Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 51
Found at i:5699003 original size:19 final size:20
Alignment explanation
Indices: 5698979--5699027 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
5698969 TCGTTTGCAA
5698979 TTTTTTGAAATTTTGTTT-T
1 TTTTTTGAAATTTTGTTTGT
*** *
5698998 TTTTTTGCCTTTTTTTTTGT
1 TTTTTTGAAATTTTGTTTGT
5699018 TTTTTTGAAA
1 TTTTTTGAAA
5699028 AAAAATAACA
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.12, C:0.04, G:0.10, T:0.73
Consensus pattern (20 bp):
TTTTTTGAAATTTTGTTTGT
Found at i:5699021 original size:11 final size:11
Alignment explanation
Indices: 5698989--5699023 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
5698979 TTTTTTGAAA
5698989 TTTTGTTTTTT
1 TTTTGTTTTTT
*
5699000 TTTTGCCTTTTT
1 TTTTG-TTTTTT
5699012 TTTTGTTTTTT
1 TTTTGTTTTTT
5699023 T
1 T
5699024 GAAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.86
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:5704175 original size:35 final size:36
Alignment explanation
Indices: 5704123--5704190 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
5704113 ATTTATAAGT
* *
5704123 TGGTGATAATATGGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATAGTGATGGAATA
*
5704158 TGGTGATGATATAGGCGTGATAATAGTGATGGA
1 TGGTGATAATATAGGCGTGATAATAGTGATGGA
5704191 CAGATTGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 19 0.66
36 10 0.34
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATAGTGATGGAATA
Found at i:5705903 original size:6 final size:6
Alignment explanation
Indices: 5705892--5705931 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
5705882 GTGCTGCAAC
*
5705892 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAA
5705932 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:5709344 original size:19 final size:20
Alignment explanation
Indices: 5709320--5709366 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
5709310 CAAGAGCATT
*
5709320 TATTTTCATT-AAAATTATG
1 TATTTTCATTAAAAATCATG
5709339 TATTTTCATTAAAAATCATG
1 TATTTTCATTAAAAATCATG
*
5709359 TGTTTTCA
1 TATTTTCA
5709367 AAGGGGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (20 bp):
TATTTTCATTAAAAATCATG
Found at i:5711061 original size:19 final size:21
Alignment explanation
Indices: 5711037--5711088 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
5711027 CGGCCAAGAG
*
5711037 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
5711056 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
5711077 CATGTATTTTCA
1 CATGTATTTTCA
5711089 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:5711933 original size:6 final size:6
Alignment explanation
Indices: 5711922--5711961 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
5711912 GTGCAGCAGC
*
5711922 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAA
5711962 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:5712016 original size:19 final size:19
Alignment explanation
Indices: 5711994--5712042 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
5711984 TGCAAAAAGA
5711994 AAAGAAAAGAAGAAAATTC
1 AAAGAAAAGAAGAAAATTC
5712013 AAAGAAAAGAAGAAAATTC
1 AAAGAAAAGAAGAAAATTC
5712032 AAAGAAAAGAA
1 AAAGAAAAGAA
5712043 AAAGAGAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.71, C:0.04, G:0.16, T:0.08
Consensus pattern (19 bp):
AAAGAAAAGAAGAAAATTC
Found at i:5712050 original size:24 final size:23
Alignment explanation
Indices: 5711989--5712050 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 23
5711979 TGGAGTGCAA
5711989 AAAGAAAAGAAAAGAAGAAAATTC
1 AAAGAAAAGAAAAG-AGAAAATTC
5712013 AAAGAAAAG---A-AGAAAATTC
1 AAAGAAAAGAAAAGAGAAAATTC
5712032 AAAGAAAAGAAAAAGAGAA
1 AAAGAAAAG-AAAAGAGAA
5712051 GAAAAAGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
19 18 0.55
21 1 0.03
23 1 0.03
24 13 0.39
ACGTcount: A:0.73, C:0.03, G:0.18, T:0.06
Consensus pattern (23 bp):
AAAGAAAAGAAAAGAGAAAATTC
Found at i:5714713 original size:7 final size:6
Alignment explanation
Indices: 5714697--5714735 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
5714687 GTGCTGCAAC
5714697 AAAAAG AAAAAG AAAAAAG AAAAAG -AAAAG -AAAAG AAAA
1 AAAAAG AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAAA
5714736 GACTGCTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 10 0.32
6 15 0.48
7 6 0.19
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:5714715 original size:13 final size:13
Alignment explanation
Indices: 5714697--5714725 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5714687 GTGCTGCAAC
5714697 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
5714710 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
5714723 AAA
1 AAA
5714726 GAAAAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:5714969 original size:16 final size:16
Alignment explanation
Indices: 5714935--5714983 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
5714925 GTAAGTTATC
* * *
5714935 TTCACTTTCTTAGTAT
1 TTCATTTTCTTATTCT
5714951 TTCATTTTCTTATTCT
1 TTCATTTTCTTATTCT
5714967 TTCATCTATTCTTATTC
1 TTCAT-T-TTCTTATTC
5714984 CATTACCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.61
Consensus pattern (16 bp):
TTCATTTTCTTATTCT
Found at i:5717498 original size:16 final size:16
Alignment explanation
Indices: 5717464--5717512 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
5717454 GTAAGTTGTC
* * *
5717464 TTCACTTTCTTAGTAT
1 TTCATTTTCTTATTCT
5717480 TTCATTTTCTTATTCT
1 TTCATTTTCTTATTCT
5717496 TTCATCTATTCTTATTC
1 TTCAT-T-TTCTTATTC
5717513 CATTACCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.61
Consensus pattern (16 bp):
TTCATTTTCTTATTCT
Found at i:5720480 original size:22 final size:22
Alignment explanation
Indices: 5720454--5720507 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
5720444 GCAAGAAGAC
5720454 CCATGTGCATTCATGTAC-ACTG
1 CCATGTGCATTCATGTACGA-TG
5720476 CCATGTGCATTCATGTACGATG
1 CCATGTGCATTCATGTACGATG
5720498 CCATGTGCAT
1 CCATGTGCAT
5720508 CATTCAAGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.31
Consensus pattern (22 bp):
CCATGTGCATTCATGTACGATG
Found at i:5721496 original size:6 final size:6
Alignment explanation
Indices: 5721485--5721524 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
5721475 GTGCTGCAAT
*
5721485 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAA
5721525 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:5721758 original size:16 final size:16
Alignment explanation
Indices: 5721724--5721772 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
5721714 GTAAGTTATC
* * *
5721724 TTCACTTTCTTACTAT
1 TTCATTTTCTTATTCT
5721740 TTCATTTTCTTATTCT
1 TTCATTTTCTTATTCT
5721756 TTCATCTATTCTTATTC
1 TTCAT-T-TTCTTATTC
5721773 CATTACCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCATTTTCTTATTCT
Found at i:5722250 original size:15 final size:15
Alignment explanation
Indices: 5722230--5722273 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
5722220 ATTAAGAAAG
*
5722230 GAAATGGAAAGGATT
1 GAAATGGAAAGAATT
*
5722245 GAAATGGAAATAATT
1 GAAATGGAAAGAATT
*
5722260 GAAATGGATAGAAT
1 GAAATGGAAAGAAT
5722274 AGTTATCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (15 bp):
GAAATGGAAAGAATT
Found at i:5722488 original size:36 final size:36
Alignment explanation
Indices: 5722415--5722555 Score: 230
Period size: 36 Copynumber: 3.9 Consensus size: 36
5722405 ATTTATAAGT
* * *
5722415 TGGTGATAATATGGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
5722450 TGGTGATGATATAGGCGTGATAATGGTGATGGTCTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
5722486 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
5722522 TGGTGATGATATAGGCATGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
5722556 AGATTGTATC
Statistics
Matches: 99, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.19
