Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003233.1 Hibiscus syriacus cultivar Beakdansim tig00006803_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: 111031
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:179 original size:20 final size:20
Alignment explanation
Indices: 154--191 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
144 ATTTGGTGCA
154 GAGGGAACCGA-TCCCCCCTT
1 GAGGGAA-CGATTCCCCCCTT
174 GAGGGAACGATTCCCCCC
1 GAGGGAACGATTCCCCCC
192 ACAGGGAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.21, C:0.39, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACGATTCCCCCCTT
Found at i:2439 original size:11 final size:11
Alignment explanation
Indices: 2423--2457 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
2413 GGGGAGAAGT
2423 GTGTGTTTTAA
1 GTGTGTTTTAA
2434 GTGTGTGTGTTAA
1 GTGTGT-T-TTAA
2447 GTGTGTTTTAA
1 GTGTGTTTTAA
2458 AATAAGTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 10 0.45
12 2 0.09
13 10 0.45
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.51
Consensus pattern (11 bp):
GTGTGTTTTAA
Found at i:2441 original size:15 final size:13
Alignment explanation
Indices: 2419--2452 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2409 AAAGGGGGAG
*
2419 AAGTGTGTGTTTT
1 AAGTGTGTGTGTT
2432 AAGTGTGTGTGTT
1 AAGTGTGTGTGTT
2445 AAGTGTGT
1 AAGTGTGT
2453 TTTAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (13 bp):
AAGTGTGTGTGTT
Found at i:2465 original size:16 final size:16
Alignment explanation
Indices: 2444--2476 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2434 GTGTGTGTGT
2444 TAAGTGTGTTTTAAAA
1 TAAGTGTGTTTTAAAA
2460 TAAGTGTGTTTTAAAA
1 TAAGTGTGTTTTAAAA
2476 T
1 T
2477 GATAAATGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (16 bp):
TAAGTGTGTTTTAAAA
Found at i:2597 original size:15 final size:15
Alignment explanation
Indices: 2577--2607 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2567 AAGGGGGAGA
2577 TTGTTGAAAACATTT
1 TTGTTGAAAACATTT
2592 TTGTTGAAAACATTT
1 TTGTTGAAAACATTT
2607 T
1 T
2608 GATATTTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (15 bp):
TTGTTGAAAACATTT
Found at i:4608 original size:41 final size:41
Alignment explanation
Indices: 4563--4642 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
4553 TCCCAATTCA
* *
4563 ATTCAATTCAATCATAACAAAATGCAATAGTTTACCATTAG
1 ATTCAATTCAATCATAACAAAATGCAATACTTCACCATTAG
** *
4604 ATTCAATTCAATCATGGCAACATGCAATACTTCACCATT
1 ATTCAATTCAATCATAACAAAATGCAATACTTCACCATT
4643 CAACTTGATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.31
Consensus pattern (41 bp):
ATTCAATTCAATCATAACAAAATGCAATACTTCACCATTAG
Found at i:4673 original size:82 final size:82
Alignment explanation
Indices: 4587--4742 Score: 217
Period size: 82 Copynumber: 1.9 Consensus size: 82
4577 TAACAAAATG
* * * *
4587 CAATAGTTTACCATT-AGA-TTCAATTCAATCATGGCAACATGCAATACTTCACCATTCAACTTG
1 CAATAGTTCACCATTCA-ACTT-AATTCAATCATGACAACATACAATAATTCACCATTCAACTTG
4650 ATTCGATCATGATAGCATA
64 ATTCGATCATGATAGCATA
* * *
4669 CAATAGTTCACCATTCAACTTGATTCGATCATGACAGCATACAATAATTCACCATTCAACTTGAT
1 CAATAGTTCACCATTCAACTTAATTCAATCATGACAACATACAATAATTCACCATTCAACTTGAT
4734 TCGATCATG
66 TCGATCATG
4743 GTAACATGCA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
82 62 0.95
83 3 0.05
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (82 bp):
CAATAGTTCACCATTCAACTTAATTCAATCATGACAACATACAATAATTCACCATTCAACTTGAT
TCGATCATGATAGCATA
Found at i:4761 original size:41 final size:41
Alignment explanation
Indices: 4609--4742 Score: 196
Period size: 41 Copynumber: 3.3 Consensus size: 41
4599 ATTAGATTCA
* * *
4609 ATTCAATCATGGCAACATGCAATACTTCACCATTCAACTTG
1 ATTCGATCATGACAACATACAATACTTCACCATTCAACTTG
* * *
4650 ATTCGATCATGATAGCATACAATAGTTCACCATTCAACTTG
1 ATTCGATCATGACAACATACAATACTTCACCATTCAACTTG
* *
4691 ATTCGATCATGACAGCATACAATAATTCACCATTCAACTTG
1 ATTCGATCATGACAACATACAATACTTCACCATTCAACTTG
4732 ATTCGATCATG
1 ATTCGATCATG
4743 GTAACATGCA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 85 1.00
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (41 bp):
ATTCGATCATGACAACATACAATACTTCACCATTCAACTTG
Found at i:6464 original size:2 final size:2
Alignment explanation
Indices: 6457--6491 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6447 CAGCTTTTGC
6457 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6492 GCAGCCTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12852 original size:26 final size:27
Alignment explanation
Indices: 12816--12867 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
12806 CTGTCTCTAC
*
12816 ATGTCCTTAAA-TTTTCTTCCCATTTT
1 ATGTCCCTAAATTTTTCTTCCCATTTT
*
12842 ATGTCCCTAAATTTTTCTTCCTATTT
1 ATGTCCCTAAATTTTTCTTCCCATTT
