Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008719.1 Hibiscus syriacus cultivar Beakdansim tig00111774_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: 4817204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 18
Found at i:281713 original size:15 final size:14
Alignment explanation
Indices: 281693--281723 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
281683 ATTCAAAAAG
281693 AAGAAAAGAAAAGAA
1 AAGAAAAG-AAAGAA
281708 AAGAAAAGAAAGAA
1 AAGAAAAGAAAGAA
281722 AA
1 AA
281724 TTGAAGCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAAAGAA
Found at i:281721 original size:4 final size:5
Alignment explanation
Indices: 281693--281723 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
281683 ATTCAAAAAG
281693 AAGAA AAGAA AAGAA AAGAA AAG-A AAGAA AA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AA
281724 TTGAAGCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:288679 original size:11 final size:13
Alignment explanation
Indices: 288647--288676 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
288637 TGGCCAAAGA
288647 TGAAAAGGTATGT
1 TGAAAAGGTATGT
288660 TGAAAAGGTATG-
1 TGAAAAGGTATGT
288672 TGAAA
1 TGAAA
288677 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:291910 original size:13 final size:13
Alignment explanation
Indices: 291888--291917 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
291878 ACTAAACACC
291888 TTTC-ACATACCT
1 TTTCAACATACCT
291900 TTTCAACATACCT
1 TTTCAACATACCT
291913 TTTCA
1 TTTCA
291918 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:297951 original size:11 final size:11
Alignment explanation
Indices: 297937--297992 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
297927 TCTTTTTGAA
297937 TTCTTTTTCTT
1 TTCTTTTTCTT
297948 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
297961 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
297974 TGTCTTTTTC-T
1 T-TCTTTTTCTT
297985 TTCTTTTT
1 TTCTTTTT
297993 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:297961 original size:19 final size:18
Alignment explanation
Indices: 297937--297992 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
297927 TCTTTTTGAA
297937 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
297955 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
297974 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
297992 T
1 T
297993 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:309275 original size:18 final size:18
Alignment explanation
Indices: 309239--309275 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
309229 TATTTTTTTC
*
309239 AAAAACAAAATAACAAAA
1 AAAAACAAAAAAACAAAA
309257 AAAAACAAAAAAGACAAAA
1 AAAAACAAAAAA-ACAAAA
309276 TTTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.03
Consensus pattern (18 bp):
AAAAACAAAAAAACAAAA
Found at i:313483 original size:22 final size:22
Alignment explanation
Indices: 313458--313499 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
313448 CAATTCATTT
313458 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
313480 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
313500 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:316843 original size:33 final size:33
Alignment explanation
Indices: 316764--316867 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
316754 ATACAATCTG
* *
316764 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
316800 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
316833 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
316866 TC
1 TC
316868 ATTTATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:319207 original size:13 final size:12
Alignment explanation
Indices: 319189--319218 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
319179 TGGCCAAATA
319189 TGAAAAGGTATG
1 TGAAAAGGTATG
319201 TTGAAAAGGTATG
1 -TGAAAAGGTATG
319214 TGAAA
1 TGAAA
319219 TGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (12 bp):
TGAAAAGGTATG
Found at i:340138 original size:19 final size:20
Alignment explanation
Indices: 340097--340147 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
340087 GAAACCCCTT
*
340097 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
340117 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
340136 TGAAGATACATG
1 TGAAAATACATG
340148 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:344345 original size:19 final size:20
Alignment explanation
Indices: 344304--344354 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
344294 GAAACCCCTT
*
344304 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
344324 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
344343 TGAAGATACATG
1 TGAAAATACATG
344355 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:349615 original size:22 final size:22
Alignment explanation
Indices: 349589--349630 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
349579 CAATTCCTTT
*
349589 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATTC-TTATATTGTTTTA
349611 ATCTTATTCTTATATTGTTT
1 ATCTTATTCTTATATTGTTT
349631 CCAGCACCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.67
Consensus pattern (22 bp):
ATCTTATTCTTATATTGTTTTA
Found at i:350034 original size:7 final size:8
Alignment explanation
Indices: 350015--350043 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
350005 AAAAAGTCAC
350015 AAAAATTG
1 AAAAATTG
350023 AAAAATTG
1 AAAAATTG
350031 AAAAATTG
1 AAAAATTG
350039 AAAAA
1 AAAAA
350044 GAAGGAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (8 bp):
AAAAATTG
Found at i:352272 original size:37 final size:35
Alignment explanation
Indices: 352176--352288 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 35
352166 TTGGTGGTTA
* * *
352176 TATAGGCATGAAATGGTGATAGAAGATGGTGATGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
352211 TATAGGCGTGCAATGGTGATGGAAGATGGTGAAGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
352246 TATAGGCGTGAAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTG--AAATGGTGATGGAAGATGGTGATGT
352283 TATAGG
1 TATAGG
352289 TAGTATCTTA
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 40 0.58
37 29 0.42
ACGTcount: A:0.33, C:0.04, G:0.37, T:0.27
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:358564 original size:28 final size:28
Alignment explanation
Indices: 358498--358562 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
358488 AAAGAAAATC
* *
358498 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAATTCAAGCACTCAAAAAGA
*
358526 A-ATAAAGAAATTCAA-CATTCAAAAAGA
1 AGA-AAAGAAATTCAAGCACTCAAAAAGA
358553 AGAAAAGAAA
1 AGAAAAGAAA
358563 ATAAAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 19 0.59
28 13 0.41
ACGTcount: A:0.63, C:0.11, G:0.14, T:0.12
Consensus pattern (28 bp):
AGAAAAGAAATTCAAGCACTCAAAAAGA
Found at i:364331 original size:11 final size:11
Alignment explanation
Indices: 364312--364342 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
364302 GATCATTCTA
*
364312 CAACACTTCCG
1 CAACCCTTCCG
364323 CAACCCTTCCG
1 CAACCCTTCCG
364334 CAACCCTTC
1 CAACCCTTC
364343 TTTGATAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.52, G:0.06, T:0.19
Consensus pattern (11 bp):
CAACCCTTCCG
Found at i:369434 original size:33 final size:33
Alignment explanation
Indices: 369392--369495 Score: 88
Period size: 33 Copynumber: 3.1 Consensus size: 33
369382 GTTGATGAAT
*
369392 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
