Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000445.1 Hibiscus syriacus cultivar Beakdansim tig00000814_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: 65290
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:12049 original size:7 final size:7
Alignment explanation
Indices: 12039--12068 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
12029 TGGAAATTAT
12039 AAATTTA
1 AAATTTA
12046 AAATTTA
1 AAATTTA
12053 AAATTTA
1 AAATTTA
12060 AAATTTA
1 AAATTTA
12067 AA
1 AA
12069 TCCGATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:14062 original size:17 final size:18
Alignment explanation
Indices: 14040--14089 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
14030 AATATATATA
*
14040 TTAAAAACTATATAT-TT
1 TTAAAAATTATATATGTT
14057 TT-AAAATTATAATATGTT
1 TTAAAAATTAT-ATATGTT
14075 TTCAAAAATTATATA
1 TT-AAAAATTATATA
14090 ATATATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 7 0.25
17 6 0.21
18 4 0.14
19 3 0.11
20 8 0.29
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (18 bp):
TTAAAAATTATATATGTT
Found at i:14123 original size:22 final size:21
Alignment explanation
Indices: 14048--14125 Score: 88
Period size: 22 Copynumber: 3.7 Consensus size: 21
14038 TATTAAAAAC
14048 TATATATTTTTAAAATTATA-
1 TATATATTTTTAAAATTATAT
* *
14068 -ATATGTTTTCAAAAATTATAT
1 TATATATTTT-TAAAATTATAT
*
14089 AATATATTTTTTAAAATTATAT
1 TATATA-TTTTTAAAATTATAT
14111 TATATATTCTTTAAA
1 TATATATT-TTTAAA
14126 CTATATATGT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 8 0.17
20 9 0.19
21 2 0.04
22 25 0.52
23 4 0.08
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (21 bp):
TATATATTTTTAAAATTATAT
Found at i:14220 original size:23 final size:23
Alignment explanation
Indices: 14177--14221 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
14167 CATACTACGT
* *
14177 AATATATATACATATCTATTATA
1 AATATATATACATAGCAATTATA
14200 AATACTATATA-ATAGCAATTAT
1 AATA-TATATACATAGCAATTAT
14222 GGGTGACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (23 bp):
AATATATATACATAGCAATTATA
Found at i:16128 original size:508 final size:497
Alignment explanation
Indices: 15184--16166 Score: 1601
Period size: 508 Copynumber: 2.0 Consensus size: 497
15174 AGCTTCATTC
15184 GTAACACCCATAACCCGTATAATTATACCTATACAGATTATAGATGTCACCTGCATTTTTAAAAC
1 GTAACACCCATAACCCGTATAATTATACCTATACAGATTATAGATGTCACCTGCATTTTTAAAAC
*
15249 CATTTCCACTTCAGAGGTGATTTAAATTTATTTTCTTTAAAATGGTAAATGATATTATCAAAATT
66 CATTTCCACTTCAGAGGTGATTTAAATTTATTTTCTTTAAAATGGTAAATGATATTATAAAAATT
*
15314 ATCATATCATATGAATTATGATTCATTATAACAAATTTAAGGCAAAAGTTTTTTTATGAATAGTT
131 ATCATATCATATGAATTATGATTCATTATAACAAATTTAAGGCAAAAGTTTTTTTATGAACAGTT
* * *
15379 ATGAACAGTACTGTACTAATATACGAGTATGTAGAATCGGGAACAATACGAAAACAAGTTCATCA
196 AAGAACAGTACTGTACTAATATACGAGTATATAGAACCGGGAACAATACGAAAACAAGTTCATCA