12868 CATTTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.19, C:0.23, G:0.04, T:0.54
Consensus pattern (27 bp):
ATGTCCCTAAATTTTTCTTCCCATTTT
Found at i:18218 original size:21 final size:21
Alignment explanation
Indices: 18194--18236 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
18184 ACTGTTGTAT
*
18194 CCATCTTTATCCTAATTATAA
1 CCATCTTCATCCTAATTATAA
*
18215 CCATCTTCATCCTGATTATAA
1 CCATCTTCATCCTAATTATAA
18236 C
1 C
18237 AGTCCAACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.28, G:0.02, T:0.40
Consensus pattern (21 bp):
CCATCTTCATCCTAATTATAA
Found at i:20878 original size:59 final size:58
Alignment explanation
Indices: 20814--20951 Score: 152
Period size: 59 Copynumber: 2.3 Consensus size: 58
20804 GAGACTAATA
* * * * * * *
20814 TAAAATAAATGTCATAATTTGGGGATAAACCTAAAATGTTAAAAATTTGATGA-CCAATT
1 TAAAATAAA-GTCACAATTTAGAGATAAAACTAAAATATTAAAAAATT-AAGATCCAATT
* * *
20873 TAAAATAAGAGTTACATTTTAGAGATAAAATTAAAATATTAAAAAATTAAGATCCAATT
1 TAAAATAA-AGTCACAATTTAGAGATAAAACTAAAATATTAAAAAATTAAGATCCAATT
20932 TAAAATAAAGTCACAATTTA
1 TAAAATAAAGTCACAATTTA
20952 ATAACATATA
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
58 13 0.20
59 51 0.78
60 1 0.02
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.32
Consensus pattern (58 bp):
TAAAATAAAGTCACAATTTAGAGATAAAACTAAAATATTAAAAAATTAAGATCCAATT
Found at i:21169 original size:17 final size:17
Alignment explanation
Indices: 21149--21188 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
21139 TTAAAATTAA
* *
21149 TTAATTAATTTTTATTT
1 TTAATTAATTTATATCT
21166 TTAATTAATTTATATCT
1 TTAATTAATTTATATCT
21183 TTAATT
1 TTAATT
21189 GACTGTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTAATTAATTTATATCT
Found at i:23999 original size:2 final size:2
Alignment explanation
Indices: 23992--24017 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23982 ATTTTAACCA
23992 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
24018 GCGCGCGCGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24517 original size:60 final size:60
Alignment explanation
Indices: 24396--24525 Score: 147
Period size: 60 Copynumber: 2.1 Consensus size: 60
24386 GTCGGGTGAT
* * * * *
24396 CATTTTATAACTTTTAATAGTCGGGGGACTTAAGAAAACAATGTCCTATAATCAGGAGAC
1 CATTTTGTAACATTTAATAGTCGGAGGACTTAAGAAAACAATCTCCTATAATCAAGAGAC
* * *
24456 CATTTTGTAACATTTAATAGTCGGAGGACTTAATAAAGCAATACT-CTATAGTCGAAG-GAC
1 CATTTTGTAACATTTAATAGTCGGAGGACTTAAGAAAACAAT-CTCCTATAATC-AAGAGAC
24516 CATTTGTGTA
1 CATTT-TGTA
24526 CTTTACCTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
60 52 0.88
61 7 0.12
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (60 bp):
CATTTTGTAACATTTAATAGTCGGAGGACTTAAGAAAACAATCTCCTATAATCAAGAGAC
Found at i:27501 original size:25 final size:25
Alignment explanation
Indices: 27472--27534 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
27462 ATGAATAGCA
*
27472 AAAAAAAACATACAAACAAAGAAAT
1 AAAAAAAACATAAAAACAAAGAAAT
** * *
27497 AAAAATTATATAAAAACAAAGGAAT
1 AAAAAAAACATAAAAACAAAGAAAT
27522 ACAAATAAAACAT
1 A-AAA-AAAACAT
27535 GTATTAAATA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
25 21 0.75
26 3 0.11
27 4 0.14
ACGTcount: A:0.71, C:0.10, G:0.05, T:0.14
Consensus pattern (25 bp):
AAAAAAAACATAAAAACAAAGAAAT
Found at i:27531 original size:31 final size:32
Alignment explanation
Indices: 27493--27552 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
27483 ACAAACAAAG
27493 AAATAAAA-AT-TATATAAA-AACAAAGGAATAC
1 AAATAAAACATGTAT-TAAATAA-AAAGGAATAC
27524 AAATAAAACATGTATTAAATAAAAAGGAA
1 AAATAAAACATGTATTAAATAAAAAGGAA
27553 ACGCAATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
31 8 0.31
32 13 0.50
33 5 0.19
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.20
Consensus pattern (32 bp):
AAATAAAACATGTATTAAATAAAAAGGAATAC
Found at i:27708 original size:2 final size:2
Alignment explanation
Indices: 27701--27768 Score: 59
Period size: 2 Copynumber: 35.0 Consensus size: 2
27691 GATGGTTATG
* * * * * *
27701 TA TA TA TA TA TA TA TA TA TA AA TA -A AA TA AA AA TG TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
27742 -A GA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27769 AAGGGAATAA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (2 bp):
TA
Found at i:29949 original size:23 final size:23
Alignment explanation
Indices: 29923--29968 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
29913 CACCACAGCT
*
29923 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
29946 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
29969 TATAATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:31760 original size:64 final size:63
Alignment explanation
Indices: 31662--31822 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
31652 TAATGAAGGT
