Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 164 of 198
Found at i:51605812 original size:20 final size:20
Alignment explanation
Indices: 51605771--51605830 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 20
51605761 TTTTAAAAAT
* *
51605771 ATATAAAATTTC-TAATAAA
1 ATATAAAATTTCAAAAGAAA
51605790 ATATAAAATTTCAAAAGAAA
1 ATATAAAATTTCAAAAGAAA
* *
51605810 ATATATAA-CTCAAAAGAAA
1 ATATAAAATTTCAAAAGAAA
51605829 AT
1 AT
51605831 CAACCTCAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
19 24 0.67
20 12 0.33
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (20 bp):
ATATAAAATTTCAAAAGAAA
Found at i:51608490 original size:19 final size:19
Alignment explanation
Indices: 51608458--51608496 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
51608448 AAAATTAAAA
51608458 AAAAAGTTCAAAATATTTAT
1 AAAAAGTTCAAAAT-TTTAT
*
51608478 AAAAATTTC-AAATTTTAT
1 AAAAAGTTCAAAATTTTAT
51608496 A
1 A
51608497 TTTTTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (19 bp):
AAAAAGTTCAAAATTTTAT
Found at i:51616295 original size:25 final size:25
Alignment explanation
Indices: 51616267--51616315 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
51616257 ATTTATTTTA
**
51616267 ATATTTTTAGTATTTTTGATATATT
1 ATATTTTTAACATTTTTGATATATT
*
51616292 ATATTTTTAACATTTTTTATATAT
1 ATATTTTTAACATTTTTGATATAT
51616316 AAAATTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (25 bp):
ATATTTTTAACATTTTTGATATATT
Found at i:51618179 original size:10 final size:10
Alignment explanation
Indices: 51618161--51618194 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
51618151 TCCCCTGCTT
*
51618161 TTATTAAAAA
1 TTATAAAAAA
51618171 TTATAAAAAAA
1 TTAT-AAAAAA
51618182 TTATAAAAAA
1 TTATAAAAAA
51618192 TTA
1 TTA
51618195 AATTCAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:51618182 original size:11 final size:11
Alignment explanation
Indices: 51618166--51618191 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
51618156 TGCTTTTATT
51618166 AAAAATTATAA
1 AAAAATTATAA
51618177 AAAAATTATAA
1 AAAAATTATAA
51618188 AAAA
1 AAAA
51618192 TTAAATTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:51618262 original size:25 final size:26
Alignment explanation
Indices: 51618210--51618261 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
51618200 AATAAAAGCT
* *
51618210 ATAAATATATTAAAATTTTTTTAAAA
1 ATAAATATATTAAAAATTATTTAAAA
51618236 ATAAA-ATATTAAAAAATTATTTAAAA
1 ATAAATATATT-AAAAATTATTTAAAA
51618262 TTATAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
ATAAATATATTAAAAATTATTTAAAA
Found at i:51618277 original size:11 final size:10
Alignment explanation
Indices: 51618245--51618366 Score: 62
Period size: 10 Copynumber: 12.5 Consensus size: 10
51618235 AATAAAATAT
51618245 TAAAAAATTA
1 TAAAAAATTA
**
51618255 TTTAAAATTA
1 TAAAAAATTA
51618265 TAAAAAA-TA
1 TAAAAAATTA
* *
51618274 T--ATAATTCG
1 TAAAAAATT-A
51618283 TAAAATAATTA
1 TAAAA-AATTA
*
51618294 TAAAAAATTG
1 TAAAAAATTA
**
51618304 TAAAATTTTA
1 TAAAAAATTA
51618314 T-AAAAA-TA
1 TAAAAAATTA
51618322 GT-AAAAATTGA
1 -TAAAAAATT-A
51618333 T-AAAAATATA
1 TAAAAAAT-TA
* *
51618343 TAGAAATTTA
1 TAAAAAATTA
51618353 -AAAAAATTA
1 TAAAAAATTA
51618362 TAAAA
1 TAAAA
51618367 TTTTATAAAG
Statistics
Matches: 83, Mismatches: 18, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
7 3 0.04
8 3 0.04
9 20 0.24
10 41 0.49
11 12 0.14
12 4 0.05
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:51618320 original size:19 final size:19
Alignment explanation
Indices: 51618277--51618375 Score: 83
Period size: 19 Copynumber: 5.0 Consensus size: 19
51618267 AAAAATATAT
*
51618277 AATTCGTAAAATAATTATAAAA
1 AATT-GTAAAAT-TTTAT-AAA
51618299 AATTGTAAAATTTTATAAA
1 AATTGTAAAATTTTATAAA
* * *
51618318 AATAGTAAAAATTGATAAA
1 AATTGTAAAATTTTATAAA
* *
51618337 AATATATAGAAA-TTTAAAAA
1 AAT-TGTA-AAATTTTATAAA
*
51618357 AATTATAAAATTTTATAAA
1 AATTGTAAAATTTTATAAA
51618376 GTCGTAAGAA
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
18 3 0.05
19 33 0.51
20 15 0.23
21 10 0.15
22 4 0.06
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (19 bp):
AATTGTAAAATTTTATAAA
Found at i:51618326 original size:29 final size:28
Alignment explanation
Indices: 51618294--51618375 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 28
51618284 AAAATAATTA
51618294 TAAAAAATTGTAAAATTTTATAAAAATAG
1 TAAAAAATTGTAAAATTTTATAAAAAT-G
* * * *
51618323 T-AAAAATTGATAAAAATATATAGAAATT
1 TAAAAAATTG-TAAAATTTTATAAAAATG
*
51618351 TAAAAAAATTATAAAATTTTATAAA
1 T-AAAAAATTGTAAAATTTTATAAA
51618376 GTCGTAAGAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
28 9 0.21
29 26 0.62
30 7 0.17
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (28 bp):
TAAAAAATTGTAAAATTTTATAAAAATG
Found at i:51618372 original size:10 final size:10
Alignment explanation
Indices: 51618291--51618375 Score: 68
Period size: 10 Copynumber: 8.7 Consensus size: 10
51618281 CGTAAAATAA
*
51618291 TTATAAAAAA
1 TTATAAAAAT
* *
51618301 TTGTAAAATT
1 TTATAAAAAT
51618311 TTATAAAAA-
1 TTATAAAAAT
51618320 -TAGTAAAAAT
1 TTA-TAAAAAT
*
51618330 TGATAAAAAT
1 TTATAAAAAT
* *
51618340 ATATAGAAAT
1 TTATAAAAAT
*
51618350 TTA-AAAAAA
1 TTATAAAAAT
*
51618359 TTATAAAATT
1 TTATAAAAAT
51618369 TTATAAA
1 TTATAAA
51618376 GTCGTAAGAA
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
8 2 0.04
9 13 0.23
10 41 0.72
11 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (10 bp):
TTATAAAAAT
Found at i:51618388 original size:58 final size:58
Alignment explanation
Indices: 51618295--51618412 Score: 150
Period size: 58 Copynumber: 2.0 Consensus size: 58
51618285 AAATAATTAT
* * *
51618295 AAAAAATTGTAAAATTTTATAAAAATAGTAAAAATTGATA-AAAATATATAGAAATTTA
1 AAAAAATTATAAAATTTTATAAAAATAGTAAAAATT-ATACAAAATATAAAGAAATATA
* * *
51618353 AAAAAATTATAAAATTTTAT-AAAGTCGTAAGAAATTATACAAAATGTAAAGAAATATA
1 AAAAAATTATAAAATTTTATAAAAATAGTAA-AAATTATACAAAATATAAAGAAATATA
51618411 AA
1 AA
51618413 TTTCGTAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
57 11 0.21
58 41 0.79
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.31
Consensus pattern (58 bp):
AAAAAATTATAAAATTTTATAAAAATAGTAAAAATTATACAAAATATAAAGAAATATA
Found at i:51618690 original size:19 final size:18
Alignment explanation
Indices: 51618641--51618692 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
51618631 TTTCTAATTT
*
51618641 TTAATATTTTTATTAAAAT
1 TTAATATTTTT-TTAAAAC
*
51618660 TTAATAGTTTTTCTAAAAC
1 TTAATA-TTTTTTTAAAAC
*
51618679 TTATTATTTTTTTA
1 TTAATATTTTTTTA
51618693 TTTTTTATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 7 0.25
19 16 0.57
20 5 0.18
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (18 bp):
TTAATATTTTTTTAAAAC
Found at i:51618849 original size:87 final size:86
Alignment explanation
Indices: 51618732--51618925 Score: 250
Period size: 87 Copynumber: 2.3 Consensus size: 86
51618722 TAAGAGCAGA
*
51618732 GGCTTAATTGC-TTTTTTGAAAAATTTTGAGGGTCTTTTTGATACATTTTGAAAATTCAAGTACC
1 GGCTTAATTGCTTTTTTTGAAAAATTTTGAGGGCCTTTTTGATACATTTTGAAAATTCAAGTACC
*
51618796 CAATTGAGTGAAAAAAAAAAGG
66 CAATTGAGTGAAAAAAAAAA-C
* * * * * *
51618818 GGCTTAATTACTTTTTTTGAAGAAA-TTTGAGGGCCTTTTTGATGCATTTTTAAAGTTTAAGTGC
1 GGCTTAATTGCTTTTTTTGAA-AAATTTTGAGGGCCTTTTTGATACATTTTGAAAATTCAAGTAC
* *
51618882 TCAATTGAGTGCAAAAAAAAAC
65 CCAATTGAGTGAAAAAAAAAAC
*
51618904 GGCTTAATTG-TTTTTTTTAAAA
1 GGCTTAATTGCTTTTTTTGAAAA
51618926 TTTAAAGACT
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
84 2 0.02
85 9 0.10
86 19 0.20
87 61 0.65
88 3 0.03
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (86 bp):
GGCTTAATTGCTTTTTTTGAAAAATTTTGAGGGCCTTTTTGATACATTTTGAAAATTCAAGTACC
CAATTGAGTGAAAAAAAAAAC
Found at i:51620424 original size:21 final size:21
Alignment explanation
Indices: 51620399--51620439 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
51620389 TTAATATAAG
*
51620399 AATAC-TTGATTATATTATTTT
1 AATACTTTAATTA-ATTATTTT
51620420 AATACTTTAATTAATTATTT
1 AATACTTTAATTAATTATTT
51620440 ATGACTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (21 bp):
AATACTTTAATTAATTATTTT
Found at i:51621813 original size:18 final size:18
Alignment explanation
Indices: 51621773--51621815 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
51621763 ATTCAAGGTG
51621773 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
51621791 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
51621809 TAATTAA
1 TAATTAA
51621816 CAACCTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:51622448 original size:16 final size:16
Alignment explanation
Indices: 51622427--51622458 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
51622417 GTGGTACATG
51622427 TATTTTTTTTCAATGT
1 TATTTTTTTTCAATGT
51622443 TATTTTTTTTCAATGT
1 TATTTTTTTTCAATGT
51622459 GGTACCTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (16 bp):
TATTTTTTTTCAATGT
Found at i:51630096 original size:15 final size:15
Alignment explanation
Indices: 51630047--51630101 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
51630037 CAAATACAAC
51630047 CAATATTCAATTCAATT
1 CAATA-TCAATTCAA-T
51630064 CAA-AT-AA-TCAAT
1 CAATATCAATTCAAT
51630076 -ATATATCAATTCAAT
1 CA-ATATCAATTCAAT
51630091 CAATATCAATT
1 CAATATCAATT
51630102 TAATAAATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
11 1 0.03
12 2 0.06
13 6 0.18
14 4 0.12
15 15 0.45
16 2 0.06
17 3 0.09
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.36
Consensus pattern (15 bp):
CAATATCAATTCAAT
Found at i:51631595 original size:25 final size:25
Alignment explanation
Indices: 51631535--51631647 Score: 76
Period size: 25 Copynumber: 4.6 Consensus size: 25
51631525 ATCTAGGCTG
* *
51631535 TATAACGGGTAGCTCCGAAGAGCCA
1 TATATCGGGAAGCTCCGAAGAGCCA
* * *
51631560 T-TAATCAGGAAGCTCCGGATAGCCA
1 TAT-ATCGGGAAGCTCCGAAGAGCCA
* *
51631585 TATATCGGGAAG-TTC-AAGCGAACC-
1 TATATCGGGAAGCTCCGAA--GAGCCA
