Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008552.1 Hibiscus syriacus cultivar Beakdansim tig00111447_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: 537591
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:385641 original size:36 final size:36
Alignment explanation
Indices: 385591--385695 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
385581 GATACAAACT
385591 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
385627 GTCCATCACTATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
385663 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
385696 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 21 0.32
36 44 0.68
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:392816 original size:14 final size:15
Alignment explanation
Indices: 392797--392826 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
392787 AGGAGTATTC
392797 TTTTTTCTT-TTTCT
1 TTTTTTCTTCTTTCT
392811 TTTTTTCTTCTTTCT
1 TTTTTTCTTCTTTCT
392826 T
1 T
392827 GTTGCTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTCTTCTTTCT
Found at i:397367 original size:19 final size:19
Alignment explanation
Indices: 397343--397379 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
397333 TCCAGCACTC
397343 AAAAAG-AAGAAAAGAAAAA
1 AAAAAGAAAG-AAAGAAAAA
397362 AAAAAGAAAGAAAGAAAA
1 AAAAAGAAAGAAAGAAAA
397380 GTTGAAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAGAAAGAAAAA
Found at i:398293 original size:15 final size:16
Alignment explanation
Indices: 398273--398309 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
398263 GATTAGAATA
398273 AAATAAACAAAAGAT-
1 AAATAAACAAAAGATG
*
398288 AAATAAATAAAAGATG
1 AAATAAACAAAAGATG
398304 AAATAA
1 AAATAA
398310 GATAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (16 bp):
AAATAAACAAAAGATG
Found at i:398307 original size:16 final size:15
Alignment explanation
Indices: 398273--398314 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
398263 GATTAGAATA
*
398273 AAATAAACAAAAGAT
1 AAATAAATAAAAGAT
398288 AAATAAATAAAAGAT
1 AAATAAATAAAAGAT
398303 GAAATAAGATAA
1 -AAATAA-ATAA
398315 TAAAAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.58
16 6 0.25
17 4 0.17
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (15 bp):
AAATAAATAAAAGAT
Found at i:402451 original size:1 final size:1
Alignment explanation
Indices: 402447--402517 Score: 52
Period size: 1 Copynumber: 71.0 Consensus size: 1
402437 TTTTTGGCTC
* *** * * * * * *
402447 TTTTTTTGTTTTTTTTTGCCTTTTTTTTGTTTTTTTTGTTTTTTTTGTTTTTTGTTTGTTTATTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
402512 TTTTTT
1 TTTTTT
402518 GAAAAAAAAA
Statistics
Matches: 53, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (1 bp):
T
Found at i:402453 original size:12 final size:11
Alignment explanation
Indices: 402436--402493 Score: 54
Period size: 9 Copynumber: 5.6 Consensus size: 11
402426 AAATTTTGGC
402436 TTTTTTGGCTCT
1 TTTTTTGGCT-T
*
402448 TTTTTT-GTTT
1 TTTTTTGGCTT
*
402458 TTTTTTGCCTT
1 TTTTTTGGCTT
402469 TTTTTT-G-TT
1 TTTTTTGGCTT
402478 TTTTTT-G-TT
1 TTTTTTGGCTT
402487 TTTTTTG
1 TTTTTTG
402494 TTTTTTGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 17 0.43
10 7 0.17
11 10 0.25
12 6 0.15
ACGTcount: A:0.00, C:0.07, G:0.12, T:0.81
Consensus pattern (11 bp):
TTTTTTGGCTT
Found at i:402459 original size:9 final size:9
Alignment explanation
Indices: 402447--402517 Score: 81
Period size: 9 Copynumber: 7.3 Consensus size: 9
402437 TTTTTGGCTC
402447 TTTTTTTGTT
1 TTTTTTTG-T
402457 TTTTTTTGCCT
1 TTTTTTTG--T
402468 TTTTTTTGT
1 TTTTTTTGT
402477 TTTTTTTGT
1 TTTTTTTGT
402486 TTTTTTTGTT
1 TTTTTTTG-T
402496 TTTTGTTTGT
1 TTTT-TTTGT
402506 TTATTTTT-T
1 TT-TTTTTGT
402515 TTT
1 TTT
402518 GAAAAAAAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
8 1 0.02
9 21 0.38
10 19 0.34
11 15 0.27
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:402460 original size:21 final size:20
Alignment explanation
Indices: 402436--402499 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 20
402426 AAATTTTGGC
*
402436 TTTTTTGGCTCTTTTTTTGTT
1 TTTTTTTGCTCTTTTTTTG-T
402457 TTTTTTTGC-CTTTTTTTTGT
1 TTTTTTTGCTC-TTTTTTTGT
402477 TTTTTTTG-T-TTTTTTTGT
1 TTTTTTTGCTCTTTTTTTGT
402495 TTTTT
1 TTTTT
402500 GTTTGTTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
18 14 0.35
20 10 0.25
21 16 0.40
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (20 bp):
TTTTTTTGCTCTTTTTTTGT
Found at i:402497 original size:25 final size:25
