Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002943.1 Hibiscus syriacus cultivar Beakdansim tig00006074_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: 111575
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:180 original size:19 final size:19
Alignment explanation
Indices: 156--192 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
146 CTCTGAGAGA
156 CGGAGATAGACGGATTCGC
1 CGGAGATAGACGGATTCGC
*
175 CGGAGATGGACGGATTCG
1 CGGAGATAGACGGATTCG
193 GAGATGGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.19, G:0.41, T:0.16
Consensus pattern (19 bp):
CGGAGATAGACGGATTCGC
Found at i:196 original size:16 final size:17
Alignment explanation
Indices: 156--199 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
146 CTCTGAGAGA
*
156 CGGAGATAGACGGATTCGC
1 CGGAGATGGACGGATT--C
175 CGGAGATGGACGGATT-
1 CGGAGATGGACGGATTC
191 CGGAGATGG
1 CGGAGATGG
200 GTGAGAGAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 9 0.38
19 15 0.62
ACGTcount: A:0.25, C:0.16, G:0.43, T:0.16
Consensus pattern (17 bp):
CGGAGATGGACGGATTC
Found at i:424 original size:39 final size:40
Alignment explanation
Indices: 364--475 Score: 131
Period size: 39 Copynumber: 2.8 Consensus size: 40
354 GCGTTTAGAA
* *
364 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
1 ATCG-ATTGCGATTATGTATTATCGCATTGCGAAAGTAAGT
* *
405 ATCG-TTGCGATTTTGTATTATCGCATTGCGATAGTAAGT
1 ATCGATTGCGATTATGTATTATCGCATTGCGAAAGTAAGT
*
444 ATCGCATTGCGA-TA-GTGAGTATCGCATTGCGA
1 ATCG-ATTGCGATTATGT-ATTATCGCATTGCGA
476 TTTCCCAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
39 37 0.60
40 15 0.24
41 10 0.16
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (40 bp):
ATCGATTGCGATTATGTATTATCGCATTGCGAAAGTAAGT
Found at i:448 original size:20 final size:20
Alignment explanation
Indices: 423--476 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
413 GATTTTGTAT
423 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
443 TATCGCATTGCGATAGTGAG
1 TATCGCATTGCGATAGTAAG
463 TATCGCATTGCGAT
1 TATCGCATTGCGAT
477 TTCCCAATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:465 original size:59 final size:61
Alignment explanation
Indices: 364--478 Score: 155
Period size: 59 Copynumber: 1.9 Consensus size: 61
354 GCGTTTAGAA
* *
364 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCG-TTGCGATTTTGTATT
1 ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGTATCGATTGCGATTTTGTATT
* *
424 ATCGCATTGCGA-TA-GTAAGTATCGCATTGCGATAGTGAGTATCGCATTGCGATTT
1 ATCGCATTGCGATTATGT-AGTATCGCATTGCGAAAGTCAGTATCG-ATTGCGATTT
479 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 2 0.04
59 25 0.52
60 12 0.25
61 9 0.19
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (61 bp):
ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGTATCGATTGCGATTTTGTATT
Found at i:488 original size:20 final size:20
Alignment explanation
Indices: 465--515 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
455 ATAGTGAGTA
*
465 TCGCATTGCGATTTCCCAAT
1 TCGCATTGCGATTTACCAAT
* **
485 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
505 TCGCATTGCGA
1 TCGCATTGCGA
516 ATTGGAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:6461 original size:20 final size:21
Alignment explanation
Indices: 6423--6464 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
6413 CGACTGATGC
6423 AAATAAAAAAGAAGCAGAGAG
1 AAATAAAAAAGAAGCAGAGAG
6444 AAATAAAAGAA-AAG-AGAGAG
1 AAATAAAA-AAGAAGCAGAGAG
6464 A
1 A
6465 GGCTCTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 11 0.55
22 2 0.10
ACGTcount: A:0.69, C:0.02, G:0.24, T:0.05
Consensus pattern (21 bp):
AAATAAAAAAGAAGCAGAGAG
Found at i:7433 original size:22 final size:21
Alignment explanation
Indices: 7398--7443 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
7388 GAGATTTGAT
7398 ATTAACTTAAATTTTAATTAAA
1 ATTAACTTAAATTTT-ATTAAA
* * *
7420 ATTAAGTTATATTTTATTATA
1 ATTAACTTAAATTTTATTAAA
7441 ATT
1 ATT
7444 CTACTAGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTAACTTAAATTTTATTAAA
Found at i:10700 original size:37 final size:38
Alignment explanation
Indices: 10620--10700 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 38