* *
31662 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
31725 GG
62 GC
*
31727 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
31791 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
31823 CCTTAAACAA
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.67
65 24 0.28
66 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:32699 original size:43 final size:43
Alignment explanation
Indices: 32638--32978 Score: 170
Period size: 43 Copynumber: 7.4 Consensus size: 43
32628 ATCAGCGGTC
*
32638 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATAT
1 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * *
32681 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGT-T-GATTGACAACCAGCGGT
1 CCTTCGTTGTGAAGTTGAACTTGCG---TTGTCTGGAGT-CCAA-TA----T
**
32731 CCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * *
32775 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGT-T-GATTGACAACCAGCGGT
1 CCTTCGTTGTGAAGTTGAACTTGCG---TTGTCTGGAGT-CCAA-TA----T
** *
32825 CCCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGTCCAATAT
1 -CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * ** **
32869 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGT-TGATTGACAACCAACGGT
1 CCTTCGTTGTGAAGTTGAACTTGCG---TTGTCTG---GA-GTCCAA-TAT
* *
32919 CCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATAT
1 -CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
32963 CCTTCGTTGTGAAGTT
1 CCTTCGTTGTGAAGTT
32979 AAAATTGGCT
Statistics
Matches: 219, Mismatches: 45, Indels: 68
0.66 0.14 0.20
Matches are distributed among these distances:
43 79 0.36
44 9 0.04
45 14 0.06
46 16 0.07
48 16 0.07
49 14 0.06
50 9 0.04
51 62 0.28
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (43 bp):
CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:32745 original size:51 final size:50
Alignment explanation
Indices: 32681--32938 Score: 192
Period size: 51 Copynumber: 5.4 Consensus size: 50
32671 AGTCCAATAT
*
32681 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAGCGGTC
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCA-CGGTC
* * * * * *
32732 CCTTCGTCATGAAGTTGAACTTGCG---TTGTCTGGAGT-CCAA-TA---T-
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGT-T-GATTGACAACCACGGTC
*
32775 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAGCGGTC
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCA-CGGTC
* * * * * *
32826 CCTTCGTCATGAAGTTGAACTT--G-CATTGTCTGGAGT-CCAA-TA---T-
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGT-T-GATTGACAACCACGGTC
*
32869 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAACGGTC
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACC-ACGGTC
32920 CCTTCGTCGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
32939 CTTGCATTGT
Statistics
Matches: 154, Mismatches: 29, Indels: 48
0.67 0.13 0.21
Matches are distributed among these distances:
43 40 0.26
44 8 0.05
45 9 0.06
46 10 0.06
47 1 0.01
48 11 0.07
49 9 0.06
50 8 0.05
51 58 0.38
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (50 bp):
CCTTCGTCGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCACGGTC
Found at i:32773 original size:94 final size:95
Alignment explanation
Indices: 32612--33300 Score: 868
Period size: 105 Copynumber: 7.0 Consensus size: 95
32602 TGGAACTGGA
* * * **
32612 AAATTGTTTATTGACAATCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGTCCA
1 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
32677 ATATCCTTCGTTGTGAAGTTGAAATTGG-G
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCG
* *
32706 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
32771 ATATCCTTCGTTGTGAAGTTGAAATTGG-G
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCG
*
32800 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGTCCA
1 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
32865 ATATCCTTCGTTGTGAAGTTGAAATTGG-G
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCG
*
32894 AAATTGTTGATTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
1 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
*
32959 ATATCCTTCGTTGTGAAGTTAAAATTGGCTCTG
66 ATATCCTTCGTTGTGAAGTTGAAATTGG--C-G
*
32992 AAATTGAGAAATGTTTG-TTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCT
1 AAA-T------TG-TTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
*
33056 GGAGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCTG
58 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG--C-G
*
33097 AAATTGAGAAATGTTTG-TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCACTGTCT
1 AAA-T------TG-TTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
* **
33161 GGAGTCTAACGTCCTTCGTTGTGAAGTTGAAATTGGCTCTG
58 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG--C-G