369425 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
*
369458 GAATATGG-TGATGAT-ATAGGCGTGATAATGGTAATG
1 G-A-A-GGATGATGTTAAT-GGCGTGA-AATGGTAATG
369494 GA
1 GA
369496 CAGATTGTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
33 22 0.39
34 9 0.16
35 15 0.26
36 11 0.19
ACGTcount: A:0.32, C:0.02, G:0.36, T:0.31
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:374111 original size:19 final size:19
Alignment explanation
Indices: 374075--374110 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
374065 AAATTTTGGA
374075 TTTTTTGGCCTTTTTTTTG
1 TTTTTTGGCCTTTTTTTTG
*
374094 TTTTTTTG-CTTTTTTTT
1 TTTTTTGGCCTTTTTTTT
374111 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.81
Consensus pattern (19 bp):
TTTTTTGGCCTTTTTTTTG
Found at i:379041 original size:23 final size:24
Alignment explanation
Indices: 378998--379046 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
378988 AAAGGTTAAG
*
378998 AAAGATGATAAGGTAATGAAAAGA
1 AAAGATGATAAGATAATGAAAAGA
*
379022 AAAGATGA-AAGAATAA-GAAATGA
1 AAAGATGATAAG-ATAATGAAAAGA
379045 AA
1 AA
379047 TAGTAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.14
Consensus pattern (24 bp):
AAAGATGATAAGATAATGAAAAGA
Found at i:382842 original size:35 final size:37
Alignment explanation
Indices: 382773--382852 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
382763 ATACTATTTC
* *
382773 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
*
382810 CATCACCATAGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
382845 CATCACCA
1 CATCACCA
382853 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.33, C:0.38, G:0.03, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:382846 original size:11 final size:11
Alignment explanation
Indices: 382806--382852 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
382796 TATCACGCCT
382806 ATATCATCACC
1 ATATCATCACC
382817 ATAGTCCATCACC
1 ATA-T-CATCACC
382830 ATATCA-CACC
1 ATATCATCACC
382840 TATATCATCACC
1 -ATATCATCACC
382852 A
1 A
382853 AATTCTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 12 0.38
12 6 0.19
13 10 0.31
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (11 bp):
ATATCATCACC
Found at i:382850 original size:22 final size:24
Alignment explanation
Indices: 382806--382852 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
382796 TATCACGCCT
382806 ATATCATCACCATAGTCCATCACC
1 ATATCATCACCATAGTCCATCACC
382830 ATATCA-CACCTATA-T-CATCACC
1 ATATCATCACC-ATAGTCCATCACC
382852 A
1 A
382853 AATTCTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 9 0.41
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (24 bp):
ATATCATCACCATAGTCCATCACC
Found at i:388469 original size:35 final size:37
Alignment explanation
Indices: 388393--388472 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
388383 ATACTATTTC
* *
388393 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
* *
388430 CATCACCATAGTCCATC-ACCA-TATCGCACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
388465 CATCACCA
1 CATCACCA
388473 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 3 0.08
37 16 0.41
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:389367 original size:10 final size:10
Alignment explanation
Indices: 389354--389396 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 10
389344 AATTTTGGCT
389354 TTTTTTTTTG
1 TTTTTTTTTG
389364 TTTTTTTTTG
1 TTTTTTTTTG
389374 CCTTTTTTGTTTTG
1 ---TTTTT-TTTTG
389388 TTTTTTTTT
1 TTTTTTTTT
389397 TGGAAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 14 0.48
11 5 0.17
13 5 0.17
14 5 0.17
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:389372 original size:23 final size:24
Alignment explanation
Indices: 389346--389396 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
389336 TTTTTTGAAA
*
389346 TTTTGGCTTTTTT-TTTTGTTTTT
1 TTTTGCCTTTTTTGTTTTGTTTTT
389369 TTTTGCCTTTTTTGTTTTGTTTTT
1 TTTTGCCTTTTTTGTTTTGTTTTT
389393 TTTT
1 TTTT
389397 TGGAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82
Consensus pattern (24 bp):
TTTTGCCTTTTTTGTTTTGTTTTT
Found at i:393379 original size:25 final size:25
Alignment explanation
Indices: 393315--393369 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
393305 TGGGATGCGG
393315 AAGTGATGTTGAATTAATATCCTTC
1 AAGTGATGTTGAATTAATATCCTTC
393340 AAGTGATGTTGAATTAATATCCTTC
1 AAGTGATGTTGAATTAATATCCTTC
393365 AAGTG
1 AAGTG
393370 TTTATGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (25 bp):
AAGTGATGTTGAATTAATATCCTTC
Found at i:393497 original size:35 final size:35
Alignment explanation
Indices: 393458--393579 Score: 149
Period size: 35 Copynumber: 3.4 Consensus size: 35
393448 GGTAAGGTAT
* *
393458 TGGTGGTTATATAGGCGTGAAATGGTGATAGAAGA
1 TGGTGATTATATAGGCGTGAAATGGTGATGGAAGA
* *
393493 TGGTGATGATATAGGCGTGCAATGGTGATGGAAGA
1 TGGTGATTATATAGGCGTGAAATGGTGATGGAAGA
*
393528 TGGTGAATT-TATAGGAGTGAAAAATGGTGATGGAAGA
1 TGGTG-ATTATATAGGCGTG--AAATGGTGATGGAAGA
393565 TGGTGATGT-TATAGG
1 TGGTGAT-TATATAGG
393580 TAGTATCTTA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
35 45 0.59
36 4 0.05
37 27 0.36
ACGTcount: A:0.31, C:0.02, G:0.38, T:0.29
Consensus pattern (35 bp):
TGGTGATTATATAGGCGTGAAATGGTGATGGAAGA
Found at i:393942 original size:20 final size:21
Alignment explanation
Indices: 393900--393943 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
393890 ATTCGGCTAG
** *
393900 ATACATGTCTTTTTAATGGAA
1 ATACATGTCTTTAAAATGAAA
393921 ATACATGTC-TTAAAATGAAA
1 ATACATGTCTTTAAAATGAAA
393941 ATA
1 ATA
393944 GATGATGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (21 bp):
ATACATGTCTTTAAAATGAAA
Found at i:395655 original size:35 final size:35
Alignment explanation
Indices: 395610--395800 Score: 253
Period size: 35 Copynumber: 5.4 Consensus size: 35
395600 TGGTAAGGGA
395610 ATGGTGATGATATAGGCGTGAAATGGTGATAGG-AG
1 ATGGTGATGATATAGGCGTGAAATGGTGAT-GGAAG
* *
395645 ATGGTGATGATATAGGCATGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
* *
395680 ATGGTGATGTTATAGGCGTGAAAATGGTGATATG-AG
1 ATGGTGATGATATAGGCGTG-AAATGGTGAT-GGAAG
* *
395716 ATGGTGATTATATAGGCGTGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
* *
395751 ATGGTGATGTTATAGGCATGAAAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTG-AAATGGTGATGGAAG
395787 ATGGTGATGA-ATAG
1 ATGGTGATGATATAG
395801 ATACTATCTT
Statistics
Matches: 136, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
34 3 0.02
35 80 0.59
36 52 0.38
37 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.37, T:0.28
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
Found at i:395717 original size:71 final size:71
Alignment explanation
Indices: 395610--395800 Score: 307
Period size: 71 Copynumber: 2.7 Consensus size: 71
395600 TGGTAAGGGA
*
395610 ATGGTGATGATATAGGCGTG-AAATGGTGATAGGAGATGGTGATGATATAGGCATGCAATGGTGA
1 ATGGTGATGTTATAGGCGTGAAAATGGTGATAGGAGATGGTGATGATATAGGCATGCAATGGTGA
395674 TGGAAG
66 TGGAAG
* * *
395680 ATGGTGATGTTATAGGCGTGAAAATGGTGATATGAGATGGTGATTATATAGGCGTGCAATGGTGA
1 ATGGTGATGTTATAGGCGTGAAAATGGTGATAGGAGATGGTGATGATATAGGCATGCAATGGTGA
395745 TGGAAG
66 TGGAAG
*
395751 ATGGTGATGTTATAGGCATGAAAATGGTGAT-GGAAGATGGTGATGA-ATAG
1 ATGGTGATGTTATAGGCGTGAAAATGGTGATAGG-AGATGGTGATGATATAG
395801 ATACTATCTT
Statistics
Matches: 112, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
70 24 0.21
71 88 0.79
ACGTcount: A:0.31, C:0.04, G:0.37, T:0.28
Consensus pattern (71 bp):
ATGGTGATGTTATAGGCGTGAAAATGGTGATAGGAGATGGTGATGATATAGGCATGCAATGGTGA
TGGAAG
Found at i:395756 original size:13 final size:13