10610 AACAAGTTGG
** *
10620 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAAATAGAAAATCAT
*
10659 -AAAATTTATATAATTTT-TTTACAAAATAGAAAAT-AT
1 AAAAATTTATAT-ATTTTCTTTAAAAAATAGAAAATCAT
10695 AAAAAT
1 AAAAAT
10701 GTTTAATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
36 2 0.06
37 26 0.72
38 8 0.22
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (38 bp):
AAAAATTTATATATTTTCTTTAAAAAATAGAAAATCAT
Found at i:11539 original size:38 final size:37
Alignment explanation
Indices: 11483--11558 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 37
11473 TCATTGTCTG
11483 ATATTCCACTTTCATCAGACGACCAACATATATATAT
1 ATATTCCACTTTCATCAGACGACCAACATATATATAT
*
11520 ATATATCCACTTTCGTCAGACGACCAACATATATATAT
1 ATAT-TCCACTTTCATCAGACGACCAACATATATATAT
11558 A
1 A
11559 GTTTTGGGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 4 0.11
38 33 0.89
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.32
Consensus pattern (37 bp):
ATATTCCACTTTCATCAGACGACCAACATATATATAT
Found at i:12632 original size:11 final size:11
Alignment explanation
Indices: 12611--12641 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
12601 AAAATTGATC
12611 GATGAATTACAT
1 GATG-ATTACAT
12623 GATGATTACAT
1 GATGATTACAT
12634 GATGATTA
1 GATGATTA
12642 GAGTTGCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (11 bp):
GATGATTACAT
Found at i:17907 original size:11 final size:11
Alignment explanation
Indices: 17891--17915 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17881 TGGAGAGATG
17891 GAACGTTTGAA
1 GAACGTTTGAA
17902 GAACGTTTGAA
1 GAACGTTTGAA
17913 GAA
1 GAA
17916 AGATTCATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.28, T:0.24
Consensus pattern (11 bp):
GAACGTTTGAA
Found at i:18009 original size:20 final size:20
Alignment explanation
Indices: 17984--18028 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
17974 TTTGGTTCAT
17984 GGAATGTAGCATTACCTCCG
1 GGAATGTAGCATTACCTCCG
* *
18004 GGAATGTAGCGTTACCTTCG
1 GGAATGTAGCATTACCTCCG
18024 GGAAT
1 GGAAT
18029 AGGATTACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (20 bp):
GGAATGTAGCATTACCTCCG
Found at i:18438 original size:15 final size:15
Alignment explanation
Indices: 18418--18447 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18408 CCCCTATGAA
*
18418 TGGGTATCGATACCC
1 TGGGTACCGATACCC
18433 TGGGTACCGATACCC
1 TGGGTACCGATACCC
18448 CTATGACTAG
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:0.20, C:0.30, G:0.27, T:0.23
Consensus pattern (15 bp):
TGGGTACCGATACCC
Found at i:18697 original size:21 final size:21
Alignment explanation
Indices: 18668--18707 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
18658 TTTTTGCAGA
*
18668 AAAATCATCCTCGAACGGCTCC
1 AAAATCATCC-CCAACGGCTCC
18690 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
18708 AGATACAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.35, C:0.38, G:0.12, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:20289 original size:29 final size:30
Alignment explanation
Indices: 20226--20299 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
20216 CTTTATTTAT
* * *
20226 ATTTTAATCATCTAACTTTTAGATTTTCTA
1 ATTTTTATCATCTAACTTTCAGATATTCTA
20256 A-TTTTATCATCTAACTTTCAGA-ATTC-A
1 ATTTTTATCATCTAACTTTCAGATATTCTA
*
20283 ATTTTTTATCCTCTAAC
1 A-TTTTTATCATCTAAC
20300 CATTAGTTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
27 2 0.05
28 3 0.08
29 32 0.84
30 1 0.03
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.50
Consensus pattern (30 bp):
ATTTTTATCATCTAACTTTCAGATATTCTA
Found at i:22006 original size:17 final size:17
Alignment explanation
Indices: 21984--22016 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21974 ATCTAAAATT
21984 TTTAAATTTTTATATAA
1 TTTAAATTTTTATATAA
*
22001 TTTAAATTTTTTTATA
1 TTTAAATTTTTATATA
22017 TTTTTTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTAAATTTTTATATAA
Found at i:25999 original size:21 final size:23
Alignment explanation
Indices: 25950--26010 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
25940 ATTTTTATTG
25950 TGTTCATTAATATTTTTTTGATAAA
1 TGTTCATTAATA-TTTTTT-ATAAA
*
25975 TGTTCATTAGTATTTTTT-T-AA