36 80 0.81
ACGTcount: A:0.28, C:0.05, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:5722526 original size:13 final size:11
Alignment explanation
Indices: 5722432--5722552 Score: 77
Period size: 11 Copynumber: 10.2 Consensus size: 11
5722422 AATATGGGCG
5722432 TGATATGGTGA
1 TGATATGGTGA
5722443 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
5722456 TGATATAGGCG-
1 TGATAT-GGTGA
5722467 TGATAATGGTGA
1 TGAT-ATGGTGA
*
5722479 TGGTCTATGGTGA
1 T-G-ATATGGTGA
*
5722492 TGATATAGGCG-
1 TGATAT-GGTGA
5722503 TGATAATGGTGA
1 TGAT-ATGGTGA
5722515 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
5722528 TGATATAGG-CA
1 TGATAT-GGTGA
5722539 TGATAATGGTGA
1 TGAT-ATGGTGA
5722551 TG
1 TG
5722553 GACAGATTGT
Statistics
Matches: 87, Mismatches: 8, Indels: 29
0.70 0.06 0.23
Matches are distributed among these distances:
11 32 0.37
12 24 0.28
13 29 0.33
14 2 0.02
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.32
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:5730826 original size:13 final size:12
Alignment explanation
Indices: 5730807--5730928 Score: 64
Period size: 13 Copynumber: 10.2 Consensus size: 12
5730797 ATATGGGCGT
5730807 GATATGGTGATG
1 GATATGGTGATG
5730819 GAATATGGTGAT-
1 G-ATATGGTGATG
*
5730831 GATATAGGCG-T-
1 GATAT-GGTGATG
5730842 GATAATGGTGATG
1 GAT-ATGGTGATG
5730855 GACTATGGTGAT-
1 GA-TATGGTGATG
*
5730867 GATATAGGCG-T-
1 GATAT-GGTGATG
*
5730878 GATAATGGTGATA
1 GAT-ATGGTGATG
5730891 GACTATGGTGAT-
1 GA-TATGGTGATG
*
5730903 GATATAGGCG-T-
1 GATAT-GGTGATG
5730914 GATAATGGTGATG
1 GAT-ATGGTGATG
5730927 GA
1 GA
5730929 CAGATTGTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 29
0.72 0.05 0.23
Matches are distributed among these distances:
11 31 0.35
12 24 0.27
13 32 0.36
14 2 0.02
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:5730851 original size:23 final size:23
Alignment explanation
Indices: 5730823--5730926 Score: 74
Period size: 23 Copynumber: 4.4 Consensus size: 23
5730813 GTGATGGAAT
5730823 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
*
5730846 ATGGTGATGGACTAT-GGTGATGAT-
1 ATGGTGAT-GA-TATAGGCG-TGATA
* *
5730870 ATAGGCG-TGATA-ATG-GTGATAGA
1 AT-GGTGATGATATAGGCGTGAT--A
5730893 CTATGGTGATGATATAGGCGTGATA
1 --ATGGTGATGATATAGGCGTGATA
5730918 ATGGTGATG
1 ATGGTGATG
5730927 GACAGATTGT
Statistics
Matches: 63, Mismatches: 5, Indels: 26
0.67 0.05 0.28
Matches are distributed among these distances:
20 4 0.06
21 1 0.02
22 3 0.05
23 19 0.30
24 11 0.17
25 18 0.29
26 2 0.03
27 5 0.08
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.31
Consensus pattern (23 bp):
ATGGTGATGATATAGGCGTGATA
Found at i:5730862 original size:36 final size:36
Alignment explanation
Indices: 5730789--5730929 Score: 239
Period size: 36 Copynumber: 3.9 Consensus size: 36
5730779 ATTTATAAGT
* * *
5730789 TGGTGATAATATGGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
5730824 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
5730860 TGGTGATGATATAGGCGTGATAATGGTGATAGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
5730896 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
5730930 AGATTGTATC
Statistics
Matches: 100, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 19 0.19
36 81 0.81
ACGTcount: A:0.28, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:5731318 original size:19 final size:20
Alignment explanation
Indices: 5731271--5731321 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
5731261 GAAACCCCTT
**
5731271 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
5731291 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
5731310 TGAAGATACATG
1 TGAAAATACATG
5731322 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:5739925 original size:26 final size:27
Alignment explanation
Indices: 5739881--5739937 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
5739871 AAACATGCAA
* *
5739881 AAAGAAAGTAAAAGGAAAGATAAAATC
1 AAAGAAAGTAAAAGCAAAGATAAAAAC
*
5739908 AAAGAAAG-AAAAGCAAAGTTAAAAAC
1 AAAGAAAGTAAAAGCAAAGATAAAAAC
5739934 AAAG
1 AAAG
5739938 GTTGTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 19 0.70
27 8 0.30
ACGTcount: A:0.68, C:0.05, G:0.18, T:0.09
Consensus pattern (27 bp):
AAAGAAAGTAAAAGCAAAGATAAAAAC
Found at i:5742988 original size:42 final size:42
Alignment explanation
Indices: 5742942--5743077 Score: 263
Period size: 42 Copynumber: 3.2 Consensus size: 42
5742932 TACCATTTCC
5742942 ATACTTCTTTCTTCCATCACCATAACATTGTTCCATATACAA
1 ATACTTCTTTCTTCCATCACCATAACATTGTTCCATATACAA
*
5742984 ATACTTCTTTCTTCGATCACCATAACATTGTTCCATATACAA
1 ATACTTCTTTCTTCCATCACCATAACATTGTTCCATATACAA
5743026 ATACTTCTTTCTTCCATCACCATAACATTGTTCCATATACAA
1 ATACTTCTTTCTTCCATCACCATAACATTGTTCCATATACAA
5743068 ATACTTCTTT
1 ATACTTCTTT
5743078 AAATCCTTTT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 92 1.00
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.40
Consensus pattern (42 bp):
ATACTTCTTTCTTCCATCACCATAACATTGTTCCATATACAA
Found at i:5770886 original size:25 final size:25
Alignment explanation
Indices: 5770858--5770917 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
5770848 ACTATTTCAT
5770858 TTCCTTTTTCTT-TCATCTTTTCTTA
1 TTCCTTTTTCTTATCATC-TTTCTTA
* **
5770883 TTCCATTACCTTATCATCTTTCTTA
1 TTCCTTTTTCTTATCATCTTTCTTA
*
5770908 -ACCTTTTTCT
1 TTCCTTTTTCT
5770918 AGCCTATCCT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
24 6 0.22
25 16 0.59
26 5 0.19
ACGTcount: A:0.13, C:0.27, G:0.00, T:0.60
Consensus pattern (25 bp):
TTCCTTTTTCTTATCATCTTTCTTA
Found at i:5790688 original size:20 final size:22
Alignment explanation
Indices: 5790659--5790698 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
5790649 GGGAGAGCTT
5790659 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
5790679 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
5790699 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:5791842 original size:18 final size:19
Alignment explanation
Indices: 5791804--5791842 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5791794 AAGGAAAAAG
*
5791804 AAGCACTCAAAAAGATTGA
1 AAGCACTCAAAAAGATAGA
5791823 AAGCACTCAAAAAGA-AGA
1 AAGCACTCAAAAAGATAGA
5791841 AA
1 AA
5791843 AAAACAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGCACTCAAAAAGATAGA
Found at i:5794394 original size:20 final size:22
Alignment explanation
Indices: 5794365--5794404 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
5794355 GGGAGAGCTT
5794365 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
5794385 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
5794405 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:5803058 original size:20 final size:19
Alignment explanation
Indices: 5803035--5803077 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5803025 TTCCAGCTAC
*
5803035 CTTTAGCCCACTTTTCAACA
1 CTTTAGCCCA-ATTTCAACA
* *
5803055 CTTTGGTCCAATTTCAACA
1 CTTTAGCCCAATTTCAACA
5803074 CTTT
1 CTTT
5803078 GGTCCAAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (19 bp):
CTTTAGCCCAATTTCAACA
Found at i:5803071 original size:19 final size:19
Alignment explanation
Indices: 5803047--5803084 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5803037 TTAGCCCACT
5803047 TTTCAACACTTTGGTCCAA
1 TTTCAACACTTTGGTCCAA
5803066 TTTCAACACTTTGGTCCAA
1 TTTCAACACTTTGGTCCAA
5803085 AGCTCTCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (19 bp):
TTTCAACACTTTGGTCCAA
Found at i:5804433 original size:24 final size:23
Alignment explanation
Indices: 5804388--5804440 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
5804378 TACTTCAATT
* *
5804388 GGTACATTCTTTCGAATTTCAAGA
1 GGTACATCCTTTCGAATGTCAA-A
5804412 GGTACATCCTTT-GAAATGTCAAA
1 GGTACATCCTTTCG-AATGTCAAA