Alignment explanation
Indices: 402469--402518 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
402459 TTTTTGCCTT
*
402469 TTTTTTGTTT-TTTTTGTTTTTTTTG
1 TTTTTTGTTTGTTTAT-TTTTTTTTG
402494 TTTTTTGTTTGTTTATTTTTTTTTG
1 TTTTTTGTTTGTTTATTTTTTTTTG
402519 AAAAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (25 bp):
TTTTTTGTTTGTTTATTTTTTTTTG
Found at i:402504 original size:20 final size:19
Alignment explanation
Indices: 402447--402517 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 19
402437 TTTTTGGCTC
402447 TTTTTTTGTTTTTTTTTGCCT
1 TTTTTTTGTTTTTTTTTG--T
402468 TTTTTTTG-TTTTTTTTGT
1 TTTTTTTGTTTTTTTTTGT
402486 TTTTTTTGTTTTTTGTTTGT
1 TTTTTTTGTTTTTT-TTTGT
402506 TTATTTTT-TTTT
1 TT-TTTTTGTTTT
402518 GAAAAAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.19
19 5 0.11
20 20 0.43
21 13 0.28
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (19 bp):
TTTTTTTGTTTTTTTTTGT
Found at i:402504 original size:29 final size:29
Alignment explanation
Indices: 402447--402517 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
402437 TTTTTGGCTC
402447 TTTTTTTGTTTTTTTTTGCCTTTTTTTTGT
1 TTTTTTTG-TTTTTTTTGCCTTTTTTTTGT
*
402477 TTTTTTTGTTTTTTTTG-TTTTTTGTTTGT
1 TTTTTTTGTTTTTTTTGCCTTTTT-TTTGT
*
402506 TTATTTT-TTTTT
1 TTTTTTTGTTTTT
402518 GAAAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 10 0.26
29 20 0.53
30 8 0.21
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (29 bp):
TTTTTTTGTTTTTTTTGCCTTTTTTTTGT
Found at i:402891 original size:15 final size:16
Alignment explanation
Indices: 402871--402907 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
402861 GATTAGAATA
402871 AAATAAACAAAAGAT-
1 AAATAAACAAAAGATG
*
402886 AAATAAATAAAAGATG
1 AAATAAACAAAAGATG
402902 AAATAA
1 AAATAA
402908 GATAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.16
Consensus pattern (16 bp):
AAATAAACAAAAGATG
Found at i:402905 original size:16 final size:15
Alignment explanation
Indices: 402871--402912 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
402861 GATTAGAATA
*
402871 AAATAAACAAAAGAT
1 AAATAAATAAAAGAT
402886 AAATAAATAAAAGAT
1 AAATAAATAAAAGAT
402901 GAAATAAGATAA
1 -AAATAA-ATAA
402913 TAAAAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.58
16 6 0.25
17 4 0.17
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (15 bp):
AAATAAATAAAAGAT
Found at i:404834 original size:2 final size:2
Alignment explanation
Indices: 404827--404890 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
404817 TATCACCAAC
404827 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
404869 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
404891 CGCTTCCATA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:405768 original size:13 final size:12
Alignment explanation
Indices: 405750--405831 Score: 50
Period size: 11 Copynumber: 6.8 Consensus size: 12
405740 AGGCGTGATT
405750 TGGTGATGGAATA
1 TGGTGATGG-ATA
405763 TGGTGAT-GATA
1 TGGTGATGGATA
*
405774 TAGGCG-T-GATAA
1 T-GGTGATGGAT-A
405786 TGGTGATGGACTA
1 TGGTGATGGA-TA
405799 TGGTGAT-GATA
1 TGGTGATGGATA
*
405810 TAGGCG-T-GATAA
1 T-GGTGATGGAT-A
405822 TGGTGATGGA
1 TGGTGATGGA
405832 CAGATTGTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.38
12 15 0.27
13 19 0.34
14 1 0.02
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.30
Consensus pattern (12 bp):
TGGTGATGGATA
Found at i:405801 original size:36 final size:36
Alignment explanation
Indices: 405728--405832 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
405718 ATTTATAAAT
* * *
405728 TGGTGATAATATAGGCGTGAT-TTGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
405763 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
405799 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
405833 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.28, C:0.05, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:424623 original size:17 final size:17
Alignment explanation
Indices: 424585--424623 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
424575 TGTAGGAGTC
424585 TTTTTCTTTTCTCTTTT
1 TTTTTCTTTTCTCTTTT
*
424602 ATTTTCTTCTT-TCTTTT
1 TTTTTCTT-TTCTCTTTT
424619 TTTTT
1 TTTTT
424624 TGTAGCACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCTTTTCTCTTTT
Found at i:425076 original size:36 final size:36
Alignment explanation
Indices: 425003--425107 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
424993 ATTTATAAGT
* * *
425003 TGGTGATAATATAGGCGTGAT-TTGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
