Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007767.1 Hibiscus syriacus cultivar Beakdansim tig00110039_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: 275075
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2635 original size:12 final size:13
Alignment explanation
Indices: 2607--2635 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2597 TTTAAACTTT
2607 TTTTTTTTTTGAC
1 TTTTTTTTTTGAC
2620 TTTTTTTTTTGA-
1 TTTTTTTTTTGAC
2632 TTTT
1 TTTT
2636 GTACTGACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (13 bp):
TTTTTTTTTTGAC
Found at i:5668 original size:20 final size:22
Alignment explanation
Indices: 5645--5693 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
5635 AATTTAGTAC
5645 TTAAATTATAAGT-TTT-ATTT
1 TTAAATTATAAGTATTTAATTT
*
5665 TT-AATT-TAATTATTTAATTT
1 TTAAATTATAAGTATTTAATTT
5685 TTAAATTAT
1 TTAAATTAT
5694 TTAAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 4 0.17
19 7 0.29
20 8 0.33
21 4 0.17
22 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTAAATTATAAGTATTTAATTT
Found at i:5703 original size:16 final size:16
Alignment explanation
Indices: 5667--5704 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5657 TTTTATTTTT
5667 AATTT-AATTATTTAA
1 AATTTAAATTATTTAA
**
5682 TTTTTAAATTATTTAA
1 AATTTAAATTATTTAA
5698 AATTTAA
1 AATTTAA
5705 TCACTTTAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 1
0.78 0.17 0.04
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTTAAATTATTTAA
Found at i:12276 original size:18 final size:18
Alignment explanation
Indices: 12249--12283 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12239 ATATACAAAT
* *
12249 TAAAATATAAATTAATAC
1 TAAAAAATAAATAAATAC
12267 TAAAAAATAAATAAATA
1 TAAAAAATAAATAAATA
12284 ATTCACAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAAATAAATAAATAC
Found at i:13326 original size:26 final size:29
Alignment explanation
Indices: 13297--13351 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
13287 ATATTTTATT
*
13297 AATTTAAT-TT-TAATCTGAAT-ATAATA
1 AATTTAATCTTATAATCTAAATAATAATA
13323 AATTTAATCTTATAATCTAAATAATAATA
1 AATTTAATCTTATAATCTAAATAATAATA
13352 TACCATTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.32
27 2 0.08
28 9 0.36
29 6 0.24
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (29 bp):
AATTTAATCTTATAATCTAAATAATAATA
Found at i:13594 original size:14 final size:13
Alignment explanation
Indices: 13577--13615 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
13567 ACTTATAGTG
13577 TTTAAAAAGATATT
1 TTTAAAAA-ATATT
*
13591 TTTAAATAATATT
1 TTTAAAAAATATT
13604 TTT-AAAAATATT
1 TTTAAAAAATATT
13616 AAAAATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 8 0.35
13 8 0.35
14 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (13 bp):
TTTAAAAAATATT
Found at i:13613 original size:12 final size:12
Alignment explanation
Indices: 13581--13615 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
13571 ATAGTGTTTA
13581 AAAAGATATTTTT
1 AAAA-ATATTTTT
13594 AAATAATATTTTT
1 AAA-AATATTTTT
13607 AAAAATATT
1 AAAAATATT
13616 AAAAATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.29
13 14 0.67
14 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (12 bp):
AAAAATATTTTT
Found at i:13899 original size:17 final size:18
Alignment explanation
Indices: 13871--13906 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
13861 CACCCACGGG
13871 TCCCTATCCTTTTAAATT
1 TCCCTATCCTTTTAAATT
*
13889 TCCCT-TCCTTTTTAATT
1 TCCCTATCCTTTTAAATT
13906 T
1 T
13907 TATTTGGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.56
Consensus pattern (18 bp):
TCCCTATCCTTTTAAATT
Found at i:14187 original size:32 final size:32
Alignment explanation
Indices: 14104--14193 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 32
14094 CTTATGTGGT
* * * *
14104 ACATTTCATGTCATCATTTTTGATTACATGAC
1 ACATGTCATGTCATCATTTTTGGTGACATAAC
14136 ACATGCTACA--TCATCATTTTTGGTGACATAAC
1 ACATG-T-CATGTCATCATTTTTGGTGACATAAC
*
14168 ACATGTCATGTCATTATTTTTGGTGA
1 ACATGTCATGTCATCATTTTTGGTGA
14194 TGTGGCATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
30 2 0.04
31 1 0.02
32 43 0.88
33 1 0.02
34 2 0.04
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (32 bp):
ACATGTCATGTCATCATTTTTGGTGACATAAC
Found at i:14244 original size:32 final size:32
Alignment explanation
Indices: 14114--14247 Score: 117
Period size: 32 Copynumber: 4.2 Consensus size: 32
14104 ACATTTCATG
* *
14114 TCATCATTTTTGATTACATGACACATG-CTACA
1 TCATCATTTTTGGTGACATGACACATGTC-ACA
* **
14146 TCATCATTTTTGGTGACATAACACATGTCATG
1 TCATCATTTTTGGTGACATGACACATGTCACA
* ** * * **
14178 TCATTATTTTTGGTGATGTGGCATATGTTGCA