Alignment explanation
Indices: 395738--395795 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
395728 TAGGCGTGCA
395738 ATGGTGATGGAAG
1 ATGGTGATGGAAG
** *
395751 ATGGTGATGTTAT
1 ATGGTGATGGAAG
* *
395764 A-GG-CAT-GAAA
1 ATGGTGATGGAAG
395774 ATGGTGATGGAAG
1 ATGGTGATGGAAG
395787 ATGGTGATG
1 ATGGTGATG
395796 AATAGATACT
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
10 2 0.06
11 4 0.12
12 4 0.12
13 23 0.70
ACGTcount: A:0.31, C:0.02, G:0.40, T:0.28
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:396270 original size:36 final size:35
Alignment explanation
Indices: 396185--396287 Score: 120
Period size: 35 Copynumber: 2.9 Consensus size: 35
396175 TATTTAGGTG
* * * * *
396185 TGAAATGGTGATAGAAGATGGTAATGATATAGGCG
1 TGAAATGGAGATGGAAGATGGTGATGTTATAGGCA
*
396220 TGCAATGGTA-ATGGAAGATGGTGATGTTATAGGCA
1 TGAAATGG-AGATGGAAGATGGTGATGTTATAGGCA
396255 TGAAAATGGAGATGGAAGATGGTGATGTT-TAGG
1 TG-AAATGGAGATGGAAGATGGTGATGTTATAGG
396288 TAGTATCTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
35 35 0.60
36 23 0.40
ACGTcount: A:0.34, C:0.03, G:0.36, T:0.27
Consensus pattern (35 bp):
TGAAATGGAGATGGAAGATGGTGATGTTATAGGCA
Found at i:402169 original size:11 final size:11
Alignment explanation
Indices: 402153--402192 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
402143 GAATGCCTTG
402153 ATGATGATTGA
1 ATGATGATTGA
402164 ATGATGATTGA
1 ATGATGATTGA
402175 ATGATGATTGA
1 ATGATGATTGA
*
402186 AGGATGA
1 ATGATGA
402193 ATAGGTGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.33
Consensus pattern (11 bp):
ATGATGATTGA
Found at i:402311 original size:36 final size:35
Alignment explanation
Indices: 402220--402328 Score: 123
Period size: 35 Copynumber: 3.1 Consensus size: 35
402210 GGTGGTTATT
* * * * *
402220 TAGGCGTGAAATGGTGATAGAAGATGGTAATGATA
1 TAGGCATGAAATGGAGATGGAAGATGGTGATGTTA
* *
402255 TAGGCATGCAATGGTA-ATGGAATATGGTGATGTTA
1 TAGGCATGAAATGG-AGATGGAAGATGGTGATGTTA
402290 TAGGCATGAAAATGGAGATGGAAGATGGTGATGTT-
1 TAGGCATG-AAATGGAGATGGAAGATGGTGATGTTA
402325 TAGG
1 TAGG
402329 TAGTATCTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
35 40 0.65
36 22 0.35
ACGTcount: A:0.34, C:0.04, G:0.35, T:0.28
Consensus pattern (35 bp):
TAGGCATGAAATGGAGATGGAAGATGGTGATGTTA
Found at i:404476 original size:22 final size:20
Alignment explanation
Indices: 404451--404505 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 20
404441 AAGTGCAAAA
404451 AGAAAGAAAAAGACAAAAGAAG
1 AGAAAGAAAAAG--AAAAGAAG
**
404473 AGAAA-AATCAGAAAAGAAG
1 AGAAAGAAAAAGAAAAGAAG
404492 A-AAAG-AAAAGAAAA
1 AGAAAGAAAAAGAAAA
404506 ATAAAAATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
18 10 0.36
19 9 0.32
21 4 0.14
22 5 0.18
ACGTcount: A:0.75, C:0.04, G:0.20, T:0.02
Consensus pattern (20 bp):
AGAAAGAAAAAGAAAAGAAG
Found at i:411099 original size:16 final size:16
Alignment explanation
Indices: 411078--411109 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
411068 TAGTTAGCTC
411078 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
411094 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
411110 TGGTGGAAGA
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:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:417350 original size:5 final size:5
Alignment explanation
Indices: 417340--417394 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
417330 GAACTTCTCT
417340 TTTTC TTTTC TTTTC TTCTT- TTCTTC TTTTC TTCTT- TTTGTC TTTTC
1 TTTTC TTTTC TTTTC TT-TTC TT-TTC TTTTC TT-TTC TTT-TC TTTTC
417387 -TTTC TTTT
1 TTTTC TTTT
417395 TGCACTGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
4 5 0.11
5 30 0.68
6 9 0.20
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:417358 original size:8 final size:8
Alignment explanation
Indices: 417347--417394 Score: 71
Period size: 8 Copynumber: 5.9 Consensus size: 8
417337 TCTTTTTCTT
417347 TTCTTTTC
1 TTCTTTTC
417355 TTCTTTTC
1 TTCTTTTC
417363 TTCTTTTC
1 TTCTTTTC
417371 TTCTTTT-
1 TTCTTTTC
417378 TGTCTTTTC
1 T-TCTTTTC
417387 TTTCTTTT
1 -TTCTTTT
417395 TGCACTGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.03
8 29 0.78
9 6 0.16
10 1 0.03
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (8 bp):
TTCTTTTC
Found at i:419628 original size:19 final size:20
Alignment explanation
Indices: 419604--419643 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
419594 TATCCTTTCT
419604 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
419623 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
419643 T
1 T
419644 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:419967 original size:28 final size:28
Alignment explanation
Indices: 419906--419968 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
419896 GCAAAAGAAG
* *
419906 AAAGA-AAAATAAGAGAAAAAAGATCAG
1 AAAGAGAAAATAAGAAAAAAAAGATCAA
*
419933 AAA-AGAAAATAA-AAAAAAAATGTTCAA
1 AAAGAGAAAATAAGAAAAAAAA-GATCAA
419960 AAAGAGAAA
1 AAAGAGAAA
419969 GCAAGCCAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 8 0.27
27 17 0.57
28 5 0.17
ACGTcount: A:0.73, C:0.03, G:0.14, T:0.10
Consensus pattern (28 bp):
AAAGAGAAAATAAGAAAAAAAAGATCAA
Found at i:424168 original size:19 final size:20
Alignment explanation
Indices: 424144--424183 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
424134 TATCCTTTCT
424144 TTATTTCATTTCATTA-TTA
1 TTATTTCATTTCATTACTTA
*
424163 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
424183 T
1 T
424184 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:437734 original size:174 final size:174
Alignment explanation
Indices: 437444--437791 Score: 680
Period size: 174 Copynumber: 2.0 Consensus size: 174
437434 GTAGTGGAGA
437444 AAATTGAAAGTGGTAAATTTGAAAAAGATGAGTGTAGAGAAGAGAAGCAGAGTGAAGGACAAATT
1 AAATTGAAAGTGGTAAATTTGAAAAAGATGAGTGTAGAGAAGAGAAGCAGAGTGAAGGACAAATT
437509 TTACCTAACAAATCTTCTTCTACTGTTTCTTTTTCCTTGTAGGATATTCAAAGATACATATA-TT
66 TTACCTAACAAATCTTCTTCTACTGTTTCTTTTTCCTTGTAGGATATTCAAAGATACATATATTT
437573 TCAAGTAGAAAATTCAAGAGAACATGTCTTTTGAAGAACCAATAG
131 TCAAGTAGAAAATTCAAGA-AACATGTCTTTTGAAGAACCAATAG
437618 AAATTGAAAGTGGTAAATTTGAAAAAGATGAGTGTAGAGAAGAGAAGCAGAGTGAAGGACAAATT
1 AAATTGAAAGTGGTAAATTTGAAAAAGATGAGTGTAGAGAAGAGAAGCAGAGTGAAGGACAAATT
437683 TTACCTAACAAATCTTCTTCTACTGTTTCTTTTTCCTTGTAGGATATTCAAAGATACATATATTT
66 TTACCTAACAAATCTTCTTCTACTGTTTCTTTTTCCTTGTAGGATATTCAAAGATACATATATTT
437748 TCAAGTAGAAAATTCAAGAAACATGTCTTTTGAAGAACCAATAG
131 TCAAGTAGAAAATTCAAGAAACATGTCTTTTGAAGAACCAATAG
437792 GTGTGACCTT
Statistics
Matches: 173, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
174 152 0.88
175 21 0.12
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (174 bp):
AAATTGAAAGTGGTAAATTTGAAAAAGATGAGTGTAGAGAAGAGAAGCAGAGTGAAGGACAAATT
TTACCTAACAAATCTTCTTCTACTGTTTCTTTTTCCTTGTAGGATATTCAAAGATACATATATTT
TCAAGTAGAAAATTCAAGAAACATGTCTTTTGAAGAACCAATAG
Found at i:440232 original size:10 final size:10
Alignment explanation
Indices: 440217--440259 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
440207 TTTGTTTTTC
440217 AAAAAAACAA
1 AAAAAAACAA
440227 AAAAAAACAA
1 AAAAAAACAA
*
440237 AAAAAAGGCAA
1 AAAAAA-ACAA
*
440248 AAAAAACCAA
1 AAAAAAACAA
440258 AA
1 AA
440260 TTTCAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.84, C:0.12, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:440248 original size:21 final size:19
Alignment explanation
Indices: 440217--440259 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