425038 TGGTGATGATGTAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
425074 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
425108 AGATTGTATC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 19 0.30
36 45 0.70
ACGTcount: A:0.27, C:0.05, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:427492 original size:26 final size:26
Alignment explanation
Indices: 427460--427526 Score: 134
Period size: 26 Copynumber: 2.6 Consensus size: 26
427450 AATGATCCTC
427460 ATGCAAGGCACATGGGGGCTGGTCAT
1 ATGCAAGGCACATGGGGGCTGGTCAT
427486 ATGCAAGGCACATGGGGGCTGGTCAT
1 ATGCAAGGCACATGGGGGCTGGTCAT
427512 ATGCAAGGCACATGG
1 ATGCAAGGCACATGG
427527 ATATTCTAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.25, C:0.19, G:0.37, T:0.18
Consensus pattern (26 bp):
ATGCAAGGCACATGGGGGCTGGTCAT
Found at i:430939 original size:23 final size:24
Alignment explanation
Indices: 430888--430941 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
430878 CTTTCTTTCT
*
430888 TTTTATTCTTTTGGAGTGCTCTCA
1 TTTTCTTCTTTTGGAGTGCTCTCA
* * *
430912 ATTTCTTCTTTT-GAGTGCTTTTA
1 TTTTCTTCTTTTGGAGTGCTCTCA
430935 TTTTCTT
1 TTTTCTT
430942 TGCTGATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.11, C:0.15, G:0.13, T:0.61
Consensus pattern (24 bp):
TTTTCTTCTTTTGGAGTGCTCTCA
Found at i:431003 original size:2 final size:2
Alignment explanation
Indices: 430996--431022 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
430986 CTTCTTTTTG
430996 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
431023 TGTTATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:435388 original size:13 final size:12
Alignment explanation
Indices: 435369--435454 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
435359 ATATAGGCGT
435369 GATATGGTGATG
1 GATATGGTGATG
435381 GAATATGGTGAT-
1 G-ATATGGTGATG
*
435393 GATATAGGCG-T-
1 GATAT-GGTGATG
435404 GATAATGGTGATG
1 GAT-ATGGTGATG
435417 GACTATGGTGAT-
1 GA-TATGGTGATG
*
435429 GATATAGGCG-T-
1 GATAT-GGTGATG
435440 GATAATGGTGATG
1 GAT-ATGGTGATG
435453 GA
1 GA
435455 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:435424 original size:36 final size:36
Alignment explanation
Indices: 435351--435455 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
435341 ATTTATAAGT
* *
435351 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
435386 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
435422 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
435456 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:441127 original size:36 final size:36
Alignment explanation
Indices: 441054--441158 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
441044 ATTTATAAGT
* * *
441054 TGGTGATAATATCGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
441089 TGGTGATGATATAGGCGTGATAATGATGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
441125 TGGTGATGATATAGGCATGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
441159 ATATTGTATC
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 19 0.30
36 44 0.70
ACGTcount: A:0.30, C:0.06, G:0.34, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:443807 original size:9 final size:10
Alignment explanation
Indices: 443794--443820 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
443784 AAAAAACAAA
443794 AAAAAAAGGC
1 AAAAAAAGGC
443804 AAAAAAAGGC
1 AAAAAAAGGC
443814 AAAAAAA
1 AAAAAAA
443821 AAATAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAAGGC
Found at i:443816 original size:23 final size:21
Alignment explanation
Indices: 443782--443823 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
443772 TTTTTTTTTT
443782 CAAAAAAACAAAAAAAAAAGG
1 CAAAAAAACAAAAAAAAAAGG
443803 CAAAAAAAGGCAAAAAAAAAA
1 CAAAAAAA--CAAAAAAAAAA
443824 TAAAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.81, C:0.10, G:0.10, T:0.00
Consensus pattern (21 bp):
CAAAAAAACAAAAAAAAAAGG
Found at i:443830 original size:23 final size:22
Alignment explanation
Indices: 443783--443842 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
443773 TTTTTTTTTC
*
443783 AAAAAAA-CAAAAAAAAAAGGCA
1 AAAAAAAGCAAAAAAAAAA-GAA
* *
443805 AAAAAAGGCAAAAAAAAAATAA
1 AAAAAAAGCAAAAAAAAAAGAA
* *
443827 AAAAAGAGCCAAAAAA
1 AAAAAAAGCAAAAAAA
443843 GCCAAAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 20 0.65
23 11 0.35
ACGTcount: A:0.80, C:0.08, G:0.10, T:0.02
Consensus pattern (22 bp):
AAAAAAAGCAAAAAAAAAAGAA
Found at i:443861 original size:32 final size:30
Alignment explanation