1 TCATCATTTTTGGTGACATGACACATGTCACA
* * *
14210 TCATCATTTTTGGTGACGTGACATATGACACA
1 TCATCATTTTTGGTGACATGACACATGTCACA
14242 TCATCA
1 TCATCA
14248 ATTGAACATA
Statistics
Matches: 80, Mismatches: 21, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
32 79 0.99
33 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (32 bp):
TCATCATTTTTGGTGACATGACACATGTCACA
Found at i:14756 original size:32 final size:32
Alignment explanation
Indices: 14718--14788 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
14708 GTTATCGTCT
* *
14718 ATCATTTTTGGTGATGTGACATATATTACATC
1 ATCATTTTTGGTGACGTGACATATATCACATC
* *
14750 ATCATTTTTGGTGACGTGACATATGTCACGTC
1 ATCATTTTTGGTGACGTGACATATATCACATC
14782 ATCATTT
1 ATCATTT
14789 GAACATATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (32 bp):
ATCATTTTTGGTGACGTGACATATATCACATC
Found at i:18813 original size:13 final size:13
Alignment explanation
Indices: 18795--18828 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
18785 ATTGGGCAAT
18795 TTTGAAAACTAA-G
1 TTTGAAAAC-AAGG
18808 TTTGAAAACAAGG
1 TTTGAAAACAAGG
18821 TTTGAAAA
1 TTTGAAAA
18829 TCAATATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.10
13 18 0.90
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (13 bp):
TTTGAAAACAAGG
Found at i:19318 original size:20 final size:22
Alignment explanation
Indices: 19293--19344 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
19283 GTGGAGGGTG
*
19293 TCGATTCCC-T-AAAGGGGGAA
1 TCGATTCCCATCAAAGGGGAAA
19313 TCGATTCCCATTCAAAGGGGAAA
1 TCGATTCCCA-TCAAAGGGGAAA
*
19336 TCGGTTCCC
1 TCGATTCCC
19345 CTTCAAGGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 9 0.33
22 1 0.04
23 17 0.63
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (22 bp):
TCGATTCCCATCAAAGGGGAAA
Found at i:19337 original size:23 final size:23
Alignment explanation
Indices: 19303--19366 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
19293 TCGATTCCCT
19303 AAAGGGGGAATCGATTCCCATTC
1 AAAGGGGGAATCGATTCCCATTC
* * *
19326 AAAGGGGAAATCGGTTCCCCTTC
1 AAAGGGGGAATCGATTCCCATTC
* *
19349 AAGGGGGGCATCGATTCC
1 AAAGGGGGAATCGATTCC
19367 TCATGCACTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (23 bp):
AAAGGGGGAATCGATTCCCATTC
Found at i:23557 original size:22 final size:21
Alignment explanation
Indices: 23515--23554 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
23505 GAGATTATTT
*
23515 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
23536 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
23555 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:29099 original size:35 final size:35
Alignment explanation
Indices: 29053--29122 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
29043 GAAGTCTCTT
*
29053 TAGGTTCAGATCGA-TCAAACTGGTAATTCCTTATA
1 TAGGTTCAGATCGATTCAAA-TGCTAATTCCTTATA
* *
29088 TAGGTTTAGATCGATTGAAATGCTAATTCCTTATA
1 TAGGTTCAGATCGATTCAAATGCTAATTCCTTATA
29123 GACCTAAGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 27 0.87
36 4 0.13
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (35 bp):
TAGGTTCAGATCGATTCAAATGCTAATTCCTTATA
Found at i:38030 original size:23 final size:25
Alignment explanation
Indices: 37971--38030 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 25
37961 TGAATCTTAG
*
37971 ATGACGCGCATTGATGACAGCATTT
1 ATGACGCGCATTCATGACAGCATTT
* * *
37996 ATGACTCACATTCA-GGCA-CATTT
1 ATGACGCGCATTCATGACAGCATTT
38019 ATGACGCGCATT
1 ATGACGCGCATT
38031 GAGCGTCATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 15 0.52
24 3 0.10
25 11 0.38
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (25 bp):
ATGACGCGCATTCATGACAGCATTT
Found at i:38040 original size:23 final size:22
Alignment explanation
Indices: 37971--38040 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 22
37961 TGAATCTTAG
37971 ATGACGCGCATTGATGACAGCATTT
1 ATGACGCGCATTGA-G-C-GCATTT
* * * *
37996 ATGACTCACATTCAGGCACATTT
1 ATGACGCGCATTGA-GCGCATTT
38019 ATGACGCGCATTGAGCGTCATT
1 ATGACGCGCATTGAGCG-CATT
38041 GAAGCCCCCG
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
22 2 0.06
23 20 0.57
24 1 0.03
25 12 0.34
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (22 bp):
ATGACGCGCATTGAGCGCATTT
Found at i:42678 original size:46 final size:46
Alignment explanation
Indices: 42562--42778 Score: 296
Period size: 46 Copynumber: 4.7 Consensus size: 46
42552 TAATATACCA
** * *
42562 TTATGCATTTTCATTGGTCG-CATCCTTTCATGCCAATTATGCACCG
1 TTATGCATTTTCATTTAT-GACATCCTTTCATGCCTATAATGCACCG
* *
42608 TTA-GCATTTTCATTTATGACATCCTTTCATGCCTATAATGTATCG
1 TTATGCATTTTCATTTATGACATCCTTTCATGCCTATAATGCACCG
* *
42653 TTATGCATTTTCATTTATGAAATCCTTTCATGCCGATAATGCACCG
1 TTATGCATTTTCATTTATGACATCCTTTCATGCCTATAATGCACCG