440207 TTTGTTTTTC
440217 AAAAAAACAAAAAAAAACA
1 AAAAAAACAAAAAAAAACA
*
440236 AAAAAAAGGCAAAAAAAACCA
1 AAAAAAA--CAAAAAAAAACA
440257 AAA
1 AAA
440260 TTTCAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
21 14 0.67
ACGTcount: A:0.84, C:0.12, G:0.05, T:0.00
Consensus pattern (19 bp):
AAAAAAACAAAAAAAAACA
Found at i:442830 original size:9 final size:9
Alignment explanation
Indices: 442816--442842 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
442806 TAATAACTCG
442816 GATATTTCT
1 GATATTTCT
442825 GATATTTCT
1 GATATTTCT
442834 GATATTTCT
1 GATATTTCT
442843 ACCCATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (9 bp):
GATATTTCT
Found at i:445151 original size:22 final size:23
Alignment explanation
Indices: 445125--445174 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
445115 GATGGCTGGT
445125 CATGTG-CTCCATCTTGGGCGTG
1 CATGTGTCTCCATCTTGGGCGTG
445147 CATGTGTCTCCATCTTGGGCGTG
1 CATGTGTCTCCATCTTGGGCGTG
445170 CATGT
1 CATGT
445175 TTGTGAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.10, C:0.26, G:0.30, T:0.34
Consensus pattern (23 bp):
CATGTGTCTCCATCTTGGGCGTG
Found at i:446726 original size:24 final size:25
Alignment explanation
Indices: 446691--446745 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
446681 ACTTGGACCC
*
446691 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
446715 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
446739 TCAAGTG
1 TCAAGTG
446746 GCATAACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:448232 original size:23 final size:24
Alignment explanation
Indices: 448194--448244 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
448184 TCCACTAAAT
* *
448194 CTCTGATTACCGCTTGATGTGAGG
1 CTCTGATTACCACTTGATGTAAGG
448218 CTCTGA-TACCACTTGATGTAAGG
1 CTCTGATTACCACTTGATGTAAGG
448241 CTCT
1 CTCT
448245 TCTGATGCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (24 bp):
CTCTGATTACCACTTGATGTAAGG
Found at i:452693 original size:36 final size:36
Alignment explanation
Indices: 452652--452800 Score: 199
Period size: 36 Copynumber: 4.1 Consensus size: 36
452642 ATTTATAAGT
* * * *
452652 TGGTGATAATATGGGCGTGATAATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * *
452688 TGGTGACGATATAGGCATGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * *
452724 TGGTGATGATAAAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
*
452760 TGGTGATGATATAGGCGTGATAATGGAGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
452796 TGGTG
1 TGGTG
452801 TTGGACAGAT
Statistics
Matches: 98, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 98 1.00
ACGTcount: A:0.30, C:0.05, G:0.38, T:0.28
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
Found at i:453192 original size:19 final size:20
Alignment explanation
Indices: 453145--453195 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
453135 GAAACCCCTT
**
453145 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
453165 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
453184 TGAAGATACATG
1 TGAAAATACATG
453196 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:465405 original size:33 final size:33
Alignment explanation
Indices: 465326--465429 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
465316 ATACAATCTG
* *
465326 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
465362 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
465395 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
465428 TC
1 TC
465430 ATTTATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:465871 original size:17 final size:18
Alignment explanation
Indices: 465849--465896 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
465839 TGGAGTGCAA
465849 AAGAAAGAAAA-AAAAAG
1 AAGAAAGAAAAGAAAAAG
*
465866 AAGAAAAGCAAAAGCAAAAG
1 AAG-AAAG-AAAAGAAAAAG
465886 AA-AAAGAAAAG
1 AAGAAAGAAAAG
465897 TGAAGCAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 8 0.30
18 8 0.30
19 4 0.15
20 7 0.26
ACGTcount: A:0.77, C:0.04, G:0.19, T:0.00
Consensus pattern (18 bp):
AAGAAAGAAAAGAAAAAG
Found at i:465884 original size:12 final size:11
Alignment explanation
Indices: 465847--465896 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
465837 TTTGGAGTGC
465847 AAAAGAAAGAA-
1 AAAAGAAA-AAG
465858 AAAA-AAAGAAG
1 AAAAGAAA-AAG
*
465869 AAAAGCAAAAG
1 AAAAGAAAAAG
465880 CAAAAGAAAAAG
1 -AAAAGAAAAAG
465892 AAAAG
1 AAAAG
465897 TGAAGCAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 6 0.18
11 16 0.47
12 12 0.35
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:469397 original size:35 final size:37
Alignment explanation
Indices: 469328--469397 Score: 108
Period size: 35 Copynumber: 1.9 Consensus size: 37
469318 ATAAGATACA
* *
469328 ATATGTCCATCACCATTATCACGCCTATATCATCACC
1 ATATGTCCATCACCATTATCACGCCAATAACATCACC
469365 ATAT-TCCATCACCA-TATCACGCCAATAACATCA
1 ATATGTCCATCACCATTATCACGCCAATAACATCA
469398 TCCTTCCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 17 0.55
36 10 0.32
37 4 0.13
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.27
Consensus pattern (37 bp):
ATATGTCCATCACCATTATCACGCCAATAACATCACC
Found at i:469412 original size:33 final size:33
Alignment explanation
Indices: 469333--469436 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
469323 ATACAATATG
* *
469333 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
469369 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
469402 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
469435 TC
1 TC
469437 ATTTATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:470497 original size:5 final size:5
Alignment explanation
Indices: 470489--470514 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
470479 ATTAAAATAA
470489 AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG A
470515 TTCTGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:482322 original size:26 final size:26
Alignment explanation
Indices: 482290--482364 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
482280 TATCCCTGCT
482290 TTATTTCATTTCATTTCTTATCTTTA
1 TTATTTCATTTCATTTCTTATCTTTA
*
482316 TTATTTCATTT-A-TTCTT-CCTTTA
1 TTATTTCATTTCATTTCTTATCTTTA
* *
482339 TTA-ATCATCTTCTTTTTCTTATCTTT
1 TTATTTCAT-TTC-ATTTCTTATCTTT
482365 GTTGCAGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
22 4 0.10
23 10 0.25
24 5 0.12
25 1 0.03
26 16 0.40
27 4 0.10
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.65
Consensus pattern (26 bp):
TTATTTCATTTCATTTCTTATCTTTA
Found at i:484109 original size:18 final size:18
Alignment explanation
Indices: 484086--484127 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
484076 TTGAAAGTGC
484086 AAAAAAAATCCGAAAATT
1 AAAAAAAATCCGAAAATT
* *
484104 AAAAAAATTCTGAAAATT
1 AAAAAAAATCCGAAAATT
484122 AAAAAA
1 AAAAAA
484128 GAAAAGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.69, C:0.07, G:0.05, T:0.19
Consensus pattern (18 bp):
AAAAAAAATCCGAAAATT
Found at i:492907 original size:16 final size:15
Alignment explanation
Indices: 492888--492926 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
492878 TTTGATAATT
492888 AAGAAATGAAAATGAA
1 AAGAAATG-AAATGAA
* *
492904 AAGAATTGAAATGGA
1 AAGAAATGAAATGAA
492919 AAGAAATG
1 AAGAAATG
492927 TTATCAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (15 bp):
AAGAAATGAAATGAA
Found at i:493160 original size:36 final size:35
Alignment explanation
Indices: 493063--493171 Score: 139
Period size: 35 Copynumber: 3.1 Consensus size: 35
493053 GGTGGTTATT
