTTTTTAAAACTATATATTATATA-G-TTTC
* * *
45434 AAAAAATGTTTTCAAAAACCATATATTATATATTTTC
1 -AAAAATGTTTT-TAAAACTATATATTATATAGTTTC
45471 -AAAATGTTTT
1 AAAAATGTTTT
45481 CTTTTTAGAA
Statistics
Matches: 230, Mismatches: 38, Indels: 50
0.72 0.12 0.16
Matches are distributed among these distances:
30 13 0.06
31 2 0.01
32 12 0.05
33 21 0.09
34 16 0.07
35 60 0.26
36 40 0.17
37 17 0.07
38 25 0.11
39 19 0.08
40 5 0.02
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (35 bp):
AAAAATGTTTTTAAAACTATATATTATATAGTTTC
Found at i:45412 original size:36 final size:36
Alignment explanation
Indices: 45335--45474 Score: 140
Period size: 36 Copynumber: 3.8 Consensus size: 36
45325 AAATGATTTT
* * * *
45335 AAAACTATATATTATATAAGTTTTCAAAAATGGTTTTA
1 AAAACTATATAATATATATGTTTTCAAAAA--ATTTCA
* *
45373 AAAACTATATAATATATATGGTTTCAAAAAAATTCA
1 AAAACTATATAATATATATGTTTTCAAAAAATTTCA
*
45409 AAAATTATATAATATATATGTTTTCAAAAAATGTTTTCA
1 AAAACTATATAATATATATGTTTTCAAAAAA---TTTCA
* *
45448 AAAACCATAT-AT-TATATATTTTCAAAA
1 AAAACTATATAATATATATGTTTTCAAAA
45475 TGTTTTCTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
36 32 0.37
37 14 0.16
38 29 0.33
39 12 0.14
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (36 bp):
AAAACTATATAATATATATGTTTTCAAAAAATTTCA
Found at i:45444 original size:13 final size:13
Alignment explanation
Indices: 45426--45451 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45416 TATAATATAT
45426 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
45439 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
45452 CCATATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
ATGTTTTCAAAAA
Found at i:45539 original size:2 final size:2
Alignment explanation
Indices: 45528--45560 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
45518 GATTTCAAAC
45528 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45561 AATAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:47364 original size:29 final size:29
Alignment explanation
Indices: 47329--47387 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
47319 AATACTTAAT
47329 TCACTTTTGTCAGTTGTGTGATTTAAATA
1 TCACTTTTGTCAGTTGTGTGATTTAAATA
47358 TCACTTTTGTCAGTTGTGTGATTTAAATA
1 TCACTTTTGTCAGTTGTGTGATTTAAATA
47387 T
1 T
47388 GTTTTTAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.49
Consensus pattern (29 bp):
TCACTTTTGTCAGTTGTGTGATTTAAATA
Found at i:55097 original size:7 final size:7
Alignment explanation
Indices: 55087--55179 Score: 57
Period size: 7 Copynumber: 13.4 Consensus size: 7
55077 GGTTTATATC
55087 TTAGGGT
1 TTAGGGT
*
55094 TTAGAGT
1 TTAGGGT
*
55101 TTAGAGT
1 TTAGGGT
**
55108 TTATAGT
1 TTAGGGT
*
55115 TTAAGGT
1 TTAGGGT
55122 TT-GGGAT
1 TTAGGG-T
*
55129 TTAGGAT
1 TTAGGGT
**
55136 TTATAGT
1 TTAGGGT
*
55143 TTAGAGT
1 TTAGGGT
*
55150 TTAGAGTT
1 TTAG-GGT
55158 TTA-GGT
1 TTAGGGT
55164 TT-GGGT
1 TTAGGGT
55170 TTAGGGT
1 TTAGGGT
55177 TTA
1 TTA
55180 TAATTTATAG
Statistics
Matches: 68, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
6 11 0.16
7 51 0.75
8 6 0.09
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (7 bp):
TTAGGGT
Found at i:55104 original size:14 final size:14
Alignment explanation
Indices: 55072--55224 Score: 91
Period size: 14 Copynumber: 11.1 Consensus size: 14
55062 GGATTAAGGC
*
55072 TTTAGGGTTTATA-
1 TTTAGGGTTTAGAG
55085 TCTTAGGGTTTAGAG
1 T-TTAGGGTTTAGAG
* *
55100 TTTAGAGTTTATAG
1 TTTAGGGTTTAGAG
* *
55114 TTTAAGGTTT-GGG
1 TTTAGGGTTTAGAG
* *
55127 ATTTAGGATTTATAG
1 -TTTAGGGTTTAGAG
*
55142 TTTAGAGTTTAGAG
1 TTTAGGGTTTAGAG
*
55156 TTTTA-GGTTT-GGG
1 -TTTAGGGTTTAGAG
* *
55169 TTTAGGGTTTATAA
1 TTTAGGGTTTAGAG
** *
55183 TTTATAGATTAGAG
1 TTTAGGGTTTAGAG
* * *
55197 ATTATGTTTTA-AG
1 TTTAGGGTTTAGAG
55210 TTTAGGGTTTAGAG
1 TTTAGGGTTTAGAG
55224 T
1 T
55225 GTAATCTAGC
Statistics
Matches: 101, Mismatches: 31, Indels: 15
0.69 0.21 0.10
Matches are distributed among these distances:
12 4 0.04