51631609 -ATATCGGGAAGCTCCGAAGAGCCA
1 TATATCGGGAAGCTCCGAAGAGCCA
*
51631633 T-TAATCGGAAAGCTC
1 TAT-ATCGGGAAGCTC
51631648 ACAAAAAACT
Statistics
Matches: 66, Mismatches: 13, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
23 16 0.24
24 6 0.09
25 43 0.65
26 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.19
Consensus pattern (25 bp):
TATATCGGGAAGCTCCGAAGAGCCA
Found at i:51632169 original size:21 final size:21
Alignment explanation
Indices: 51632145--51632184 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
51632135 GTAAATTTAG
*
51632145 CTCAATTTAATACAATTCATA
1 CTCAATTCAATACAATTCATA
*
51632166 CTCAATTCAATCCAATTCA
1 CTCAATTCAATACAATTCA
51632185 CATCTTAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (21 bp):
CTCAATTCAATACAATTCATA
Found at i:51633363 original size:47 final size:47
Alignment explanation
Indices: 51633289--51633422 Score: 146
Period size: 47 Copynumber: 2.9 Consensus size: 47
51633279 TTGGCAGTTT
* * * *
51633289 ATCTGTTCGACCAGTGGTTTATCCACAATGTATTTTA-TTCAGCAATC
1 ATCTGCTCAACCAGTGGTTTATCCACAAAGTATTTTAGTTC-CCAATC
* * * *
51633336 ATCTGCTCAACCAATGGTTCATTCACAACA-TATTTTAGTTCCCAGTC
1 ATCTGCTCAACCAGTGGTTTATCCACAA-AGTATTTTAGTTCCCAATC
* *
51633383 ATCTGCTCAGCCAGTGTTTTATCCACAAAGTATTTTAGTT
1 ATCTGCTCAACCAGTGGTTTATCCACAAAGTATTTTAGTT
51633423 GGCAGTTCAT
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
46 1 0.01
47 67 0.94
48 3 0.04
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.37
Consensus pattern (47 bp):
ATCTGCTCAACCAGTGGTTTATCCACAAAGTATTTTAGTTCCCAATC
Found at i:51638283 original size:3 final size:3
Alignment explanation
Indices: 51638275--51638327 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
51638265 TGTACATGAA
51638275 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
51638323 AAC AA
1 AAC AA
51638328 TAATAATAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:51638332 original size:3 final size:3
Alignment explanation
Indices: 51638326--51638351 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
51638316 CAACAACAAC
51638326 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
51638352 GGAGAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:51641869 original size:132 final size:132
Alignment explanation
Indices: 51641534--51641869 Score: 498
Period size: 132 Copynumber: 2.5 Consensus size: 132
51641524 TGCCGACCAG
* * *
51641534 GGAGTTAGAATTACTGGCTTCAATATACTCCACTGTAACCTCAGAGAGGTAAAATCTACCATCTT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTACCATCTT
* * * * *
51641599 CGATCTACTCCACTACTGTCTAGGGAGATAAGATCTGTAATCTTCAATTTATTCAACTGTTGCTC
66 TGATCTGCTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCAACTGCTGCTC
51641664 AA
131 AA
*
51641666 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAAT-TCACCAGCT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCT-ACCATCT
**
51641730 TTGATCTGCTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCGCTGCTG-T
65 TTGATCTGCTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCAACTGCTGCT
*
51641794 CTA
130 CAA
* *
51641797 GG-GAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATC
1 GGAG-A-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTACCATC
51641861 TTTGATCTG
64 TTTGATCTG
51641870 TTTCGCTGTC
Statistics
Matches: 185, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
130 1 0.01
131 7 0.04
132 176 0.95
133 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (132 bp):
GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTACCATCTT
TGATCTGCTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCAACTGCTGCTC
AA
Found at i:51646613 original size:17 final size:17
Alignment explanation
Indices: 51646587--51646622 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
51646577 TTATATGATG
*
51646587 AAATGCCATGCAGTCAA
1 AAATGCCATGCAGCCAA
*
51646604 AAATGTCATGCAGCCAA
1 AAATGCCATGCAGCCAA
51646621 AA
1 AA
51646623 CAAAACACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (17 bp):
AAATGCCATGCAGCCAA
Found at i:51649634 original size:3 final size:3
Alignment explanation
Indices: 51649628--51649681 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
51649618 ATTACAATAT
51649628 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
51649676 CAA CAA
1 CAA CAA
51649682 TAATAATAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:51649686 original size:3 final size:3
Alignment explanation
Indices: 51649680--51649705 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
51649670 CAACAACAAC
51649680 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
51649706 GGAGAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:51657733 original size:18 final size:19
Alignment explanation
Indices: 51657701--51657740 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
51657691 TTGTTGAAGA
*
51657701 GCTTGCAGCTTGTATGCAT
1 GCTTGCAGCTCGTATGCAT
*
51657720 GCTT-CAGCTCGTATGCTT
1 GCTTGCAGCTCGTATGCAT
51657738 GCT
1 GCT
51657741 GCAATAGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.12, C:0.25, G:0.25, T:0.38
Consensus pattern (19 bp):
GCTTGCAGCTCGTATGCAT
Found at i:51662988 original size:16 final size:16
Alignment explanation
Indices: 51662967--51663018 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
51662957 TTTGGTTCGC
51662967 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
51662983 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGG
51662999 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
51663015 TGTA
1 TGTA
51663019 ATAGCTAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:51663106 original size:39 final size:40
Alignment explanation
Indices: 51663004--51663112 Score: 112
Period size: 44 Copynumber: 2.6 Consensus size: 40
51662994 AGAGATGTAT
*
51663004 TGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGGAATAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
* ***
51663044 TGTAATGTAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TG----G-AATAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
51663088 TGGAATAGAGGTGTAATAGCATAAT
1 TGGAATAGAGGTGTAATAGC-TAAT
51663113 GGAAAAAACT
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
39 15 0.27
40 3 0.05
41 4 0.07
44 20 0.36
45 14 0.25
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.35
Consensus pattern (40 bp):
TGGAATAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:51663337 original size:61 final size:60
Alignment explanation
Indices: 51663269--51663469 Score: 203
Period size: 61 Copynumber: 3.3 Consensus size: 60
51663259 TTTTAATTAA
*
51663269 AATATATGATACTGTAAAATTCTTAATAATTAATATTCTTATATTAAATTACTGAAATCAT
1 AATATATGATACTGTAAAATT-TTAATAATTAATATTCTTATATTAAATTACTCAAATCAT
* * ** * ** * *
51663330 AATATATGATACTGTAAAA-TAT-A-AATTAACATAATTATTATTAAATATATTTTAATTAA
1 AATATATGATACTGTAAAATTTTAATAATTAATATTCTTA-TATTAAAT-TACTCAAATCAT
* * * *
51663389 AATATTTGAT-TTAATAAAATTATTAATAATTAATATTCTTATATTAATTTACTCAAATCAT
1 AATATATGATACT-GTAAAATT-TTAATAATTAATATTCTTATATTAAATTACTCAAATCAT
51663450 AATATATGATACTGTAAAAT
1 AATATATGATACTGTAAAAT
51663470 ATAAATTAAC
Statistics
Matches: 107, Mismatches: 25, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
57 11 0.10
58 10 0.09
59 22 0.21
60 2 0.02
61 42 0.39
62 9 0.08
63 11 0.10
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (60 bp):
AATATATGATACTGTAAAATTTTAATAATTAATATTCTTATATTAAATTACTCAAATCAT
Found at i:51663377 original size:43 final size:42
Alignment explanation
Indices: 51663330--51663499 Score: 108
Period size: 44 Copynumber: 4.2 Consensus size: 42
51663320 CTGAAATCAT
51663330 AATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
1 AATATATGATACT-TAAAATATAAATTAACATAATTATTATTA
** * * * * * *
51663373 AATATATTTTAATTAAAATATTTGATTTAATAAAATTATTAATA
1 AATATATGATACTTAAAATA--TAAATTAACATAATTATTATTA
* * * * *
51663417 ATTA-AT-ATTCTT---ATATTAATTTAC-TCAA--ATCA-T-
1 AATATATGATACTTAAAATATAAATTAACAT-AATTATTATTA
51663450 AATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
1 AATATATGATACT-TAAAATATAAATTAACATAATTATTATTA
51663493 AATATAT
1 AATATAT
51663500 TTTAATTAAA
Statistics
Matches: 90, Mismatches: 23, Indels: 28
0.64 0.16 0.20
Matches are distributed among these distances:
33 3 0.03
34 3 0.03
35 7 0.08
36 1 0.01
37 7 0.08
39 15 0.17
40 1 0.01
41 3 0.03
42 11 0.12
43 19 0.21
44 20 0.22
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (42 bp):
AATATATGATACTTAAAATATAAATTAACATAATTATTATTA
Found at i:51663450 original size:120 final size:120
Alignment explanation
Indices: 51663237--51663548 Score: 511
Period size: 120 Copynumber: 2.6 Consensus size: 120
51663227 ATCATATTTA
* * *
51663237 AACATAATAATTATTAAATATATTTTAATTAAAATATATGATACT-GTAAAATTCTTAATAATTA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATGAT-TTAATAAAATTCTTAATAATTA
*
51663301 ATATTCTTATATTAAATTACTGAAATCATAATATATGATACTGTAAAATATAAATT
65 ATATTCTTATATTAAATTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* *
51663357 AACATAATTATTATTAAATATATTTTAATTAAAATATTTGATTTAATAAAATTATTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATTAA
*
51663422 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAAATTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* *
51663477 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAAT-ATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATT-A
51663541 ATATTCTT
65 ATATTCTT
51663549 NNNNNNNNNN
Statistics
Matches: 179, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
119 4 0.02
120 175 0.98
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAAATTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:51670268 original size:11 final size:11
Alignment explanation
Indices: 51670252--51670279 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
51670242 AATCGGGAGG
51670252 CGAAGGTAGAA
1 CGAAGGTAGAA
51670263 CGAAGGTAGAA
1 CGAAGGTAGAA
51670274 CGAAGG
1 CGAAGG