1 TGTTCATTAATATTTTTTATAAA
*
25996 TGTTAATTAATATTT
1 TGTTCATTAATATTT
26011 AATATGTGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 15 0.45
22 1 0.03
24 6 0.18
25 11 0.33
ACGTcount: A:0.30, C:0.03, G:0.08, T:0.59
Consensus pattern (23 bp):
TGTTCATTAATATTTTTTATAAA
Found at i:26926 original size:20 final size:20
Alignment explanation
Indices: 26882--27109 Score: 162
Period size: 20 Copynumber: 11.2 Consensus size: 20
26872 AATGACCAAC
**
26882 AAAATCGCAACGCGA-TATC
1 AAAATCGCAACGCGATTAAG
*
26901 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
26921 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
26941 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
26961 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
26982 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
27003 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
* *
27024 AAGAATCGCAATGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
27045 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
27067 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
** *
27085 AAAATCGCAATACGATTCAG
1 AAAATCGCAACGCGATTAAG
27105 AAAAT
1 AAAAT
27110 GAGTAAATTC
Statistics
Matches: 166, Mismatches: 29, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
18 4 0.02
19 15 0.09
20 105 0.63
21 13 0.08
22 29 0.17
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:27009 original size:42 final size:42
Alignment explanation
Indices: 26958--27094 Score: 224
Period size: 42 Copynumber: 3.3 Consensus size: 42
26948 CAACGGTCAA
26958 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
* *
27000 AAGAGAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
* *
27042 CAGAAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
27082 AAGAAAATCGCAA
1 AAGAAAATCGCAA
27095 TACGATTCAG
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 33 0.38
42 55 0.62
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (42 bp):
AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
Found at i:27080 original size:40 final size:40
Alignment explanation
Indices: 26882--27094 Score: 220
Period size: 42 Copynumber: 5.2 Consensus size: 40
26872 AATGACCAAC
*
26882 AAAATCGCAACGCGATAT-CAA-AATCGCAACGCGATTTAG
1 AAAATCGCAACGCGAT-TCCAAGAATCGCAACGCGATTAAG
* **** *
26921 AAAATCGCAACGTTGAAAAGAA-AATCGCAACG-G-TCAAAAG
1 AAAATCGCAACG-CGATTCCAAGAATCGCAACGCGAT--TAAG
*
26961 AAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATTAAG
* * *
27003 AGAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTAAG
27045 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
27085 AAAATCGCAA
1 AAAATCGCAA
27095 TACGATTCAG
Statistics
Matches: 145, Mismatches: 18, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
38 1 0.01
39 14 0.10
40 62 0.43
41 3 0.02
42 63 0.43
43 1 0.01
44 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (40 bp):
AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
Found at i:27204 original size:6 final size:6
Alignment explanation
Indices: 27193--27247 Score: 96
Period size: 6 Copynumber: 9.5 Consensus size: 6
27183 GACACGTATT
27193 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
27240 ACC-CG ACC
1 ACCACG ACC
27248 CGAGACGAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.20
6 39 0.80
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:27755 original size:6 final size:6
Alignment explanation
Indices: 27744--27776 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
27734 TCTCGTCTCG
27744 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
27777 AATACGTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:27904 original size:20 final size:20
Alignment explanation
Indices: 27879--28137 Score: 282
Period size: 20 Copynumber: 12.8 Consensus size: 20
27869 CTCATTTTCT
*
27879 GAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
27899 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
* ***
27919 GAATCGCATTGCGATTCCAA
1 GAATCGCGTTGCGATTCTTG
27939 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
27960 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