15444 AAGAGATAAAAGGTACATGCTATAATCTCAGGAGCATCTCTATCATCATCAGTCTTGATGTGATA
261 AAGAGATAAAAGGTACATGCTATAATCTCAGGAGCATCTCTATCATCATCAGTCTTGATGTGATA
* * *
15509 AACTATTGCAGTAGTTCTGCCTTCACGATTAGATGCAGCCTCAAATGTACCATGTTTACCTATTT
326 AACTATTGCAGTAGTTCTGCCTTCACGAATAAATGCAGCCTCAAATGTACCAGGTTTACCTATTT
* * *
15574 TGCCACCTCTACCCCTATGGGGTCCCAATACTTTCTGATCTGGATGAAGTTATGGACAATTCCTC
391 TGCCACCTATACCCCTATGGGGTACCAATACTGTCTGATCTGGATGAAGTTATGGACAATTCCTC
15639 CTAAAATGCCCCGA-TTTACCTGTAGCTCTGATGCCAATAAAT
456 CTAAAATGCCCC-ACTTTACCTGTAGCTCTGATGCCAATAAAT
*
15681 GTAACACCTATAACCCGTATAATTATACCTATACAGATTATAGATGTCACCTGCATTTTTAAAA-
1 GTAACACCCATAACCCGTATAATTATACCTATACAGATTATAGATGTCACCTGCATTTTTAAAAC
* *
15745 CATTTTCACTTCAGAGGTGATTTAAATTTATTTTCTTTAAAATGGTAAATGGTATTATAAAAATT
66 CATTTCCACTTCAGAGGTGATTTAAATTTATTTTCTTTAAAATGGTAAATGATATTATAAAAATT
15810 ATCATATCATATGAATTATGATTCATTATAACAAATTTAAGGCAAAAGTTTTTTTTATGAACAGT
131 ATCATATCATATGAATTATGATTCATTATAACAAATTTAAGGCAAAAG-TTTTTTTATGAACAGT
**
15875 TAAGAACAATACCGTGACATTACTGTACTAATATACGAGTATATAGAACCGGGATTAATACGAAA
195 TAAGAAC---A----G----TACTGTACTAATATACGAGTATATAGAACCGGGAACAATACGAAA
* *
15940 ACAGGTTCATCAAAGAGATAAAAGGTACATGCTATAATCTCAGGAGTATCTCTATCATCATCAGT
249 ACAAGTTCATCAAAGAGATAAAAGGTACATGCTATAATCTCAGGAGCATCTCTATCATCATCAGT
* *
16005 CTTGATGTGATAAACTCTTGCAGTAGTTCTGCCTTCACGAATAAATGCAGCCTCAGATGTACCAG
314 CTTGATGTGATAAACTATTGCAGTAGTTCTGCCTTCACGAATAAATGCAGCCTCAAATGTACCAG
* * * * *
16070 GTTTACCTATTTTGCCACCTATATCCCTCTGGGGTATCGATACTGTCTGATCTGGATGAAGTTCT
379 GTTTACCTATTTTGCCACCTATACCCCTATGGGGTACCAATACTGTCTGATCTGGATGAAGTTAT
*
16135 GGACATTTCCTCCTAAAATGCCCCACTTTACC
444 GGACAATTCCTCCTAAAATGCCCCACTTTACC
16167 AAAATGAAAG
Statistics
Matches: 447, Mismatches: 26, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
496 110 0.25
497 84 0.19
500 1 0.00
504 1 0.00
507 1 0.00
508 250 0.56
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (497 bp):
GTAACACCCATAACCCGTATAATTATACCTATACAGATTATAGATGTCACCTGCATTTTTAAAAC
CATTTCCACTTCAGAGGTGATTTAAATTTATTTTCTTTAAAATGGTAAATGATATTATAAAAATT
ATCATATCATATGAATTATGATTCATTATAACAAATTTAAGGCAAAAGTTTTTTTATGAACAGTT
AAGAACAGTACTGTACTAATATACGAGTATATAGAACCGGGAACAATACGAAAACAAGTTCATCA
AAGAGATAAAAGGTACATGCTATAATCTCAGGAGCATCTCTATCATCATCAGTCTTGATGTGATA
AACTATTGCAGTAGTTCTGCCTTCACGAATAAATGCAGCCTCAAATGTACCAGGTTTACCTATTT
TGCCACCTATACCCCTATGGGGTACCAATACTGTCTGATCTGGATGAAGTTATGGACAATTCCTC
CTAAAATGCCCCACTTTACCTGTAGCTCTGATGCCAATAAAT
Found at i:20876 original size:22 final size:22
Alignment explanation
Indices: 20848--20892 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
20838 AGTTTTTTTT
*
20848 ATGAACAGTACCGTGAACATTG
1 ATGAACAATACCGTGAACATTG
*
20870 ATGAACAATACTGTGAACATTG
1 ATGAACAATACCGTGAACATTG
20892 A
1 A
20893 ACAGTGTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (22 bp):