* *
33202 AAATTGAGAAATGTTTG-TTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
1 AAA-T------TG-TTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
*
33266 GGAGTCCAATATCCTTCGTTGAGAAGTTGAAATTG
58 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
33301 ACTCTGGGTA
Statistics
Matches: 559, Mismatches: 24, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
94 272 0.49
98 4 0.01
99 1 0.00
105 279 0.50
106 3 0.01
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (95 bp):
AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
ATATCCTTCGTTGTGAAGTTGAAATTGGCG
Found at i:34081 original size:21 final size:21
Alignment explanation
Indices: 34057--34098 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34047 ACCTTATTTT
34057 CTCTTCTT-TTGTTCTTTTCTC
1 CTCTT-TTCTTGTTCTTTTCTC
*
34078 CTCTTTTCTTTTTCTTTTCTC
1 CTCTTTTCTTGTTCTTTTCTC
34099 AATTTAGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (21 bp):
CTCTTTTCTTGTTCTTTTCTC
Found at i:34178 original size:24 final size:25
Alignment explanation
Indices: 34135--34181 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
34125 ACCCTAAACG
34135 TTCTTTTCTTCTTCTTCTTTTTTCC
1 TTCTTTTCTTCTTCTTCTTTTTTCC
*
34160 TTCTTTT-TTTTTCTTCTTTTTT
1 TTCTTTTCTTCTTCTTCTTTTTT
34182 TTTTAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (25 bp):
TTCTTTTCTTCTTCTTCTTTTTTCC
Found at i:34184 original size:13 final size:13
Alignment explanation
Indices: 34138--34184 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
34128 CTAAACGTTC
*
34138 TTTTCTTCTTCTT
1 TTTTTTTCTTCTT
*
34151 CTTTTTTCCTTCTT
1 -TTTTTTTCTTCTT
34165 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
34178 TTTTTTT
1 TTTTTTT
34185 TAACTTAGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTCTTCTT
Found at i:34184 original size:14 final size:14
Alignment explanation
Indices: 34138--34185 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
34128 CTAAACGTTC
* *
34138 TTTTCTTCTTCTTC
1 TTTTTTTCTTCTTT
*
34152 TTTTTTCCTTC-TT
1 TTTTTTTCTTCTTT
34165 TTTTTTTCTTCTTT
1 TTTTTTTCTTCTTT
34179 TTTTTTT
1 TTTTTTT
34186 AACTTAGGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTTCTTCTTT
Found at i:43630 original size:20 final size:19
Alignment explanation
Indices: 43588--43630 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
43578 AATGTTAGTA
*
43588 AAATAAAAAAAATGGAAAT
1 AAATAAAAAAAATAGAAAT
*
43607 AAATAAAAATAATAAGAAAT
1 AAATAAAAAAAAT-AGAAAT
43627 AAAT
1 AAAT
43631 GGCAAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (19 bp):
AAATAAAAAAAATAGAAAT
Found at i:44840 original size:2 final size:2
Alignment explanation
Indices: 44833--45062 Score: 174
Period size: 2 Copynumber: 118.5 Consensus size: 2
44823 AATAAAAGAA
44833 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
44875 AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * *
44917 AT AT AT GT TT AT AT ACG CT AT CA- AT A- AT AC CT A- AA AT A- AT
1 AT AT AT AT AT AT AT A-T AT AT -AT AT AT AT AT AT AT AT AT AT AT
* * * *
44957 AA AA AT A- AT GAT GT -T AT GT AT AT AT AT -T AT AT AT AT -T AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * *
44996 AT AT AT AT AT AT AA AT A- AA AT AA AT AA AT AA AA AT GT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
45037 A- AG AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
45063 AGGGAATAAA
Statistics
Matches: 182, Mismatches: 33, Indels: 26
0.76 0.14 0.11
Matches are distributed among these distances:
1 10 0.05
2 169 0.93
3 3 0.02
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:44840 original size:18 final size:20
Alignment explanation
Indices: 44803--44911 Score: 62
Period size: 20 Copynumber: 5.3 Consensus size: 20
44793 TAAATGAAAA
44803 AATATAAAGAATATACATAT
1 AATATAAAGAATATACATAT
*
44823 AATA-AAAGAAATATATATAT
1 AATATAAAG-AATATACATAT
* * *
44843 ATATATATA-TATATATATAT
1 A-ATATAAAGAATATACATAT
* * *
44863 ATATATATA-TATATATATAT
1 A-ATATAAAGAATATACATAT
* *
44883 ATATATAAATATATATATATAT
1 A-ATATAAAGA-ATATACATAT
44905 ATATATA
1 A-ATATA
44912 TATATATATA
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.05
20 53 0.67
21 3 0.04
22 19 0.24
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (20 bp):
AATATAAAGAATATACATAT
Found at i:44989 original size:9 final size:9
Alignment explanation
Indices: 44975--45008 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
44965 TGATGTTATG
44975 TATATATAT
1 TATATATAT
44984 TATATATAT
1 TATATATAT
44993 TATATATA-
1 TATATATAT
45001 TATATATA
1 TATATATA
45009 AATAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TATATATAT
Found at i:45095 original size:50 final size:50
Alignment explanation
Indices: 44993--45096 Score: 115
Period size: 50 Copynumber: 2.1 Consensus size: 50