27979 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
28000 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
28019 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
28040 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
28059 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
28079 GAAAATCGCGTTGCGATT-TTAT
1 G--AATCGCGTTGCGATTCTT-G
*
28101 GAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
28121 GAAGATCGCGTTGCGAT
1 G-A-ATCGCGTTGCGAT
28138 CTTCTTTTCA
Statistics
Matches: 206, Mismatches: 13, Indels: 38
0.80 0.05 0.15
Matches are distributed among these distances:
18 15 0.07
19 2 0.01
20 143 0.69
21 5 0.02
22 41 0.20
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:27927 original size:40 final size:40
Alignment explanation
Indices: 27872--28199 Score: 358
Period size: 40 Copynumber: 8.1 Consensus size: 40
27862 GAATTTACTC
* *
27872 ATTTTCTGAATCGCATTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
* * ***
27912 ATTTTCTGAATCGCATTGCGATTCCAAGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
27952 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
27992 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
28032 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
*** * *
28072 ATTCTTGGAAAATCGCGTTGCGATT-TTATGAATCGCATTGCG
1 ATT-TT-CTTAATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
*** **** *
28114 ATTCTTGGAAGATCGCGTTGCGA-TCTTCTTTTCAACGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCGATTCTTGGAATC-GCGTTGCG
* * *
28156 CTTTTCTAAATCGCGTTGCGGTT-TT-GATATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGA-ATCGCGTTGCG
28195 ATTTT
1 ATTTT
28200 GTTAGTCATT
Statistics
Matches: 251, Mismatches: 29, Indels: 17
0.85 0.10 0.06
Matches are distributed among these distances:
39 11 0.04
40 170 0.68
41 15 0.06
42 55 0.22
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (40 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:28172 original size:20 final size:20
Alignment explanation
Indices: 27872--28199 Score: 229
Period size: 20 Copynumber: 16.2 Consensus size: 20
27862 GAATTTACTC
* *
27872 ATTTTCTGAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
27892 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
* *
27912 ATTTTCTGAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
* *
27932 A-TTCCAAGAATCGCGTTGCG
1 ATTTTCTA-AATCGCGTTGCG
*
27952 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
27972 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
27992 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
28012 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
28032 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
28052 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
**
28072 ATTCTTGGAAAATCGCGTTGCG
1 ATT-TT-CTAAATCGCGTTGCG
* * *
28094 ATTTTATGAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
28114 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* ** *
28136 ATCTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
*
28156 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
* * *
28176 GTTTT-GATATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
28195 ATTTT
1 ATTTT
28200 GTTAGTCATT
Statistics
Matches: 247, Mismatches: 46, Indels: 31
0.76 0.14 0.10
Matches are distributed among these distances:
19 27 0.11
20 173 0.70
21 20 0.08
22 27 0.11
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:28998 original size:2 final size:2
Alignment explanation
Indices: 28991--29037 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
28981 GACGTTATTG
28991 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
29033 AT AT A
1 AT AT A
29038 AATTAACATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35809 original size:13 final size:13
Alignment explanation
Indices: 35791--35815 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35781 CGGTAGCGAC
35791 AGATTGCCAAAAT
1 AGATTGCCAAAAT
35804 AGATTGCCAAAA
1 AGATTGCCAAAA
35816 GGATGCAATC
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:0.16, G:0.16, T:0.20
Consensus pattern (13 bp):
AGATTGCCAAAAT
Found at i:44052 original size:24 final size:24