ATGAACAATACCGTGAACATTG
Found at i:23835 original size:31 final size:31
Alignment explanation
Indices: 23798--23867 Score: 124
Period size: 30 Copynumber: 2.3 Consensus size: 31
23788 GTCTTTTCTC
23798 TTTGTTTTTTTTAGTTTCTAATAAGAATAAG
1 TTTGTTTTTTTTAGTTTCTAATAAGAATAAG
23829 TTTG-TTTTTTTAGTTTCTAATAAGAATAAG
1 TTTGTTTTTTTTAGTTTCTAATAAGAATAAG
*
23859 TTTATTTTT
1 TTTGTTTTT
23868 GTGACACGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
30 29 0.78
31 8 0.22
ACGTcount: A:0.27, C:0.03, G:0.11, T:0.59
Consensus pattern (31 bp):
TTTGTTTTTTTTAGTTTCTAATAAGAATAAG
Found at i:25644 original size:60 final size:57
Alignment explanation
Indices: 25580--25743 Score: 168
Period size: 59 Copynumber: 2.7 Consensus size: 57
25570 GCCCTCATTT
25580 TAAATTGGTCTCTAAACTTTTAAACATTTCAATTTCATCCATAAACTATGAT-TATCATAC
1 TAAATTGGTC-CTAAACTTTT-AACATTTCAATTTCATCC-TAAACTATGATCT-TCATAC
* * * * *
25640 TAAATTAGTCCTTAAACTTTTAACATTTCATTTTCATCCCCAAACTCTGATCTTCATTC
1 TAAATTGGTCC-TAAACTTTTAACATTTCAATTTCAT-CCTAAACTATGATCTTCATAC
* * *
25699 TAAATTGGCCCCCAAACTTTTTGAACATTTCAATTTAATCCTAAA
1 TAAATTGG-TCCTAAAC-TTTT-AACATTTCAATTTCATCCTAAA
25744 TTATACATGT
Statistics
Matches: 87, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
59 41 0.47
60 32 0.37
61 14 0.16
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.40
Consensus pattern (57 bp):
TAAATTGGTCCTAAACTTTTAACATTTCAATTTCATCCTAAACTATGATCTTCATAC
Found at i:28221 original size:25 final size:23
Alignment explanation
Indices: 28184--28232 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
28174 TAAATTTTTT
* *
28184 ATAAGATGGAATTCTATAGAAATTA
1 ATAACATGAAATTCTA-A-AAATTA
28209 ATAACATGAAATTCTAAAAATTA
1 ATAACATGAAATTCTAAAAATTA
28232 A
1 A
28233 GTAAATTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 1 0.05
25 14 0.64
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.31
Consensus pattern (23 bp):
ATAACATGAAATTCTAAAAATTA
Found at i:28327 original size:18 final size:17
Alignment explanation
Indices: 28304--28346 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
28294 TTGTTAAACT
28304 TTTAATTATCATGTTTTA
1 TTTAATTATCAT-TTTTA
*
28322 TTTAATATATTATTTTTA
1 TTTAAT-TATCATTTTTA
*
28340 TTAAATT
1 TTTAATT
28347 TTACAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 16 0.73
19 5 0.23
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTAATTATCATTTTTA
Found at i:31607 original size:12 final size:12
Alignment explanation
Indices: 31590--31644 Score: 94
Period size: 12 Copynumber: 4.7 Consensus size: 12
31580 ACATCAATTT
31590 AGTTAGGTGAAG
1 AGTTAGGTGAAG
31602 AGTTAGGTGAAG
1 AGTTAGGTGAAG
*
31614 AATTAGGTGAAG
1 AGTTAGGTGAAG
31626 AGTTAGGTG-AG
1 AGTTAGGTGAAG
31637 AGTTAGGT
1 AGTTAGGT
31645 ATTTGTATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
11 10 0.24