13 19 0.19
14 72 0.71
15 6 0.06
ACGTcount: A:0.25, C:0.01, G:0.27, T:0.48
Consensus pattern (14 bp):
TTTAGGGTTTAGAG
Found at i:55144 original size:42 final size:41
Alignment explanation
Indices: 55087--55220 Score: 151
Period size: 41 Copynumber: 3.2 Consensus size: 41
55077 GGTTTATATC
* *
55087 TTAGGGTTTAGAGTTTAGAGTTTATAGTTTAAGGTTTGGGAT
1 TTAGGGTTTATAGTTTAGAGTTTAGAGTTTAAGGTTTGGG-T
* *
55129 TTAGGATTTATAGTTTAGAGTTTAGAGTTTTAGGTTTGGGT
1 TTAGGGTTTATAGTTTAGAGTTTAGAGTTTAAGGTTTGGGT
* * * * * * **
55170 TTAGGGTTTATAATTTATAGATTAGAGATTATGTTTTAAGT
1 TTAGGGTTTATAGTTTAGAGTTTAGAGTTTAAGGTTTGGGT
55211 TTAGGGTTTA
1 TTAGGGTTTA
55221 GAGTGTAATC
Statistics
Matches: 78, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
41 42 0.54
42 36 0.46
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (41 bp):
TTAGGGTTTATAGTTTAGAGTTTAGAGTTTAAGGTTTGGGT
Found at i:55402 original size:14 final size:14
Alignment explanation
Indices: 55383--55423 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
55373 TATAATTATC
55383 AATAATGTATTTTT
1 AATAATGTATTTTT
55397 AATAAT-T-TTTTT
1 AATAATGTATTTTT
*
55409 -ATAATGTAATTTT
1 AATAATGTATTTTT
55422 AA
1 AA
55424 AAAATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 5 0.22
12 6 0.26
13 5 0.22
14 7 0.30
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:58785 original size:21 final size:20
Alignment explanation
Indices: 58761--58947 Score: 148
Period size: 21 Copynumber: 8.9 Consensus size: 20
58751 ACTTCGACTA
58761 TCGCATTGCGATAGTCCAAGT
1 TCGC-TTGCGATAGTCCAAGT
*
58782 TCGCGTTGCGATAGTCGAAGT
1 TCGC-TTGCGATAGTCCAAGT
* *
58803 TCGCGTTGCGATTTATTCCAAAT
1 TCGC-TTGCGA--TAGTCCAAGT
* *
58826 TCG-TTGCGATTTATTCCAAAT
1 TCGCTTGCGA--TAGTCCAAGT
58847 TCG-TTGCGATAGTCCAAGT
1 TCGCTTGCGATAGTCCAAGT
*
58866 TCGCGTTGCGATTTATTCCAAGT
1 TCGC-TTGCGA--TAGTCCAAGT
*
58889 TCG-TTGCGATAGTCGAAGT
1 TCGCTTGCGATAGTCCAAGT
* *
58908 TCGCGTTGCGATTTATTCCAAAT
1 TCGC-TTGCGA--TAGTCCAAGT
58931 TCG-TTGCGATAGTCCAA
1 TCGCTTGCGATAGTCCAA
58948 AATCGCAACG
Statistics
Matches: 142, Mismatches: 14, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
19 29 0.20
21 81 0.57
23 32 0.23
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (20 bp):
TCGCTTGCGATAGTCCAAGT
Found at i:58813 original size:42 final size:41
Alignment explanation
Indices: 58766--58947 Score: 217
Period size: 42 Copynumber: 4.3 Consensus size: 41
58756 GACTATCGCA
* *
58766 TTGCGATAGTCCAAGTTCGCGTTGCGA-TAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTATTCCAAGTT--CG
* * *
58808 TTGCGATTTATTCCAAATT--CGTTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
58850 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
* *
58892 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCG
58934 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
58948 AATCGCAACG
Statistics
Matches: 123, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
40 9 0.07
42 97 0.79
44 17 0.14
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (41 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTATTCCAAGTTCG
Found at i:58860 original size:84 final size:82
Alignment explanation
Indices: 58766--58947 Score: 251
Period size: 84 Copynumber: 2.2 Consensus size: 82
58756 GACTATCGCA
* *
58766 TTGCGATAGTCCAAGTTCGCGTTGCGA-TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT-CG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTAGTCCAAGTT--CGTTGCGA--TAGTCCAAATTCCG
58829 TTGCGATTTATTCCAAATTCG
62 TTGCGATTTATTCCAAATTCG
* * *
58850 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTAGTCCAAGTTCGTTGCGATAGTCCAAATTC-CGTT
58915 GCGATTTATTCCAAATTCG
64 GCGATTTATTCCAAATTCG
58934 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
58948 AATCGCAACG
Statistics
Matches: 89, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
82 8 0.09
84 72 0.81
86 9 0.10
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (82 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTAGTCCAAGTTCGTTGCGATAGTCCAAATTCCGTTGC