44983 TTATATATAT
* *
44993 TATATATATATATATAAATAAAATAAATAAATAAAAATGTACATAAGATA
1 TATATATATATATATAAATAAAATAAATAAATAAAAATGAAAATAAGATA
* * *
45043 TATATATATATATATATATAAGGGAATAAA-ATATAATAATGAAAAT-AG-TA
1 TATATATATATATATAAATAA---AATAAATAAATAAAAATGAAAATAAGATA
45093 TATA
1 TATA
45097 ATAATAGTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
50 26 0.57
51 2 0.04
52 12 0.26
53 6 0.13
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.34
Consensus pattern (50 bp):
TATATATATATATATAAATAAAATAAATAAATAAAAATGAAAATAAGATA
Found at i:48698 original size:56 final size:56
Alignment explanation
Indices: 48621--48731 Score: 159
Period size: 56 Copynumber: 2.0 Consensus size: 56
48611 ATGGTCCCGA
* * * * *
48621 TTATATGATATTATTTATTAAGTACTTTGATTATTAAAAGTTACAACATGGTCATT
1 TTATATAATATTATTTATTAAGTACTTCGACTATTAAAAGTTACAAAATGATCATT
* *
48677 TTATATAATATTATTTTTTAAGTTCTTCGACTATTAAAAGTTACAAAATGATCAT
1 TTATATAATATTATTTATTAAGTACTTCGACTATTAAAAGTTACAAAATGATCAT
48732 CCAACTATTG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (56 bp):
TTATATAATATTATTTATTAAGTACTTCGACTATTAAAAGTTACAAAATGATCATT
Found at i:49960 original size:17 final size:17
Alignment explanation
Indices: 49933--49971 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
49923 AATTTACAAT
49933 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
49949 TAATTATAAATAATATC
1 TAATTATAAATAATATC
49966 TAATTA
1 TAATTA
49972 ATTGATTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:50815 original size:158 final size:156
Alignment explanation
Indices: 50504--50819 Score: 614
Period size: 158 Copynumber: 2.0 Consensus size: 156
50494 ACCAATCGGC
50504 GTTCAGGGAAATCGAGGCCTTGCAAATGCTTCATAACTGCCCCACATAGTCGTCTTGCACGAGTA
1 GTTCAGGGAAATCGAGGCCTTGCAAATGCTTCATAACTGCCCCACATAGTCGTCTTGCACGAGTA
50569 CTTTTGGCGGGAAGACGAGGACGCCGTGCTCGTTTGGAGTTCTTGAGGACCGATTTGGCGGCGGT
66 CTTTTGGCGGGAAGACGAGGACGCCGTGCTCGTTTGGAGTTCTTGAGGACCGATTTGGCGGCGGT
50634 TATCCGCGACGCGAAAAAGAAGGAAG
131 TATCCGCGACGCGAAAAAGAAGGAAG
50660 GTTCAGGGAAATCGAGGCCTTGCAAATGCTTCATAACTGCCCCAACATAGTCGTCTTGCACGAGT
1 GTTCAGGGAAATCGAGGCCTTGCAAATGCTTCATAACTGCCCC-ACATAGTCGTCTTGCACGAGT
50725 ACTTTTGGCGGGAAGACGAGGACGCCGTGCTCGTTTTGGAGTTCTTGAGGACCGATTTGGCGGCG
65 ACTTTTGGCGGGAAGACGAGGACGCCGTGCTCG-TTTGGAGTTCTTGAGGACCGATTTGGCGGCG
50790 GTTATCCGCGACGCGAAAAAGAAGGAAG
129 GTTATCCGCGACGCGAAAAAGAAGGAAG
50818 GT
1 GT
50820 GGGATCCGGG
Statistics
Matches: 158, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
156 43 0.27
157 54 0.34
158 61 0.39
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (156 bp):
GTTCAGGGAAATCGAGGCCTTGCAAATGCTTCATAACTGCCCCACATAGTCGTCTTGCACGAGTA
CTTTTGGCGGGAAGACGAGGACGCCGTGCTCGTTTGGAGTTCTTGAGGACCGATTTGGCGGCGGT
TATCCGCGACGCGAAAAAGAAGGAAG
Found at i:55508 original size:24 final size:24
Alignment explanation
Indices: 55476--55542 Score: 116
Period size: 24 Copynumber: 2.8 Consensus size: 24
55466 TAGAGCAGTG
55476 GAGTGCTGAAACACTGAAGCTCTA
1 GAGTGCTGAAACACTGAAGCTCTA
55500 GAGTGCTGAAACACTGAAGCTCTA
1 GAGTGCTGAAACACTGAAGCTCTA
* *
55524 GAGTGTTGAAGCACTGAAG
1 GAGTGCTGAAACACTGAAG
55543 TGCTGGAGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (24 bp):
GAGTGCTGAAACACTGAAGCTCTA
Found at i:64313 original size:36 final size:36
Alignment explanation
Indices: 64271--64346 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
64261 TTATAGCTAA
*
64271 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
64307 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
64343 AAAA
1 AAAA
64347 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:68692 original size:15 final size:15
Alignment explanation
Indices: 68674--68703 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
68664 CCACGGTGCT
68674 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
68689 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
68704 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:69168 original size:36 final size:36
Alignment explanation
Indices: 69126--69201 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
69116 TTATAGCTAA
*
69126 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
69162 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
69198 AAAA
1 AAAA
69202 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:74573 original size:2 final size:2
Alignment explanation
Indices: 74566--74595 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
74556 TCAAACCCGA
74566 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
74596 TAGAAGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82658 original size:13 final size:13
Alignment explanation
Indices: 82640--82664 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
82630 TTACCGAACA
82640 TTAAATGAACATG