* * * *
493063 TAGGCGTGAAATGGTGATAGAAGATGGTAAGGATA
1 TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
* * *
493098 TAGGCGTGCAATGATAATGGAAGATGGTGATGTTA
1 TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
493133 TAGGCGTGAAAATGGTGATGGAAGATGGTGATGTT-
1 TAGGCGTG-AAATGGTGATGGAAGATGGTGATGTTA
493168 TAGG
1 TAGG
493172 TAGTATCTTA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 40 0.63
36 23 0.37
ACGTcount: A:0.32, C:0.04, G:0.38, T:0.27
Consensus pattern (35 bp):
TAGGCGTGAAATGGTGATGGAAGATGGTGATGTTA
Found at i:493882 original size:16 final size:15
Alignment explanation
Indices: 493845--493883 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
493835 TCTTTGATAA
493845 CATTTCTTTCCATTT
1 CATTTCTTTCCATTT
*
493860 CAATTCTTTCCATTTT
1 CATTTCTTTCCA-TTT
493876 CATTTCTT
1 CATTTCTT
493884 AATTATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (15 bp):
CATTTCTTTCCATTT
Found at i:494929 original size:2 final size:2
Alignment explanation
Indices: 494922--494957 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
494912 TCATAATAAC
494922 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
494958 GAAAATAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:499279 original size:19 final size:21
Alignment explanation
Indices: 499250--499298 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 21
499240 AATGAAATAG
499250 AAATGGAAAAAAG-AAAGAAT
1 AAATGGAAAAAAGAAAAGAAT
499270 AAATGG-AAAAAGAAAAGAATT
1 AAATGGAAAAAAGAAAAGAA-T
499291 GAAATGGA
1 -AAATGGA
499299 TAGAAAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.24
20 12 0.48
21 1 0.04
22 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.12
Consensus pattern (21 bp):
AAATGGAAAAAAGAAAAGAAT
Found at i:499469 original size:11 final size:11
Alignment explanation
Indices: 499449--499548 Score: 62
Period size: 11 Copynumber: 8.5 Consensus size: 11
499439 ATGGAATTTT
499449 GTGATGATATAG
1 GTGATGATAT-G
499461 GTG-TGATATG
1 GTGATGATATG
499471 GTGATGGACTATG
1 GTGAT-GA-TATG
499484 GTGATGATATAG
1 GTGATGATAT-G
*
499496 GCG-TGATAATG
1 GTGATGAT-ATG
*
499507 GTGATGGAAGATG
1 GTGAT-G-ATATG
*
499520 GCGATGATATAG
1 GTGATGATAT-G
*
499532 GCG-TGATAATG
1 GTGATGAT-ATG
499543 GTGATG
1 GTGATG
499549 GACATATTGT
Statistics
Matches: 71, Mismatches: 6, Indels: 22
0.72 0.06 0.22
Matches are distributed among these distances:
10 4 0.06
11 27 0.38
12 22 0.31
13 17 0.24
14 1 0.01
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.30
Consensus pattern (11 bp):
GTGATGATATG
Found at i:499526 original size:36 final size:36
Alignment explanation
Indices: 499451--499550 Score: 157
Period size: 36 Copynumber: 2.8 Consensus size: 36
499441 GGAATTTTGT
* ** *
499451 GATGATATAGGTGTGAT-ATGGTGATGGACTATGGT
1 GATGATATAGGCGTGATAATGGTGATGGAAGATGGC
499486 GATGATATAGGCGTGATAATGGTGATGGAAGATGGC
1 GATGATATAGGCGTGATAATGGTGATGGAAGATGGC
499522 GATGATATAGGCGTGATAATGGTGATGGA
1 GATGATATAGGCGTGATAATGGTGATGGA
499551 CATATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 16 0.27
36 44 0.73
ACGTcount: A:0.29, C:0.04, G:0.38, T:0.29
Consensus pattern (36 bp):
GATGATATAGGCGTGATAATGGTGATGGAAGATGGC
Found at i:508833 original size:20 final size:21
Alignment explanation
Indices: 508807--508855 Score: 91
Period size: 20 Copynumber: 2.4 Consensus size: 21
508797 AAATGAAATA
508807 GAAATGGAAAAAGGAAAGAAT
1 GAAATGGAAAAAGGAAAGAAT
508828 -AAATGGAAAAAGGAAAGAAT
1 GAAATGGAAAAAGGAAAGAAT
508848 GAAATGGA
1 GAAATGGA
508856 TAGAAAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.61, C:0.00, G:0.29, T:0.10
Consensus pattern (21 bp):
GAAATGGAAAAAGGAAAGAAT
Found at i:509039 original size:13 final size:12
Alignment explanation
Indices: 509016--509096 Score: 54
Period size: 11 Copynumber: 7.2 Consensus size: 12
509006 ATATAGGCGT
509016 GATAT-GTGATG
1 GATATGGTGATG
509027 GACTATGGTGAT-
1 GA-TATGGTGATG
509039 GATATAGGCTGAT-
1 GATAT-GG-TGATG
509052 -A-ATGGTGATG
1 GATATGGTGATG
509062 GAATATGGTGAT-
1 G-ATATGGTGATG
*
509074 GATATCGTGAT-
1 GATATGGTGATG
509085 -A-ATGGTGATG
1 GATATGGTGATG
509095 GA
1 GA
509097 CAGATTGTAT
Statistics
Matches: 58, Mismatches: 2, Indels: 20
0.73 0.03 0.25
Matches are distributed among these distances:
9 11 0.19
10 3 0.05
11 17 0.29
12 10 0.17
13 17 0.29
ACGTcount: A:0.30, C:0.04, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:509041 original size:34 final size:35
Alignment explanation
Indices: 508992--509096 Score: 146
Period size: 34 Copynumber: 3.1 Consensus size: 35
508982 GGAATGAAAA
*
508992 GGAATTTGGTGATGATATAGGCGTGAT-AT-GTGAT
1 GGAATATGGTGATGATATAGGC-TGATAATGGTGAT
*
509026 GGACTATGGTGATGATATAGGCTGATAATGGTGAT
1 GGAATATGGTGATGATATAGGCTGATAATGGTGAT
*
509061 GGAATATGGTGATGATAT-CG-TGATAATGGTGAT
1 GGAATATGGTGATGATATAGGCTGATAATGGTGAT
509094 GGA
1 GGA
509097 CAGATTGTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
33 20 0.31
34 23 0.35
35 22 0.34
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.32
Consensus pattern (35 bp):
GGAATATGGTGATGATATAGGCTGATAATGGTGAT
Found at i:509090 original size:33 final size:34
Alignment explanation
Indices: 508992--509096 Score: 135
Period size: 35 Copynumber: 3.1 Consensus size: 34
508982 GGAATGAAAA
*
508992 GGAATTTGGTGATGATATAGGCGTGAT-AT-GTGAT
1 GGAATATGGTGATGATATA--CGTGATAATGGTGAT
* *
509026 GGACTATGGTGATGATATAGGCTGATAATGGTGAT
1 GGAATATGGTGATGATATACG-TGATAATGGTGAT
509061 GGAATATGGTGATGATAT-CGTGATAATGGTGAT
1 GGAATATGGTGATGATATACGTGATAATGGTGAT
509094 GGA
1 GGA
509097 CAGATTGTAT
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
32 1 0.02
33 20 0.32
34 20 0.32
35 22 0.35
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.32
Consensus pattern (34 bp):
GGAATATGGTGATGATATACGTGATAATGGTGAT
Found at i:514131 original size:24 final size:24
Alignment explanation
Indices: 514104--514149 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
514094 GATGTTAACG
*
514104 GACACAACTCTTGGCACTTCAAGT
1 GACACAACTCTTGGAACTTCAAGT
***
514128 GACATTTCTCTTGGAACTTCAA
1 GACACAACTCTTGGAACTTCAA
514150 ACGACATTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (24 bp):
GACACAACTCTTGGAACTTCAAGT
Found at i:514155 original size:24 final size:24
Alignment explanation
Indices: 514111--514157 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
514101 ACGGACACAA
* **
514111 CTCTTGGCACTTCAAGTGACATTT
1 CTCTTGGAACTTCAAACGACATTT
514135 CTCTTGGAACTTCAAACGACATT
1 CTCTTGGAACTTCAAACGACATT
514158 ATCTTTGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (24 bp):
CTCTTGGAACTTCAAACGACATTT
Found at i:514173 original size:24 final size:24
Alignment explanation
Indices: 514128--514173 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
514118 CACTTCAAGT
* *
514128 GACATTTCTCTTGGAACTTCAAAC
1 GACATTTCTCTTGAAACATCAAAC
514152 GACATTATCT-TTGAAACATCAA
1 GACATT-TCTCTTGAAACATCAA
514174 GAGATATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (24 bp):
GACATTTCTCTTGAAACATCAAAC
Found at i:515517 original size:20 final size:20
Alignment explanation
Indices: 515480--515516 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
515470 GTTGTATGAG
*
515480 TCTTTCCTTTTTGTTTTTAT
1 TCTTTCCTTGTTGTTTTTAT
515500 TCTTT-CTTGTTGTTTTT
1 TCTTTCCTTGTTGTTTTT
515517 TGTTGTAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.03, C:0.14, G:0.08, T:0.76
Consensus pattern (20 bp):
TCTTTCCTTGTTGTTTTTAT
Found at i:517848 original size:21 final size:21
Alignment explanation