12 31 0.76
ACGTcount: A:0.33, C:0.00, G:0.40, T:0.27
Consensus pattern (12 bp):
AGTTAGGTGAAG
Found at i:39712 original size:2 final size:2
Alignment explanation
Indices: 39705--39729 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39695 TATTTGTGTT
39705 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39730 CGTTAGTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39880 original size:2 final size:2
Alignment explanation
Indices: 39875--39940 Score: 57
Period size: 2 Copynumber: 33.5 Consensus size: 2
39865 ATTATGTAAT
* * *
39875 TA TA TA TA T- TA TA TA AA TA -A TCA -A TA TGA AA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T-A TA TA TA TA TA TA
*
39916 TA AA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39941 GGAAAAAACG
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
1 3 0.06
2 46 0.90
3 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:45349 original size:22 final size:22
Alignment explanation
Indices: 45324--45385 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
45314 GACATATGAA
*
45324 ATTTGTCCCGAAGGACCTATGT
1 ATTTGTCCCGAAGGACCGATGT
* *
45346 ATTTGTCCCGAATGACCGCTGT
1 ATTTGTCCCGAAGGACCGATGT
*
45368 ATATGTCCCGAAGGACCG
1 ATTTGTCCCGAAGGACCG
45386 CGTAGACCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCGATGT
Found at i:46713 original size:10 final size:10
Alignment explanation
Indices: 46698--46729 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
46688 TTTCACGGGG
46698 AGGAGGAAGA
1 AGGAGGAAGA
46708 AGGAGGAAGA
1 AGGAGGAAGA
46718 AGGAGGAAGA
1 AGGAGGAAGA
46728 AG
1 AG
46730 AAGAAGAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (10 bp):
AGGAGGAAGA
Found at i:46714 original size:13 final size:13
Alignment explanation
Indices: 46696--46735 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
46686 GCTTTCACGG
*
46696 GGAGGAGGAAGAA
1 GGAGGAAGAAGAA
*
46709 GGAGGAAGAAGGA
1 GGAGGAAGAAGAA
*
46722 GGAAGAAGAAGAA
1 GGAGGAAGAAGAA
46735 G
1 G
46736 AGAGTTTTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (13 bp):
GGAGGAAGAAGAA
Found at i:47411 original size:18 final size:19
Alignment explanation
Indices: 47388--47434 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
47378 CGTTTTGCAT
*
47388 TTGCATTTTA-CTTTCGCA
1 TTGCATTTTACCTTTCACA
47406 TTGCATTTTACCTTTCACA
1 TTGCATTTTACCTTTCACA
*
47425 TTACATTTTA
1 TTGCATTTTA
47435 TTCATTCGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.51
Consensus pattern (19 bp):
TTGCATTTTACCTTTCACA
Found at i:54625 original size:17 final size:17
Alignment explanation
Indices: 54605--54655 Score: 70
Period size: 17 Copynumber: 3.0 Consensus size: 17
54595 TGACTGAAGA
54605 AAAAAAAAAGAGAAATG
1 AAAAAAAAAGAGAAATG
54622 AAAAGAAAAA-AGAAATG
1 AAAA-AAAAAGAGAAATG
54639 AAAAAATAAAGA-AAATG
1 AAAAAA-AAAGAGAAATG