51670280 AAGACGCGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.11, G:0.39, T:0.07
Consensus pattern (11 bp):
CGAAGGTAGAA
Found at i:51682084 original size:19 final size:18
Alignment explanation
Indices: 51682049--51682091 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
51682039 ATTTACATCT
*
51682049 TTCTCTTAACTCTCTCAA
1 TTCTCTTAACCCTCTCAA
51682067 TTCTCTTAAACCCTCTCAA
1 TTCTCTT-AACCCTCTCAA
*
51682086 GTCTCT
1 TTCTCT
51682092 CAAGTCTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.21, C:0.35, G:0.02, T:0.42
Consensus pattern (18 bp):
TTCTCTTAACCCTCTCAA
Found at i:51694760 original size:21 final size:21
Alignment explanation
Indices: 51694707--51694768 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
51694697 TTTTTTAGAT
51694707 AATT-ATGT-TTATTTTCTTTA
1 AATTAATGTATTATTTT-TTTA
51694727 AATTAA-G-AGTTATTTTTTTA
1 AATTAATGTA-TTATTTTTTTA
*
51694747 ATTTAATGTATTATTTATTTTA
1 AATTAATGTATTATTT-TTTTA
51694769 TTACTTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
20 14 0.40
21 15 0.43
22 6 0.17
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (21 bp):
AATTAATGTATTATTTTTTTA
Found at i:51700342 original size:23 final size:23
Alignment explanation
Indices: 51700298--51700342 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
51700288 TCTTATTTTG
* *
51700298 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
51700321 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
51700343 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:51700639 original size:21 final size:22
Alignment explanation
Indices: 51700598--51700640 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
51700588 ATGCGCATGC
*
51700598 ATTGTTTTTATGTAATATATAT
1 ATTGTTTTTATATAATATATAT
*
51700620 ATTGTTTTATATATAGTATAT
1 ATTGTTTT-TATATAATATAT
51700641 GTATGCTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (22 bp):
ATTGTTTTTATATAATATATAT
Found at i:51702210 original size:146 final size:146
Alignment explanation
Indices: 51702018--51702284 Score: 367
Period size: 146 Copynumber: 1.8 Consensus size: 146
51702008 ATTCAGGTAG
* * * *
51702018 ATTAATAATATGTAGATCTATATATAGGTATGCTATTATAATGTATATTTTTACATTAATGAGAT
1 ATTAATAATATGTAGATCTATATAAAAGTATGATATTATAATGTATATTTTTACATTAATGAGAC
* * * *
51702083 GTAAGC-TTAAACCCTAAATGTATAACTAACTGTATGGTATATTATAATATATACAACAAACATA
66 GCAA-CATTAAACCCTAAACGTATAACTAACTGTATAGTAGATTATAATATATACAACAAACATA
51702147 TATAATTAAGATACATT
130 TATAATTAAGATACATT
* * *
51702164 ATTAATAATATGTA-ATCCTATATAAAATTATGATATTATAATGTATATTTTTATATTAATGATA
1 ATTAATAATATGTAGAT-CTATATAAAAGTATGATATTATAATGTATATTTTTACATTAATGAGA
* * * *
51702228 CGCAACATTAAACTCTAAACGTGTAATTAACTTTATAGTAGATTATAATATATACAA
65 CGCAACATTAAACCCTAAACGTATAACTAACTGTATAGTAGATTATAATATATACAA
51702285 TTAGCATGGA
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
145 3 0.03
146 101 0.97
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (146 bp):
ATTAATAATATGTAGATCTATATAAAAGTATGATATTATAATGTATATTTTTACATTAATGAGAC
GCAACATTAAACCCTAAACGTATAACTAACTGTATAGTAGATTATAATATATACAACAAACATAT
ATAATTAAGATACATT
Found at i:51702976 original size:48 final size:48
Alignment explanation
Indices: 51702905--51703002 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
51702895 GTAGCTGGAG
51702905 TTAGTCATATTTTCTTGTTGCCTTTGCTTCCCTCGCTGCTGCCTCCGC
1 TTAGTCATATTTTCTTGTTGCCTTTGCTTCCCTCGCTGCTGCCTCCGC
51702953 TTAGTCATATTTTCTTGTTGCCTTTGCTTCCCTCGCTGCTGCCTCCGC
1 TTAGTCATATTTTCTTGTTGCCTTTGCTTCCCTCGCTGCTGCCTCCGC
51703001 TT
1 TT
51703003 TAAGTTATAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.06, C:0.33, G:0.16, T:0.45
Consensus pattern (48 bp):
TTAGTCATATTTTCTTGTTGCCTTTGCTTCCCTCGCTGCTGCCTCCGC
Found at i:51704734 original size:73 final size:73
Alignment explanation
Indices: 51704653--51704806 Score: 308
Period size: 73 Copynumber: 2.1 Consensus size: 73
51704643 TAACTTGATA
51704653 TTCTCTCTCATCCAACTTCTATTTTCTTGAATCCAAGGTGATTTTCTTATTCTCCATAGTCTCCT
1 TTCTCTCTCATCCAACTTCTATTTTCTTGAATCCAAGGTGATTTTCTTATTCTCCATAGTCTCCT
51704718 TATCACTT
66 TATCACTT
51704726 TTCTCTCTCATCCAACTTCTATTTTCTTGAATCCAAGGTGATTTTCTTATTCTCCATAGTCTCCT
1 TTCTCTCTCATCCAACTTCTATTTTCTTGAATCCAAGGTGATTTTCTTATTCTCCATAGTCTCCT
51704791 TATCACTT
66 TATCACTT
51704799 TTCTCTCT
1 TTCTCTCT
51704807 TGGTGGTTAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 81 1.00
ACGTcount: A:0.18, C:0.28, G:0.06, T:0.47
Consensus pattern (73 bp):
TTCTCTCTCATCCAACTTCTATTTTCTTGAATCCAAGGTGATTTTCTTATTCTCCATAGTCTCCT
TATCACTT
Found at i:51705005 original size:11 final size:11
Alignment explanation
Indices: 51704989--51705033 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
51704979 TAGCTATTTA
51704989 TAATAAAATAT
1 TAATAAAATAT
51705000 TAATAAAATAT
1 TAATAAAATAT
*
51705011 CCTATTAAAATAT
1 --TAATAAAATAT
*
51705024 TAATTAAATA
1 TAATAAAATA
51705034 ATATTTATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 19 0.66
13 10 0.34
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:51707683 original size:23 final size:23
Alignment explanation
Indices: 51707611--51707676 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
51707601 TATCAAATTT
* *
51707611 TCATAATCAATCTCATTTTCT-TTC
1 TCAT-ATCAATTTCA-TTTCTACTC
51707635 TCATATCAATTTCATTTCTACTC
1 TCATATCAATTTCATTTCTACTC
* *
51707658 TCATTTCCATTCTCATTTC
1 TCATATCAATT-TCATTTC
51707677 AGTCTCAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.14
23 20 0.56
24 11 0.31
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (23 bp):
TCATATCAATTTCATTTCTACTC
Found at i:51709781 original size:11 final size:11
Alignment explanation
Indices: 51709765--51709809 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
51709755 TAGCTATTTA
51709765 TAATAAAATAT
1 TAATAAAATAT
51709776 TAATAAAATATCT
1 TAATAAAATA--T
*
51709789 TATTAAAATAT
1 TAATAAAATAT
*
51709800 TAATTAAATA
1 TAATAAAATA
51709810 ATATTTATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 19 0.66
13 10 0.34
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:51710778 original size:43 final size:43
Alignment explanation
Indices: 51710730--51710815 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
51710720 TATGTGATTG
*
51710730 ATATTGAAATGG-AAATGGCGAGAAATGAAAATGAGATGAGAAA
1 ATATTGAAATGGCAAA-GACGAGAAATGAAAATGAGATGAGAAA
* **
51710773 ATATTGAAATGGCAAAGATGAGAAATGATTATGAGATGAGAAA
1 ATATTGAAATGGCAAAGACGAGAAATGAAAATGAGATGAGAAA
51710816 TGAAATATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 35 0.92
44 3 0.08
ACGTcount: A:0.50, C:0.02, G:0.27, T:0.21
Consensus pattern (43 bp):
ATATTGAAATGGCAAAGACGAGAAATGAAAATGAGATGAGAAA
Found at i:51714036 original size:23 final size:24
Alignment explanation
Indices: 51714009--51714060 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
51713999 AAACTTCAAA
* *
51714009 TTTTATTAGATT-TTTTTATGATT
1 TTTTATAAGATTGTCTTTATGATT
*
51714032 TTTTATAATATTGTCTTTATGATT
1 TTTTATAAGATTGTCTTTATGATT
51714056 TTTTA
1 TTTTA
51714061 AATAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.23, C:0.02, G:0.08, T:0.67
Consensus pattern (24 bp):
TTTTATAAGATTGTCTTTATGATT
Found at i:51714811 original size:13 final size:13
Alignment explanation
Indices: 51714793--51714822 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
51714783 TGTTCCTTTT
51714793 ATTTTTCTCTTAA
1 ATTTTTCTCTTAA
*
51714806 ATTTTTCTTTTAA
1 ATTTTTCTCTTAA
51714819 ATTT
1 ATTT
51714823 CGACCCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTTTCTCTTAA
Found at i:51715935 original size:34 final size:33
Alignment explanation
Indices: 51715852--51715936 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 33
51715842 AATACATAAA
* * *
51715852 AAGCATTATTTTTGCTACTGAGTTGATCTATCAT
1 AAGCA-TATTTTTGCTACTGAATCGAACTATCAT
* * *
51715886 AAGCATATTAATTGCTACTGAATCGAACTGTTAT
1 AAGCATATT-TTTGCTACTGAATCGAACTATCAT
51715920 AAGCATATTGTTTGCTA
1 AAGCATATT-TTTGCTA
51715937 TTGTATTATT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 4 0.10
34 38 0.90
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (33 bp):
AAGCATATTTTTGCTACTGAATCGAACTATCAT
Found at i:51717942 original size:25 final size:26
Alignment explanation
Indices: 51717893--51717943 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
51717883 ATATTGGAAT
*
51717893 TATTAAATAAACTAATAATTTAAAAA
1 TATTAAATAAACTAATAATTGAAAAA
* *
51717919 TATTATATAAA-TACTAATTGAAAAA
1 TATTAAATAAACTAATAATTGAAAAA
51717944 CAGAGATGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (26 bp):
TATTAAATAAACTAATAATTGAAAAA
Found at i:51721763 original size:20 final size:20
Alignment explanation
Indices: 51721719--51721756 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
51721709 TCTAGAATAT
**
51721719 TAAAAATAAATTTAAAAAAA
1 TAAAAATAAAAATAAAAAAA
51721739 TAAAAATAAAAATAAAAA
1 TAAAAATAAAAATAAAAA
51721757 GCTAAAATTT
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:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (20 bp):
TAAAAATAAAAATAAAAAAA
Found at i:51726626 original size:40 final size:40
Alignment explanation
Indices: 51726550--51726627 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
51726540 ATAGTGTTGA
* * * * *
51726550 TTTTACCATATTTTCTTATATTTTCTTCTCATCAAACAAT
1 TTTTACCAAATTTTATTACATTTTCTTCTAACCAAACAAT
51726590 TTTTACCAAATTTTATTACATTTTC-TCATAACCAAACA
1 TTTTACCAAATTTTATTACATTTTCTTC-TAACCAAACA
51726628 CACACACGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 2 0.06
40 30 0.94
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (40 bp):
TTTTACCAAATTTTATTACATTTTCTTCTAACCAAACAAT
Found at i:51727083 original size:22 final size:22
Alignment explanation
Indices: 51727036--51727096 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
51727026 TATTTGCTTA
*
51727036 TTTGAATCGATTATTT-TGTTG
1 TTTGAATCGATTCTTTATGTTG
* *
51727057 ATTGACTCGATTCTTTATGTTG
1 TTTGAATCGATTCTTTATGTTG
*
51727079 TTTGAATCAATTCTTTAT
1 TTTGAATCGATTCTTTAT