* *
42699 TTATGCATTTTCATTTATGGCATCCTTTCATGCTTATAATGCACCG
1 TTATGCATTTTCATTTATGACATCCTTTCATGCCTATAATGCACCG
*
42745 TTATGCATGTTCATTTATCG-CATCCTTTCATGCC
1 TTATGCATTTTCATTTAT-GACATCCTTTCATGCC
42779 GAAGGCATTT
Statistics
Matches: 152, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
44 1 0.01
45 37 0.24
46 113 0.74
47 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (46 bp):
TTATGCATTTTCATTTATGACATCCTTTCATGCCTATAATGCACCG
Found at i:42928 original size:81 final size:81
Alignment explanation
Indices: 42780--43018 Score: 361
Period size: 81 Copynumber: 3.0 Consensus size: 81
42770 TTTCATGCCG
* * * * * *
42780 AAGGCATTTAAACTTTCATCTAACTAGCATGATTGACACATTTCTGTCAAATGCACAGCTAGTCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGACA
*
42845 ATTAATATTTTACTCA
66 ATTAATCTTTTACTCA
* *
42861 AAGGTATTTAACCTTTCATCTAACTGGCATGACTGACACCTTTCTGTCCAATGCACAACTAGACA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGACA
42926 ATTAATCTTTTACTCA
66 ATTAATCTTTTACTCA
* * * *
42942 AAGGTATTTAACCTTTCATCTAACTGGAATGATTAACACCTTTCTGTCAAATGCATAACTAGGCA
1 AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGACA
43007 ATTAATCTTTTA
66 ATTAATCTTTTA
43019 TTTTAAAACA
Statistics
Matches: 143, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 143 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (81 bp):
AAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGACA
ATTAATCTTTTACTCA
Found at i:48300 original size:46 final size:46
Alignment explanation
Indices: 48250--48452 Score: 246
Period size: 46 Copynumber: 4.4 Consensus size: 46
48240 TTTTCGTTGG
* * *
48250 TGGCATCCTTTCATGCCAATTATGTACCGTTAAGCATTTTCATTTA
1 TGGCATCCTTTCATGCCAATAATGCACCGTTATGCATTTTCATTTA
* *****
48296 TGGCA-CCATTTCATGCCTATAATATGTTGTTATGCATTTTCATTTA
1 TGGCATCC-TTTCATGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
48342 TGGCATCCTTTCATGCCGATAATGCACCGTTATGTATTTTCTTTTA
1 TGGCATCCTTTCATGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * *
48388 TGGTATCCTTTTATGCCTATAATGCACCATTATGCATTTTCATTTA
1 TGGCATCCTTTCATGCCAATAATGCACCGTTATGCATTTTCATTTA
48434 TGGCATCCTTTCATGCCAA
1 TGGCATCCTTTCATGCCAA
48453 AGGCATTTAA
Statistics
Matches: 131, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
45 2 0.02
46 127 0.97
47 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (46 bp):
TGGCATCCTTTCATGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:48585 original size:81 final size:80
Alignment explanation
Indices: 48450--48852 Score: 529
Period size: 81 Copynumber: 5.0 Consensus size: 80
48440 CCTTTCATGC
* ** * * *
48450 CAAAGGCATTTAACCTTTCATCTAACTTTCATTATTGACACCTTTCTGCCAAATGCATAGTTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCATA-CTAGG
48515 CAATTAATCTTTTACT
65 CAATTAATCTTTTACT
* * *
48531 CAAAGGTATTTAACCTCTCATCTAACTGGCATGATTTACATCTTTCTGTCAAATGCACTACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCA-TACTAGG
48596 CAATTAATCTTTTACT
65 CAATTAATCTTTTACT
* * * *
48612 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTATGTAAAATACATATCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCATA-CTAGG
*
48677 TAATTAAT-TTTTAACT
65 CAATTAATCTTTT-ACT
* * * *
48693 CAAAGGTATTTAACCTTTCATCTAACTGACATGATTGAAACCTTTCTGTCCAATGCACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCA-TACTAGG
*
48758 AAATTAATCTTTTACT
65 CAATTAATCTTTTACT
* * * *
48774 CAAAGGTATTTGACCTGTCATCTAACTGGCATGATTGACATCTTTCTGTCAAATGCACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCA-TACTAGG
*
48839 CAATTAATTTTTTA
65 CAATTAATCTTTTA
48853 TTTTAAAATA
Statistics
Matches: 283, Mismatches: 34, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
80 6 0.02
81 270 0.95
82 7 0.02
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (80 bp):
CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCATACTAGGC
AATTAATCTTTTACT
Found at i:58979 original size:21 final size:21
Alignment explanation
Indices: 58953--59023 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
58943 ATTTTTGTGC
58953 AAAGTGCATCGATACACTATG
1 AAAGTGCATCGATACACTATG
* * *
58974 AAAGTGTACCGATGCATTCCT-TG
1 AAAGTGCATCGATACA---CTATG
*
58997 AATGTGCATCGATACACTATG
1 AAAGTGCATCGATACACTATG
59018 AAAGTG
1 AAAGTG
59024 TACCGACGCA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 2 0.05
21 20 0.53
23 14 0.37
24 2 0.05
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (21 bp):
AAAGTGCATCGATACACTATG
Found at i:59009 original size:23 final size:23
Alignment explanation
Indices: 58972--59053 Score: 71
Period size: 23 Copynumber: 3.7 Consensus size: 23
58962 CGATACACTA
* *
58972 TGAAAGTGTACCGATGCATTCCT
1 TGAATGTGTATCGATGCATTCCT
* *
58995 TGAATGTGCATCGATACA---CT