5804435 GG-ACAT
1 GGTACAT
5804441 GTCTTGTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 4 0.15
23 4 0.15
24 18 0.69
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (23 bp):
GGTACATCCTTTCGAATGTCAAA
Found at i:5810808 original size:13 final size:12
Alignment explanation
Indices: 5810790--5810873 Score: 54
Period size: 11 Copynumber: 7.0 Consensus size: 12
5810780 ATGGGCGTGT
5810790 TATGGTGATGGAA
1 TATGGTGATGG-A
5810803 TATGGTGAT-GA
1 TATGGTGATGGA
*
5810814 TATAGGCG-T-GA
1 TAT-GGTGATGGA
5810825 TAATGGTGATGGA
1 T-ATGGTGATGGA
5810838 CTATGGTGAT-GA
1 -TATGGTGATGGA
*
5810850 TATAGGCG-T-GA
1 TAT-GGTGATGGA
5810861 TAATGGTGATGGA
1 T-ATGGTGATGGA
5810874 CAGATTGTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.36
12 15 0.26
13 21 0.36
14 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.37, T:0.31
Consensus pattern (12 bp):
TATGGTGATGGA
Found at i:5810843 original size:36 final size:36
Alignment explanation
Indices: 5810770--5810874 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
5810760 ATTTATAAGT
* * * *
5810770 TGGTGATAATATGGGCGTG-TTATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
5810805 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
5810841 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
5810875 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 17 0.26
36 48 0.74
ACGTcount: A:0.27, C:0.05, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:5812950 original size:13 final size:12
Alignment explanation
Indices: 5812931--5813016 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
5812921 ATATGGGCGT
5812931 GATATGGTGATG
1 GATATGGTGATG
5812943 GAATATGGTGAT-
1 G-ATATGGTGATG
*
5812955 GATATAGGCG-T-
1 GATAT-GGTGATG
5812966 GATAATGGTGATG
1 GAT-ATGGTGATG
5812979 GACTATGGTGAT-
1 GA-TATGGTGATG
*
5812991 GATATAGGCG-T-
1 GATAT-GGTGATG
5813002 GATAATGGTGATG
1 GAT-ATGGTGATG
5813015 GA
1 GA
5813017 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:5812986 original size:36 final size:36
Alignment explanation
Indices: 5812913--5813017 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
5812903 ATTTATAAGT
* * *
5812913 TGGTGATAATATGGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
5812948 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
5812984 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
5813018 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.28, C:0.05, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:5818158 original size:19 final size:20
Alignment explanation
Indices: 5818134--5818176 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
5818124 CGGCCAAGAG
5818134 CATGTATCTTCATT-AAAAT
1 CATGTATCTTCATTAAAAAT
*
5818153 CATGTATTTTCATTAAAAAT
1 CATGTATCTTCATTAAAAAT
5818173 CATG
1 CATG
5818177 CATTTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (20 bp):
CATGTATCTTCATTAAAAAT
Found at i:5818173 original size:20 final size:19
Alignment explanation
Indices: 5818134--5818184 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
5818124 CGGCCAAGAG
*
5818134 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
5818153 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATT-AAAAT
*
5818173 CATGCATTTTCA
1 CATGTATTTTCA
5818185 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:5818989 original size:19 final size:19
Alignment explanation
Indices: 5818953--5818990 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5818943 CAAAAAAAGT
*
5818953 AACAAGAAAGAAGAAAAAA
1 AACAAGAAAGAAAAAAAAA
5818972 AACAA-AAAGAAAAGAAAAA
1 AACAAGAAAGAAAA-AAAAA
5818991 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:5819048 original size:14 final size:15
Alignment explanation
Indices: 5819014--5819060 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
5819004 AATTTGGAGT
5819014 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
5819029 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
5819043 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
5819060 G
1 G
5819061 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:5822293 original size:19 final size:20
Alignment explanation
Indices: 5822269--5822311 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
5822259 CGGCCAAGAG
5822269 CATGTATCTTCATT-AAAAT
1 CATGTATCTTCATTAAAAAT
*
5822288 CATGTATTTTCATTAAAAAT
1 CATGTATCTTCATTAAAAAT
5822308 CATG
1 CATG
5822312 CATTTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (20 bp):
CATGTATCTTCATTAAAAAT
Found at i:5822308 original size:20 final size:19
Alignment explanation
Indices: 5822269--5822319 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
5822259 CGGCCAAGAG
*
5822269 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
5822288 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATT-AAAAT
*
5822308 CATGCATTTTCA
1 CATGTATTTTCA
5822320 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:5822861 original size:15 final size:16
Alignment explanation
Indices: 5822836--5822865 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5822826 CTTTGATAAC
5822836 ATTCATTTCCATTTCA
1 ATTCATTTCCATTTCA
5822852 ATTC-TTTCCATTTC
1 ATTCATTTCCATTTC
5822866 TATTTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTCATTTCCATTTCA
Found at i:5825535 original size:19 final size:21
Alignment explanation
Indices: 5825492--5825543 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
5825482 GAAACCCCTT
*
5825492 TGAAAATATATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
5825513 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
5825532 TGAAGATACATG
1 TGAAAATACATG
5825544 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.46, C:0.04, G:0.13, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:5829469 original size:19 final size:21
Alignment explanation
Indices: 5829421--5829472 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
5829411 GAAACCCCTT
*
5829421 TGAAAATACATGATTTTTATA
1 TGAAAATACATGATTTGTATA
5829442 TGAAAATACATGA-TTGTA-A
1 TGAAAATACATGATTTGTATA
*
5829461 TGAAGATACATG
1 TGAAAATACATG
5829473 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 13 0.45
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTGTATA
Found at i:5840253 original size:8 final size:8
Alignment explanation
Indices: 5840242--5840266 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5840232 GAGAAAAATC
5840242 AGAAAAGA
1 AGAAAAGA
5840250 AGAAAAGA
1 AGAAAAGA
5840258 AGAAAAGA
1 AGAAAAGA
5840266 A
1 A
5840267 AAGAAAAAGA
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:5840276 original size:16 final size:16
Alignment explanation
Indices: 5840225--5840276 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
5840215 TTGGAGTGCA
5840225 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGA-AAAAA--AG
*
5840244 AAAAGAAGAAAAGAAG
1 AAAAGAAGAAAAAAAG
5840260 AAAAGAA-AAGAAAAAG
1 AAAAGAAGAA-AAAAAG
5840276 A
1 A
5840277 GAAGTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.07
16 15 0.50
18 4 0.13
19 9 0.30
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (16 bp):
AAAAGAAGAAAAAAAG
Found at i:5841760 original size:20 final size:22
Alignment explanation
Indices: 5841731--5841770 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
5841721 GGGAGAGCTT
5841731 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
5841751 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
5841771 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:5845462 original size:20 final size:22
Alignment explanation
Indices: 5845433--5845472 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
5845423 GGGAGAGCTT
5845433 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
5845453 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