Alignment explanation
Indices: 44025--44077 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
44015 CGTTCATTTA
44025 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
44049 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
44073 CGTTC
1 CGTTC
44078 ATTTATGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.47
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:44077 original size:14 final size:14
Alignment explanation
Indices: 44035--44066 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
44025 CGTTCGTGAA
44035 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
44049 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
44063 CGTT
1 CGTT
44067 TATGTTCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:44083 original size:24 final size:24
Alignment explanation
Indices: 44036--44086 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
44026 GTTCGTGAAC
*
44036 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
* *
44060 GTTCGTTTATGTTCGTTCATTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
44084 GTT
1 GTT
44087 TAACCCAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.12, G:0.24, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCGTTCAGTTAT
Found at i:46148 original size:14 final size:14
Alignment explanation
Indices: 46131--46157 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46121 AAATCAAGTT
46131 TTGAAATTAGAAAA
1 TTGAAATTAGAAAA
46145 TTGAAATTAGAAA
1 TTGAAATTAGAAA
46158 TTACTCCCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.30
Consensus pattern (14 bp):
TTGAAATTAGAAAA
Found at i:48485 original size:19 final size:20
Alignment explanation
Indices: 48439--48498 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 20
48429 TTCCCCTGTG
48439 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TC-AA
48462 GGGGGAATCGGTTCCCTC-A
1 GGGGGAATCGGTTCCCTCAA
* *
48481 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
48499 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Found at i:52353 original size:22 final size:21
Alignment explanation
Indices: 52311--52350 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
52301 GAGTTTGTTT
*
52311 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
52332 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
52351 ACAATTTCTC
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:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:59982 original size:22 final size:22
Alignment explanation
Indices: 59954--60001 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
59944 CATCGGCACC
59954 TGTTTTAGACTGTACAGAGATT
1 TGTTTTAGACTGTACAGAGATT
*
59976 TGTTTTAGATTGTACAGAGATT
1 TGTTTTAGACTGTACAGAGATT
59998 TGTT
1 TGTT
60002 CAACCTGCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.46
Consensus pattern (22 bp):
TGTTTTAGACTGTACAGAGATT
Found at i:68871 original size:23 final size:23
Alignment explanation
Indices: 68818--68904 Score: 81
Period size: 23 Copynumber: 3.7 Consensus size: 23
68808 AATCTTATAT
* *
68818 GGCACTACGGTGCAATTCTACTT
1 GGCACTTCGGTGCAATTCTACTC
*
68841 GGCACTTCGGTGCATTTCTACTC
1 GGCACTTCGGTGCAATTCTACTC
68864 GGTC-CTTCGG-GACAAATTCTACGT-
1 GG-CACTTCGGTG-C-AATTCTAC-TC
*
68888 GACACTTCGGTGCAATT
1 GGCACTTCGGTGCAATT
68905 TATATGAGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
22 1 0.02
23 34 0.64
24 16 0.30
25 2 0.04
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACTC
Found at i:70334 original size:23 final size:23
Alignment explanation
Indices: 70298--70341 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
70288 TTCTGGGCTA
* *
70298 GGGGAATCGGTACCCATTCAAGT
1 GGGGAACCGATACCCATTCAAGT
*
70321 GGGGAACCGATACCCCTTCAA
1 GGGGAACCGATACCCATTCAA
70342 ACGAACAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (23 bp):
GGGGAACCGATACCCATTCAAGT
Found at i:73912 original size:20 final size:21
Alignment explanation
Indices: 73880--73938 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
73870 AGATTGTGCA
* * *
73880 GGGGGAATAGATTCCCCT-TG
1 GGGGGTATCGATTCCCCTGAG
73900 GGGGGTATCGATTCCCCCTGAG
1 GGGGGTATCGATT-CCCCTGAG
73922 GGGGGTATCGATTCCCC
1 GGGGGTATCGATTCCCC