1 TGAATGTGTATCGATGCATTCCT
* * *
59015 ATGAAAGTGTACCGACGCATTCCT
1 -TGAATGTGTATCGATGCATTCCT
59039 TGAATGTGTATCGAT
1 TGAATGTGTATCGAT
59054 ACACTCAGGA
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
20 2 0.05
21 13 0.30
23 26 0.60
24 2 0.05
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (23 bp):
TGAATGTGTATCGATGCATTCCT
Found at i:59019 original size:44 final size:44
Alignment explanation
Indices: 58956--59058 Score: 188
Period size: 44 Copynumber: 2.3 Consensus size: 44
58946 TTTGTGCAAA
*
58956 GTGCATCGATACACTATGAAAGTGTACCGATGCATTCCTTGAAT
1 GTGCATCGATACACTATGAAAGTGTACCGACGCATTCCTTGAAT
59000 GTGCATCGATACACTATGAAAGTGTACCGACGCATTCCTTGAAT
1 GTGCATCGATACACTATGAAAGTGTACCGACGCATTCCTTGAAT
*
59044 GTGTATCGATACACT
1 GTGCATCGATACACT
59059 CAGGAGTGTA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (44 bp):
GTGCATCGATACACTATGAAAGTGTACCGACGCATTCCTTGAAT
Found at i:63777 original size:21 final size:21
Alignment explanation
Indices: 63754--63800 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
63744 TGTTGTGTGC
63754 TTTCAACTTTTCTTCTTTTTCT
1 TTTC-ACTTTTCTTCTTTTTCT
** *
63776 TTTCTTTTTTCTTCTTTTTAT
1 TTTCACTTTTCTTCTTTTTCT
63797 TTTC
1 TTTC
63801 TTCATTTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTCACTTTTCTTCTTTTTCT
Found at i:63779 original size:14 final size:15
Alignment explanation
Indices: 63760--63793 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
63750 GTGCTTTCAA
63760 CTTTTCTTCTTT-TT
1 CTTTTCTTCTTTCTT
*
63774 CTTTTCTTTTTTCTT
1 CTTTTCTTCTTTCTT
63789 CTTTT
1 CTTTT
63794 TATTTTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
CTTTTCTTCTTTCTT
Found at i:63790 original size:10 final size:10
Alignment explanation
Indices: 63761--63794 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
63751 TGCTTTCAAC
63761 TTTTCTTCTT
1 TTTTCTTCTT
*
63771 TTTCTTTTCTT
1 TTT-TCTTCTT
63782 TTTTCTTCTT
1 TTTTCTTCTT
63792 TTT
1 TTT
63795 ATTTTCTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTCTTCTT
Found at i:63801 original size:21 final size:21
Alignment explanation
Indices: 63761--63802 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
63751 TGCTTTCAAC
*
63761 TTTTCTTCTTTTTCTTTTCTT
1 TTTTCTTCTTTTTATTTTCTT
63782 TTTTCTTCTTTTTATTTTCTT
1 TTTTCTTCTTTTTATTTTCTT
63803 CATTTGAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTCTTCTTTTTATTTTCTT
Found at i:83602 original size:90 final size:90
Alignment explanation
Indices: 83449--83621 Score: 303
Period size: 90 Copynumber: 1.9 Consensus size: 90
83439 CCTAACACAC
*
83449 CCTTTTATATCCAAGTTACCCTAATCATATTACGGTTTTCATTATTTTAAATTAATTAAATCTAT
1 CCTTTTATATCCAAGTTACCCTAATCATATTACGGTTTTCATTATTTCAAATTAATTAAATCTAT
*
83514 ATTTAATTAATTGGAATTTAATCAT
66 ATTTAATTAATTGAAATTTAATCAT
*
83539 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTT-ATTATTTCAAATTAATTAAATCTA
1 CCTTTTATATCCAAGTTACCCTAATCATATTACGG-TTTTCATTATTTCAAATTAATTAAATCTA
83603 TATTTAATTAATTGAAATT
65 TATTTAATTAATTGAAATT
83622 AAATATTCGG
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
90 75 0.95
91 4 0.05
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (90 bp):
CCTTTTATATCCAAGTTACCCTAATCATATTACGGTTTTCATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTTAATCAT
Found at i:88887 original size:14 final size:14
Alignment explanation
Indices: 88855--88895 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
88845 AAAGGTTTAT
88855 AAAATTTCCTGTCCA
1 AAAATTTCCTG-CCA
*
88870 AAAATTTCCTGCCC
1 AAAATTTCCTGCCA
88884 AAAATTTCCTGC
1 AAAATTTCCTGC
88896 GCTTCTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (14 bp):
AAAATTTCCTGCCA
Found at i:94328 original size:22 final size:21
Alignment explanation
Indices: 94303--94344 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
94293 TGTTATTTGG
94303 CTTTTTGATT-TTTCTTTTTTTC
1 CTTTTT-ATTCTTT-TTTTTTTC
94325 CTTTTTATTCTTTTTTTTTT
1 CTTTTTATTCTTTTTTTTTT
94345 GAAAAATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (21 bp):
CTTTTTATTCTTTTTTTTTTC
Found at i:104210 original size:18 final size:18
Alignment explanation
Indices: 104172--104212 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
104162 GTCAACGGCA
*
104172 GTCAACGGGTCGAGTCGG
1 GTCAACGGGTCGAGTCAG
* *
104190 GTCAACGGGTCGGGTTAG
1 GTCAACGGGTCGAGTCAG
104208 GTCAA
1 GTCAA
104213 ACCGGTTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.41, T:0.20
Consensus pattern (18 bp):
GTCAACGGGTCGAGTCAG
Found at i:107403 original size:20 final size:21
Alignment explanation
Indices: 107378--107428 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
107368 AAAACCCCTT
*
107378 TGAAAATACATGAT-TTTTGA
1 TGAAAATACATGATATTTTAA