Indices: 517807--517848 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
517797 TTATACCTAT
*
517807 AGATACTTATTTCATGTTATA
1 AGATACTTATTTCATGATATA
*
517828 AGATAGTTATTTTCAT-ATATA
1 AGATACTTA-TTTCATGATATA
517849 TATTATACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (21 bp):
AGATACTTATTTCATGATATA
Found at i:520117 original size:18 final size:19
Alignment explanation
Indices: 520080--520117 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
520070 AATTCCTAAT
520080 AAATAATAAATCTGATCCTA
1 AAATAATAAATC-GATCCTA
*
520100 AAATAATTAATC-ATCCTA
1 AAATAATAAATCGATCCTA
520118 TATTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.32
Consensus pattern (19 bp):
AAATAATAAATCGATCCTA
Found at i:527007 original size:23 final size:24
Alignment explanation
Indices: 526968--527021 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
526958 ATTTCCTTTT
526968 CATTTCCTAAAAAATAGGGTCGGC
1 CATTTCCTAAAAAATAGGGTCGGC
526992 CATTTCCT-AAAAATAGGGTCGGC
1 CATTTCCTAAAAAATAGGGTCGGC
527015 CATTTCC
1 CATTTCC
527022 ATTTTAAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 22 0.73
24 8 0.27
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.28
Consensus pattern (24 bp):
CATTTCCTAAAAAATAGGGTCGGC
Found at i:527177 original size:20 final size:19
Alignment explanation
Indices: 527135--527177 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
527125 ATCAACCACT
* *
527135 TCCATTTGATACTTGTGGT
1 TCCATTTGATACTAGTGGG
527154 TCCATTTGATATCTAGTGGG
1 TCCATTTGATA-CTAGTGGG
527174 TCCA
1 TCCA
527178 AGTCCTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (19 bp):
TCCATTTGATACTAGTGGG
Found at i:533013 original size:6 final size:6
Alignment explanation
Indices: 533002--533041 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
532992 GTGTTGCAAT
*
533002 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAA
533042 GACTCCTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.17
6 19 0.63
7 6 0.20
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:533254 original size:16 final size:16
Alignment explanation
Indices: 533225--533284 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
533215 GAGTTGTAAG
*
533225 TTATCTTCACTTTCTTA
1 TTAT-TTCATTTTCTTA
*
533242 TTATTTCATTTTCCTTT
1 TTATTTCATTTT-CTTA
* * *
533259 TTCTTTCATTTTTTTC
1 TTATTTCATTTTCTTA
533275 TTATTTCATT
1 TTATTTCATT
533285 ACCTTATCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
16 18 0.50
17 18 0.50
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTCATTTTCTTA
Found at i:537180 original size:15 final size:16
Alignment explanation
Indices: 537137--537182 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
537127 TATGAAATAA
*
537137 GAAATGGAAGAAGAATG
1 GAAATGG-AGAAGAAAG
*
537154 GAAAT-GATAAGAAAG
1 GAAATGGAGAAGAAAG
537169 GAAATGGA-AAGAAA
1 GAAATGGAGAAGAAA
537183 TGATATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 18 0.69
16 3 0.12
17 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.30, T:0.11
Consensus pattern (16 bp):
GAAATGGAGAAGAAAG
Found at i:545278 original size:19 final size:19
Alignment explanation
Indices: 545228--545278 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
545218 CCAGGTTAGT
* * *
545228 AAAAAAATAAAATAAAGTA
1 AAAAAAATTAAAGAAAGAA
*
545247 AAAAAAAGT-AAGAAAGAA
1 AAAAAAATTAAAGAAAGAA
545265 AAAAAAATTAAAGA
1 AAAAAAATTAAAGA
545279 GAGAGGGAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (19 bp):
AAAAAAATTAAAGAAAGAA
Found at i:558907 original size:11 final size:13
Alignment explanation
Indices: 558875--558904 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
558865 TGGCCAAAGA
558875 TGAAAAGGTATGT
1 TGAAAAGGTATGT
558888 TGAAAAGGTATG-
1 TGAAAAGGTATGT
558900 TGAAA
1 TGAAA
558905 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:562184 original size:20 final size:20
Alignment explanation
Indices: 562148--562185 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
562138 TAAAATAAAG
*
562148 AAATGATTAAAATGGAAAAC
1 AAATGATTAAAAAGGAAAAC
562168 AAATGA-TAAGAAAGGAAA
1 AAATGATTAA-AAAGGAAA
562186 TGGATATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.63, C:0.03, G:0.18, T:0.16
Consensus pattern (20 bp):
AAATGATTAAAAAGGAAAAC
Found at i:576942 original size:29 final size:28
Alignment explanation
Indices: 576877--576943 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
576867 ACTTCTTTCT
* **
576877 TTTCTTTTC-TTCTTTTTGAGTGCTGGA
1 TTTCTTTTCTTTCTTTTGGAGTGCTCAA
*
576904 TTTTTCTTTCTTTCTTTTGGAGTGCTTCAA
1 TTTCT-TTTCTTTCTTTTGGAGTGC-TCAA
576934 TTTCTTTTCT
1 TTTCTTTTCT
576944 GATTTTCTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
27 4 0.12
28 4 0.12
29 18 0.56
30 6 0.19
ACGTcount: A:0.07, C:0.16, G:0.13, T:0.63
Consensus pattern (28 bp):
TTTCTTTTCTTTCTTTTGGAGTGCTCAA
Found at i:580432 original size:2 final size:2
Alignment explanation
Indices: 580425--580458 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
580415 AACTATCACC
580425 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
580459 TCCGCTGCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:581599 original size:26 final size:26
Alignment explanation
Indices: 581560--581627 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
581550 CTAGAACACA
* * *
581560 CCCATGTGCTTTGCATATGATCAGGC
1 CCCATGTGCCTTGCATATGACCAGCC
581586 CCCATGTGCCTTGCATATGACCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
581612 CCCATGTGCCTTGCAT
1 CCCATGTGCCTTGCAT
581628 GTGGGTTCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.18, C:0.34, G:0.21, T:0.28
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGACCAGCC
Found at i:585146 original size:37 final size:37
Alignment explanation
Indices: 585096--585169 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
585086 AGGAATCTAG
585096 TAGCTAGTGGAACACCAAGGAGAGCACCAGACCAGTT
1 TAGCTAGTGGAACACCAAGGAGAGCACCAGACCAGTT
585133 TAGCTAGTGGAACACCAAGGAGAGCACCAGACCAGTT
1 TAGCTAGTGGAACACCAAGGAGAGCACCAGACCAGTT
585170 AATAACTTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.24, G:0.27, T:0.14
Consensus pattern (37 bp):
TAGCTAGTGGAACACCAAGGAGAGCACCAGACCAGTT
Found at i:585865 original size:22 final size:23
Alignment explanation
Indices: 585823--585866 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
585813 GGACATAACT
* *
585823 TTTGGGATGCCAAGGGTCATGAA
1 TTTGGGATGACAAGGGACATGAA
585846 TTTGGGAT-ACAAGGGACATGA
1 TTTGGGATGACAAGGGACATGA
585867 TCATTCAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.30, C:0.11, G:0.34, T:0.25
Consensus pattern (23 bp):
TTTGGGATGACAAGGGACATGAA
Found at i:588683 original size:36 final size:36
Alignment explanation
Indices: 588628--588732 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
588618 GATACAATCT
588628 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
588664 GTTCATCTCCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
588700 GTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
588733 ACTTATAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 21 0.33
36 43 0.67
ACGTcount: A:0.30, C:0.35, G:0.06, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:589588 original size:35 final size:34
Alignment explanation
Indices: 589538--589623 Score: 136
Period size: 35 Copynumber: 2.5 Consensus size: 34
589528 TAAGATACTA
589538 CCTATATCATCACCATCTTCCATCACCATATCAC
1 CCTATATCATCACCATCTTCCATCACCATATCAC
* *
589572 GCCTATATCATTACCATCTTCCATCACCATTTCAC
1 -CCTATATCATCACCATCTTCCATCACCATATCAC
*
589607 CCTAAATCATCACCATC
1 CCTATATCATCACCATC