Indices: 443784--443849 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 30
443774 TTTTTTTTCA
*
443784 AAAAAACAAAAAAAAAAGGCAAAAAAAGGC
1 AAAAAACAAAAAAAAAAGGCAAAAAAAGCC
* *
443814 AAAAAAAAAATAAAAAAAGAGCCAAAAAAGCC
1 AAAAAACAAA-AAAAAAAG-GCAAAAAAAGCC
443846 AAAA
1 AAAA
443850 TTTCAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 9 0.29
31 8 0.26
32 14 0.45
ACGTcount: A:0.77, C:0.11, G:0.11, T:0.02
Consensus pattern (30 bp):
AAAAAACAAAAAAAAAAGGCAAAAAAAGCC
Found at i:453458 original size:32 final size:33
Alignment explanation
Indices: 453397--453463 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
453387 ACAAAATTAA
* *
453397 AAGAAAGAAATGATTAAAATGGAATATGGA-AG
1 AAGAAAGAAATGATTAAAATAGAAAATGGATAG
453429 AAGAAAGGAAATGA-TAAGAA-AGAAAATGGATAG
1 AAGAAA-GAAATGATTAA-AATAGAAAATGGATAG
453462 AA
1 AA
453464 ATGTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.60, C:0.00, G:0.25, T:0.15
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAATAGAAAATGGATAG
Found at i:453512 original size:22 final size:22
Alignment explanation
Indices: 453487--453538 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
453477 TGGGCTGCGG
*
453487 AAGTGTTGAATAAATCTCCTTC
1 AAGTGATGAATAAATCTCCTTC
453509 AAGTGATGAATAAATCTCCTTC
1 AAGTGATGAATAAATCTCCTTC
453531 AAGTGATG
1 AAGTGATG
453539 TTGACTTCGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (22 bp):
AAGTGATGAATAAATCTCCTTC
Found at i:459965 original size:35 final size:35
Alignment explanation
Indices: 459862--459965 Score: 172
Period size: 36 Copynumber: 2.9 Consensus size: 35
459852 ATTTATAAGT
* * *
459862 TGGTGATAATATAGGCGTGATATGGTGAAGGAATA
1 TGGTGATGATATAGGCGTGATATGGTGATGGACTA
459897 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
459933 TGGTGATGATATAGGCGTGATATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATATGGTGATGGAC
459966 AGATTGTATC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 32 0.49
36 33 0.51
ACGTcount: A:0.29, C:0.05, G:0.37, T:0.30
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGTGATGGACTA
Found at i:466667 original size:13 final size:13
Alignment explanation
Indices: 466649--466708 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
466639 TATAGGCGTG
466649 ATATGGTGATGGA
1 ATATGGTGATGGA
466662 ATATGGTGAT-G-
1 ATATGGTGATGGA
* *
466673 ATATAGG-CATGGT
1 ATAT-GGTGATGGA
466686 A-ATGGTGATGGA
1 ATATGGTGATGGA
*
466698 CTATGGTGATG
1 ATATGGTGATG
466709 ATATAGGCGT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
11 8 0.21
12 10 0.26
13 20 0.53
ACGTcount: A:0.28, C:0.03, G:0.37, T:0.32
Consensus pattern (13 bp):
ATATGGTGATGGA
Found at i:466703 original size:36 final size:36
Alignment explanation
Indices: 466630--466734 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
466620 ATTTATAAGT
* *
466630 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
* *
466665 TGGTGATGATATAGGCATGGTAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
466701 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
466735 AGATTGTATC
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 18 0.29
36 45 0.71
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:469060 original size:15 final size:16
Alignment explanation
Indices: 469029--469065 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
469019 CTTTATTATC
469029 TTATTTCATCTTCTGT
1 TTATTTCATCTTCTGT
*
469045 TTATTT-ATCTTTTGT
1 TTATTTCATCTTCTGT
469060 TTATTT
1 TTATTT
469066 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTCTGT
Found at i:469434 original size:13 final size:12
Alignment explanation
Indices: 469416--469475 Score: 66
Period size: 12 Copynumber: 4.9 Consensus size: 12
469406 CTATTTTTTT
469416 CAAAAACAAAAAA
1 CAAAAA-AAAAAA
*
469429 CAAAAAAAAAAG
1 CAAAAAAAAAAA
469441 CAAAAAAAAAAA
1 CAAAAAAAAAAA
****
469453 GGGCAAAAAAAA
1 CAAAAAAAAAAA
469465 CAAAAAAAAAA
1 CAAAAAAAAAA
469476 GCCAAAAAAG
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
12 31 0.84
13 6 0.16
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:469448 original size:15 final size:15
Alignment explanation
Indices: 469430--469470 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
469420 AACAAAAAAC
469430 AAAAAAAAAAGCAAA
1 AAAAAAAAAAGCAAA
**
469445 AAAAAAAAGGGCAAA
1 AAAAAAAAAAGCAAA
469460 AAAAACAAAAA
1 AAAAA-AAAAA
469471 AAAAAGCCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGCAAA
Found at i:469481 original size:13 final size:13
Alignment explanation
Indices: 469416--469484 Score: 58