107398 TGAAAATACA--ATATTTTAA
1 TGAAAATACATGATATTTTAA
*
107417 TGAATATACATG
1 TGAAAATACATG
107429 CTCTTAGCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
20 10 0.38
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATATTTTAA
Found at i:110690 original size:11 final size:11
Alignment explanation
Indices: 110673--110737 Score: 55
Period size: 11 Copynumber: 5.9 Consensus size: 11
110663 TCTTTTTGAA
110673 TTTTTCTTTT-
1 TTTTTCTTTTC
110683 TCTTTTCTTTTC
1 T-TTTTCTTTTC
*
110695 TTCTTT-TCTTC
1 TT-TTTCTTTTC
*
110706 TTTTTCTCTTC
1 TTTTTCTTTTC
110717 TTTTGTCTTTT-
1 TTTT-TCTTTTC
*
110728 TCTTTCTTTT
1 TTTTTCTTTT
110738 TGCACTCCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
10 10 0.21
11 28 0.60
12 9 0.19
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:110717 original size:27 final size:28
Alignment explanation
Indices: 110675--110738 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 28
110665 TTTTTGAATT
* *
110675 TTTCTTTTTCTTTTCTTTTCT-TCTTTTC
1 TTTCTTTTTCTCTTCTTTTGTCT-TTTTC
110703 -TTCTTTTTCTCTTCTTTTGTCTTTTTC
1 TTTCTTTTTCTCTTCTTTTGTCTTTTTC
110730 TTTCTTTTT
1 TTTCTTTTT
110739 GCACTCCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 23 0.72
28 9 0.28
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (28 bp):
TTTCTTTTTCTCTTCTTTTGTCTTTTTC
Found at i:110738 original size:18 final size:18
Alignment explanation
Indices: 110657--110739 Score: 79
Period size: 18 Copynumber: 4.8 Consensus size: 18
110647 TTTCCTTGGC
**
110657 TTTCTTTCTTTTTGAATT
1 TTTCTTTCTTTTTGTCTT
110675 TTTCTTT-TTCTTT-TC-T
1 TTTCTTTCTT-TTTGTCTT
110691 TTTC-TTCTTTTCT-TCTT
1 TTTCTTTCTTTT-TGTCTT
110708 TTTCTCTTC-TTTTGTCTT
1 TTTCT-TTCTTTTTGTCTT
110726 TTTCTTTCTTTTTG
1 TTTCTTTCTTTTTG
110740 CACTCCAATT
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
15 4 0.07
16 10 0.18
17 11 0.20
18 27 0.49
19 3 0.05
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTCTTTCTTTTTGTCTT
Found at i:111480 original size:20 final size:21
Alignment explanation
Indices: 111455--111505 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
111445 GAAACCCCTT
*
111455 TGAAAATACATGAT-TTTTGA
1 TGAAAATACATGATATTTTAA
111475 TGAAAATACA--ATATTTTAA
1 TGAAAATACATGATATTTTAA
*
111494 TGAAGATACATG
1 TGAAAATACATG
111506 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
20 10 0.38
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATATTTTAA
Found at i:113484 original size:15 final size:15
Alignment explanation
Indices: 113447--113478 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
113437 AAGTCTTGTT
113447 TTTGCATTAAAAATC
1 TTTGCATTAAAAATC
113462 TTTGCATTAAAAATC
1 TTTGCATTAAAAATC
113477 TT
1 TT
113479 GTCATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (15 bp):
TTTGCATTAAAAATC
Found at i:114206 original size:15 final size:15
Alignment explanation
Indices: 114186--114222 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
114176 ATCCAACACT
114186 CAAAAAGAAGAAAAG
1 CAAAAAGAAGAAAAG
*
114201 CAAAAAAAAGAAAAG
1 CAAAAAGAAGAAAAG
*
114216 AAAAAAG
1 CAAAAAG
114223 TTGAAGCACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.00
Consensus pattern (15 bp):
CAAAAAGAAGAAAAG
Found at i:115544 original size:24 final size:25
Alignment explanation
Indices: 115498--115552 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
115488 ACAGTTATGC
*
115498 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
115522 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
115547 CA-TTGA
1 CACTTGA
115553 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:118792 original size:2 final size:2
Alignment explanation
Indices: 118787--118826 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
118777 TTCTTATCAA
118787 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
118827 GTAAGAAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:120379 original size:27 final size:27
Alignment explanation
Indices: 120349--120412 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
120339 TTAAGGTGTA
*
120349 AAAAAATTTA-TTTTGGGTGTTAAATTT
1 AAAAAATTTATTTTTAGGTGTT-AATTT
**
120376 AAAAAAAATATTTTTAGGTGTTAATTT
1 AAAAAATTTATTTTTAGGTGTTAATTT
*
120403 ATAAAATTTA
1 AAAAAATTTA
120413 AAAATATTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
27 20 0.67
28 10 0.33
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (27 bp):
AAAAAATTTATTTTTAGGTGTTAATTT
Found at i:120380 original size:28 final size:28
Alignment explanation
Indices: 120347--120412 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
120337 TTTTAAGGTG
*
120347 TAAAAAAATTTA-TTTTGGGTGTTAAATT
1 TAAAAAAATTTATTTTTAGGTGTT-AATT
*
120375 TAAAAAAA-ATATTTTTAGGTGTTAATT