51727097 TGTAAAAATC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 13 0.39
22 20 0.61
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (22 bp):
TTTGAATCGATTCTTTATGTTG
Found at i:51730949 original size:32 final size:32
Alignment explanation
Indices: 51730903--51730967 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
51730893 GCTTAGTCAC
*
51730903 TAGTTTTGGTCCTTTGGAGCTATCCATCTTTG
1 TAGTTTTGGCCCTTTGGAGCTATCCATCTTTG
51730935 TAGTTTTGGCCCTTTGGAGCTATCCATCTTTG
1 TAGTTTTGGCCCTTTGGAGCTATCCATCTTTG
51730967 T
1 T
51730968 TGCAAAATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (32 bp):
TAGTTTTGGCCCTTTGGAGCTATCCATCTTTG
Found at i:51737060 original size:24 final size:26
Alignment explanation
Indices: 51737002--51737061 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 26
51736992 TTAAACATAC
51737002 ATATTTAATTATTTATATTTAATAAA
1 ATATTTAATTATTTATATTTAATAAA
**
51737028 ATAAATAATTA-TTA-ATTTAATAAA
1 ATATTTAATTATTTATATTTAATAAA
*
51737052 TTATTTAATT
1 ATATTTAATT
51737062 TAATATTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 17 0.59
25 3 0.10
26 9 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
ATATTTAATTATTTATATTTAATAAA
Found at i:51737069 original size:24 final size:24
Alignment explanation
Indices: 51737012--51737069 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
51737002 ATATTTAATT
51737012 ATTT-ATATTTAATAAAATAAATA
1 ATTTAATATTTAATAAAATAAATA
* * **
51737035 A-TTATTAATTTAATAAATTATTTA
1 ATTTAAT-ATTTAATAAAATAAATA
51737059 ATTTAATATTT
1 ATTTAATATTT
51737070 TATTTTAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
22 2 0.07
23 2 0.07
24 19 0.70
25 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTTAATATTTAATAAAATAAATA
Found at i:51737074 original size:17 final size:17
Alignment explanation
Indices: 51737034--51737066 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
51737024 TAAAATAAAT
51737034 AATTA-TTAATTTAATA
1 AATTATTTAATTTAATA
51737050 AATTATTTAATTTAATA
1 AATTATTTAATTTAATA
51737067 TTTTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTATTTAATTTAATA
Found at i:51737433 original size:14 final size:14
Alignment explanation
Indices: 51737414--51737446 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
51737404 ATTTTAATTA
51737414 AAAATAACTTTT-AG
1 AAAATAA-TTTTAAG
51737428 AAAATAATTTTAAG
1 AAAATAATTTTAAG
51737442 AAAAT
1 AAAAT
51737447 TTGTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (14 bp):
AAAATAATTTTAAG
Found at i:51741339 original size:16 final size:17
Alignment explanation
Indices: 51741318--51741351 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
51741308 TTCTATCATG
51741318 TAAGAATCATT-TTGAT
1 TAAGAATCATTATTGAT
51741334 TAAGAATCATTATTGAT
1 TAAGAATCATTATTGAT
51741351 T
1 T
51741352 TGTCCTGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (17 bp):
TAAGAATCATTATTGAT
Found at i:51750799 original size:12 final size:12
Alignment explanation
Indices: 51750768--51750810 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
51750758 ATGATTAAAA
* *
51750768 ACTTGATGGAAA
1 ACTTGATTGAAG
51750780 ACTTGATTGAAG
1 ACTTGATTGAAG
* *
51750792 ACTTGATTTATG
1 ACTTGATTGAAG
51750804 ACTTGAT
1 ACTTGAT
51750811 GAATAAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (12 bp):
ACTTGATTGAAG
Found at i:51752197 original size:6 final size:6
Alignment explanation
Indices: 51752186--51752222 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
51752176 GAATAGAAGG
51752186 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA A
51752223 TGTGTAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:51773916 original size:23 final size:22
Alignment explanation
Indices: 51773829--51773915 Score: 124
Period size: 23 Copynumber: 4.0 Consensus size: 22
51773819 CTGATTAGTA
51773829 TACGACACAT-AAGTGCCTGA-
1 TACGACACATAAAGTGCCTGAG
*
51773849 TACGACACATAAAGTACCTGAG
1 TACGACACATAAAGTGCCTGAG
51773871 ATACGACACATAAAGTGCCTGATG
1 -TACGACACATAAAGTGCCTGA-G
*
51773895 TACGACACATAAAGTGTCTGA
1 TACGACACATAAAGTGCCTGA
51773916 TCGGCAAAGC
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
20 10 0.17
21 9 0.15
23 40 0.67
24 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (22 bp):
TACGACACATAAAGTGCCTGAG
Found at i:51774893 original size:4 final size:4
Alignment explanation
Indices: 51774879--51774941 Score: 55
Period size: 4 Copynumber: 16.8 Consensus size: 4
51774869 GTTTTTCCTT
* *
51774879 TTTC TTTTC TTTC TTTC TTT- TTCC TTTC TTTC -TT- TTTG TTTC TTTC
1 TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
51774925 TTT- TGT- TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTT
51774942 TGTTCACTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
3 10 0.20
4 35 0.71
5 4 0.08
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:51774914 original size:14 final size:14
Alignment explanation
Indices: 51774871--51774942 Score: 78
Period size: 14 Copynumber: 5.3 Consensus size: 14
51774861 AACCTTTAGT
51774871 TTTTCC-TT-TTTC
1 TTTTCCTTTCTTTC
51774883 TTTT-CTTTCTTTC
1 TTTTCCTTTCTTTC
51774896 TTTTTCCTTTCTTTC
1 -TTTTCCTTTCTTTC
**
51774911 TTTTTGTTTCTTTC
1 TTTTCCTTTCTTTC
**
51774925 TTTTGTTTTCTTTC
1 TTTTCCTTTCTTTC
51774939 TTTT
1 TTTT
51774943 GTTCACTAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
11 1 0.02
12 6 0.12
13 4 0.08
14 32 0.62
15 9 0.17
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (14 bp):
TTTTCCTTTCTTTC
Found at i:51774933 original size:18 final size:18
Alignment explanation
Indices: 51774876--51774941 Score: 77
Period size: 18 Copynumber: 3.8 Consensus size: 18
51774866 TTAGTTTTTC
51774876 CTTTTTCTTTTCTTTCTTT
1 CTTTTTC-TTTCTTTCTTT
51774895 CTTTTTC---CTTTCTTT
1 CTTTTTCTTTCTTTCTTT
*
51774910 CTTTTTGTTTCTTTCTTT
1 CTTTTTCTTTCTTTCTTT
51774928 -TGTTTTCTTTCTTT
1 CT-TTTTCTTTCTTT
51774942 TGTTCACTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 14 0.34
17 1 0.02
18 19 0.46
19 7 0.17
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (18 bp):
CTTTTTCTTTCTTTCTTT
Found at i:51774945 original size:14 final size:13
Alignment explanation
Indices: 51774879--51774942 Score: 83
Period size: 14 Copynumber: 4.6 Consensus size: 13
51774869 GTTTTTCCTT
*
51774879 TTTCTTTTCTTTC
1 TTTCTTTTTTTTC
51774892 TTTCTTTTTCCTTTC
1 TTTCTTTTT--TTTC
51774907 TTTCTTTTTGTTTC
1 TTTCTTTTT-TTTC
51774921 TTTCTTTTGTTTTC
1 TTTCTTTT-TTTTC
51774935 TTTCTTTT
1 TTTCTTTT
51774943 GTTCACTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.17
14 24 0.52
15 14 0.30
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (13 bp):
TTTCTTTTTTTTC
Found at i:51783417 original size:23 final size:23
Alignment explanation
Indices: 51783387--51783510 Score: 73
Period size: 23 Copynumber: 5.4 Consensus size: 23
51783377 ATTATAATAA
*
51783387 TATGTATTAGTGTTAAATTTCAT
1 TATGTATTAGTCTTAAATTTCAT
* *
51783410 TATGTATTATTTTTAAA--TCAAT
1 TATGTATTAGTCTTAAATTTC-AT
*
51783432 ATAT-TATTAGCATCATAAATTTTCAT
1 -TATGTATTAG--TCTTAAA-TTTCAT
*
51783458 GTAT-TATTAG-CTTAGATTT-AT
1 -TATGTATTAGTCTTAAATTTCAT
* *
51783479 TATGTATTTGTTTTTAAA-TTCAT
1 TATGTATTAG-TCTTAAATTTCAT
51783502 TATGTATTA
1 TATGTATTA
51783511 TCATTTCGAA
Statistics
Matches: 78, Mismatches: 12, Indels: 22
0.70 0.11 0.20
Matches are distributed among these distances:
20 3 0.04
21 9 0.12
22 12 0.15
23 36 0.46
24 5 0.06
26 11 0.14
27 2 0.03
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (23 bp):
TATGTATTAGTCTTAAATTTCAT
Found at i:51785051 original size:25 final size:25
Alignment explanation
Indices: 51785019--51785081 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
51785009 TAGCTCTCAT
51785019 GAGCTTCCCGTTATATGGTTCTTAC
1 GAGCTTCCCGTTATATGGTTCTTAC
*
51785044 GAGCTTCCCGTTATATGGTTCTTGC
1 GAGCTTCCCGTTATATGGTTCTTAC
51785069 GAGCTTCCCGTTA
1 GAGCTTCCCGTTA
51785082 ATAGCTCTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.14, C:0.25, G:0.22, T:0.38
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGTTCTTAC
Found at i:51785177 original size:25 final size:25
Alignment explanation
Indices: 51785149--51785246 Score: 108
Period size: 25 Copynumber: 3.8 Consensus size: 25
51785139 TAGCTCTTAT
51785149 GAGCTTCCCGATTAATGGCTCTCCG
1 GAGCTTCCCGATTAATGGCTCTCCG
* * **
51785174 GAGCTTCCTGATTTAAAGGCTCTTTCAT
1 GAGCTTCCCGA-TTAATGGCTC--TCCG
51785202 GAGCTTCCCGATTAATGGCTCTCCG
1 GAGCTTCCCGATTAATGGCTCTCCG
* *
51785227 GAGCTTCTCGA-TATTGGCTC
1 GAGCTTCCCGATTAATGGCTC
51785247 ACTTGAACCT
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
24 8 0.13
25 22 0.37
26 9 0.15
27 9 0.15
28 12 0.20
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (25 bp):
GAGCTTCCCGATTAATGGCTCTCCG
Found at i:51785294 original size:25 final size:26
Alignment explanation
Indices: 51785266--51785336 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 26
51785256 TTCTCGATAT
51785266 TGGCTCGTAT-AAGCTTCCCATTACA
1 TGGCTCGTATGAAGCTTCCCATTACA
* * * *
51785291 TGGCTC-TCTGGAGCTTCCCGTTATA
1 TGGCTCGTATGAAGCTTCCCATTACA
* *
51785316 TGGCTCGAAAGAAAGCTTCCC
1 TGGCTCGTATG-AAGCTTCCC
51785337 GTTTATATGT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
24 2 0.06
25 24 0.69
26 1 0.03
27 8 0.23
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (26 bp):
TGGCTCGTATGAAGCTTCCCATTACA
Found at i:51790436 original size:29 final size:25
Alignment explanation
Indices: 51790389--51790442 Score: 63
Period size: 29 Copynumber: 2.0 Consensus size: 25
51790379 ATTAATTTAT
*
51790389 TAATTTTATATAAATATAACTATAA
1 TAATTTTATATAAATATAAATATAA
51790414 TAATTTCTATTATAATATTATAAATATAA
1 TAATTT-TA-TATAA-A-TATAAATATAA
51790443 AAGTTTAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 6 0.25
26 2 0.08
27 5 0.21
28 1 0.04
29 10 0.42
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (25 bp):
TAATTTTATATAAATATAAATATAA
Found at i:51791443 original size:15 final size:15
Alignment explanation