73939 CCTAAATGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.32
21 9 0.26
22 14 0.41
ACGTcount: A:0.15, C:0.25, G:0.36, T:0.24
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCTGAG
Found at i:74991 original size:23 final size:23
Alignment explanation
Indices: 74965--75052 Score: 88
Period size: 23 Copynumber: 3.8 Consensus size: 23
74955 CAATCTTATA
*
74965 TGGCACTACGGTACAATTCTACG
1 TGGCACTTCGGTACAATTCTACG
* * *
74988 TGGCACTTCAGTGCATTTCTACG
1 TGGCACTTCGGTACAATTCTACG
* *
75011 CGGTC-CTTCGGGACAAATTCTACG
1 TGG-CACTTCGGTAC-AATTCTACG
*
75035 TGGCACTTCGGTGCAATT
1 TGGCACTTCGGTACAATT
75053 TATATGAGCT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
23 32 0.64
24 18 0.36
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTACAATTCTACG
Found at i:84930 original size:6 final size:6
Alignment explanation
Indices: 84919--84952 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
84909 ACACCTATTT
84919 AAAACA AAAACA AAAACA AAAA-A AAAACCA AAAA
1 AAAACA AAAACA AAAACA AAAACA AAAA-CA AAAA
84953 TAATCTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 16 0.62
7 5 0.19
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:85579 original size:20 final size:20
Alignment explanation
Indices: 85543--85580 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
85533 CCAAGACAAA
*
85543 ATTAAAATAGTAGTTTATAT
1 ATTAAAATAGTAATTTATAT
85563 ATTAAACAT-GTAATTTAT
1 ATTAAA-ATAGTAATTTAT
85581 CATAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (20 bp):
ATTAAAATAGTAATTTATAT
Found at i:89428 original size:21 final size:21
Alignment explanation
Indices: 89404--89448 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
89394 CCCTAACTTA
*
89404 AAACCCTAAATTGATAACC-CT
1 AAACCCTAAACT-ATAACCTCT
89425 AAACCCTAAACTATAACCTCT
1 AAACCCTAAACTATAACCTCT
89446 AAA
1 AAA
89449 TCTAAATCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.22
Consensus pattern (21 bp):
AAACCCTAAACTATAACCTCT
Found at i:97778 original size:2 final size:2
Alignment explanation
Indices: 97771--97831 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
97761 ATTATCACTT
97771 TA TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
97813 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
97832 TGGGATACTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:104820 original size:25 final size:25
Alignment explanation
Indices: 104784--104832 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
104774 ATCAGCTATT
* * *
104784 TTTAATTTTATATAATTTTAAAAAA
1 TTTAATTGTATAAAATATTAAAAAA
104809 TTTAATTGTATAAAATATTAAAAA
1 TTTAATTGTATAAAATATTAAAAA
104833 CTGTAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TTTAATTGTATAAAATATTAAAAAA
Found at i:108432 original size:12 final size:12
Alignment explanation
Indices: 108410--108441 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
108400 AGGCCAACTC
108410 CCACT-CTTTGA
1 CCACTACTTTGA
108421 CCACTACTTTGA
1 CCACTACTTTGA
108433 CCACTACTT
1 CCACTACTT
108442 CCCTCATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.22, C:0.38, G:0.06, T:0.34
Consensus pattern (12 bp):
CCACTACTTTGA
Found at i:108542 original size:31 final size:31
Alignment explanation
Indices: 108499--108609 Score: 136
Period size: 31 Copynumber: 3.6 Consensus size: 31
108489 TGTTGAGCTC
108499 GACTCGACTCGAAAACTCTGAAA-ATAAGTTT
1 GACTCGACTCGAAAACTCTGAAATA-AAGTTT
*
108530 GACTTGACTCGAAAACTCTGAAATAAAGTTT
1 GACTCGACTCGAAAACTCTGAAATAAAGTTT
* * * *
108561 CGACTTGACTCG-AAACTCTTAAATGAAGTTC
1 -GACTCGACTCGAAAACTCTGAAATAAAGTTT
*
108592 GACTCGGCTCGAAAACTC
1 GACTCGACTCGAAAACTC
108610 GCGAGCTTAA
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.13
31 50 0.70
32 12 0.17
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (31 bp):
GACTCGACTCGAAAACTCTGAAATAAAGTTT
Found at i:111128 original size:11 final size:11
Alignment explanation
Indices: 111112--111136 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
111102 TGTATATATA
111112 AATTTTAATTT
1 AATTTTAATTT
111123 AATTTTAATTT
1 AATTTTAATTT
111134 AAT
1 AAT
111137 ATGGTGATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
AATTTTAATTT
Done.