589624 CCTTAACCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 15 0.32
35 32 0.68
ACGTcount: A:0.29, C:0.40, G:0.01, T:0.30
Consensus pattern (34 bp):
CCTATATCATCACCATCTTCCATCACCATATCAC
Found at i:590626 original size:18 final size:18
Alignment explanation
Indices: 590603--590643 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
590593 AGAGTGCATG
* *
590603 ACATGTGTGACAGTATTC
1 ACATGTATGACAATATTC
*
590621 ACATGTATGACAATGTTC
1 ACATGTATGACAATATTC
590639 ACATG
1 ACATG
590644 CGTGGAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (18 bp):
ACATGTATGACAATATTC
Found at i:591424 original size:12 final size:13
Alignment explanation
Indices: 591403--591427 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
591393 AAAAATTAGA
591403 AAATTAAAAAAAC
1 AAATTAAAAAAAC
591416 AAATTAAAAAAA
1 AAATTAAAAAAA
591428 TTACGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (13 bp):
AAATTAAAAAAAC
Found at i:592730 original size:2 final size:2
Alignment explanation
Indices: 592723--592777 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
592713 AGTTATTTTC
592723 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
592765 AT TT AT AT CT AT A
1 AT AT AT AT AT AT A
592778 GTTATTATGA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:594414 original size:25 final size:27
Alignment explanation
Indices: 594349--594415 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 27
594339 ACAAAAAGAA
594349 AGAAAAGAAGAAAAAGAAGAAAAAAATTC
1 AGAAAAG-AG-AAAAGAAGAAAAAAATTC
* *
594378 AGAAAATAAGAAAAGAA-AAAGAAATTC
1 AGAAAA-GAGAAAAGAAGAAAAAAATTC
594405 A-AAAAGAGAAA
1 AGAAAAGAGAAA
594416 GCAAGCCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 5 0.15
26 4 0.12
27 10 0.29
28 7 0.21
29 8 0.24
ACGTcount: A:0.73, C:0.03, G:0.16, T:0.07
Consensus pattern (27 bp):
AGAAAAGAGAAAAGAAGAAAAAAATTC
Found at i:599137 original size:152 final size:152
Alignment explanation
Indices: 598861--599166 Score: 612
Period size: 152 Copynumber: 2.0 Consensus size: 152
598851 GCATACATGA
598861 GTAATCCCAATGAAACAAAGGAATTACAAAGACAAATCAAAGAACTCCTAGACAAAGGTTACATT
1 GTAATCCCAATGAAACAAAGGAATTACAAAGACAAATCAAAGAACTCCTAGACAAAGGTTACATT
598926 TGGGAAAGTTTAAGCCCTTGTGTTGTACCCGTTTTGTTGGTACCAAAGAAAGATGGAACTTGGAG
66 TGGGAAAGTTTAAGCCCTTGTGTTGTACCCGTTTTGTTGGTACCAAAGAAAGATGGAACTTGGAG
598991 AATGTGCATGGATTGTAGGGCT
131 AATGTGCATGGATTGTAGGGCT
599013 GTAATCCCAATGAAACAAAGGAATTACAAAGACAAATCAAAGAACTCCTAGACAAAGGTTACATT
1 GTAATCCCAATGAAACAAAGGAATTACAAAGACAAATCAAAGAACTCCTAGACAAAGGTTACATT
599078 TGGGAAAGTTTAAGCCCTTGTGTTGTACCCGTTTTGTTGGTACCAAAGAAAGATGGAACTTGGAG
66 TGGGAAAGTTTAAGCCCTTGTGTTGTACCCGTTTTGTTGGTACCAAAGAAAGATGGAACTTGGAG
599143 AATGTGCATGGATTGTAGGGCT
131 AATGTGCATGGATTGTAGGGCT
599165 GT
1 GT
599167 GAACCAAATC
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
152 154 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (152 bp):
GTAATCCCAATGAAACAAAGGAATTACAAAGACAAATCAAAGAACTCCTAGACAAAGGTTACATT
TGGGAAAGTTTAAGCCCTTGTGTTGTACCCGTTTTGTTGGTACCAAAGAAAGATGGAACTTGGAG
AATGTGCATGGATTGTAGGGCT
Found at i:604335 original size:36 final size:36
Alignment explanation
Indices: 604265--604377 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
604255 AATGGAAGGA
* * *
604265 TGATGTTATTGGCGTGAT-ATGGTGAAGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
604300 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
604336 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
604372 TGATGA
1 TGATGA
604378 AAATAATATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:604760 original size:19 final size:20
Alignment explanation
Indices: 604713--604763 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
604703 GAAACCCCTT
**
604713 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
604733 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
604752 TGAAGATACATG
1 TGAAAATACATG
604764 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:607835 original size:14 final size:15
Alignment explanation
Indices: 607807--607850 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
607797 TTGCTTCAAT
*
607807 TTTTCTTTGCTTTTTT
1 TTTTCTTT-CTTTTTC
607823 TTATTC-TTCTTTTTC
1 TT-TTCTTTCTTTTTC
607838 TTTTCTTTCTTTT
1 TTTTCTTTCTTTT
607851 GCACTCCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 3 0.12
15 15 0.60
16 4 0.16
17 3 0.12
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTCTTTCTTTTTC
Found at i:608337 original size:38 final size:37
Alignment explanation
Indices: 608297--608411 Score: 155
Period size: 38 Copynumber: 3.2 Consensus size: 37
608287 AATGGAAGGA
* *
608297 TGATG-TTATTGGCGTGAT-ATGGTGAAGGAATATGG
1 TGATGATTATAGGCGTGATAATGGTGATGGAATATGG
*
608332 TGATGA-TATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATTATAGGCGTGATAATGGTGATGGAATATGG
* *
608368 TGATGATATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGAT-TATAGGCGTGATAATGGTGATGGAATATGG
608406 TGATGA
1 TGATGA
608412 AAATAGTATC
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 16 0.23
36 21 0.30
38 34 0.48
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.32
Consensus pattern (37 bp):
TGATGATTATAGGCGTGATAATGGTGATGGAATATGG
Found at i:608798 original size:19 final size:20
Alignment explanation
Indices: 608751--608801 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
608741 GAAACCCCTT
**
608751 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
608771 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
608790 TGAAGATACATG
1 TGAAAATACATG
608802 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:611745 original size:35 final size:36
Alignment explanation
Indices: 611664--611749 Score: 102
Period size: 35 Copynumber: 2.4 Consensus size: 36
611654 ATACTTCCTA
* *
611664 AACATCACCATCTTCCATCACCATTTTCACGCCTAT
1 AACATCACCATCTTCCATCACCATTTGCACGCATAT
* *
611700 AACATCACCATCTTCCATTATCA-TTGCACGCATAT
1 AACATCACCATCTTCCATCACCATTTGCACGCATAT
* * *
611735 ATCCTTACCATCTTC
1 AACATCACCATCTTC
611750 TAATTTCACG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 22 0.51
36 21 0.49
ACGTcount: A:0.28, C:0.36, G:0.03, T:0.33
Consensus pattern (36 bp):
AACATCACCATCTTCCATCACCATTTGCACGCATAT
Found at i:611949 original size:16 final size:15
Alignment explanation
Indices: 611911--611950 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
611901 TCTTTGATAA
611911 CATTTCTTTTCCATTT
1 CATTTC-TTTCCATTT
*
611927 CAATTCTTTCCATTTT
1 CATTTCTTTCCA-TTT
611943 CATTTCTT
1 CATTTCTT
611951 AATTATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.15, C:0.25, G:0.00, T:0.60
Consensus pattern (15 bp):
CATTTCTTTCCATTT
Found at i:615316 original size:23 final size:23
Alignment explanation
Indices: 615271--615316 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
615261 TTATACCTAT
*
615271 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
615294 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
615317 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:618254 original size:19 final size:20
Alignment explanation
Indices: 618230--618280 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
618220 CGGCCAAGAG
* *
618230 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
618249 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
618269 CATGTATTTTCA
1 CATGTATTTTCA
618281 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:619710 original size:35 final size:36
Alignment explanation
Indices: 619639--619729 Score: 114