Indices: 51791420--51791472 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
51791410 ATGGATTAAT
*
51791420 AATCTAGAAATATCA
1 AATCAAGAAATATCA
*
51791435 AATCAAG-AAT-TAA
1 AATCAAGAAATATCA
*
51791448 TAATCTAGAAATATCA
1 -AATCAAGAAATATCA
51791464 AATCAAGAA
1 AATCAAGAA
51791473 TTAAGTACAC
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
13 2 0.07
14 9 0.30
15 17 0.57
16 2 0.07
ACGTcount: A:0.57, C:0.11, G:0.08, T:0.25
Consensus pattern (15 bp):
AATCAAGAAATATCA
Found at i:51791448 original size:29 final size:29
Alignment explanation
Indices: 51791414--51791476 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
51791404 TCAAACATGG
51791414 ATTAATAATCTAGAAATATCAAATCAAGA
1 ATTAATAATCTAGAAATATCAAATCAAGA
51791443 ATTAATAATCTAGAAATATCAAATCAAGA
1 ATTAATAATCTAGAAATATCAAATCAAGA
51791472 ATTAA
1 ATTAA
51791477 GTACACATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.56, C:0.10, G:0.06, T:0.29
Consensus pattern (29 bp):
ATTAATAATCTAGAAATATCAAATCAAGA
Found at i:51793784 original size:9 final size:9
Alignment explanation
Indices: 51793767--51793803 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
51793757 TGAGTTTTCG
51793767 AATTCGAAT
1 AATTCGAAT
*
51793776 AACTCGAAT
1 AATTCGAAT
51793785 AATTCGAAT
1 AATTCGAAT
51793794 AATTCGAAT
1 AATTCGAAT
51793803 A
1 A
51793804 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:51794058 original size:30 final size:31
Alignment explanation
Indices: 51794022--51794081 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
51794012 AAACCTTTTA
*
51794022 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
51794052 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
51794082 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:51795403 original size:31 final size:31
Alignment explanation
Indices: 51795365--51795425 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
51795355 TGCCCAAAGG
51795365 ATATCCCATAGGAAAAGAACATTGATGTGTA
1 ATATCCCATAGGAAAAGAACATTGATGTGTA
51795396 ATATCCCATAGGAAAAGAACATTGATGTGT
1 ATATCCCATAGGAAAAGAACATTGATGTGT
51795426 TACAAAGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (31 bp):
ATATCCCATAGGAAAAGAACATTGATGTGTA
Found at i:51801455 original size:28 final size:28
Alignment explanation
Indices: 51801424--51801489 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
51801414 ACCAATAAAA
51801424 GTCCTTTTTTTAA-AAATTACCGAAATGG
1 GTCCTTTTTTTAATAAATTACCGAAAT-G
* * * * *
51801452 GTCCATTATTTAATTATTTACCGGAATG
1 GTCCTTTTTTTAATAAATTACCGAAATG
51801480 GTCCTTTTTT
1 GTCCTTTTTT
51801490 CCGCGAAATC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
28 20 0.67
29 10 0.33
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (28 bp):
GTCCTTTTTTTAATAAATTACCGAAATG
Found at i:51801667 original size:12 final size:11
Alignment explanation
Indices: 51801650--51801706 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 11
51801640 AACAAATCCT
51801650 CTCTCATATTTC
1 CTCTCA-ATTTC
51801662 CTCTCAA-TTC
1 CTCTCAATTTC
51801672 CTCTCAATTTC
1 CTCTCAATTTC
*
51801683 CT-TCCAAAATT-
1 CTCT-C-AATTTC
51801694 CTCTCAATTTC
1 CTCTCAATTTC
51801705 CT
1 CT
51801707 TCCAAAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 15 0.39
11 12 0.32
12 11 0.29
ACGTcount: A:0.21, C:0.35, G:0.00, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:51801697 original size:22 final size:22
Alignment explanation
Indices: 51801667--51801722 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
51801657 ATTTCCTCTC
51801667 AATTCCTCTCAATTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
51801690 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
51801712 AATTCTCTCAA
1 AATTCTCTCAA
51801723 ACCATATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:51802911 original size:7 final size:7
Alignment explanation
Indices: 51802901--51802925 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
51802891 ATTCGATTGA
51802901 TATTTAG
1 TATTTAG
51802908 TATTTAG
1 TATTTAG
51802915 TATTTAG
1 TATTTAG
51802922 TATT
1 TATT
51802926 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:51803145 original size:29 final size:29
Alignment explanation
Indices: 51803069--51803642 Score: 624
Period size: 29 Copynumber: 21.1 Consensus size: 29
51803059 TCAACTACGC
51803069 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* * *
51803098 AACCCCTAACTTAAATTAATTACAAACCCT
1 AA-CCCTAACCTAATTTAATTAAAAACCCT
51803128 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
51803157 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
**
51803186 AAACCCT----T-A---GCTTAAAAACCCT
1 -AACCCTAACCTAATTTAATTAAAAACCCT
* *
51803208 AACCTTAACCTAAATTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
51803237 AACCCTAACCTAAATTAATTAAAACCCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
51803266 AACCCTAACCTAAATTAATTAAAAACCTT
1 AACCCTAACCTAATTTAATTAAAAACCCT
51803295 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
51803324 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
51803353 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
51803382 AA----ATCC----TTAACTTAAAAATCCT
1 AACCCTAACCTAATTTAA-TTAAAAACCCT
*
51803404 AACCTTAACCTAATTTAATT--AAA----
1 AACCCTAACCTAATTTAATTAAAAACCCT
51803427 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
51803456 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
51803485 -A----AA-CT--CTTAACTTAAAAACCCT
1 AACCCTAACCTAATTTAA-TTAAAAACCCT
* *
51803507 AACCTTAACCTAAATTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
51803536 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
51803565 AAACCCT----T-A---ACTTAAAAACCCT
1 -AACCCTAACCTAATTTAATTAAAAACCCT
*
51803587 AACCTTAACCTAATTTAATT--AAA----
1 AACCCTAACCTAATTTAATTAAAAACCCT
51803610 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
51803639 AACC
1 AACC
51803643 TAAGTTAACA
Statistics
Matches: 467, Mismatches: 29, Indels: 98
0.79 0.05 0.16
Matches are distributed among these distances:
21 18 0.04
22 46 0.10
23 41 0.09
24 2 0.00
25 13 0.03
26 7 0.01
27 8 0.02
28 3 0.01
29 283 0.61
30 46 0.10
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:51803396 original size:22 final size:20
Alignment explanation
Indices: 51803367--51803412 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
51803357 CTAACCTAAT
51803367 TTAA-TTAAAAACCCTAAATCC
1 TTAACTTAAAAACCCT-AA-CC
*
51803388 TTAACTTAAAAATCCTAACC
1 TTAACTTAAAAACCCTAACC
51803408 TTAAC
1 TTAAC
51803413 CTAATTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 6 0.26
22 10 0.43
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (20 bp):
TTAACTTAAAAACCCTAACC
Found at i:51803457 original size:18 final size:20
Alignment explanation
Indices: 51803411--51803453 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 20
51803401 CCTAACCTTA
51803411 ACCTAATTTAATTAAAAACCC
1 ACCTAATTTAATTAAAAA-CC
51803432 TAACCTAATTTAATTAAAAACC
1 --ACCTAATTTAATTAAAAACC
51803454 CTAACCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (20 bp):
ACCTAATTTAATTAAAAACC
Found at i:51803458 original size:103 final size:103
Alignment explanation
Indices: 51803208--51803571 Score: 446
Period size: 103 Copynumber: 3.3 Consensus size: 103
51803198 TAAAAACCCT
* * * *
51803208 AACCTTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAAATTAATTAAAACCCCTAACCCTA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT-A----A
*
51803273 ACCTAAATTAA-TTAAAAACCTTAACCCTAACCTAATTTAATTAAAAACCC
61 ACC----TTAACTTAAAAACC-TAACCTTAACCTAATTTAATT-AAAA--C
51803323 TAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAATCC
1 -AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAA-CC
51803388 TTAACTTAAAAATCCTAACCTTAACCTAATTTAATT-AAA-
64 TTAACTTAAAAA-CCTAACCTTAACCTAATTTAATTAAAAC
51803427 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACTCT
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAAC-CT
*
51803492 TAACTTAAAAACCCTAACCTTAACCTAAATTAATTAAAAACCC
65 TAACTTAAAAA-CCTAACCTTAACCTAATTTAATT-AAAA--C
51803535 TAACCCTAACCTAATTTAATTAAAAACCCTAAACCCT
1 -AACCCTAACCTAATTTAATTAAAAACCCT-AACCCT
51803572 TAACTTAAAA
Statistics
Matches: 230, Mismatches: 7, Indels: 28
0.87 0.03 0.11
Matches are distributed among these distances:
102 1 0.00
103 96 0.42
105 3 0.01
107 3 0.01
108 4 0.02
109 56 0.24
110 8 0.03
111 2 0.01
112 2 0.01
115 1 0.00
116 54 0.23
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (103 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCTT
AACTTAAAAACCTAACCTTAACCTAATTTAATTAAAAC
Found at i:51803515 original size:20 final size:22
Alignment explanation
Indices: 51803470--51803520 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
51803460 CTAACCTAAT
51803470 TTAA-TTAAAAACCCTAAACTC
1 TTAACTTAAAAACCCTAAACTC
51803491 TTAACTTAAAAACCCT-AAC-C
1 TTAACTTAAAAACCCTAAACTC
*
51803511 TTAACCTAAA
1 TTAACTTAAA
51803521 TTAATTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 10 0.36
21 7 0.25
22 11 0.39
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.27
Consensus pattern (22 bp):
TTAACTTAAAAACCCTAAACTC
Found at i:51803531 original size:80 final size:80
Alignment explanation
Indices: 51803427--51803640 Score: 359
Period size: 80 Copynumber: 2.8 Consensus size: 80
51803417 TTTAATTAAA
* *
51803427 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACTCT
1 AACCTTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCT
51803492 TAACTTAAAAACCCT
66 TAACTTAAAAACCCT
*
51803507 AACCTTAACCTAAATTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCT
1 AACCTTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCT
51803572 TAACTTAAAAACCCT
66 TAACTTAAAAACCCT
51803587 AACCTTAACCTAATTTAATT--AAA----AACCCTAACCTAATTTAATTAAAAACCCTAA
1 AACCTTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA
51803641 CCTAAGTTAA
Statistics
Matches: 130, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
74 31 0.24
78 3 0.02