1 TAAAAAAATTTATTTTTAGGTGTTAATT
*
120402 T-ATAAAATTTA
1 TAAAAAAATTTA
120413 AAAATATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
26 5 0.16
27 9 0.28
28 18 0.56
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (28 bp):
TAAAAAAATTTATTTTTAGGTGTTAATT
Found at i:142154 original size:23 final size:24
Alignment explanation
Indices: 142101--142151 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
142091 TTTCTTTTCT
* *
142101 TTTTCTTCTTTTTGAGTGCTGGAA
1 TTTTCTTCTTTTGGAGTGCTGCAA
* *
142125 TTTTCTTCTTTTGGAGTTCTTCAA
1 TTTTCTTCTTTTGGAGTGCTGCAA
142149 TTT
1 TTT
142152 CTTTTATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.14, G:0.16, T:0.59
Consensus pattern (24 bp):
TTTTCTTCTTTTGGAGTGCTGCAA
Found at i:144061 original size:17 final size:17
Alignment explanation
Indices: 144041--144093 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
144031 TTCATGCATT
144041 TAGTTCATTAATCAAAC
1 TAGTTCATTAATCAAAC
* * *
144058 TAGTTCATTTATTAAGC
1 TAGTTCATTAATCAAAC
* *
144075 TAGTGCATTAATCTAAC
1 TAGTTCATTAATCAAAC
144092 TA
1 TA
144094 ACACTTTAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (17 bp):
TAGTTCATTAATCAAAC
Found at i:149249 original size:17 final size:17
Alignment explanation
Indices: 149227--149262 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
149217 AATTAAGATT
149227 TAGTTTAA-TAATTGAAC
1 TAGTTTAATTAA-TGAAC
149244 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
149261 TA
1 TA
149263 AATTTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.42
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:152132 original size:17 final size:17
Alignment explanation
Indices: 152110--152162 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
152100 AATTAAGAGT
*
152110 TAGTTTAATAAATAAAC
1 TAGTTTAATAAATGAAC
* *
152127 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
152144 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
152161 TA
1 TA
152163 AATTTATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:152171 original size:17 final size:17
Alignment explanation
Indices: 152113--152172 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
152103 TAAGAGTTAG
* * *
152113 TTTAATAAATAAACTAG
1 TTTAATTAATGAACTAA
* * *
152130 TTTGATGAATGAACTAG
1 TTTAATTAATGAACTAA
152147 TTTAATTAATGAACTAAA
1 TTTAATTAATGAACT-AA
152165 TTT-ATTAA
1 TTTAATTAA
152173 ATGGGTAGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
17 32 0.89
18 4 0.11
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (17 bp):
TTTAATTAATGAACTAA
Found at i:159400 original size:20 final size:20
Alignment explanation
Indices: 159375--159416 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
159365 CCATGACATG
159375 TAAATG-ATATAGAAACATAA
1 TAAATGAATATA-AAACATAA
*
159395 TAAATGAATCTAAAACATAA
1 TAAATGAATATAAAACATAA
159415 TA
1 TA
159417 TAAAGCTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (20 bp):
TAAATGAATATAAAACATAA
Found at i:164281 original size:20 final size:21
Alignment explanation
Indices: 164233--164281 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
164223 TATTCTTTTA
*
164233 CATCTTTTATATTATTATGAT
1 CATCTTTTATATTATTATAAT
164254 CATC-TTTATA-T-TTATAAT
1 CATCTTTTATATTATTATAAT
164272 CTATCTTTTA
1 C-ATCTTTTA
164282 ACATATGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.28
19 4 0.16
20 10 0.40
21 4 0.16
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.57
Consensus pattern (21 bp):
CATCTTTTATATTATTATAAT
Found at i:183046 original size:35 final size:35
Alignment explanation
Indices: 183007--183118 Score: 134
Period size: 35 Copynumber: 3.1 Consensus size: 35
182997 ATTGATGGTT
* *
183007 ATATAGTCGTGAAATGGTGATAGAAGTTGGTGATG
1 ATATAGGCGTGAAATGGTGATAGAAGATGGTGATG
* *
183042 ATATAGGCGTGCAATGGTGATTGAAGATGGTGATG
1 ATATAGGCGTGAAATGGTGATAGAAGATGGTGATG
* * *
183077 TTATAGGCGTAAAAAATGGTGATGGAAGATGGTGATG
1 ATATAGGCGT--GAAATGGTGATAGAAGATGGTGATG
*
183114 TTATA
1 ATATA
183119 TGTAGTATCT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 40 0.60
37 27 0.40
ACGTcount: A:0.32, C:0.04, G:0.34, T:0.30
Consensus pattern (35 bp):
ATATAGGCGTGAAATGGTGATAGAAGATGGTGATG
Found at i:188775 original size:35 final size:35
Alignment explanation
Indices: 188727--188812 Score: 109
Period size: 35 Copynumber: 2.5 Consensus size: 35
188717 TGGTAAGGGA
* * *
188727 TTGGTGGTTATATAGGCGTGAAATGGTGATAGAAG
1 TTGGTGATGATATAGGCGAGAAATGGTGATAGAAG
* *
188762 TTGGTGATGATATAGGCGAGCAATGGTGATGGAAG
1 TTGGTGATGATATAGGCGAGAAATGGTGATAGAAG
* *
188797 ATGGTGATGTTATAGG
1 TTGGTGATGATATAGG
188813 TAGTATCTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.30
Consensus pattern (35 bp):