5845473 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:5848982 original size:18 final size:18
Alignment explanation
Indices: 5848961--5848998 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5848951 CCTTACACAC
5848961 TTTGCCACAACAACACCA
1 TTTGCCACAACAACACCA
* *
5848979 TTTGCCACGACAACGCCA
1 TTTGCCACAACAACACCA
5848997 TT
1 TT
5848999 CATACTTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.37, G:0.11, T:0.21
Consensus pattern (18 bp):
TTTGCCACAACAACACCA
Found at i:5855504 original size:19 final size:21
Alignment explanation
Indices: 5855480--5855531 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
5855470 CGGCCAAGAG
*
5855480 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
5855499 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
5855520 CATGTATTTTCA
1 CATGTATTTTCA
5855532 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:5856996 original size:18 final size:18
Alignment explanation
Indices: 5856975--5857012 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5856965 CCTTACACAC
5856975 TTTGCCACAACAACACCA
1 TTTGCCACAACAACACCA
* *
5856993 TTTGCCACGACAACGCCA
1 TTTGCCACAACAACACCA
5857011 TT
1 TT
5857013 CATACTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.37, G:0.11, T:0.21
Consensus pattern (18 bp):
TTTGCCACAACAACACCA
Found at i:5862863 original size:167 final size:167
Alignment explanation
Indices: 5862587--5862921 Score: 607
Period size: 167 Copynumber: 2.0 Consensus size: 167
5862577 CACCAACGCC
* *
5862587 ACCTTCAAAGGATATGGAAGTAATGCCACAAGGACCAATAACTCGATCAAGGGCCAAACTTTTCA
1 ACCTTCAAAGGATATGGAAGTAATGCCACAAGGACCAATAACTCAACCAAGGGCCAAACTTTTCA
*
5862652 GGGAAGCTCATACTACCAAATGCATTAAAACCTTTGAATCATTTAGAAATGCATCCCCAAACAAT
66 GGAAAGCTCATACTACCAAATGCATTAAAACCTTTGAATCATTTAGAAATGCATCCCCAAACAAT
*
5862717 AGATTATATAATATGTTTTATGTTGACATATAATATA
131 AGATTATATAATATGTTTTATGCTGACATATAATATA
5862754 ACCTTCAAAGGATATGGAAGTAATGCCACAAGGACCAATAACTCAACCAAGGGCCAAACTTTTCA
1 ACCTTCAAAGGATATGGAAGTAATGCCACAAGGACCAATAACTCAACCAAGGGCCAAACTTTTCA
* *
5862819 GGAAAGCTCTTACTACCAAATGCATTAAAACCTTTGAATCATTTAGAAATGTATCCCCAAACAAT
66 GGAAAGCTCATACTACCAAATGCATTAAAACCTTTGAATCATTTAGAAATGCATCCCCAAACAAT
*
5862884 AGATTTTATAATATGTTTTATGCTGACATATAATATA
131 AGATTATATAATATGTTTTATGCTGACATATAATATA
5862921 A
1 A
5862922 TCTATGAACC
Statistics
Matches: 161, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
167 161 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (167 bp):
ACCTTCAAAGGATATGGAAGTAATGCCACAAGGACCAATAACTCAACCAAGGGCCAAACTTTTCA
GGAAAGCTCATACTACCAAATGCATTAAAACCTTTGAATCATTTAGAAATGCATCCCCAAACAAT
AGATTATATAATATGTTTTATGCTGACATATAATATA
Found at i:5864069 original size:13 final size:11
Alignment explanation
Indices: 5864028--5864112 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
5864018 ACAATTTGTC
5864028 CATCACCATTAT
1 CATCACCA-TAT
*
5864040 CA-CGCCTATAT
1 CATCACC-ATAT
5864051 CATCACCATAGT
1 CATCACCATA-T
5864063 CCATCACCATTAT
1 -CATCACCA-TAT
*
5864076 CA-CGCCTATAT
1 CATCACC-ATAT
5864087 CATCACCATATT
1 CATCACCATA-T
5864099 CCATCACCATAT
1 -CATCACCATAT
5864111 CA
1 CA
5864113 CGCCCATATT
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:5864072 original size:36 final size:36
Alignment explanation
Indices: 5864025--5864129 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
5864015 GATACAATTT
5864025 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
5864061 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
5864097 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
5864130 ACTTATAAAT
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:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:5864545 original size:17 final size:17
Alignment explanation
Indices: 5864506--5864548 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
5864496 AAAGTTCTAC
5864506 AAAA-AAAATAACAAGA
1 AAAAGAAAATAACAAGA
5864522 AAGAAGAAAATAA-AAGA
1 AA-AAGAAAATAACAAGA
5864539 GAAAAGAAAA
1 -AAAAGAAAA
5864549 AGACTCCTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 13 0.54
18 9 0.38
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAGAAAATAACAAGA
Found at i:5869783 original size:13 final size:11
Alignment explanation
Indices: 5869742--5869826 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
5869732 ACAATCTGTC
5869742 CATCACCATTAT
1 CATCACCA-TAT
*
5869754 CATGC-CTATAT
1 CAT-CACCATAT
5869765 CATCACCATAGT
1 CATCACCATA-T
5869777 CCATCACCATTAT
1 -CATCACCA-TAT
*
5869790 CA-CGCCTATAT
1 CATCACC-ATAT
5869801 CATCACCATATT
1 CATCACCATA-T
5869813 CCATCACCATAT
1 -CATCACCATAT
5869825 CA
1 CA
5869827 CGCCCATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
10 1 0.02
11 23 0.38
12 14 0.23
13 20 0.33
14 2 0.03
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:5869786 original size:36 final size:36
Alignment explanation
Indices: 5869739--5869841 Score: 163
Period size: 36 Copynumber: 2.9 Consensus size: 36
5869729 GATACAATCT
*
5869739 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
5869775 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
5869811 TTCCATCACCA-TATCACGCCCATATTATCAC
1 GTCCATCACCATTATCACGCCTATATCATCAC
5869842 TAACTTATAA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 18 0.29
36 45 0.71
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:5870675 original size:17 final size:18
Alignment explanation
Indices: 5870653--5870692 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
5870643 TTTACTAGAA
5870653 TTTTCTTTCTTTTTG-GC
1 TTTTCTTTCTTTTTGTGC
5870670 TTTTC-TTCTTTTTGTGC
1 TTTTCTTTCTTTTTGTGC
5870687 TTTTCT
1 TTTTCT
5870693 CTTTTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.00, C:0.17, G:0.10, T:0.72
Consensus pattern (18 bp):
TTTTCTTTCTTTTTGTGC
Found at i:5870680 original size:16 final size:17
Alignment explanation
Indices: 5870653--5870697 Score: 67
Period size: 16 Copynumber: 2.7 Consensus size: 17
5870643 TTTACTAGAA
5870653 TTTTCTTTCTTTTTG-GC
1 TTTTC-TTCTTTTTGTGC
5870670 TTTTCTTCTTTTTGTGC
1 TTTTCTTCTTTTTGTGC
5870687 TTTTC-TCTTTT
1 TTTTCTTCTTTT
5870698 GTTTTGAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.00, C:0.18, G:0.09, T:0.73
Consensus pattern (17 bp):
TTTTCTTCTTTTTGTGC
Found at i:5872942 original size:14 final size:14
Alignment explanation
Indices: 5872923--5872966 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5872913 TTTTTTTAAA
5872923 TGAATAGTGAACAG
1 TGAATAGTGAACAG
* *
5872937 TGAATAATGAATAG
1 TGAATAGTGAACAG
* *
5872951 TAAAAAGTGAACAG
1 TGAATAGTGAACAG
5872965 TG
1 TG
5872967 CATCGATGCA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.48, C:0.05, G:0.25, T:0.23
Consensus pattern (14 bp):
TGAATAGTGAACAG
Found at i:5872945 original size:21 final size:21
Alignment explanation
Indices: 5872921--5872961 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5872911 TATTTTTTTA
* *
5872921 AATGAATAGTGAACAGTGAAT
1 AATGAATAGTAAAAAGTGAAT
5872942 AATGAATAGTAAAAAGTGAA
1 AATGAATAGTAAAAAGTGAA
5872962 CAGTGCATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.02, G:0.22, T:0.22
Consensus pattern (21 bp):
AATGAATAGTAAAAAGTGAAT
Found at i:5873028 original size:21 final size:21
Alignment explanation
Indices: 5873002--5873041 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5872992 AAAAATGTGT
*
5873002 ATCGATGCACTGCTACAGTGC
1 ATCGATACACTGCTACAGTGC
5873023 ATCGATACACTGCTACAGT
1 ATCGATACACTGCTACAGT
5873042 ACTACTATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (21 bp):
ATCGATACACTGCTACAGTGC
Found at i:5879657 original size:272 final size:275
Alignment explanation
Indices: 5879283--5879831 Score: 1020
Period size: 272 Copynumber: 2.0 Consensus size: 275
5879273 CACCAACTTT
5879283 CTGCATGACATACTCACATCATTGAAGAACCATCAAACACAATATAAGGGAGTTCTACCATACTT
1 CTGCATGACATACTCACATCATTGAAGAACCATCAAACACAATATAAGGGAGTTCTACCATACTT