1 TTAAATGAACATG
82653 TTAAATGAACAT
1 TTAAATGAACAT
82665 ATTCACGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (13 bp):
TTAAATGAACATG
Found at i:85928 original size:18 final size:18
Alignment explanation
Indices: 85886--85929 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
85876 TGGTGGCGGG
*
85886 GGGGAGGTGGATGATGTA
1 GGGGAGGTGGATGAAGTA
85904 GGCGGAGGT-GATGAAGTA
1 GG-GGAGGTGGATGAAGTA
85922 GAGGGAGG
1 G-GGGAGG
85930 AGGACGGGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.25, C:0.02, G:0.57, T:0.16
Consensus pattern (18 bp):
GGGGAGGTGGATGAAGTA
Found at i:86144 original size:48 final size:47
Alignment explanation
Indices: 86003--86165 Score: 145
Period size: 48 Copynumber: 3.5 Consensus size: 47
85993 AATAGCAGGT
* * * *
86003 GGTGGGGAAGGAGTAGTAGTTGGCGGCGGAGCCGCAGCGGCTGGTGGT
1 GGTGTGGAAGGAGT-GTAGTTGGCGGCGGAGCTGCAGCTGCTGGTGGG
* * * *
86051 GGTGTGG-AGGAAGTGGTGGTTGGCGGCGGAGTTGCTGCTGTTGGTGGG
1 GGTGTGGAAGG-AGT-GTAGTTGGCGGCGGAGCTGCAGCTGCTGGTGGG
* * * *
86099 GGTGTGGAAGGAGTGCTAGTTGGCGGCGGAACTGAAGCTACTGGT-GA
1 GGTGTGGAAGGAGTG-TAGTTGGCGGCGGAGCTGCAGCTGCTGGTGGG
*
86146 GG-GTGG-AGGAGTATAGTTGG
1 GGTGTGGAAGGAGTGTAGTTGG
86166 TTGATGGTGG
Statistics
Matches: 94, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
44 7 0.07
45 6 0.06
46 4 0.04
47 7 0.07
48 67 0.71
49 3 0.03
ACGTcount: A:0.15, C:0.10, G:0.52, T:0.22
Consensus pattern (47 bp):
GGTGTGGAAGGAGTGTAGTTGGCGGCGGAGCTGCAGCTGCTGGTGGG
Found at i:86570 original size:25 final size:21
Alignment explanation
Indices: 86519--86570 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
86509 ATTTATATAT
86519 TCAATTAATTCAGTTATAGTG
1 TCAATTAATTCAGTTATAGTG
86540 TCAATTAATTCAGTTATAGTG
1 TCAATTAATTCAGTTATAGTG
* *
86561 TAAAATAATT
1 TCAATTAATT
86571 TAATAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (21 bp):
TCAATTAATTCAGTTATAGTG
Found at i:87894 original size:5 final size:5
Alignment explanation
Indices: 87878--87911 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
87868 CGTATTACCA
87878 CGACC ACGACC CGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC CGACC CGACC CGACC CGACC CGA
87912 GACGAGACGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.24, C:0.56, G:0.21, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:88416 original size:5 final size:5
Alignment explanation
Indices: 88408--88448 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
88398 CCGTCTCGTC
88408 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG
88449 TGGTAATACG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.27
Consensus pattern (5 bp):
TCGGG
Found at i:88437 original size:6 final size:6
Alignment explanation
Indices: 88411--88452 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
88401 TCTCGTCTCG
88411 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
88453 AATACGTGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.00, C:0.17, G:0.55, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:88594 original size:21 final size:19
Alignment explanation
Indices: 88542--88597 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
88532 CGTTGCGATT
*
88542 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
*
88561 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
88584 TTGGACTATCGCAA
1 TTGGACTATCGCAA
88598 TGTGAATATG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 6 0.20
21 14 0.47
23 10 0.33
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:88655 original size:21 final size:20
Alignment explanation
Indices: 88629--88824 Score: 148
Period size: 21 Copynumber: 9.4 Consensus size: 20
88619 GCGATATTCA
*
88629 CATTGCGATAGTCGACTATCG
1 CATTGCGATAGTCAACT-TCG
*
88650 CATTGCGAT-TTACATA-TTCG
1 CATTGCGATAGT-CA-ACTTCG
*
88670 CATTGCGATAGTCCAAGTTCG
1 CATTGCGATAGT-CAACTTCG
*
88691 CAATTGCGATAGTCCAAGTTCG
1 C-ATTGCGATAGT-CAACTTCG
* *
88713 CATTGCGATAGTCGACTATCA
1 CATTGCGATAGTCAACT-TCG
*
88734 CATTGCGAT-TTACATA-TTCG
1 CATTGCGATAGT-CA-ACTTCG
*
88754 CATTGCGATAGTTCAAGTTCG
1 CATTGCGATAG-TCAACTTCG
* *
88775 CAATGCGATAGTCCAAGTTCG
1 CATTGCGATAGT-CAACTTCG
*
88796 CATTGCGATAGTCGAAGTTCG
1 CATTGCGATAGTC-AACTTCG
*
88817 CGTTGCGA
1 CATTGCGA
88825 ATCTGGAAAC
Statistics
Matches: 148, Mismatches: 14, Indels: 26
0.79 0.07 0.14
Matches are distributed among these distances:
20 32 0.22
21 92 0.62
22 24 0.16
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (20 bp):
CATTGCGATAGTCAACTTCG
Found at i:88679 original size:41 final size:41
Alignment explanation
Indices: 88622--88824 Score: 189
Period size: 42 Copynumber: 4.9 Consensus size: 41
88612 TCGCAATGCG
* *
88622 ATATTCACATTGCGATAGTCGACTATCGCATTGCGAT-TTAC
1 ATATTCGCATTGCGATAGTCGACT-TCGCATTGCGATAGTAC
* * *
88663 ATATTCGCATTGCGATAGTCCAAGTTCGCAATTGCGATAGTCC