Period size: 13 Copynumber: 5.5 Consensus size: 13
469406 CTATTTTTTT
*
469416 CAAAAACAAAAA-A
1 CAAAAA-AAAAAGC
469429 CAAAAAAAAAAGC
1 CAAAAAAAAAAGC
* *
469442 AAAAAAAAAAAGGG
1 CAAAAAAAAAA-GC
469456 C--AAAAAAAA--
1 CAAAAAAAAAAGC
469465 CAAAAAAAAAAGC
1 CAAAAAAAAAAGC
469478 CAAAAAA
1 CAAAAAA
469485 GCCAAAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
9 1 0.02
11 8 0.17
12 13 0.28
13 23 0.50
14 1 0.02
ACGTcount: A:0.81, C:0.12, G:0.07, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAGC
Found at i:469490 original size:22 final size:23
Alignment explanation
Indices: 469434--469491 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
469424 AAAAACAAAA
* *
469434 AAAAAAGCAAAAAAAAAAAGGGC
1 AAAAAAGCCAAAAAAAAAAGGCC
**
469457 AAAAAAAACAAAAAAAAAA-GCC
1 AAAAAAGCCAAAAAAAAAAGGCC
469479 AAAAAAGCCAAAA
1 AAAAAAGCCAAAA
469492 TTTAAAAACA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
22 13 0.45
23 16 0.55
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (23 bp):
AAAAAAGCCAAAAAAAAAAGGCC
Found at i:476548 original size:13 final size:11
Alignment explanation
Indices: 476507--476591 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
476497 ACAATTTATC
476507 CATCACCATTAT
1 CATCACCA-TAT
*
476519 CA-CGCCTATAT
1 CATCACC-ATAT
476530 CATCACCATAGT
1 CATCACCATA-T
476542 CCATCACCATTAT
1 -CATCACCA-TAT
*
476555 CA-CGCCTATAT
1 CATCACC-ATAT
476566 CATCACCATATT
1 CATCACCATA-T
476578 CCATCACCATAT
1 -CATCACCATAT
476590 CA
1 CA
476592 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:476552 original size:36 final size:36
Alignment explanation
Indices: 476505--476608 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
476495 ATACAATTTA
476505 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
476541 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
476577 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
476609 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:476648 original size:18 final size:18
Alignment explanation
Indices: 476625--476669 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
476615 AAATTTCCAT
476625 TTCTTCATCTTTGAATTA
1 TTCTTCATCTTTGAATTA
476643 TTCTTCATCTTTGAATTA
1 TTCTTCATCTTTGAATTA
*
476661 TCCTTCATC
1 TTCTTCATC
476670 CTCAACAAGG
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:0.20, C:0.22, G:0.04, T:0.53
Consensus pattern (18 bp):
TTCTTCATCTTTGAATTA
Found at i:477051 original size:19 final size:19
Alignment explanation
Indices: 477015--477052 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
477005 AACAAAAAGC
*
477015 AACAAGAAAGAAGAAAAAA
1 AACAAGAAAGAAAAAAAAA
477034 AACAA-AAAGAAAAGAAAAA
1 AACAAGAAAGAAAA-AAAAA
477053 GACTCCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (19 bp):
AACAAGAAAGAAAAAAAAA
Found at i:489530 original size:13 final size:11
Alignment explanation
Indices: 489489--489573 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
489479 ACAATTTATC
489489 CATCACCATTAT
1 CATCACCA-TAT
*
489501 CA-CGCCTATAT
1 CATCACC-ATAT
489512 CATCACCATAGT
1 CATCACCATA-T
489524 CCATCACCATTAT
1 -CATCACCA-TAT
*
489537 CA-CGCCTATAT
1 CATCACC-ATAT
489548 CATCACCATATT
1 CATCACCATA-T
489560 CCATCACCATAT
1 -CATCACCATAT
489572 CA
1 CA
489574 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:489534 original size:36 final size:36
Alignment explanation
Indices: 489487--489590 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
489477 ATACAATTTA
489487 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
489523 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
489559 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
489591 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:489632 original size:18 final size:18
Alignment explanation
Indices: 489609--489651 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
489599 ATTTCCATTT
489609 CTTCATCTTTGAATTATC
1 CTTCATCTTTGAATTATC
489627 CTTCATCTTTGAATTATC
1 CTTCATCTTTGAATTATC
489645 CTTCATC
1 CTTCATC
489652 CTTAATAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.21, C:0.26, G:0.05, T:0.49
Consensus pattern (18 bp):
CTTCATCTTTGAATTATC
Found at i:493984 original size:19 final size:19
Alignment explanation
Indices: 493960--494009 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
493950 CGGCCAAGAG
* **
493960 CATGTATCTTCATTTAAAT
1 CATGTATTTTCATCAAAAT
493979 CATGTATTTTCATCAAAAT
1 CATGTATTTTCATCAAAAT
493998 CATGTATTTTCA
1 CATGTATTTTCA