5879348 TATATTATATTTACTTATTATGCACTATATATATTATGAGCATACACTTGCATATTAGACTATAC
66 TATATTATATTTACTTATTATGCACTATATATATTATGAGCATACACTTGCATATTAGACTATAC
5879413 TTGAATTATCATAGTATGTGCATTCATTCATTATATCCTATGGTTTGCATCATTGATTGATATTC
131 TTGAATTATCATAGTATGTGCATTCATTCATTATATCCTATGGTTTGCATCATTGATTGATATTC
5879478 ATG-TATAATCTATAGTTATAATATTAATA-TCATTCATTATCATATGATGCATGAATTATTATT
196 ATGATATAATCTATAGTTATAATATTAATATTCATTCATTATCATATGATGCATGAATTATTATT
5879541 ATAACCTA-TGTTCA
261 ATAACCTATTGTTCA
5879555 CTGCATGACATACTCACATCATTGAAGAACCATC-AACACAATATAAGGGAGTTCTACCATACTT
1 CTGCATGACATACTCACATCATTGAAGAACCATCAAACACAATATAAGGGAGTTCTACCATACTT
5879619 TATA-T-TATTTACTTATTATGCACTATATATATTATTATGAGCATACACTTGCATATTAGACTA
66 TATATTATATTTACTTATTATGCAC--TATATA-TATTATGAGCATACACTTGCATATTAGACTA
5879682 TACTTGAATTATCATAGTATGTGCATTCATTCATTATATCCTATGGTTTGCATCATTGATTGATA
128 TACTTGAATTATCATAGTATGTGCATTCATTCATTATATCCTATGGTTTGCATCATTGATTGATA
5879747 TTCATGTATATAATCTATAGTTATAATATTAATATTCATTCATTATCATATGATGCATGAATTAT
193 TTCATG-ATATAATCTATAGTTATAATATTAATATTCATTCATTATCATATGATGCATGAATTAT
5879812 TATTATAACCTATTGTTCA
257 TATTATAACCTATTGTTCA
5879831 C
1 C
5879832 ATCTTTATAA
Statistics
Matches: 270, Mismatches: 0, Indels: 10
0.96 0.00 0.04
Matches are distributed among these distances:
269 18 0.07
270 1 0.00
271 40 0.15
272 136 0.50
274 26 0.10
275 42 0.16
276 7 0.03
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.40
Consensus pattern (275 bp):
CTGCATGACATACTCACATCATTGAAGAACCATCAAACACAATATAAGGGAGTTCTACCATACTT
TATATTATATTTACTTATTATGCACTATATATATTATGAGCATACACTTGCATATTAGACTATAC
TTGAATTATCATAGTATGTGCATTCATTCATTATATCCTATGGTTTGCATCATTGATTGATATTC
ATGATATAATCTATAGTTATAATATTAATATTCATTCATTATCATATGATGCATGAATTATTATT
ATAACCTATTGTTCA
Found at i:5880696 original size:20 final size:21
Alignment explanation
Indices: 5880671--5880723 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
5880661 CGGCCAAGAG
*
5880671 CATGTATCTTCA-TTAAAAAT
1 CATGTATTTTCATTTAAAAAT
*
5880691 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAAT
5880712 CATGTATTTTCA
1 CATGTATTTTCA
5880724 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 11 0.37
21 19 0.63
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:5886822 original size:12 final size:10
Alignment explanation
Indices: 5886813--5886852 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
5886803 GCTTTTTGGC
5886813 TTTTTTTTTG
1 TTTTTTTTTG
5886823 TTTTTTTTT-
1 TTTTTTTTTG
5886832 TATTTTTTTTG
1 T-TTTTTTTTG
5886843 TTTTGTTTTT
1 TTTT-TTTTT
5886853 TAGAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 1 0.04
10 20 0.74
11 6 0.22
ACGTcount: A:0.03, C:0.00, G:0.07, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:5886837 original size:20 final size:21
Alignment explanation
Indices: 5886814--5886854 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
5886804 CTTTTTGGCT
5886814 TTTTTTTTGTTTT-TTTTTTA
1 TTTTTTTTGTTTTGTTTTTTA
5886834 TTTTTTTTGTTTTGTTTTTTA
1 TTTTTTTTGTTTTGTTTTTTA
5886855 GAAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.05, C:0.00, G:0.07, T:0.88
Consensus pattern (21 bp):
TTTTTTTTGTTTTGTTTTTTA
Found at i:5893998 original size:26 final size:27
Alignment explanation
Indices: 5893969--5894025 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
5893959 ATGAAACAAC
*
5893969 CTTTGTTTTTAACTTTACTTTT-CTTG
1 CTTTGATTTTAACTTTACTTTTACTTG
* * *
5893995 CTTTGATTTTATCTTTCCTTTTACTTT
1 CTTTGATTTTAACTTTACTTTTACTTG
5894022 CTTT
1 CTTT
5894026 TTGCACGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.11, C:0.18, G:0.05, T:0.67
Consensus pattern (27 bp):
CTTTGATTTTAACTTTACTTTTACTTG
Found at i:5895738 original size:19 final size:20
Alignment explanation
Indices: 5895714--5895756 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5895704 AGCATTTATC
*
5895714 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
5895733 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
5895753 TTCA
1 TTCA
5895757 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:5896869 original size:17 final size:17
Alignment explanation
Indices: 5896847--5896880 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5896837 TATCCTACCC
5896847 CTATACCATAACCATTT
1 CTATACCATAACCATTT
*
5896864 CTATACCCTAACCATTT
1 CTATACCATAACCATTT
5896881 TTTTAAGCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (17 bp):
CTATACCATAACCATTT
Found at i:5899783 original size:19 final size:20
Alignment explanation
Indices: 5899759--5899801 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5899749 AGCATTTATC
*
5899759 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
5899778 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
5899798 TTCA
1 TTCA
5899802 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:5908136 original size:23 final size:23
Alignment explanation
Indices: 5908108--5908228 Score: 83
Period size: 23 Copynumber: 5.1 Consensus size: 23
5908098 ACAATCTGTC
*
5908108 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCACC-ATAT
5908131 CATCACCA-TAGTCCATCACCAT-T
1 CATCACCATTA-T-CATCACCATAT
*
5908154 -ATCACGCCTATATCATCACCATAGT
1 CATCAC-CAT-TATCATCACCATA-T
*
5908179 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
5908203 CATCACCA-TATTCCATCACCATAT
1 CATCACCATTA-T-CATCACCATAT
5908227 CA
1 CA
5908229 CGCCCATATT
Statistics
Matches: 79, Mismatches: 5, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
22 9 0.11
23 29 0.37
24 17 0.22
25 17 0.22
26 2 0.03
27 5 0.06
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.28
Consensus pattern (23 bp):
CATCACCATTATCATCACCATAT
Found at i:5908149 original size:13 final size:11
Alignment explanation
Indices: 5908108--5908228 Score: 86
Period size: 11 Copynumber: 10.2 Consensus size: 11
5908098 ACAATCTGTC
5908108 CATCACCATTAT
1 CATCACCA-TAT
*
5908120 CA-CGCCTATAT
1 CATCACC-ATAT
5908131 CATCACCATAGT
1 CATCACCATA-T
5908143 CCATCACCATTAT
1 -CATCACCA-TAT
*
5908156 CA-CGCCTATAT
1 CATCACC-ATAT
5908167 CATCACCATAGT
1 CATCACCATA-T
5908179 CCATCACCATTAT
1 -CATCACCA-TAT
*
5908192 CA-CGCCTATAT
1 CATCACC-ATAT
5908203 CATCACCATATT
1 CATCACCATA-T
5908215 CCATCACCATAT
1 -CATCACCATAT
5908227 CA
1 CA
5908229 CGCCCATATT
Statistics
Matches: 89, Mismatches: 6, Indels: 29
0.72 0.05 0.23
Matches are distributed among these distances:
11 35 0.39
12 22 0.25
13 28 0.31
14 4 0.04
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:5908152 original size:36 final size:36
Alignment explanation
Indices: 5908105--5908245 Score: 248
Period size: 36 Copynumber: 3.9 Consensus size: 36
5908095 GATACAATCT
5908105 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
5908141 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
5908177 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
5908213 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
5908246 ACTTATAAAT
Statistics
Matches: 102, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.20
36 82 0.80
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:5912345 original size:13 final size:11
Alignment explanation
Indices: 5912304--5912388 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
5912294 ACAATCTGTC
5912304 CATCACCATTAT
1 CATCACCA-TAT
*
5912316 CA-CGCCTATAT
1 CATCACC-ATAT
5912327 CATCACCATAGT
1 CATCACCATA-T
5912339 CCATCACCATTAT
1 -CATCACCA-TAT
*
5912352 CA-CGCCTATAT
1 CATCACC-ATAT
5912363 CATCACCATATT
1 CATCACCATA-T
5912375 CCATCACCATAT
1 -CATCACCATAT
5912387 CA
1 CA
5912389 CGCCCATATT
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:5912348 original size:36 final size:36
Alignment explanation
Indices: 5912301--5912405 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
5912291 GATACAATCT