1 ATATTCGCATTGCGATAGT-CGACTTCGC-ATTGCGATAGTAC
* *
88706 A-AGTTCGCATTGCGATAGTCGACTATCACATTGCGAT-TTAC
1 ATA-TTCGCATTGCGATAGTCGACT-TCGCATTGCGATAGTAC
* * * *
88747 ATATTCGCATTGCGATAGTTCAAGTTCGCAATGCGATAGTCC
1 ATATTCGCATTGCGATAG-TCGACTTCGCATTGCGATAGTAC
* *
88789 A-AGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGA
1 ATA-TTCGCATTGCGATAGTCG-ACTTCGCATTGCGA
88825 ATCTGGAAAC
Statistics
Matches: 133, Mismatches: 19, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
41 53 0.40
42 58 0.44
43 22 0.17
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (41 bp):
ATATTCGCATTGCGATAGTCGACTTCGCATTGCGATAGTAC
Found at i:88771 original size:84 final size:83
Alignment explanation
Indices: 88629--88810 Score: 337
Period size: 84 Copynumber: 2.2 Consensus size: 83
88619 GCGATATTCA
*
88629 CATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCAA
1 CATTGCGATAGTCGACTATCACATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCAA
88694 TTGCGATAGTCCAAGTTCG
66 -TGCGATAGTCCAAGTTCG
*
88713 CATTGCGATAGTCGACTATCACATTGCGATTTACATATTCGCATTGCGATAGTTCAAGTTCGCAA
1 CATTGCGATAGTCGACTATCACATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCAA
88778 TGCGATAGTCCAAGTTCG
66 TGCGATAGTCCAAGTTCG
88796 CATTGCGATAGTCGA
1 CATTGCGATAGTCGA
88811 AGTTCGCGTT
Statistics
Matches: 96, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
83 33 0.34
84 63 0.66
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (83 bp):
CATTGCGATAGTCGACTATCACATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCAA
TGCGATAGTCCAAGTTCG
Found at i:88800 original size:62 final size:63
Alignment explanation
Indices: 88687--88804 Score: 168
Period size: 62 Copynumber: 1.9 Consensus size: 63
88677 ATAGTCCAAG
* *
88687 TTCGCAATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCACATTGCGATTTACATA
1 TTCGCAATTGCGATAGTCCAAGTTCGCAATGCGATAGTCAACTATCACATTGCGATTTACATA
* * *
88750 TTCGC-ATTGCGATAGTTCAAGTTCGCAATGCGATAGTCCAAGT-TCGCATTGCGAT
1 TTCGCAATTGCGATAGTCCAAGTTCGCAATGCGATAGT-CAACTATCACATTGCGAT
88805 AGTCGAAGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
62 41 0.84
63 8 0.16
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (63 bp):
TTCGCAATTGCGATAGTCCAAGTTCGCAATGCGATAGTCAACTATCACATTGCGATTTACATA
Found at i:89449 original size:18 final size:19
Alignment explanation
Indices: 89422--89462 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
89412 AATCCTTATT
89422 TTTTTAAATAAAAATAATA
1 TTTTTAAATAAAAATAATA
* *
89441 TTTTT-AATAAATATATTA
1 TTTTTAAATAAAAATAATA
89459 TTTT
1 TTTT
89463 GGATTGAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTTAAATAAAAATAATA
Found at i:93535 original size:29 final size:29
Alignment explanation
Indices: 93493--93585 Score: 159
Period size: 29 Copynumber: 3.2 Consensus size: 29
93483 ATCAAACTAA
* *
93493 AATTTATTTGAAAATTATTAACCGAATCG
1 AATTAATTTGAAAATTATTAACCGAACCG
*
93522 AATTAATTTGAAAATTATTAACCAAACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
93551 AATTAATTTGAAAATTATTAACCGAACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
93580 AATTAA
1 AATTAA
93586 CCGATTGTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCGAACCG
Found at i:93699 original size:29 final size:29
Alignment explanation
Indices: 93649--93725 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
93639 ATCGGTTTGC
* * *
93649 TTAATCGAATCAAAATTTATTTGAAAATTA
1 TTAATCGAA-CCAAATTAATTTAAAAATTA
93679 TTAATCGAACCAAATTAATTTAAAAATTA
1 TTAATCGAACCAAATTAATTTAAAAATTA
*
93708 TTAACCGAACCAAATTAA
1 TTAATCGAACCAAATTAA
93726 CCGTTTTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 34 0.79
30 9 0.21
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (29 bp):
TTAATCGAACCAAATTAATTTAAAAATTA
Found at i:93819 original size:30 final size:29
Alignment explanation
Indices: 93785--93863 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
93775 TTTTGGTTCG
* *
93785 ATTAATCGAACCAAAATTTACTTGAAAATT
1 ATTAACCGAACC-AAATTAACTTGAAAATT
* * *
93815 ATTAACCGAATCGAATTAATTTGAAAATT
1 ATTAACCGAACCAAATTAACTTGAAAATT
* * *
93844 ATTAACTGAATCGAATTAAC
1 ATTAACCGAACCAAATTAAC
93864 CAATTTTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 32 0.76
30 10 0.24
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.33
Consensus pattern (29 bp):
ATTAACCGAACCAAATTAACTTGAAAATT
Found at i:93832 original size:137 final size:138
Alignment explanation
Indices: 93529--93873 Score: 453
Period size: 137 Copynumber: 2.5 Consensus size: 138
93519 TCGAATTAAT
*
93529 TTGAAAATTATTAACCAAACCGAATTAATTTGAAAATTATTAACCGAACCGAATTAACCGATTGT
1 TTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTATTAACCGAACCGAATTAACCGA-TGT
* * * *
93594 TTTTGAAAATTATTAACCGAATTAATCGAAGCAAAAATTCGGTTAATCGGTTTGCTTAATCGAAT