Period size: 35 Copynumber: 2.6 Consensus size: 36
619629 ATAAGATACT
*
619639 GCCTA-AACATCACCATCTTCCATCACCATTTTCAC
1 GCCTATAACATCACCATCTTCCATCACCATTTGCAC
* *
619674 GCCTATAACATCACCATCTTCCATTATCA-TTGCAC
1 GCCTATAACATCACCATCTTCCATCACCATTTGCAC
* * *
619709 GCCTATATCCTTACCATCTTC
1 GCCTATAACATCACCATCTTC
619730 TAATTTCATG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
35 28 0.57
36 21 0.43
ACGTcount: A:0.26, C:0.37, G:0.04, T:0.32
Consensus pattern (36 bp):
GCCTATAACATCACCATCTTCCATCACCATTTGCAC
Found at i:619787 original size:11 final size:11
Alignment explanation
Indices: 619771--619799 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
619761 TACCATATAT
619771 TCATCATTCAA
1 TCATCATTCAA
619782 TCATCATTCAA
1 TCATCATTCAA
619793 TCATCAT
1 TCATCAT
619800 CAAGGCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (11 bp):
TCATCATTCAA
Found at i:619928 original size:16 final size:15
Alignment explanation
Indices: 619891--619929 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
619881 TATTTGATAA
619891 CATTTCTTTCCATTT
1 CATTTCTTTCCATTT
*
619906 CAATTCTTTCCATTTT
1 CATTTCTTTCCA-TTT
619922 CATTTCTT
1 CATTTCTT
619930 AATTATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (15 bp):
CATTTCTTTCCATTT
Found at i:624816 original size:15 final size:15
Alignment explanation
Indices: 624796--624835 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
624786 AATATGGAAG
624796 AAGAAAAGAAATGAT
1 AAGAAAAGAAATGAT
*
624811 AAGAAATGAAATGAT
1 AAGAAAAGAAATGAT
624826 AAG-AAAGAAA
1 AAGAAAAGAAA
624836 ATGGATAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.12
Consensus pattern (15 bp):
AAGAAAAGAAATGAT
Found at i:630666 original size:6 final size:6
Alignment explanation
Indices: 630652--630686 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
630642 TGTAAGAGTC
*
630652 TTTTCT TTTTGT TTTTCT TCTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTT
630687 GTTGCTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:630681 original size:13 final size:12
Alignment explanation
Indices: 630652--630686 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
630642 TGTAAGAGTC
*
630652 TTTTCTTTTTGT
1 TTTTCTTTTTCT
630664 TTTTCTTCTTTCT
1 TTTTCTT-TTTCT
630677 TTTTCTTTTT
1 TTTTCTTTTT
630687 GTTGCTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:632642 original size:28 final size:27
Alignment explanation
Indices: 632611--632664 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
632601 TTTGAATGTG
632611 CTTTGCAA-CTTTCTTCACTTTTCTTTTT
1 CTTTG-AATCTTTCTTC-CTTTTCTTTTT
* *
632639 CTTTGAATTTTTCTTCTTTTTCTTTT
1 CTTTGAATCTTTCTTCCTTTTCTTTT
632665 ATTTCTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.09, C:0.20, G:0.04, T:0.67
Consensus pattern (27 bp):
CTTTGAATCTTTCTTCCTTTTCTTTTT
Found at i:634314 original size:208 final size:210
Alignment explanation
Indices: 633953--634373 Score: 819
Period size: 208 Copynumber: 2.0 Consensus size: 210
633943 CATAGACCAT
633953 ATTTTAAGTACTCTATGTGGTGGTGATGATGGTGTAACTCTCCAGCTGAAATGAAACCTCTAGCT
1 ATTTTAAGTACTCTA-GTGGTGGTGATGATGGTGTAACTCTCCAGCTGAAATGAAACCTCTAGCT
634018 AGCTCAAAAGTCCAGCTCAAGTCAGCTATGAGCTCGGGGGTCAGCTGGCAACTTTGTCCCAGAAT
65 AGCTCAAAAGTCCAGCTCAAGTCAGCTATGAGCTCGGGGGTCAGCTGGCAACTTTGTCCCAGAAT
634083 GTTCTTGAGCTGTCTCGGAGTTGTCCTAGTCAAGTTTCCATAGCTCTTGGACTCCAATGCTTGCT
130 GTTCTTGAGCTGTCTCGGAGTTGTCCTAGTCAAGTTTCCATAGCTCTTGGACTCCAATGCTTGCT
634148 TTAAGTCAGCTCTATC
195 TTAAGTCAGCTCTATC
634164 ATTTTAAGTACTCTA-T-GTGGTGATGATGGTGTAACTCTCCAGCTGAAATGAAACCTCTAGCTA
1 ATTTTAAGTACTCTAGTGGTGGTGATGATGGTGTAACTCTCCAGCTGAAATGAAACCTCTAGCTA
634227 GCTCAAAAGTCCAGCTCAAGTCAGCTATGAGCTCGGGGGTCAGCTGGCAACTTTGTCCCAGAATG
66 GCTCAAAAGTCCAGCTCAAGTCAGCTATGAGCTCGGGGGTCAGCTGGCAACTTTGTCCCAGAATG
634292 TTCTTGAGCTGTCTCGGAGTTGTCCTAGTCAAGTTTCCATAGCTCTTGGACTCCAATGCTTGCTT
131 TTCTTGAGCTGTCTCGGAGTTGTCCTAGTCAAGTTTCCATAGCTCTTGGACTCCAATGCTTGCTT
634357 TAAGTCAGCTCTATC
196 TAAGTCAGCTCTATC
634372 AT
1 AT
634374 GTGGTCAAAC
Statistics
Matches: 210, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
208 194 0.92
209 1 0.00
211 15 0.07
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (210 bp):
ATTTTAAGTACTCTAGTGGTGGTGATGATGGTGTAACTCTCCAGCTGAAATGAAACCTCTAGCTA
GCTCAAAAGTCCAGCTCAAGTCAGCTATGAGCTCGGGGGTCAGCTGGCAACTTTGTCCCAGAATG
TTCTTGAGCTGTCTCGGAGTTGTCCTAGTCAAGTTTCCATAGCTCTTGGACTCCAATGCTTGCTT
TAAGTCAGCTCTATC
Found at i:640936 original size:22 final size:23
Alignment explanation
Indices: 640911--640962 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 23
640901 TGAATTTATT
*
640911 TTTCTTTTCTTTTATG-GTTTTC-
1 TTTCTTTTCTTTT-TGTCTTTTCT
640933 TTTC-TTTCTTTTTGTCTTTTCT
1 TTTCTTTTCTTTTTGTCTTTTCT
640955 TTTCTTTT
1 TTTCTTTT
640963 TGCACTCCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 2 0.08
21 13 0.50
22 8 0.31
23 3 0.12
ACGTcount: A:0.02, C:0.15, G:0.06, T:0.77
Consensus pattern (23 bp):
TTTCTTTTCTTTTTGTCTTTTCT
Found at i:641944 original size:30 final size:31
Alignment explanation
Indices: 641904--641963 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
641894 ACATGCTGCC
**
641904 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
641935 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
641964 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:644357 original size:8 final size:8
Alignment explanation
Indices: 644346--644370 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
644336 TCTTTTTCTT
644346 TTCTTTTC
1 TTCTTTTC
644354 TTCTTTTC
1 TTCTTTTC
644362 TTCTTTTC
1 TTCTTTTC
644370 T
1 T
644371 GATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:646079 original size:30 final size:31
Alignment explanation
Indices: 646039--646098 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
646029 AAATGCTGCC
**
646039 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
646070 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
646099 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:646496 original size:19 final size:21
Alignment explanation
Indices: 646456--646507 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
646446 GAAACCCCTT
646456 TGAAAATACATGATTGTTTAA
1 TGAAAATACATGATTGTTTAA
646477 TGAAAATACATGA-T-TTTAA
1 TGAAAATACATGATTGTTTAA
* *
646496 TGCATATACATG
1 TGAAAATACATG
646508 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 15 0.52
20 1 0.03
21 13 0.45
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTGTTTAA
Found at i:650353 original size:36 final size:35
Alignment explanation
Indices: 650259--650369 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 35
650249 TAGGTGGTTA
* * *
650259 TATAGGCGTGAAATGGTGATAGAAGATGGTAATGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
650294 TATAGGCGTGCAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
650329 TATAGGCGTGAAGATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTGAA-ATGGTGATGGAAGATGGTGATGT
650365 T-TAGG
1 TATAGG
650370 TAGTATCTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 45 0.66
36 23 0.34
ACGTcount: A:0.31, C:0.04, G:0.38, T:0.28
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:650356 original size:13 final size:13
Alignment explanation
Indices: 650338--650363 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
650328 TTATAGGCGT
650338 GAAGATGGTGATG
1 GAAGATGGTGATG
650351 GAAGATGGTGATG
1 GAAGATGGTGATG
650364 TTTAGGTAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.46, T:0.23
Consensus pattern (13 bp):
GAAGATGGTGATG
Done.