80 96 0.74
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (80 bp):
AACCTTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCT
TAACTTAAAAACCCT
Found at i:51803580 original size:51 final size:50
Alignment explanation
Indices: 51803521--51803642 Score: 183
Period size: 51 Copynumber: 2.4 Consensus size: 50
51803511 TTAACCTAAA
51803521 TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACC-C
1 TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT-AACCAC
* *
51803571 TTAACTTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCTAAT
1 TTAA-TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACC--AC
51803624 TTAATTAAAAACCCTAACC
1 TTAATTAAAAACCCTAACC
51803643 TAAGTTAACA
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
50 8 0.12
51 39 0.59
52 15 0.23
53 4 0.06
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (50 bp):
TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCAC
Found at i:51803640 original size:18 final size:20
Alignment explanation
Indices: 51803594--51803636 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 20
51803584 CCTAACCTTA
51803594 ACCTAATTTAATTAAAAACCC
1 ACCTAATTTAATTAAAAA-CC
51803615 TAACCTAATTTAATTAAAAACC
1 --ACCTAATTTAATTAAAAACC
51803637 CTAACCTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (20 bp):
ACCTAATTTAATTAAAAACC
Found at i:51803792 original size:116 final size:116
Alignment explanation
Indices: 51803647--51803884 Score: 404
Period size: 116 Copynumber: 2.1 Consensus size: 116
51803637 CTAACCTAAG
* * *
51803647 TTAACAATGTTACATTCACGTAATGTTAGATTTGGAAAAATGTTTTGACTAGTACTAACAAATAA
1 TTAATAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACCAGTACTAACAAATAA
51803712 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
* * * *
51803763 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACCGGTACTATCAATTAA
1 TTAATAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACCAGTACTAACAAATAA
*
51803828 TAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
51803879 TTAATA
1 TTAATA
51803885 CAATTTATCA
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
116 114 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (116 bp):
TTAATAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACCAGTACTAACAAATAA
TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
Found at i:51803901 original size:17 final size:18
Alignment explanation
Indices: 51803860--51803901 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
51803850 TTTACTAACC
* *
51803860 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
51803878 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
51803895 ATTAATA
1 ATTAATA
51803902 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:51807260 original size:126 final size:126
Alignment explanation
Indices: 51806914--51807250 Score: 490
Period size: 126 Copynumber: 2.7 Consensus size: 126
51806904 CCCAAACATG
* * * * *
51806914 CTACAGTAGCAAAAGAGCGTCCACGATGG-CGCGATTTCACAAATTCTTCTCAAATAGCATCCTA
1 CTACTGTAGCAAAAGCGCGTCCATGACGGACGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
* *
51806978 CTAGAAGCGATTTTATATTATTTGCTCAGAAACGTC-AAAAAAACTTATTTCTTACATGAC
66 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
*
51807038 TTACTGTAGCAAAAGCGCG--C-TGACGAGAC-CGTAATTTCACAAATTCTTCTCAAATAGCATC
1 CTACTGTAGCAAAAGCGCGTCCATGACG-GACGCG--ATTTCACAAATTCTTCTCAAATAGCATC
* *
51807099 CTGCTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
63 CTGCTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTCTTACATGAC
51807164 CTACTGTAGCAAAAGCGCGTCCATGA-GGACGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCATGACGGACGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
*
51807228 CTAGAAGAGATTTTATACTATTT
66 CTAGAAGCGATTTTATACTATTT
51807251 TATTAGAAAC
Statistics
Matches: 191, Mismatches: 12, Indels: 18
0.86 0.05 0.08
Matches are distributed among these distances:
121 3 0.02
122 4 0.02
123 1 0.01
124 81 0.42
125 6 0.03
126 86 0.45
127 3 0.02
128 4 0.02
129 3 0.02
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCATGACGGACGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
Found at i:51816934 original size:2 final size:2
Alignment explanation
Indices: 51816927--51816957 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
51816917 ATTAATATCT
51816927 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51816958 TTATTGAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51824474 original size:30 final size:30
Alignment explanation
Indices: 51824438--51824500 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
51824428 ACTTAATAAG
*
51824438 CAAATGTCTCTAAAATCATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
51824468 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
51824498 CAA
1 CAA
51824501 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.14, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:51826436 original size:29 final size:31
Alignment explanation
Indices: 51826384--51826452 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
51826374 CCATTTTCAT
** *
51826384 ATATTTTTTAATTGAGTTGATAAAATATGAA
1 ATATTTTTTAACCGAGTTGATAAAATACGAA
51826415 A-ATTTTTTAACCGAGTTG-TAAAATACGAA
1 ATATTTTTTAACCGAGTTGATAAAATACGAA
51826444 ATATTTTTT
1 ATATTTTTT
51826453 TAATCAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 11 0.32
30 22 0.65
31 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (31 bp):
ATATTTTTTAACCGAGTTGATAAAATACGAA
Found at i:51832719 original size:27 final size:27
Alignment explanation
Indices: 51832689--51832740 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
51832679 GTACGTGGTC
* *
51832689 GCTCCAAAGGGACGTCTGAGGGTAGTG
1 GCTCCAAAGGGACCTCTGAGCGTAGTG
51832716 GCTCCAAAGGGACCTCTGAGCGTAG
1 GCTCCAAAGGGACCTCTGAGCGTAG
51832741 AGCAAGGCGA
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:0.23, C:0.23, G:0.37, T:0.17
Consensus pattern (27 bp):
GCTCCAAAGGGACCTCTGAGCGTAGTG
Found at i:51834588 original size:24 final size:24
Alignment explanation
Indices: 51834556--51834601 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
51834546 ACTTCCGCTG
51834556 CTGTGGCAATA-GCAGCAGCTGCTT
1 CTGTGGCAA-AGGCAGCAGCTGCTT
* *
51834580 CTGTTGCAAAGGCTGCAGCTGC
1 CTGTGGCAAAGGCAGCAGCTGC
51834602 AGCTGCCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.20, C:0.26, G:0.30, T:0.24
Consensus pattern (24 bp):
CTGTGGCAAAGGCAGCAGCTGCTT
Found at i:51845881 original size:3 final size:3
Alignment explanation
Indices: 51845875--51845907 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
51845865 GCTAAAAGAC
51845875 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
51845908 TATTTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:51850310 original size:7 final size:7
Alignment explanation
Indices: 51850300--51850338 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
51850290 TAGGGTTAAA
51850300 GGTTAGG
1 GGTTAGG
51850307 GGTTAGG
1 GGTTAGG
51850314 GGTTAGG
1 GGTTAGG
51850321 GGTTAGG
1 GGTTAGG
51850328 GGTTAGG
1 GGTTAGG
51850335 GGTT
1 GGTT
51850339 TATAGTTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.13, C:0.00, G:0.56, T:0.31
Consensus pattern (7 bp):
GGTTAGG
Found at i:51850318 original size:21 final size:21
Alignment explanation
Indices: 51850292--51850338 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
51850282 TAAGTGTTTA
51850292 GGGTTAAAGGTTAGGGGTTAG
1 GGGTTAAAGGTTAGGGGTTAG
**
51850313 GGGTTAGGGGTTAGGGGTTAG
1 GGGTTAAAGGTTAGGGGTTAG
51850334 GGGTT
1 GGGTT
51850339 TATAGTTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.53, T:0.30
Consensus pattern (21 bp):
GGGTTAAAGGTTAGGGGTTAG
Found at i:51850647 original size:21 final size:21
Alignment explanation
Indices: 51850623--51850673 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
51850613 TATGGTTTAG
51850623 GGTTTAGGGGATAAGGGTTAT
1 GGTTTAGGGGATAAGGGTTAT
*
51850644 GGTTTAGGGGATAAGGGTTGT
1 GGTTTAGGGGATAAGGGTTAT
51850665 GGTTTAGGG
1 GGTTTAGGG
51850674 TCTAGGTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (21 bp):
GGTTTAGGGGATAAGGGTTAT
Found at i:51852203 original size:22 final size:22
Alignment explanation
Indices: 51852176--51852222 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
51852166 GTCTTTCTAC
51852176 TTAGGTTTAATCAGTATAAAAT
1 TTAGGTTTAATCAGTATAAAAT
51852198 TTAGGTTTAATCAGTATAAAAT
1 TTAGGTTTAATCAGTATAAAAT
51852220 TTA
1 TTA
51852223 AGAAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.43
Consensus pattern (22 bp):
TTAGGTTTAATCAGTATAAAAT
Found at i:51853493 original size:18 final size:18
Alignment explanation
Indices: 51853470--51853514 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
51853460 AAACAAATTT
51853470 TAAATTATATAACTTACA
1 TAAATTATATAACTTACA
51853488 TAAATTATATAACTTACA
1 TAAATTATATAACTTACA
*
51853506 TAACTTATA
1 TAAATTATA
51853515 AATATTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATTATATAACTTACA
Found at i:51853499 original size:9 final size:9
Alignment explanation
Indices: 51853474--51853514 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
51853464 AAATTTTAAA
51853474 TTATATAAC
1 TTATATAAC
* *
51853483 TTACATAAA
1 TTATATAAC
51853492 TTATATAAC
1 TTATATAAC
*
51853501 TTACATAAC
1 TTATATAAC
51853510 TTATA
1 TTATA
51853515 AATATTTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (9 bp):
TTATATAAC
Found at i:51853670 original size:23 final size:23
Alignment explanation
Indices: 51853641--51853745 Score: 63
Period size: 23 Copynumber: 4.3 Consensus size: 23
51853631 AAACTTACAT
51853641 AATACATATCTTAAATAACATAC
1 AATACATATCTTAAATAACATAC
* *
51853664 AATACATAAACTTACATAAC-T-C
1 AATACAT-ATCTTAAATAACATAC
* * *
51853686 AAATTTATCA-ATCATATCATAACTTATAT
1 -AA--TA-CATATCTTA-AATAAC--ATAC
*
51853715 AATACATATCTTAAATACCATAC
1 AATACATATCTTAAATAACATAC
51853738 AATACATA
1 AATACATA
51853746 AACTTACATA
Statistics