494010 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46
Consensus pattern (19 bp):
CATGTATTTTCATCAAAAT
Found at i:494392 original size:13 final size:11
Alignment explanation
Indices: 494351--494435 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
494341 ACAATCTGTC
494351 CATCACCATTAT
1 CATCACCA-TAT
*
494363 CA-CGCCTATAT
1 CATCACC-ATAT
494374 CATCACCATAGT
1 CATCACCATA-T
494386 CCATCACCATTAT
1 -CATCACCA-TAT
*
494399 CA-CGCCTATAT
1 CATCACC-ATAT
494410 CATCACCATATT
1 CATCACCATA-T
494422 CCATCACCATAT
1 -CATCACCATAT
494434 CA
1 CA
494436 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:494395 original size:36 final size:36
Alignment explanation
Indices: 494348--494452 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
494338 GATACAATCT
494348 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
494384 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
494420 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
494453 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:495089 original size:15 final size:15
Alignment explanation
Indices: 495069--495120 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
495059 GTAAGTTATC
495069 TTCATTTTTTTTCAT
1 TTCATTTTTTTTCAT
495084 TTCATTTCTTTATTC-T
1 TTCATTT-TTT-TTCAT
495100 TTCATCTTTTTTT-AT
1 TTCAT-TTTTTTTCAT
495115 TTCATT
1 TTCATT
495121 GCCATATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.03
15 15 0.45
16 12 0.36
17 5 0.15
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.71
Consensus pattern (15 bp):
TTCATTTTTTTTCAT
Found at i:495928 original size:19 final size:20
Alignment explanation
Indices: 495878--495920 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
495868 GAAACTCCTT
*
495878 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
495898 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
495917 TGAA
1 TGAA
495921 GATGCATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:500003 original size:19 final size:20
Alignment explanation
Indices: 499962--500012 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
499952 GAAACCCCTT
*
499962 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
499982 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
500001 TGAAGATACATG
1 TGAAAATACATG
500013 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:504301 original size:23 final size:23
Alignment explanation
Indices: 504273--504446 Score: 98
Period size: 23 Copynumber: 7.3 Consensus size: 23
504263 ACAATCTGTC
*
504273 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCACC-ATAT
504296 CATCACCA-TAGTCCATCACCATTAT
1 CATCACCATTA-T-CATCACCA-TAT
504321 CA-CACC-TATATCATCACCATATT
1 CATCACCAT-TATCATCACCATA-T
*
504344 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
504368 CATCACCA-TAGTCCATCACCAT-T
1 CATCACCATTA-T-CATCACCATAT
*
504391 -ATCACGCCTATATCATCACCATATT
1 CATCAC-CAT-TATCATCACCATA-T
*
504416 CCATCACCA-TATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
*
504439 TATCACCA
1 CATCACCA
504447 ACTTATAAAT
Statistics
Matches: 122, Mismatches: 7, Indels: 45
0.70 0.04 0.26
Matches are distributed among these distances:
22 18 0.15
23 42 0.34
24 27 0.22
25 28 0.23
26 2 0.02
27 5 0.04
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (23 bp):
CATCACCATTATCATCACCATAT
Found at i:504314 original size:13 final size:11
Alignment explanation
Indices: 504273--504429 Score: 115
Period size: 11 Copynumber: 13.2 Consensus size: 11
504263 ACAATCTGTC
504273 CATCACCATTAT
1 CATCACCA-TAT
*
504285 CA-CGCCTATAT
1 CATCACC-ATAT
504296 CATCACCATAGT
1 CATCACCATA-T
504308 CCATCACCATTAT
1 -CATCACCA-TAT
504321 CA-CACCTATAT
1 CATCACC-ATAT
504332 CATCACCATATT
1 CATCACCATA-T
504344 CCATCACCATTAT
1 -CATCACCA-TAT
*
504357 CA-CGCCTATAT
1 CATCACC-ATAT
504368 CATCACCATAGT
1 CATCACCATA-T
504380 CCATCACCATTAT
1 -CATCACCA-TAT
*
504393 CA-CGCCTATAT
1 CATCACC-ATAT
504404 CATCACCATATT
1 CATCACCATA-T
504416 CCATCACCATAT
1 -CATCACCATAT
504428 CA
1 CA
504430 CGCCTATATT
Statistics
Matches: 120, Mismatches: 6, Indels: 39
0.73 0.04 0.24
Matches are distributed among these distances:
11 47 0.39
12 30 0.25
13 37 0.31
14 6 0.05
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:504317 original size:36 final size:36
Alignment explanation
Indices: 504270--504446 Score: 311
Period size: 36 Copynumber: 4.9 Consensus size: 36
504260 GATACAATCT
504270 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
504306 GTCCATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