TTGGTGATGATATAGGCGAGAAATGGTGATAGAAG
Found at i:192069 original size:11 final size:11
Alignment explanation
Indices: 192053--192100 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
192043 GTACTACAAT
192053 AAAATAAAAAG
1 AAAATAAAAAG
192064 AAAATAGAAAAG
1 AAAATA-AAAAG
* *
192076 AAAATGAAATG
1 AAAATAAAAAG
*
192087 AAAA-GAAAAG
1 AAAATAAAAAG
192097 AAAA
1 AAAA
192101 AGGCTCCTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
10 9 0.27
11 14 0.42
12 10 0.30
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAATAAAAAG
Found at i:192091 original size:16 final size:16
Alignment explanation
Indices: 192059--192099 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
192049 CAATAAAATA
192059 AAAAGAAAATAGAAAAG
1 AAAAG-AAATAGAAAAG
192076 AAAATGAAAT-GAAAAG
1 AAAA-GAAATAGAAAAG
192092 AAAAGAAA
1 AAAAGAAA
192100 AAGGCTCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.17
16 10 0.43
17 8 0.35
18 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (16 bp):
AAAAGAAATAGAAAAG
Found at i:192101 original size:11 final size:11
Alignment explanation
Indices: 192059--192102 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
192049 CAATAAAATA
192059 AAAAGAAAATAG
1 AAAAGAAAA-AG
*
192071 AAAAGAAAATG
1 AAAAGAAAAAG
*
192082 AAATG-AAAAG
1 AAAAGAAAAAG
192092 AAAAGAAAAAG
1 AAAAGAAAAAG
192103 GCTCCTACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 8 0.30
11 10 0.37
12 9 0.33
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:207911 original size:17 final size:17
Alignment explanation
Indices: 207891--207957 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 17
207881 AATTTGTACA
207891 ATTAAATGAAAGAAATG
1 ATTAAATGAAAGAAATG
* **
207908 ATTAAATGGAAATAAGAAA
1 ATTAAAT-GAAAGAA-ATG
207927 ATTAAA-GAAAGAAATG
1 ATTAAATGAAAGAAATG
207943 AATTGAAAATGAAAG
1 -ATT--AAATGAAAG
207958 GAAGGAATAG
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
16 1 0.03
17 16 0.42
18 6 0.16
19 10 0.26
20 5 0.13
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (17 bp):
ATTAAATGAAAGAAATG
Found at i:216049 original size:25 final size:25
Alignment explanation
Indices: 215991--216049 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
215981 AAAAATAAAC
* *
215991 AAAAGAAATTGAAGCACTCCAAAAG
1 AAAAGAAAATAAAGCACTCCAAAAG
*
216016 AAAAAAAAATAAAGCACTCCGAAAA-
1 AAAAGAAAATAAAGCACTCC-AAAAG
*
216041 ATAAGAAAA
1 AAAAGAAAA
216050 AAAAAGAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.64, C:0.14, G:0.12, T:0.10
Consensus pattern (25 bp):
AAAAGAAAATAAAGCACTCCAAAAG
Found at i:224131 original size:195 final size:195
Alignment explanation
Indices: 223799--224189 Score: 737
Period size: 195 Copynumber: 2.0 Consensus size: 195
223789 CACTGGAGGC
*
223799 TTATTCTTCCTAATGACTTCCATACTCTTTTTTCATATGAATCTGGTGATGTGATCATGCTCACT
1 TTATTCTTCCTAATGACTTCCATACTCTTTTTTCATATGAATCTGGTGATGTGATCATGCCCACT
223864 TTGGATCCAGAAGTCATGCTACAAGGTCCTATTACTAGATCAAGGGCCAAACGATTCAGGGAAGT
66 TTGGATCCAGAAGTCATGCTACAAGGTCCTATTACTAGATCAAGGGCCAAACGATTCAGGGAAGT
*
223929 ACTCTTAACTAAGTGTATTGAAGCTTTCGATTCATTTAACAACTTGACACCCTCTATTGTTAAGT
131 ACTCTTAACTAAGTGTATTGAAGCTTTCGATTCATTTAACAACTTGACACCCTCTAATGTTAAGT
223994 TTATTCTTCCTAATGACTTCCATACTCTTTTTTCATATGAATCTGGTGATGTGATCATGCCCACT
1 TTATTCTTCCTAATGACTTCCATACTCTTTTTTCATATGAATCTGGTGATGTGATCATGCCCACT
* * *
224059 TTGGATCTAGAAGTCATGTTATAAGGTCCTATTACTAGATCAAGGGCCAAACGATTCAGGGAAGT
66 TTGGATCCAGAAGTCATGCTACAAGGTCCTATTACTAGATCAAGGGCCAAACGATTCAGGGAAGT
224124 ACTCTTAACTAAGTGTATTGAAGCTTTCGATTCATTTAACAACTTGACACCCTCTAATGTTAAGT
131 ACTCTTAACTAAGTGTATTGAAGCTTTCGATTCATTTAACAACTTGACACCCTCTAATGTTAAGT
224189 T
1 T
224190 ATATAATGTT
Statistics
Matches: 191, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
195 191 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (195 bp):
TTATTCTTCCTAATGACTTCCATACTCTTTTTTCATATGAATCTGGTGATGTGATCATGCCCACT
TTGGATCCAGAAGTCATGCTACAAGGTCCTATTACTAGATCAAGGGCCAAACGATTCAGGGAAGT
ACTCTTAACTAAGTGTATTGAAGCTTTCGATTCATTTAACAACTTGACACCCTCTAATGTTAAGT
Found at i:240473 original size:11 final size:11
Alignment explanation
Indices: 240459--240484 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
240449 AATACAAAAA
240459 GAAGTGCAAGT
1 GAAGTGCAAGT
240470 GAAGTGCAAGT
1 GAAGTGCAAGT
240481 GAAG
1 GAAG
240485 AAATCAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.38, T:0.15
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:240542 original size:23 final size:23
Alignment explanation
Indices: 240501--240552 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
240491 AATTCCAACA
240501 AAGAAATCGAAGCAATC-AAAAG
1 AAGAAATCGAAGCAATCAAAAAG
* *
240523 AAGAAATTGAAAGCACTCAAAAAG