Matches: 62, Mismatches: 9, Indels: 22
0.67 0.10 0.24
Matches are distributed among these distances:
22 1 0.02
23 21 0.34
24 14 0.23
25 14 0.23
26 9 0.15
28 3 0.05
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (23 bp):
AATACATATCTTAAATAACATAC
Found at i:51853673 original size:40 final size:40
Alignment explanation
Indices: 51853629--51853755 Score: 144
Period size: 40 Copynumber: 3.3 Consensus size: 40
51853619 TAACTTATAT
51853629 ATAAACTTACATAATACATATCTTAAATAACATACAATAC
1 ATAAACTTACATAATACATATCTTAAATAACATACAATAC
* *
51853669 ATAAACTTACATAACT-CAAAT-TT--ATCA-AT-C-ATATC
1 ATAAACTTACATAA-TACATATCTTAAATAACATACAATA-C
* *
51853704 AT-AACTTATATAATACATATCTTAAATACCATACAATAC
1 ATAAACTTACATAATACATATCTTAAATAACATACAATAC
51853743 ATAAACTTACATA
1 ATAAACTTACATA
51853756 TAAACTTGCA
Statistics
Matches: 70, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
33 1 0.01
34 17 0.24
35 6 0.09
36 2 0.03
37 5 0.07
38 2 0.03
39 6 0.09
40 30 0.43
41 1 0.01
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (40 bp):
ATAAACTTACATAATACATATCTTAAATAACATACAATAC
Found at i:51853794 original size:9 final size:9
Alignment explanation
Indices: 51853784--51854138 Score: 316
Period size: 9 Copynumber: 39.2 Consensus size: 9
51853774 TTTAAATTAT
*
51853784 ATAACTTAT
1 ATAACTTAC
* *
51853793 ATAAATTAT
1 ATAACTTAC
51853802 ATAACTTAC
1 ATAACTTAC
*
51853811 ATAACTTGC
1 ATAACTTAC
*
51853820 ATACCTTAC
1 ATAACTTAC
* *
51853829 ATAAATTAA
1 ATAACTTAC
51853838 ATAACTTAC
1 ATAACTTAC
51853847 ATAACTTAC
1 ATAACTTAC
*
51853856 ATAACTTAA
1 ATAACTTAC
51853865 ATAACTTAC
1 ATAACTTAC
51853874 ATAA--TAC
1 ATAACTTAC
*
51853881 ATAACCTAC
1 ATAACTTAC
* *
51853890 CTAACTTAA
1 ATAACTTAC
* *
51853899 ATTATTTAC
1 ATAACTTAC
51853908 ATAA--TAC
1 ATAACTTAC
51853915 ATAACTTAGTAC
1 ATAAC-T--TAC
*
51853927 ATAATTTAC
1 ATAACTTAC
51853936 ATAA--TAC
1 ATAACTTAC
51853943 ATAACTTATAC
1 ATAAC-T-TAC
51853954 ATAACTTAC
1 ATAACTTAC
* *
51853963 ATAATTTTTTC
1 ATAA--CTTAC
51853974 -TAAATTGCTTAC
1 AT-AA---CTTAC
* *
51853986 ATAAATTAT
1 ATAACTTAC
51853995 ATAACTTAC
1 ATAACTTAC
*
51854004 ATAACTTAT
1 ATAACTTAC
* *
51854013 ATAAATTAA
1 ATAACTTAC
51854022 ATAACTTAC
1 ATAACTTAC
51854031 ATAACTTAC
1 ATAACTTAC
51854040 ATAACTTAC
1 ATAACTTAC
*
51854049 ATAACTTAA
1 ATAACTTAC
51854058 ATAACTTAC
1 ATAACTTAC
51854067 ATAACTTAC
1 ATAACTTAC
*
51854076 ATAAATTAC
1 ATAACTTAC
51854085 ATAACTTAC
1 ATAACTTAC
51854094 ATAACTTAC
1 ATAACTTAC
51854103 ATAACTTAC
1 ATAACTTAC
51854112 ATAA--TAC
1 ATAACTTAC
51854119 ATAACCTT-C
1 ATAA-CTTAC
*
51854128 CTAACTTAC
1 ATAACTTAC
51854137 AT
1 AT
51854139 TATTGTCTAA
Statistics
Matches: 284, Mismatches: 42, Indels: 40
0.78 0.11 0.11
Matches are distributed among these distances:
7 28 0.10
8 3 0.01
9 222 0.78
10 3 0.01
11 14 0.05
12 13 0.05
13 1 0.00
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.36
Consensus pattern (9 bp):
ATAACTTAC
Found at i:51859699 original size:21 final size:21
Alignment explanation
Indices: 51859673--51859747 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
51859663 CAACAACTTA
* *
51859673 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGAG
*
51859694 AAGCAGATGCCGCAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
** *
51859715 AAGCAGCGAGAGAAGCAGCGATAG
1 AAGCA--GAG-GCCGCAGCGAGAG
51859739 AAGCAGAGG
1 AAGCAGAGG
51859748 TTCAAAAGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
21 24 0.55
22 3 0.07
23 2 0.05
24 15 0.34
ACGTcount: A:0.36, C:0.19, G:0.43, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:51859722 original size:12 final size:12
Alignment explanation
Indices: 51859705--51859744 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
51859695 AGCAGATGCC
51859705 GCAGCGAGAGAA
1 GCAGCGAGAGAA
51859717 GCAGCGAGAGAA
1 GCAGCGAGAGAA
*
51859729 GCAGCGATAGAA
1 GCAGCGAGAGAA
51859741 GCAG
1 GCAG
51859745 AGGTTCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.40, C:0.17, G:0.40, T:0.03
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:51861455 original size:15 final size:15
Alignment explanation
Indices: 51861435--51861465 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
51861425 GAGTAACAAA
51861435 AATGTAATTTTAATT
1 AATGTAATTTTAATT
*
51861450 AATGTAATTTTGATT
1 AATGTAATTTTAATT
51861465 A
1 A
51861466 GGGAAAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (15 bp):
AATGTAATTTTAATT
Found at i:51862754 original size:84 final size:84
Alignment explanation
Indices: 51862613--51862797 Score: 257
Period size: 84 Copynumber: 2.2 Consensus size: 84
51862603 AAAAAGAGCA
* * * *
51862613 TATGGAAAATAGAGAATCAAATGTGGGAAATGAAAGAGAATAACGTATATGAAAAATAGAGATAT
1 TATGGAAAATAGAGAATCAAATATGGGAAATGAAAAAGAATAACGAAAATGAAAAATAGAGATAT
*
51862678 GAAAGGAAATTTAATATTT
66 GAAAGGAAATTGAATATTT
* *
51862697 TATGGAAAATAGATAATCAAATATGGGAAA-GAAAAAAGAATAAC-AACAATGTAAAATAGAGAT
1 TATGGAAAATAGAGAATCAAATATGGGAAATG-AAAAAGAATAACGAA-AATGAAAAATAGAGAT
*
51862760 ATGAAAGGGAATTGAATATTT
64 ATGAAAGGAAATTGAATATTT
*
51862781 TATGAAAAATAGAGAAT
1 TATGGAAAATAGAGAAT
51862798 TTAATTATTT
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
83 2 0.02
84 87 0.98
ACGTcount: A:0.54, C:0.03, G:0.20, T:0.24
Consensus pattern (84 bp):
TATGGAAAATAGAGAATCAAATATGGGAAATGAAAAAGAATAACGAAAATGAAAAATAGAGATAT
GAAAGGAAATTGAATATTT
Found at i:51864070 original size:20 final size:21
Alignment explanation
Indices: 51864032--51864072 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
51864022 ACAGACAACC
*
51864032 CATTCATGTTTTAAAATATAA
1 CATTCATGTATTAAAATATAA
*
51864053 CATTCAT-TATTAATATATAA
1 CATTCATGTATTAAAATATAA
51864073 ATTTATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (21 bp):
CATTCATGTATTAAAATATAA
Found at i:51872280 original size:112 final size:113
Alignment explanation
Indices: 51872107--51872340 Score: 294
Period size: 112 Copynumber: 2.1 Consensus size: 113
51872097 ATCTGAAGAT
* ** * *
51872107 CAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGTTTATGGAAAAACGCCGCTA
1 CAAAACGCATCGTTTTGATCCCGATGTATACTAGAATTAGTGGCGCTTATCGAAAAACGCCGCTA
* *
51872172 AAGGAAGTATTAGCGGCGCATTGCCGAAAGCGCCGCAA-AAATCTTAAC
66 AAGGAAGTATTAGCGGCGC-TTACCAAAAGCGCCGCAACAAATCTTAAC
* * * * *
51872220 GAAAACGCATCGTTTT-ATCCCGCTGTATATTAGCATTAGTGGCGCTTA-CGAAAACCCGCCGCT
1 CAAAACGCATCGTTTTGATCCCGATGTATACTAGAATTAGTGGCGCTTATCGAAAA-ACGCCGCT
* * *
51872283 AAAGGAAGTATTAGCGGCGCTTACCAAAAGCGCTGCAACATATGTTAAC
65 AAAGGAAGTATTAGCGGCGCTTACCAAAAGCGCCGCAACAAATCTTAAC
51872332 CAAAACGCA
1 CAAAACGCA
51872341 GAGTTTGGTC
Statistics
Matches: 103, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
111 20 0.19
112 68 0.66
113 15 0.15
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (113 bp):
CAAAACGCATCGTTTTGATCCCGATGTATACTAGAATTAGTGGCGCTTATCGAAAAACGCCGCTA
AAGGAAGTATTAGCGGCGCTTACCAAAAGCGCCGCAACAAATCTTAAC
Found at i:51872375 original size:112 final size:112
Alignment explanation
Indices: 51872132--51872379 Score: 268
Period size: 112 Copynumber: 2.2 Consensus size: 112
51872122 TGGTCTTGAT
* * * * *
51872132 GTATACTAGAATTAGTGGCGTTTATGGAAAA-ACGCCGCTAAAGGAAGTATTAGCGGCGCATTGC
1 GTATATTAGAATTAGTGGCGCTTA-CGAAAACCCGCCGCTAAAGGAAGTATTAGCGGCGCATTAC
* * ** * * **
51872196 CGAAAGCGCCGCAAAAATCTTAACGAAAACGCATCGTTTTATCCCGCT
65 CAAAAGCGCCGCAAAAATCTTAACCAAAACGCAGAGTTTGATCCAGAG
*
51872244 GTATATTAGCATTAGTGGCGCTTACGAAAACCCGCCGCTAAAGGAAGTATTAGCGGCGC-TTACC
1 GTATATTAGAATTAGTGGCGCTTACGAAAACCCGCCGCTAAAGGAAGTATTAGCGGCGCATTACC
* * * * *
51872308 AAAAGCGCTGCAACATATGTTAACCAAAACGCAGAGTTTGGTCTAGAG
66 AAAAGCGCCGCAA-AAATCTTAACCAAAACGCAGAGTTTGATCCAGAG
*
51872356 GTATGTTAGAATTTA-TGGCGCTTA
1 GTATATTAGAA-TTAGTGGCGCTTA
51872380 TGGAAAAACA
Statistics
Matches: 112, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
111 20 0.18
112 89 0.79
113 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (112 bp):
GTATATTAGAATTAGTGGCGCTTACGAAAACCCGCCGCTAAAGGAAGTATTAGCGGCGCATTACC
AAAAGCGCCGCAAAAATCTTAACCAAAACGCAGAGTTTGATCCAGAG
Found at i:51872752 original size:115 final size:114
Alignment explanation
Indices: 51872459--51873000 Score: 433
Period size: 115 Copynumber: 4.7 Consensus size: 114
51872449 GCGTTTAAGG
* * * *
51872459 GAAAACACCGCTAAAGCATAATATTAGCGGCG-TTTTGAGGAAAGCGCCGCAAAATATCTTAACC
1 GAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTCAAG-AAGCGCCGCAAAATATCTTAACC
***
51872523 AAAACGCAGAG-TTTGGTCTTGAGGTATACTAGAATTAGTGGCGCA-AAGG
65 AAAACGCAGAGTTTTGGTCTTGAGGTATAC-AGAATTAGTGGCGCATATCA
* * * * * ** * * **
51872572 GTACACGCCACTAAGGCATACTATTAGCGGCG-TTTTCAGAGAAGCGCAACAACATTTGGTAACC
1 GAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTCA-AGAAGCGCCGCAAAATATCTTAACC
* * *
51872636 AAAACGCA-ACGTTTTTGTCTTGATGTATACAGTTATTAGTGGCGCATATCA
65 AAAACGCAGA-GTTTTGGTCTTGAGGTATACAG-AATTAGTGGCGCATATCA
* * ** *
51872687 AAAAACGCCGCTAAATCATAGTATTAGCGGCGCTTGGCAAAAAGCGCCGCAAAATATGCTT-ACC
1 GAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTCAAGAAGCGCCGCAAAATAT-CTTAACC
* * * * * * **
51872751 AAAACGCAGAATTTT-TTCGTGAGGTATATTAGACTTAGTGGCGCTTATGG
65 AAAACGCAGAGTTTTGGTCTTGAGGTATA-CAGAATTAGTGGCGCATATCA
** * * * * *
51872801 GGGAACGCCGCTAAAGCATATTATTTGCGGCGC-TTTCTGAGAAGCGCCGCAAAATATATTAACA
1 GAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTC-AAGAAGCGCCGCAAAATATCTTAACC
** * *
51872865 AAAACGCA-ACGTTTAAGTCTTGATGTATACTGGAATTAGT-G-GCATCCA-CGA
65 AAAACGCAGA-GTTTTGGTCTTGAGGTATAC-AGAATTAGTGGCGCAT--ATC-A
* * ** *
51872916 GAAATCGCCGCTAAAGCATCGTATTAGCGGCGCTTTTTGAGAAGCGCCGAAAAATATCTTAACCA
1 GAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTCAAGAAGCGCCGCAAAATATCTTAACCA
51872981 AAACGCAGAGTTTTGGTCTT
66 AAACGCAGAGTTTTGGTCTT
51873001 AACCATGCAT
Statistics
Matches: 329, Mismatches: 81, Indels: 36
0.74 0.18 0.08
Matches are distributed among these distances:
112 1 0.00
113 67 0.20
114 110 0.33
115 141 0.43
116 10 0.03