5912301 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
5912337 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
5912373 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
5912406 ACTTATAAAT
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:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:5912597 original size:15 final size:15
Alignment explanation
Indices: 5912547--5912590 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
5912537 TTTGATAACT
*
5912547 ATTCTATCCATTTCA
1 ATTCTTTCCATTTCA
*
5912562 ATTCTTTCTATTTCA
1 ATTCTTTCCATTTCA
5912577 ATTCTTTCCATTTC
1 ATTCTTTCCATTTC
5912591 CTTTCTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.20, C:0.25, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTCTTTCCATTTCA
Found at i:5913851 original size:16 final size:16
Alignment explanation
Indices: 5913818--5913867 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
5913808 TAAGGTAACG
5913818 GAATAAGAATAGATGAAA
1 GAATAAGAA-A-ATGAAA
5913836 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* * *
5913852 TAGTAAGAAAGTGAAA
1 GAATAAGAAAATGAAA
5913868 ATAACTTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 19 0.66
17 1 0.03
18 9 0.31
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:5914100 original size:7 final size:6
Alignment explanation
Indices: 5914066--5914111 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
5914056 TGTAGGAGTC
* *
5914066 TTTTC- TTTTCT TTATCT TTTTGT TTTTCT TCTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTT
5914112 ATTGCAGCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
5 5 0.14
6 24 0.69
7 6 0.17
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:5914406 original size:22 final size:22
Alignment explanation
Indices: 5914381--5914454 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
5914371 GCTGCGAAAG
*
5914381 TGTTGTTGAATTGTCCTTCAAA
1 TGTTGATGAATTGTCCTTCAAA
*
5914403 TGTTGATGAATTCG-AC--C--A
1 TGTTGATGAATT-GTCCTTCAAA
* *
5914421 CGTTGTTGAATTGTCCTTCAAA
1 TGTTGATGAATTGTCCTTCAAA
5914443 TGTTGATGAATT
1 TGTTGATGAATT
5914455 CGACCACCAT
Statistics
Matches: 39, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
17 1 0.03
18 12 0.31
20 2 0.05
22 23 0.59
23 1 0.03
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (22 bp):
TGTTGATGAATTGTCCTTCAAA
Found at i:5914426 original size:40 final size:40
Alignment explanation
Indices: 5914382--5914461 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
5914372 CTGCGAAAGT
5914382 GTTGTTGAATTGTCCTTCAAATGTTGATGAATTCGACCAC
1 GTTGTTGAATTGTCCTTCAAATGTTGATGAATTCGACCAC
5914422 GTTGTTGAATTGTCCTTCAAATGTTGATGAATTCGACCAC
1 GTTGTTGAATTGTCCTTCAAATGTTGATGAATTCGACCAC
5914462 CATTGGTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (40 bp):
GTTGTTGAATTGTCCTTCAAATGTTGATGAATTCGACCAC
Found at i:5915981 original size:20 final size:19
Alignment explanation
Indices: 5915945--5915983 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
5915935 AGTAAAGATG
**
5915945 TGAAAACATATGTTATGCA
1 TGAAAACATATAATATGCA
5915964 TGAAAATCATATAATATGCA
1 TGAAAA-CATATAATATGCA
5915984 AGTGAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (19 bp):
TGAAAACATATAATATGCA
Found at i:5919396 original size:24 final size:24
Alignment explanation
Indices: 5919345--5919396 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
5919335 TCTTGGCACT
* * **
5919345 TCAAGTGGCATATCTTTTTTAACA
1 TCAAGTGGCATAGCTGTTGGAACA
*
5919369 TCAAGTGGCATAGCTGTTGGAACG
1 TCAAGTGGCATAGCTGTTGGAACA
5919393 TCAA
1 TCAA
5919397 AGGACATGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (24 bp):
TCAAGTGGCATAGCTGTTGGAACA
Found at i:5920718 original size:23 final size:23
Alignment explanation
Indices: 5920668--5920720 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
5920658 TTTCTTTCTT
5920668 TTTTCTTCTTTTGAGTGTCTTCA
1 TTTTCTTCTTTTGAGTGTCTTCA
* *
5920691 ATTTCTTCTTTTGAGTG-CTTTGA
1 TTTTCTTCTTTTGAGTGTC-TTCA
5920714 TTTTCTT
1 TTTTCTT
5920721 TGCTGGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 1 0.04
23 25 0.96
ACGTcount: A:0.09, C:0.15, G:0.13, T:0.62
Consensus pattern (23 bp):
TTTTCTTCTTTTGAGTGTCTTCA
Found at i:5923044 original size:23 final size:25
Alignment explanation
Indices: 5922999--5923050 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 25
5922989 AATAAAGGGG
*
5922999 ATAATAATATAAGTAATGAAAATAA
1 ATAATAATATAAGAAATGAAAATAA
*
5923024 ATAATAATA-ATGAAATG-AAATAA
1 ATAATAATATAAGAAATGAAAATAA
5923047 ATAA
1 ATAA
5923051 AGGATAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.40
24 6 0.24
25 9 0.36
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (25 bp):
ATAATAATATAAGAAATGAAAATAA
Found at i:5923505 original size:19 final size:21
Alignment explanation
Indices: 5923458--5923509 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
5923448 GAAACCCCTT
*
5923458 TGAAAATACATGATTTTTAAA
1 TGAAGATACATGATTTTTAAA
*
5923479 TAAAGATACATGA-TTTT-AA
1 TGAAGATACATGATTTTTAAA
5923498 TGAAGATACATG
1 TGAAGATACATG
5923510 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 13 0.46
20 4 0.14
21 11 0.39
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAGATACATGATTTTTAAA
Found at i:5926066 original size:33 final size:33
Alignment explanation
Indices: 5926024--5926099 Score: 152
Period size: 33 Copynumber: 2.3 Consensus size: 33
5926014 TTGTGAAAAC
5926024 GTACCTTTTCGCGAATAGTTGCCATCTCAAGAG
1 GTACCTTTTCGCGAATAGTTGCCATCTCAAGAG
5926057 GTACCTTTTCGCGAATAGTTGCCATCTCAAGAG
1 GTACCTTTTCGCGAATAGTTGCCATCTCAAGAG
5926090 GTACCTTTTC
1 GTACCTTTTC
5926100 ACAAGGAGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (33 bp):
GTACCTTTTCGCGAATAGTTGCCATCTCAAGAG
Found at i:5926113 original size:33 final size:33
Alignment explanation
Indices: 5926024--5926114 Score: 112
Period size: 33 Copynumber: 2.8 Consensus size: 33
5926014 TTGTGAAAAC
* * *
5926024 GTACCTTTTCGCGAATAGTTGCCATCTCAAGAG
1 GTACCTTTTCACGAAGAGCTGCCATCTCAAGAG
* * *
5926057 GTACCTTTTCGCGAATAGTTGCCATCTCAAGAG
1 GTACCTTTTCACGAAGAGCTGCCATCTCAAGAG
5926090 GTACCTTTTCAC-AAGGAGCTGCCAT
1 GTACCTTTTCACGAA-GAGCTGCCAT
5926115 AATGTTATGC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 2 0.04
33 52 0.96
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (33 bp):
GTACCTTTTCACGAAGAGCTGCCATCTCAAGAG
Found at i:5929090 original size:18 final size:19
Alignment explanation
Indices: 5929052--5929090 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5929042 AAGGAAAAAG
*
5929052 AAGCACTCAAAAAGATTGA
1 AAGCACTCAAAAAGATAGA
5929071 AAGCACTCAAAAAGA-AGA
1 AAGCACTCAAAAAGATAGA
5929089 AA
1 AA
5929091 AAGAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGCACTCAAAAAGATAGA
Found at i:5934591 original size:22 final size:20
Alignment explanation
Indices: 5934566--5934605 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5934556 ATGTTTGTTT
5934566 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
5934588 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
5934606 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:5939287 original size:21 final size:19
Alignment explanation
Indices: 5939261--5939306 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
5939251 GAGGCTCCTT
*
5939261 TGAAAACACATGATTTTTTAA
1 TGAAAACACAT-A-ATTTTAA
*
5939282 TGAAAATACATAATTTTAA
1 TGAAAACACATAATTTTAA
5939301 TGAAAA
1 TGAAAA
5939307 TAAATGTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 12 0.52
20 1 0.04
21 10 0.43
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.35
Consensus pattern (19 bp):
TGAAAACACATAATTTTAA
Found at i:5940365 original size:25 final size:22
Alignment explanation
Indices: 5940336--5940381 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5940326 TTTTTAACCC
5940336 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