65 TTTT-AAAACTATTAACCGAATTAATCGAAGCAAAAATTCGGTTAATCGGTTCGATTAATCGAAC
*
93659 CAAAATTTAT
129 CAAAATTTAC
* * * *
93669 TTGAAAATTATTAATCGAACCAAATTAATTTAAAAATTATTAACCGAACCAAATTAACCG-T-TT
1 TTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTATTAACCGAACCGAATTAACCGATGTT
** * * *
93732 TTT-CCACTATTAATCGAATTAATCGAAGTAAAAATTCGGTTAATTTTGGTTCGATTAATCGAAC
66 TTTAAAACTATTAACCGAATTAATCGAAGCAAAAATTCGGTTAA--TCGGTTCGATTAATCGAAC
93796 CAAAATTTAC
129 CAAAATTTAC
* * * * *
93806 TTGAAAATTATTAACCGAATCGAATTAATTTGAAAATTATTAACTGAATCGAATTAACCAATTTT
1 TTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTATTAACCGAACCGAATTAACCGATGTT
93871 TTT
66 TTT
93874 TCTTTAACCA
Statistics
Matches: 178, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
135 35 0.20
137 81 0.46
138 2 0.01
139 5 0.03
140 55 0.31
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.35
Consensus pattern (138 bp):
TTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTATTAACCGAACCGAATTAACCGATGTT
TTTAAAACTATTAACCGAATTAATCGAAGCAAAAATTCGGTTAATCGGTTCGATTAATCGAACCA
AAATTTAC
Found at i:93838 original size:29 final size:29
Alignment explanation
Indices: 93806--93862 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
93796 CAAAATTTAC
93806 TTGAAAATTATTAACCGAATCGAATTAAT
1 TTGAAAATTATTAACCGAATCGAATTAAT
*
93835 TTGAAAATTATTAACTGAATCGAATTAA
1 TTGAAAATTATTAACCGAATCGAATTAA
93863 CCAATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.35
Consensus pattern (29 bp):
TTGAAAATTATTAACCGAATCGAATTAAT
Found at i:102125 original size:31 final size:31
Alignment explanation
Indices: 102087--102154 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
102077 ATTTAAGCTA
* *
102087 AGGGACTAAAATGGAACGGATCAATAATATT
1 AGGGACTAAAATCGAACAGATCAATAATATT
* * *
102118 AGGGACTAAAATCGAATAGATTAATAATGTT
1 AGGGACTAAAATCGAACAGATCAATAATATT
102149 AGGGAC
1 AGGGAC
102155 CATTTATACT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.24
Consensus pattern (31 bp):
AGGGACTAAAATCGAACAGATCAATAATATT
Found at i:102266 original size:18 final size:18
Alignment explanation
Indices: 102243--102277 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
102233 ACCGCATAGT
102243 TTACCCATATTAAAAAGC
1 TTACCCATATTAAAAAGC
102261 TTACCCATATTAAAAAG
1 TTACCCATATTAAAAAG
102278 TTTGACGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.29
Consensus pattern (18 bp):
TTACCCATATTAAAAAGC
Found at i:103089 original size:19 final size:20
Alignment explanation
Indices: 103067--103106 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
103057 TCCATTTGTA
103067 AACCCAAA-CGCCATGAATC
1 AACCCAAAGCGCCATGAATC
*
103086 AACCCAAAGCGCCATTAATC
1 AACCCAAAGCGCCATGAATC
103106 A
1 A
103107 TGACTGTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.42, C:0.35, G:0.10, T:0.12
Consensus pattern (20 bp):
AACCCAAAGCGCCATGAATC
Found at i:107336 original size:16 final size:16
Alignment explanation
Indices: 107315--107347 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
107305 TAAAATATAC
107315 ACTTCAAAAACTGCTG
1 ACTTCAAAAACTGCTG
107331 ACTTCAAAAACTGCTG
1 ACTTCAAAAACTGCTG
107347 A
1 A
107348 GACATACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (16 bp):
ACTTCAAAAACTGCTG
Found at i:108812 original size:21 final size:20
Alignment explanation
Indices: 108788--108827 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
108778 TGGCTACAAC
*
108788 AAACTAAGCTTAGAATACTTG
1 AAACTAAGCTT-GAAAACTTG
108809 AAACTAAGCTTGAAAACTT
1 AAACTAAGCTTGAAAACTT
108828 ACAAAATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (20 bp):
AAACTAAGCTTGAAAACTTG
Found at i:110418 original size:56 final size:57
Alignment explanation
Indices: 110334--110459 Score: 191
Period size: 56 Copynumber: 2.2 Consensus size: 57
110324 TTTACCCTAT
* *
110334 CGGTAATTAGCGTTGCGAATTTGAAAATCGTGTTGCGATAACACTGTTTACCTACAG
1 CGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGATAACACTATTTACCTACAG
* ** *
110391 CGGTAATTAGCGTTGTGAATTTG-AAATCGCGTTGCGATAGTACTATTTACCTACAT
1 CGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGATAACACTATTTACCTACAG
110447 CGGTAATTAGCGT
1 CGGTAATTAGCGT
110460 ATTTCGATAA
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
56 41 0.65
57 22 0.35
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (57 bp):
CGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGATAACACTATTTACCTACAG
Found at i:110521 original size:20 final size:20
Alignment explanation
Indices: 110498--110541 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
110488 GTAATTAGCT
110498 TTGCGAATTTGTAAATCGCG
1 TTGCGAATTTGTAAATCGCG
*
110518 TTGCGAATTTTTAAATCGCG
1 TTGCGAATTTGTAAATCGCG
110538 TTGC
1 TTGC
110542 TCCTGTGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (20 bp):
TTGCGAATTTGTAAATCGCG
Done.