504342 TTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
504378 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
504414 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
504447 ACTTATAAAT
Statistics
Matches: 135, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
35 21 0.16
36 114 0.84
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:508760 original size:33 final size:33
Alignment explanation
Indices: 508681--508784 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
508671 ATACAATCTG
* *
508681 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
508717 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
508750 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
508783 TC
1 TC
508785 ATTCATCAAC
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:509193 original size:17 final size:18
Alignment explanation
Indices: 509171--509218 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
509161 TGGAGTGCAA
509171 AAGAAAGAAAA-AAAAAG
1 AAGAAAGAAAAGAAAAAG
*
509188 AAGAAAAGCAAAAGCAAAAG
1 AAG-AAAG-AAAAGAAAAAG
509208 AA-AAAGAAAAG
1 AAGAAAGAAAAG
509219 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:509206 original size:12 final size:11
Alignment explanation
Indices: 509169--509218 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
509159 TTTGGAGTGC
509169 AAAAGAAAGAA-
1 AAAAGAAA-AAG
509180 AAAA-AAAGAAG
1 AAAAGAAA-AAG
*
509191 AAAAGCAAAAG
1 AAAAGAAAAAG
509202 CAAAAGAAAAAG
1 -AAAAGAAAAAG
509214 AAAAG
1 AAAAG
509219 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:512785 original size:33 final size:33
Alignment explanation
Indices: 512706--512809 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
512696 ATACAATCTG
* *
512706 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
512742 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
512775 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
512808 TC
1 TC
512810 ATTCATCAAC
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:521813 original size:25 final size:26
Alignment explanation
Indices: 521776--521834 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 26
521766 TTCTTTTTTC
*
521776 TTTTTTTTAAATTTTCGGAATT-TGT
1 TTTTTTTTAAATTTTCGGAATTCTCT
* *
521801 TTTTTTTTTAATTTTTGGAATTCTCT
1 TTTTTTTTAAATTTTCGGAATTCTCT
521827 TTTTTTTT
1 TTTTTTTT
521835 CAAGATGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 20 0.67
26 10 0.33
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.71
Consensus pattern (26 bp):
TTTTTTTTAAATTTTCGGAATTCTCT
Found at i:521816 original size:26 final size:26
Alignment explanation
Indices: 521776--521834 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
521766 TTCTTTTTTC
*
521776 TTTTTTTTAAATTTTCGGAATT-TGTT
1 TTTTTTTTAAATTTT-GGAATTCTCTT
*
521802 TTTTTTTTAATTTTTGGAATTCTCTT
1 TTTTTTTTAAATTTTGGAATTCTCTT
521828 TTTTTTT
1 TTTTTTT
521835 CAAGATGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 6 0.20
26 24 0.80
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.71
Consensus pattern (26 bp):
TTTTTTTTAAATTTTGGAATTCTCTT
Found at i:522637 original size:69 final size:69
Alignment explanation
Indices: 522554--522703 Score: 300
Period size: 69 Copynumber: 2.2 Consensus size: 69
522544 CCAAATCATG
522554 CACATGGGTGTTGTTTTGTTCCCAATGGTGAGTTACACTCCTTCACGTGATTTGCTGGCCATGTG
1 CACATGGGTGTTGTTTTGTTCCCAATGGTGAGTTACACTCCTTCACGTGATTTGCTGGCCATGTG
522619 GATT
66 GATT
522623 CACATGGGTGTTGTTTTGTTCCCAATGGTGAGTTACACTCCTTCACGTGATTTGCTGGCCATGTG
1 CACATGGGTGTTGTTTTGTTCCCAATGGTGAGTTACACTCCTTCACGTGATTTGCTGGCCATGTG
522688 GATT
66 GATT
522692 CACATGGGTGTT
1 CACATGGGTGTT
522704 CTTAGAAAAA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 81 1.00
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (69 bp):
CACATGGGTGTTGTTTTGTTCCCAATGGTGAGTTACACTCCTTCACGTGATTTGCTGGCCATGTG
GATT
Found at i:527298 original size:13 final size:11
Alignment explanation
Indices: 527257--527341 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
527247 ACAATCTGTC
527257 CATCACCATTAT
1 CATCACCA-TAT
*
527269 CA-CGCCTATAT
1 CATCACC-ATAT
527280 CATCACCATAGT
1 CATCACCATA-T
527292 CCATCACCATTAT
1 -CATCACCA-TAT
*
527305 CA-CGCCTATAT
1 CATCACC-ATAT
527316 CATCACCATATT
1 CATCACCATA-T
527328 CCATCACCATAT
1 -CATCACCATAT
527340 CA
1 CA
527342 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:527301 original size:36 final size:36
Alignment explanation
Indices: 527254--527358 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