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (114 bp):
GAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTTCAAGAAGCGCCGCAAAATATCTTAACCA
AAACGCAGAGTTTTGGTCTTGAGGTATACAGAATTAGTGGCGCATATCA
Found at i:51872942 original size:229 final size:227
Alignment explanation
Indices: 51872460--51872995 Score: 598
Period size: 229 Copynumber: 2.3 Consensus size: 227
51872450 CGTTTAAGGG
* * * *
51872460 AAAACACCGCTAAAGCATAATATTAGCGGCGTTTTGAGGAAAGCGCCGCAAAATATCTTAACCAA
1 AAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTGA-AAAAGCGCCGCAAAATATCTTAACCAA
* * * *
51872525 AACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGCGCAAAGGGTACACGCCACTAAGGCA
65 AACGCAGAGTTTTGTCGTGAGGTATACTAGAATTAGTGGCGCAAAGGGGACACGCCACTAAAGCA
* * * * * **
51872590 TACTATTAGCGGCGTTTTCAGAGAAGCGCAACAACATTTGGTAACCAAAACGCAACGTTTTTGTC
130 TACTATTAGCGGCGCTTTCAGAGAAGCGCAACAAAATATAGTAACAAAAACGCAACGTTTAAGTC
**
51872655 TTGATGTATACAGTTATTAGTGGCGCATATCAA
195 TTGATGTATACAGGAATTAGTGGCGCATATCAA
* *
51872688 AAAACGCCGCTAAATCATAGTATTAGCGGCGCTTGGCAAAAAGCGCCGCAAAATATGCTT-ACCA
1 AAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTG-AAAAAGCGCCGCAAAATAT-CTTAACCA
* * * * ** *
51872752 AAACGCAGAATTTTTTCGTGAGGTATATTAGACTTAGTGGCGCTTATGGGGGA-ACGCCGCTAAA
64 AAACGCAGAGTTTTGTCGTGAGGTATACTAGAATTAGTGGCGC--AAAGGGGACACGCCACTAAA
* * * ** *
51872816 GCATATTATTTGCGGCGCTTTCTGAGAAGCGCCGCAAAATATATTAACAAAAACGCAACGTTTAA
127 GCATACTATTAGCGGCGCTTTCAGAGAAGCGCAACAAAATATAGTAACAAAAACGCAACGTTTAA
* *
51872881 GTCTTGATGTATACTGGAATTAGT-G-GCATCCA-CGAG
192 GTCTTGATGTATACAGGAATTAGTGGCGCAT--ATC-AA
* * * *
51872917 AAATCGCCGCTAAAGCATCGTATTAGCGGCGCTTTTTG-AGAAGCGCCGAAAAATATCTTAACCA
1 AAAACGCCGCTAAAGCATAGTATTAGCGGCGC--TTTGAAAAAGCGCCGCAAAATATCTTAACCA
51872981 AAACGCAGAGTTTTG
64 AAACGCAGAGTTTTG
51872996 GTCTTAACCA
Statistics
Matches: 256, Mismatches: 42, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
227 4 0.02
228 94 0.37
229 150 0.59
230 5 0.02
231 3 0.01
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (227 bp):
AAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTGAAAAAGCGCCGCAAAATATCTTAACCAAA
ACGCAGAGTTTTGTCGTGAGGTATACTAGAATTAGTGGCGCAAAGGGGACACGCCACTAAAGCAT
ACTATTAGCGGCGCTTTCAGAGAAGCGCAACAAAATATAGTAACAAAAACGCAACGTTTAAGTCT
TGATGTATACAGGAATTAGTGGCGCATATCAA
Found at i:51873932 original size:14 final size:15
Alignment explanation
Indices: 51873913--51873947 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
51873903 ACACTTGCAT
*
51873913 GGATTTAGGGTTTA-
1 GGATTTAAGGTTTAG
51873927 GGATTTAAGGTTTAG
1 GGATTTAAGGTTTAG
51873942 GGATTT
1 GGATTT
51873948 TGGGGCCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.23, C:0.00, G:0.34, T:0.43
Consensus pattern (15 bp):
GGATTTAAGGTTTAG
Found at i:51877848 original size:18 final size:17
Alignment explanation
Indices: 51877821--51878166 Score: 296
Period size: 18 Copynumber: 19.7 Consensus size: 17
51877811 AGGGTTCACA
*
51877821 AATTAAATAACTTACATT
1 AATTACATAACTTACA-T
*
51877839 AATTACATAACTTACAAA
1 AATTACATAACTTAC-AT
*
51877857 AATTAAATAACTTACAT
1 AATTACATAACTTACAT
*
51877874 AACTTACATAAATT--A-
1 AA-TTACATAACTTACAT
* *
51877889 ACTTACATAACTTACAAA
1 AATTACATAACTTAC-AT
* *
51877907 AATTAAATATCTTACAT
1 AATTACATAACTTACAT
51877924 AACTTACATAACTTA-AGT
1 AA-TTACATAACTTACA-T
51877942 AACTTACATAACTTACAT
1 AA-TTACATAACTTACAT
*
51877960 AACTTACATAAATTA-AGT
1 AA-TTACATAACTTACA-T
51877978 AACTTACATAACTTACAT
1 AA-TTACATAACTTACAT
*
51877996 AAATTAAATAACTTACAT
1 -AATTACATAACTTACAT
51878014 AACTTACATAACTTACAT
1 AA-TTACATAACTTACAT
*
51878032 AAATTAAATAACTTACAT
1 -AATTACATAACTTACAT
* *
51878050 AACTTACATAAATTAAAT
1 AA-TTACATAACTTACAT
*
51878068 ATCTTACATAACTTACAT
1 A-ATTACATAACTTACAT
*
51878086 AAATGTA-GTAACTTACAT
1 -AAT-TACATAACTTACAT
51878104 AACTTACATAACTTACAGT
1 AA-TTACATAACTTACA-T
*
51878123 ACTTACATAACTTACAGT
1 AATTACATAACTTACA-T
*
51878141 ACTTACATAA--TACAT
1 AATTACATAACTTACAT
51878156 AA-TACATAACT
1 AATTACATAACT
51878167 GGCGTTTTAA
Statistics
Matches: 275, Mismatches: 30, Indels: 48
0.78 0.08 0.14
Matches are distributed among these distances:
14 17 0.06
15 3 0.01
16 5 0.02
17 17 0.06
18 221 0.80
19 12 0.04
ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34
Consensus pattern (17 bp):
AATTACATAACTTACAT
Found at i:51877863 original size:36 final size:36
Alignment explanation
Indices: 51877827--51878166 Score: 366
Period size: 36 Copynumber: 9.7 Consensus size: 36
51877817 CACAAATTAA
* * *
51877827 ATAACTTACATTAA-TTACATAACTTACAAAAATTAA
1 ATAACTTACA-TAACTTACATAACTTACATAACTTAC
*
51877863 ATAACTTACATAACTTACATAA---A-TTAACTTAC
1 ATAACTTACATAACTTACATAACTTACATAACTTAC
* * * *
51877895 ATAACTTACAAAAATTAAATATCTTACATAACTTAC
1 ATAACTTACATAACTTACATAACTTACATAACTTAC
51877931 ATAACTTA-AGTAACTTACATAACTTACATAACTTAC
1 ATAACTTACA-TAACTTACATAACTTACATAACTTAC
* * *
51877967 ATAAATTA-AGTAACTTACATAACTTACATAAATTAA
1 ATAACTTACA-TAACTTACATAACTTACATAACTTAC
* *
51878003 ATAACTTACATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAACTTACATAACTTAC
* * *
51878039 ATAACTTACATAACTTACATAAATTAAATATCTTAC
1 ATAACTTACATAACTTACATAACTTACATAACTTAC
* *
51878075 ATAACTTACATAAATGTA-GTAACTTACATAACTTAC
1 ATAACTTACATAACT-TACATAACTTACATAACTTAC
51878111 ATAACTTACAGT-ACTTACATAACTTACAGT-ACTTAC
1 ATAACTTACA-TAACTTACATAACTTACA-TAACTTAC
51878147 ATAA--TACATAA--TACATAACT
1 ATAACTTACATAACTTACATAACT
51878167 GGCGTTTTAA
Statistics
Matches: 263, Mismatches: 29, Indels: 28
0.82 0.09 0.09
Matches are distributed among these distances:
32 32 0.12
33 2 0.01
34 5 0.02
35 7 0.03
36 212 0.81
37 5 0.02
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.34
Consensus pattern (36 bp):
ATAACTTACATAACTTACATAACTTACATAACTTAC
Found at i:51878144 original size:27 final size:27
Alignment explanation
Indices: 51877827--51878166 Score: 366
Period size: 27 Copynumber: 12.9 Consensus size: 27
51877817 CACAAATTAA
51877827 ATAACTTACATTAA-TTACATAACTTAC
1 ATAACTTACA-TAACTTACATAACTTAC
* * *
51877854 AAAAATTAAATAACTTACATAACTTAC
1 ATAACTTACATAACTTACATAACTTAC
*
51877881 ATAA---A-TTAACTTACATAACTTAC
1 ATAACTTACATAACTTACATAACTTAC
* * * *
51877904 AAAAATTAAATATCTTACATAACTTAC
1 ATAACTTACATAACTTACATAACTTAC
51877931 ATAACTTA-AGTAACTTACATAACTTAC
1 ATAACTTACA-TAACTTACATAACTTAC
*
51877958 ATAACTTACATAAATTA-AGTAACTTAC
1 ATAACTTACATAACTTACA-TAACTTAC
* *
51877985 ATAACTTACATAAATTAAATAACTTAC
1 ATAACTTACATAACTTACATAACTTAC
* *
51878012 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAACTTAC
* *
51878039 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAACTTAC
* *
51878066 ATATCTTACATAACTTACATAAATGTA-
1 ATAACTTACATAACTTACATAACT-TAC
*
51878093 GTAACTTACATAACTTACATAACTTAC
1 ATAACTTACATAACTTACATAACTTAC
51878120 AGT-ACTTACATAACTTACAGT-ACTTAC
1 A-TAACTTACATAACTTACA-TAACTTAC
51878147 ATAA--TACATAA--TACATAACT
1 ATAACTTACATAACTTACATAACT
51878167 GGCGTTTTAA
Statistics
Matches: 277, Mismatches: 21, Indels: 34
0.83 0.06 0.10
Matches are distributed among these distances:
22 1 0.00
23 27 0.10
24 1 0.00
25 7 0.03
26 9 0.03
27 226 0.82
28 6 0.02
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.34
Consensus pattern (27 bp):
ATAACTTACATAACTTACATAACTTAC
Found at i:51886522 original size:21 final size:21
Alignment explanation
Indices: 51886492--51886557 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
51886482 CAACAACTTA
* * *
51886492 AAGCAAAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGAG
**
51886513 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
51886534 AAGCAGAGGCCGCAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
51886555 AAG
1 AAG
51886558 TAGGGATAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.36, C:0.20, G:0.42, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:51887064 original size:42 final size:42
Alignment explanation
Indices: 51887009--51887212 Score: 234
Period size: 42 Copynumber: 4.8 Consensus size: 42
51886999 GTGAAATAAC
*
51887009 CGCCGCTAAAGAACACTACTTTTAGCGGCGTTTTTGACC-AAG
1 CGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTT-ACCAAAG
* *
51887051 CGCCGCTATAGAACATTACTTTTAGCGGCGTTTTCATCCAAAG
1 CGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTA-CCAAAG
* * *
51887094 CGCCGCTAAAGAACATGA-TCTTTAGCGGCGTTTTTTCCCAAG
1 CGCCGCTAAAGAACATTACT-TTTAGCGGCGTTTTTACCAAAG
* * * * *
51887136 CGCCGCTATAGAACATTAATTTTAGCGGCATTTTTTCCTAAG
1 CGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTACCAAAG
* *
51887178 CGCCGCTAAAGAACATGA-TCTTTAACGGCGTTTTT
1 CGCCGCTAAAGAACATTACT-TTTAGCGGCGTTTTT
51887213 TTCTGTAAGC
Statistics
Matches: 141, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
41 2 0.01
42 105 0.74
43 34 0.24
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (42 bp):
CGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTACCAAAG
Found at i:51887215 original size:85 final size:85
Alignment explanation
Indices: 51887009--51887213 Score: 308
Period size: 85 Copynumber: 2.4 Consensus size: 85
51886999 GTGAAATAAC
** *
51887009 CGCCGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTTGACCAAGCGCCGCTATAGAACATTACTT
1 CGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTTTCCCAAGCGCCGCTATAGAACATTAATT
*
51887072 TTAGCGGCGTTTTCATCCAAAG
64 TTAGCGGCATTTTCATCCAAAG
51887094 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCCAAGCGCCGCTATAGAACATTAATTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCCAAGCGCCGCTATAGAACATTAATTTT
* *
51887159 AGCGGCATTTT-TTCCTAAG
66 AGCGGCATTTTCATCCAAAG
*
51887178 CGCCGCTAAAGAACATGATCTTTAACGGCGTTTTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
51887214 TCTGTAAGCG
Statistics
Matches: 111, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
84 42 0.38
85 68 0.61
86 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (85 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCCAAGCGCCGCTATAGAACATTAATTTT
AGCGGCATTTTCATCCAAAG
Done.