5940361 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
5940382 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:5944036 original size:11 final size:10
Alignment explanation
Indices: 5944022--5944059 Score: 58
Period size: 10 Copynumber: 3.6 Consensus size: 10
5944012 TTTTTTACCC
5944022 TTTTTTTGCTTT
1 TTTTTTTG--TT
5944034 TTTTTTTGTT
1 TTTTTTTGTT
5944044 TTTTTTTGTT
1 TTTTTTTGTT
5944054 TTTTTT
1 TTTTTT
5944060 GAAAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.69
12 8 0.31
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:5947902 original size:8 final size:8
Alignment explanation
Indices: 5947891--5947915 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5947881 GTGAAAAATT
5947891 AGAAAAGA
1 AGAAAAGA
5947899 AGAAAAGA
1 AGAAAAGA
5947907 AGAAAAGA
1 AGAAAAGA
5947915 A
1 A
5947916 AAGAAAAAGA
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:5957239 original size:49 final size:50
Alignment explanation
Indices: 5957184--5957283 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 50
5957174 GCATGGTTAT
5957184 GATAGAATATAATGTATAAATG-ATAATATAAGATAGGGTAAGGAAGAAC
1 GATAGAATATAATGTATAAATGAATAATATAAGATAGGGTAAGGAAGAAC
5957233 GATAGAATATAATGTATAAATGATATAATATAAGATAGGGTAAGGAAGAAC
1 GATAGAATATAATGTATAAATGA-ATAATATAAGATAGGGTAAGGAAGAAC
5957284 TCCCTTAGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 22 0.45
51 27 0.55
ACGTcount: A:0.51, C:0.02, G:0.22, T:0.25
Consensus pattern (50 bp):
GATAGAATATAATGTATAAATGAATAATATAAGATAGGGTAAGGAAGAAC
Found at i:5972927 original size:89 final size:89
Alignment explanation
Indices: 5972776--5972938 Score: 220
Period size: 89 Copynumber: 1.8 Consensus size: 89
5972766 CAACTTCTCA
* * *
5972776 ACCATGTATGTGCTTGCAAGATTTGCACAACTACCACCATCAATGGCTACAAGGCATACTTTATC
1 ACCATGTATGTGCTTGCAAGATTTGCACAACTACCACCATCAATAGCTACAAGACATACTTTACC
5972841 ATTCACATGAAAATGAGTGTTTTG
66 ATTCACATGAAAATGAGTGTTTTG
* * * * * *
5972865 ACCATGTATGTGTTTGCAATG-TTTGTATAACTTCCTCCGTCAATAGCTACAAGACATACTTTAC
1 ACCATGTATGTGCTTGCAA-GATTTGCACAACTACCACCATCAATAGCTACAAGACATACTTTAC
*
5972929 CATTTACATG
65 CATTCACATG
5972939 GCAACGAGTG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
89 62 0.98
90 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33
Consensus pattern (89 bp):
ACCATGTATGTGCTTGCAAGATTTGCACAACTACCACCATCAATAGCTACAAGACATACTTTACC
ATTCACATGAAAATGAGTGTTTTG
Found at i:5973371 original size:16 final size:16
Alignment explanation
Indices: 5973339--5973386 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5973329 AAGGTAATGA
5973339 AATAAGAATAGATGAAAG
1 AATAAGAA-A-ATGAAAG
*
5973357 AATAAGAAAATGAAAT
1 AATAAGAAAATGAAAG
* *
5973373 AGTAAGAAAGTGAA
1 AATAAGAAAATGAA
5973387 GATAACTTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 18 0.67
17 1 0.04
18 8 0.30
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (16 bp):
AATAAGAAAATGAAAG
Found at i:5973600 original size:6 final size:6
Alignment explanation
Indices: 5973586--5973620 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
5973576 TGTAGGAGTC
*
5973586 TTTTCT TTTTGT TTTTCT TCTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTT
5973621 GTTACAGCAC
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:5973615 original size:13 final size:12
Alignment explanation
Indices: 5973586--5973620 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
5973576 TGTAGGAGTC
*
5973586 TTTTCTTTTTGT
1 TTTTCTTTTTCT
5973598 TTTTCTTCTTTCT
1 TTTTCTT-TTTCT
5973611 TTTTCTTTTT
1 TTTTCTTTTT
5973621 GTTACAGCAC
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:5973870 original size:25 final size:25
Alignment explanation
Indices: 5973836--5973890 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
5973826 AAGAAGAAAG
*
5973836 GAAATGATAAGAATTGAAATGGATA
1 GAAATCATAAGAATTGAAATGGATA
*
5973861 GAAATCATAAGCATTGAAATGGATA
1 GAAATCATAAGAATTGAAATGGATA
5973886 GAAAT
1 GAAAT
5973891 GTTATCAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.24
Consensus pattern (25 bp):
GAAATCATAAGAATTGAAATGGATA
Found at i:5980138 original size:20 final size:21
Alignment explanation
Indices: 5980113--5980160 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
5980103 ATTCATTCAG
*
5980113 TAGCTCATGTCATG-TTATTT
1 TAGCTCATGTCATGTTTATAT
*
5980133 TAGCTCATGTTATGTTTATAT
1 TAGCTCATGTCATGTTTATAT
5980154 TAGCTCA
1 TAGCTCA
5980161 CTAACTTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.48
Consensus pattern (21 bp):
TAGCTCATGTCATGTTTATAT
Found at i:5982585 original size:19 final size:19
Alignment explanation
Indices: 5982555--5982606 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
5982545 TTCGGCCAAG
*
5982555 AGCATGTGTTTTCATTAAA
1 AGCATGTATTTTCATTAAA
*
5982574 ATCATGTATTTTCATTAAA
1 AGCATGTATTTTCATTAAA
*
5982593 AGCATATATTTTCA
1 AGCATGTATTTTCA
5982607 AAGGGATTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.44
Consensus pattern (19 bp):
AGCATGTATTTTCATTAAA
Found at i:5984397 original size:13 final size:11
Alignment explanation
Indices: 5984356--5984440 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
5984346 ACAATCTGTC
5984356 CATCACCATTAT
1 CATCACCA-TAT
*
5984368 CA-CGCCTATAT
1 CATCACC-ATAT
5984379 CATCACCATAGT
1 CATCACCATA-T
5984391 CCATCACCATTAT
1 -CATCACCA-TAT
*
5984404 CA-CGCCTATAT
1 CATCACC-ATAT
5984415 CATCACCATATT
1 CATCACCATA-T
5984427 CCATCACCATAT
1 -CATCACCATAT
5984439 CA
1 CA
5984441 CTCGCCATTA
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:5984400 original size:36 final size:36
Alignment explanation
Indices: 5984353--5984441 Score: 162
Period size: 36 Copynumber: 2.5 Consensus size: 36
5984343 GATACAATCT
5984353 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
5984389 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
5984425 TTCCATCACCA-TATCAC
1 GTCCATCACCATTATCAC
5984442 TCGCCATTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
35 6 0.12
36 46 0.88
ACGTcount: A:0.30, C:0.37, G:0.04, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:5984863 original size:24 final size:23
Alignment explanation
Indices: 5984822--5984869 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
5984812 AAAGTGCTAC
*
5984822 AAAAAAAAAGCAACAAGAAAGAAG
1 AAAAAAAAAGCAAAAAGAAA-AAG
5984846 AAAAAAAAAG-AGAAAAGAAAAAG
1 AAAAAAAAAGCA-AAAAGAAAAAG
5984869 A
1 A
5984870 CTCTACATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAGCAAAAAGAAAAAG
Found at i:5985013 original size:66 final size:65
Alignment explanation
Indices: 5984810--5985013 Score: 195
Period size: 66 Copynumber: 3.1 Consensus size: 65
5984800 GGATTGACAT
*
5984810 TCAAAGTGCTACAAAAAAAAAGCAACAAGAAAGAAGAAAAAAAAAGAGAAAAGAAAAAGACTCTA
1 TCAAAGTGCTAC-AAAAAAAAGCAACAAGAAAGAAGAAAATAAAAGAGAAAAG-AAAAGACTCTA
5984875 CA
64 CA
* * * * * * *
5984877 TCAAATTTGGAGTGCAAAAGAAAG-AA-AAGAAA-AAAAAAATCAAAAG-CAAAAGAAAAG--TG
1 TCAAA-GT-G-CTACAAAAAAAAGCAACAAGAAAGAAGAAAAT-AAAAGAGAAAAGAAAAGACTC
*
5984936 AAGCAA
62 TA-C-A
5984942 GTCAAAGTGCTACAAAAAAAAGCAACAAGAAAGAAGAAAATAAAAGAGAAAAGAAAAGACTCCTA
1 -TCAAAGTGCTACAAAAAAAAGCAACAAGAAAGAAGAAAATAAAAGAGAAAAGAAAAGACT-CTA
5985007 CA
64 CA
5985009 TCAAA
1 TCAAA
5985014 TTTGGAGTGC
Statistics
Matches: 106, Mismatches: 17, Indels: 29
0.70 0.11 0.19
Matches are distributed among these distances:
63 12 0.11
64 4 0.04
65 18 0.17
66 38 0.36
67 17 0.16
68 5 0.05
69 10 0.09
70 2 0.02
ACGTcount: A:0.63, C:0.11, G:0.16, T:0.09
Consensus pattern (65 bp):
TCAAAGTGCTACAAAAAAAAGCAACAAGAAAGAAGAAAATAAAAGAGAAAAGAAAAGACTCTACA
Found at i:5985042 original size:132 final size:130
Alignment explanation
Indices: 5984810--5985072 Score: 467
Period size: 132 Copynumber: 2.0 Consensus size: 130
5984800 GGATTGACAT
5984810 TCAAAGTGCTACAAAAAAAAAGCAACAAGAAAGAAGAAAAAAAAAGAGAAAAGAAAAAGACTCTA