527244 GATACAATCT
527254 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
527290 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
527326 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
527359 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:527997 original size:17 final size:16
Alignment explanation
Indices: 527970--528022 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
527960 GAGTTGTAAG
527970 TTATC-TTCATTTTTT
1 TTATCTTTCATTTTTT
*
527985 TTATCATTTCA-TTTCT
1 TTATC-TTTCATTTTTT
528001 TTATTCTTTCATCTTTTT
1 TTA-TCTTTCAT-TTTTT
528019 TTAT
1 TTAT
528023 TTCATTGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 7 0.23
18 7 0.23
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATCTTTCATTTTTT
Found at i:528827 original size:19 final size:20
Alignment explanation
Indices: 528786--528836 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
528776 GAAACTCCTT
*
528786 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
528806 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
528825 TGAAGATACATG
1 TGAAAATACATG
528837 CTCTTGGCCA
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:532912 original size:19 final size:20
Alignment explanation
Indices: 532871--532921 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
532861 GAAACCCCTT
*
532871 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
532891 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
532910 TGAAGATACATG
1 TGAAAATACATG
532922 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:537207 original size:23 final size:23
Alignment explanation
Indices: 537179--537352 Score: 98
Period size: 23 Copynumber: 7.3 Consensus size: 23
537169 ACAATCTGTC
*
537179 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCACC-ATAT
537202 CATCACCA-TAGTCCATCACCATTAT
1 CATCACCATTA-T-CATCACCA-TAT
537227 CA-CACC-TATATCATCACCATATT
1 CATCACCAT-TATCATCACCATA-T
*
537250 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
537274 CATCACCA-TAGTCCATCACCAT-T
1 CATCACCATTA-T-CATCACCATAT
*
537297 -ATCACGCCTATATCATCACCATATT
1 CATCAC-CAT-TATCATCACCATA-T
*
537322 CCATCACCA-TATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
*
537345 TATCACCA
1 CATCACCA
537353 ACTTATAAAT
Statistics
Matches: 122, Mismatches: 7, Indels: 45
0.70 0.04 0.26
Matches are distributed among these distances:
22 18 0.15
23 42 0.34
24 27 0.22
25 28 0.23
26 2 0.02
27 5 0.04
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (23 bp):
CATCACCATTATCATCACCATAT
Found at i:537220 original size:13 final size:11
Alignment explanation
Indices: 537179--537335 Score: 115
Period size: 11 Copynumber: 13.2 Consensus size: 11
537169 ACAATCTGTC
537179 CATCACCATTAT
1 CATCACCA-TAT
*
537191 CA-CGCCTATAT
1 CATCACC-ATAT
537202 CATCACCATAGT
1 CATCACCATA-T
537214 CCATCACCATTAT
1 -CATCACCA-TAT
537227 CA-CACCTATAT
1 CATCACC-ATAT
537238 CATCACCATATT
1 CATCACCATA-T
537250 CCATCACCATTAT
1 -CATCACCA-TAT
*
537263 CA-CGCCTATAT
1 CATCACC-ATAT
537274 CATCACCATAGT
1 CATCACCATA-T
537286 CCATCACCATTAT
1 -CATCACCA-TAT
*
537299 CA-CGCCTATAT
1 CATCACC-ATAT
537310 CATCACCATATT
1 CATCACCATA-T
537322 CCATCACCATAT
1 -CATCACCATAT
537334 CA
1 CA
537336 CGCCTATATT
Statistics
Matches: 120, Mismatches: 6, Indels: 39
0.73 0.04 0.24
Matches are distributed among these distances:
11 47 0.39
12 30 0.25
13 37 0.31
14 6 0.05
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:537223 original size:36 final size:36
Alignment explanation
Indices: 537176--537352 Score: 311
Period size: 36 Copynumber: 4.9 Consensus size: 36
537166 GATACAATCT
537176 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
537212 GTCCATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
537248 TTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
537284 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
537320 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
537353 ACTTATAAAT
Statistics
Matches: 135, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
35 21 0.16
36 114 0.84
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:537551 original size:15 final size:16
Alignment explanation
Indices: 537531--537562 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
537521 TTCTATTTAC
537531 TTATCATATT-CTTAA
1 TTATCATATTACTTAA
537546 TTATCATATTACTTAA
1 TTATCATATTACTTAA
537562 T
1 T
537563 GCAGATTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATCATATTACTTAA
Done.