1 AAGAAATCG-AAGCAATCAAAAAG
240547 AAGAAA
1 AAGAAA
240553 AAGAAATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 8 0.31
23 7 0.27
24 11 0.42
ACGTcount: A:0.62, C:0.12, G:0.17, T:0.10
Consensus pattern (23 bp):
AAGAAATCGAAGCAATCAAAAAG
Found at i:240558 original size:24 final size:23
Alignment explanation
Indices: 240510--240558 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
240500 AAAGAAATCG
**
240510 AAGCAATCAAAAGAAGAAATTGA
1 AAGCAATCAAAAGAAGAAAAAGA
*
240533 AAGCACTCAAAAAGAAGAAAAAGA
1 AAGCAATC-AAAAGAAGAAAAAGA
240557 AA
1 AA
240559 TGAAAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.65, C:0.10, G:0.16, T:0.08
Consensus pattern (23 bp):
AAGCAATCAAAAGAAGAAAAAGA
Found at i:248840 original size:21 final size:21
Alignment explanation
Indices: 248816--248864 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
248806 AACAAGAAAT
*
248816 AAGAAAAAAAAGAAAAA-ATGA
1 AAGAAAAAAAACAAAAAGA-GA
* *
248837 AAGAAGAAATACAAAAAGAGA
1 AAGAAAAAAAACAAAAAGAGA
248858 AAGAAAA
1 AAGAAAA
248865 GACTCCTACA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (21 bp):
AAGAAAAAAAACAAAAAGAGA
Found at i:248901 original size:6 final size:6
Alignment explanation
Indices: 248890--248928 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
248880 TTTGGAGTGC
*
248890 AAAAGA AAAAGA AAAAGA AAAAGA AAAAAA AAACAGA AA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAA-AGA AA
248929 TTCAAAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 26 0.87
7 4 0.13
ACGTcount: A:0.85, C:0.03, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:253129 original size:15 final size:17
Alignment explanation
Indices: 253093--253126 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
253083 TTCGATAACA
253093 TTTC-TATCTATTTCCT
1 TTTCTTATCTATTTCCT
253109 TTTCTTATC-ATTTCCT
1 TTTCTTATCTATTTCCT
253125 TT
1 TT
253127 CTTCTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCTTATCTATTTCCT
Found at i:256487 original size:15 final size:16
Alignment explanation
Indices: 256467--256499 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
256457 TTAGGAGGGA
*
256467 AATGAAATA-AAAGGT
1 AATGAAAAACAAAGGT
256482 AATGAAAAACAAAGGT
1 AATGAAAAACAAAGGT
256498 AA
1 AA
256500 ATAAAAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.64, C:0.03, G:0.18, T:0.15
Consensus pattern (16 bp):
AATGAAAAACAAAGGT
Found at i:269464 original size:14 final size:16
Alignment explanation
Indices: 269441--269478 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
269431 TTGTTGTAAC
269441 AAGAAAAAA-A-AGAA
1 AAGAAAAAAGAGAGAA
269455 GAAGAAAAAAGAGAGAA
1 -AAGAAAAAAGAGAGAA
269472 AAGAAAA
1 AAGAAAA
269479 GACTCTACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 8 0.38
17 4 0.19
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAGAGAGAA
Found at i:269479 original size:14 final size:12
Alignment explanation
Indices: 269441--269480 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 12
269431 TTGTTGTAAC
269441 AAGAAAAAAAAG
1 AAGAAAAAAAAG
269453 AAGAAGAAAAAAG
1 AAGAA-AAAAAAG
269466 AGAGAAAAGAAAAG
1 A-AGAAAA-AAAAG
269480 A
1 A
269481 CTCTACACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.20
13 10 0.40
14 10 0.40
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAG
Found at i:269712 original size:13 final size:15
Alignment explanation
Indices: 269694--269725 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
269684 GTTATCTTCA
269694 TCATTT-CTTTA-TT
1 TCATTTCCTTTACTT
269707 TCATTTCCTTTACTT
1 TCATTTCCTTTACTT
269722 TCAT
1 TCAT
269726 ATTTCCCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 5 0.29
15 6 0.35
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (15 bp):
TCATTTCCTTTACTT
Found at i:272710 original size:20 final size:20
Alignment explanation
Indices: 272667--272709 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
272657 ATAAGAGGTG
*
272667 AAAA-CATATATTATGCAAT
1 AAAATCATATAATATGCAAT
272686 AAAATCATATAATATGCAAGT
1 AAAATCATATAATATGCAA-T
272707 AAA
1 AAA
272710 TGATAACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (20 bp):
AAAATCATATAATATGCAAT
Found at i:272719 original size:25 final size:22
Alignment explanation
Indices: 272669--272720 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 22
272659 AAGAGGTGAA
*
272669 AACATATATTATGCAATAAAAT
1 AACATATAATATGCAATAAAAT
272691 --CATATAATATGCAAGTAAATGAT
1 AACATATAATATGCAA-TAAA--AT
272714 AACATAT
1 AACATAT
272721 GATTATTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
20 13 0.54
21 4 0.17
23 2 0.08
25 5 0.21
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.31
Consensus pattern (22 bp):
AACATATAATATGCAATAAAAT
Done.