GATTTATTCCAAATTCG
Found at i:58915 original size:63 final size:63
Alignment explanation
Indices: 58766--58919 Score: 231
Period size: 63 Copynumber: 2.4 Consensus size: 63
58756 GACTATCGCA
*
58766 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * *
58829 TTGCGATTTATTCCAAATT--CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
58892 TTGCGATAGTCGAAGTTCGCGTTGCGAT
1 TTGCGATAGTCCAAGTTCGCGTTGCGAT
58920 TTATTCCAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
61 8 0.10
63 63 0.79
65 9 0.11
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (63 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:59047 original size:6 final size:6
Alignment explanation
Indices: 59036--59061 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
59026 ACGTATTACT
59036 ACGACC ACGACC ACGACC ACGACC AC
1 ACGACC ACGACC ACGACC ACGACC AC
59062 TAGACGAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.50, G:0.15, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:59700 original size:19 final size:21
Alignment explanation
Indices: 59663--59705 Score: 72
Period size: 19 Copynumber: 2.1 Consensus size: 21
59653 ACCAGTCGTT
59663 ACGAATTTGGAATAAATCGCA
1 ACGAATTTGGAATAAATCGCA
59684 ACGAATTTGG-A-AAATCGCA
1 ACGAATTTGGAATAAATCGCA
59703 ACG
1 ACG
59706 CGAACTTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 11 0.50
20 1 0.05
21 10 0.45
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (21 bp):
ACGAATTTGGAATAAATCGCA
Found at i:59709 original size:21 final size:20
Alignment explanation
Indices: 59664--59729 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
59654 CCAGTCGTTA
59664 CGAATTTGGAATAAATCGCAA-
1 CGAATTTGG-A-AAATCGCAAG
59685 CGAATTTGGAAAATCGCAACG
1 CGAATTTGGAAAATCGCAA-G
* **
59706 CGAACTTGGACTATCGCAATG
1 CGAATTTGGAAAATCGCAA-G
59727 CGA
1 CGA
59730 TAGTCGAAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.23
20 1 0.03
21 29 0.74
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (20 bp):
CGAATTTGGAAAATCGCAAG
Found at i:59791 original size:21 final size:21
Alignment explanation
Indices: 59767--59877 Score: 150
Period size: 21 Copynumber: 5.3 Consensus size: 21
59757 AATTTGGAAA
*
59767 ATCGCAACGCAAACTTCGACT
1 ATCGCAATGCAAACTTCGACT
*
59788 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCAAACTTCGACT
*
59809 ATCGCAATGCAAACTTTGACT
1 ATCGCAATGCAAACTTCGACT
* * *
59830 ATCGAAATGCGAACTTCAACT
1 ATCGCAATGCAAACTTCGACT
* *
59851 ATCGCAACGCAAACTTCGATT
1 ATCGCAATGCAAACTTCGACT
59872 ATCGCA
1 ATCGCA
59878 TTGCGAATAT
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.23
Consensus pattern (21 bp):
ATCGCAATGCAAACTTCGACT
Found at i:59830 original size:42 final size:42
Alignment explanation
Indices: 59767--59884 Score: 182
Period size: 42 Copynumber: 2.8 Consensus size: 42
59757 AATTTGGAAA
*
59767 ATCGCAACGCAAACTTCGACTATCGCAATGCGAACTTCGACT
1 ATCGCAACGCAAACTTCGACTATCGCAATGCGAACTTCAACT
* * *
59809 ATCGCAATGCAAACTTTGACTATCGAAATGCGAACTTCAACT
1 ATCGCAACGCAAACTTCGACTATCGCAATGCGAACTTCAACT
* *
59851 ATCGCAACGCAAACTTCGATTATCGCATTGCGAA
1 ATCGCAACGCAAACTTCGACTATCGCAATGCGAA
59885 TATGTAAATC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (42 bp):
ATCGCAACGCAAACTTCGACTATCGCAATGCGAACTTCAACT
Found at i:59923 original size:21 final size:21
Alignment explanation
Indices: 59893--59987 Score: 136
Period size: 21 Copynumber: 4.5 Consensus size: 21
59883 AATATGTAAA
* *
59893 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
59914 TCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
59935 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
**
59956 TCGCATTGCGATAGTTGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
59977 TCGCGTTGCGA
1 TCGCATTGCGA
59988 ATCTGGAAAC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 67 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Done.