1 TCAAAGTGCTACAAAAAAAAAGCAACAAGAAAGAAGAAAAAAAAAGAGAAAAGAAAAAGACTCTA
5984875 CATCAAATTTGGAGTGCAAAAGAAAGAAAAGAAAAAAAAAATCAAAAGCAAAAGAAAAGTGAAGC
66 CATCAAATTTGGAGTGCAAAA-AAA-AAAA-AAAAAAAAAATCAAAAGCAAAAGAAAAGTGAAGC
5984940 AAG
128 AAG
*
5984943 TCAAAGTGCTAC-AAAAAAAAGCAACAAGAAAGAAGAAAATAAAAGAGAAAAG-AAAAGACTCCT
1 TCAAAGTGCTACAAAAAAAAAGCAACAAGAAAGAAGAAAAAAAAAGAGAAAAGAAAAAGACT-CT
5985006 ACATCAAATTTGGAGTGCAAAAAAAAAAAAAAAAAAAAATCAAAAGCAAAAGAAAAGTGAAGCAA
65 ACATCAAATTTGGAGTGCAAAAAAAAAAAAAAAAAAAAATCAAAAGCAAAAGAAAAGTGAAGCAA
5985071 G
130 G
5985072 T
1 T
5985073 TGCAAAGTAC
Statistics
Matches: 128, Mismatches: 1, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
129 38 0.30
130 4 0.03
131 11 0.09
132 63 0.49
133 12 0.09
ACGTcount: A:0.63, C:0.10, G:0.16, T:0.10
Consensus pattern (130 bp):
TCAAAGTGCTACAAAAAAAAAGCAACAAGAAAGAAGAAAAAAAAAGAGAAAAGAAAAAGACTCTA
CATCAAATTTGGAGTGCAAAAAAAAAAAAAAAAAAAAATCAAAAGCAAAAGAAAAGTGAAGCAAG
Found at i:5990223 original size:22 final size:23
Alignment explanation
Indices: 5990173--5990226 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
5990163 TACAATCTGT
*
5990173 CCATCACCATTATCACGCCTATA
1 CCATCACCATTATCACGCCCATA
5990196 CCATCACCA-TATCACGCCCATA
1 CCATCACCATTATCACGCCCATA
**
5990218 TTATCACCA
1 CCATCACCA
5990227 ACTTATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.31, C:0.41, G:0.04, T:0.24
Consensus pattern (23 bp):
CCATCACCATTATCACGCCCATA
Found at i:5992950 original size:19 final size:20
Alignment explanation
Indices: 5992926--5992965 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
5992916 TATCATTTCT
5992926 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
5992945 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
5992965 T
1 T
5992966 ATTATTATTC
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:5992968 original size:19 final size:18
Alignment explanation
Indices: 5992922--5992968 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
5992912 TCTCTATCAT
5992922 TTCTT-TATTTCATTTCA
1 TTCTTATATTTCATTTCA
*
5992939 TTCTTATTATTTCTTTTCA
1 TTCTTA-TATTTCATTTCA
5992958 TTACTTATATT
1 TT-CTTATATT
5992969 ATTATTCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
19 17 0.65
20 4 0.15
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.66
Consensus pattern (18 bp):
TTCTTATATTTCATTTCA
Found at i:5994398 original size:45 final size:45
Alignment explanation
Indices: 5994347--5994548 Score: 361
Period size: 45 Copynumber: 4.5 Consensus size: 45
5994337 CAATTTAATC
*
5994347 CCATAAGCTTGTAAGCTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
*
5994392 CCATAAGCTCATAAGCTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
*
5994437 CCATAAGCTCGTAAGCTTATTGTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
*
5994482 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTGCCA-TTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
5994526 CCATAAGCTCGTAAGCTTATTTT
1 CCATAAGCTCGTAAGCTTATTTT
5994549 CATACTTACC
Statistics
Matches: 151, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
44 28 0.19
45 123 0.81
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.38
Consensus pattern (45 bp):
CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
Found at i:5995776 original size:19 final size:21
Alignment explanation
Indices: 5995733--5995784 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
5995723 GAAACCCCTT
5995733 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
5995754 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
5995773 TGAAGATACATG
1 TGAAAATACATG
5995785 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:5998708 original size:15 final size:15
Alignment explanation
Indices: 5998674--5998710 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5998664 TCCGAAAATT
5998674 AAAAAA-AA-AAAAA
1 AAAAAAGAAGAAAAA
5998687 AAAAAAGAAGAAAAA
1 AAAAAAGAAGAAAAA
*
5998702 GAAAAAGAA
1 AAAAAAGAA
5998711 TTCTGGTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.29
14 2 0.10
15 13 0.62
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAGAAAAA
Found at i:6001880 original size:23 final size:24
Alignment explanation
Indices: 6001852--6001905 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
6001842 AAAATCAGGA
6001852 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* * *
6001875 AAGAAATTGATAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
6001899 AAGAAAA
1 AAGAAAA
6001906 AGAAAGAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.61, C:0.11, G:0.17, T:0.11
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:6004712 original size:24 final size:24
Alignment explanation
Indices: 6004666--6004717 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
6004656 TTCTTGGACT
* * *
6004666 TCAAGTGGCACATCTTTTTGAACA
1 TCAAGTGGCACAGCTGTTGGAACA
* *
6004690 TCAAGTGGCATAGCTGTTGGAACG
1 TCAAGTGGCACAGCTGTTGGAACA
6004714 TCAA
1 TCAA
6004718 AGGACATGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (24 bp):
TCAAGTGGCACAGCTGTTGGAACA
Found at i:6006032 original size:23 final size:22
Alignment explanation
Indices: 6005983--6006034 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
6005973 TTTCTTTCTT
*
6005983 TTTTCTTCTTTGAGTGTTTTCA
1 TTTTCTTCTTTGAGTGCTTTCA
* *
6006005 ATTTCTTCTTTTGAGTGCTTTGA
1 TTTTCTTC-TTTGAGTGCTTTCA
6006028 TTTTCTT
1 TTTTCTT
6006035 TGCTGGATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.10, C:0.13, G:0.13, T:0.63
Consensus pattern (22 bp):
TTTTCTTCTTTGAGTGCTTTCA
Found at i:6017742 original size:45 final size:45
Alignment explanation
Indices: 6017691--6017892 Score: 298
Period size: 45 Copynumber: 4.5 Consensus size: 45
6017681 CAATTTAATC
* *
6017691 CCATAAGCTTGTAAGCTTATTTTACCAACAAACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
* **
6017736 CCATAAGCTCATAAGCTTATTTTACCAACATACTTATAATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
*
6017781 CCATAAGCTCGTAAGCTTATTGTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
* * * *
6017826 CAATATGCTCATAAGCTTATTTTACCAACATACTTGCCA-TTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
*
6017870 TCATAAGCTCGTAAGCTTATTTT
1 CCATAAGCTCGTAAGCTTATTTT
6017893 CATACTTACC
Statistics
Matches: 139, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
44 24 0.17
45 115 0.83
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (45 bp):
CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
Found at i:6020058 original size:15 final size:15
Alignment explanation
Indices: 6020034--6020063 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6020024 TATGATAATT
6020034 AAGAAATGAAATGGA
1 AAGAAATGAAATGGA
*
6020049 AAGAATTGAAATGGA
1 AAGAAATGAAATGGA
6020064 TAAAATAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.17
Consensus pattern (15 bp):
AAGAAATGAAATGGA
Found at i:6020248 original size:13 final size:12
Alignment explanation
Indices: 6020229--6020293 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
6020219 ATATAGGCGT
6020229 GATATGGTGATG
1 GATATGGTGATG
6020241 GAATATGGTGAT-
1 G-ATATGGTGATG
*
6020253 GATATAGGCG-T-
1 GATAT-GGTGATG
6020264 GATAATGGTGATG
1 GAT-ATGGTGATG
6020277 GACTATGGTGAT-
1 GA-TATGGTGATG
6020289 GATAT
1 GATAT
6020294 AGGCGTTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:6020284 original size:36 final size:36
Alignment explanation
Indices: 6020211--6020315 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
6020201 ATTTATAAGT
* *
6020211 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
6020246 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
6020282 TGGTGATGATATAGGCGTTATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
6020316 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:0.29, C:0.05, G:0.35, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Done.