54656 GGGTTCAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
16 2 0.06
17 23 0.74
18 6 0.19
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (17 bp):
AAAAAAAAAGAGAAATG
Found at i:54636 original size:12 final size:11
Alignment explanation
Indices: 54601--54653 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 11
54591 ACTTTGACTG
54601 AAGAAAAAAAA
1 AAGAAAAAAAA
**
54612 AAGAGAAATGAA
1 AAGA-AAAAAAA
54624 AAGAAAAAAGAA
1 AAGAAAAAA-AA
* *
54636 ATGAAAAAATA
1 AAGAAAAAAAA
54647 AAGAAAA
1 AAGAAAA
54654 TGGGGTTCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
11 14 0.42
12 19 0.58
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:54735 original size:45 final size:44
Alignment explanation
Indices: 54651--54735 Score: 98
Period size: 45 Copynumber: 1.9 Consensus size: 44
54641 AAAATAAAGA
* * * * * *
54651 AAATGGGGTTCAAGATGAAAATCTGTAAAGGGTGTCTTGAAACC
1 AAATGAGGTTCAAGATGAAAACCCGCAAAGGGCGGCTTGAAACC
*
54695 AAATGAGGTCTCAAGTTGAAAACCCGCAAAGGGCGGCTTGA
1 AAATGAGGT-TCAAGATGAAAACCCGCAAAGGGCGGCTTGA
54736 GTTGTCAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
44 8 0.24
45 25 0.76
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.21
Consensus pattern (44 bp):
AAATGAGGTTCAAGATGAAAACCCGCAAAGGGCGGCTTGAAACC
Found at i:55445 original size:27 final size:27
Alignment explanation
Indices: 55410--55463 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
55400 ATTTGTTCAG
* *
55410 GATTGGACCAAGTCACAAGACGACCAA
1 GATTAGACCAAGTCACAAGACAACCAA
55437 GATTAGACCAAGTCACAAGACAACCAA
1 GATTAGACCAAGTCACAAGACAACCAA
55464 CAAGTGAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.11
Consensus pattern (27 bp):
GATTAGACCAAGTCACAAGACAACCAA
Found at i:56081 original size:137 final size:134
Alignment explanation
Indices: 55921--56426 Score: 511
Period size: 130 Copynumber: 3.8 Consensus size: 134
55911 GGGGAAGATC
* *
55921 CTTCTTCTTTCAGATTTGATCTTCCTGAAGAGCAGCT-AAGCAAATCAAAGTTTGATTCAATCTT
1 CTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAG-TGAAGCAAATC-AAGTTCGATTCAATCTT
* * *
55985 CCCTGAAGAGCAACGAAGTGGATCAAAATTTTTCGAG-TCTGATCTCCCCTAAAAAGTAATGGAG
64 CCCTAAAGAGCAACGAAGTGAATCAAAA-TTTTCAAGATCTGATCTCCCCTAAAAAGT-ATGGAG
*
56049 CATATTATT
127 CACA-TATT
* * * * *
56058 CTTCTTCTTTCAGATTTGGTCTTCCTGAAGAACAGTGAAACAAATCAAGTTCAATTCAATTTTAC
1 CTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCAAGTTCGATTCAATCTTCC
** * * *
56123 CTAAAGAAAAACAAAGTGAATCAATAATTTTCAAGATATGAT-T-ACCTGAAAAAG--TGGA--A
66 CTAAAGAGCAACGAAGTGAATCAA-AATTTTCAAGATCTGATCTCCCCT-AAAAAGTATGGAGCA
*
56182 CAGATT
129 CATATT
* **
56188 CTTCTTCTTTCAGATTTGGTATTCCTGAAGAGCAGCAAAGCAAATCAAGTTCGATTCAATCTTCC
1 CTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCAAGTTCGATTCAATCTTCC
* * * * * *
56253 TTAAAGAGCAACGAAGTGGATCAAAATTTACAAG-TTTGATCTCCCCCAAAGAGTAGTGGAGTCG
66 CTAAAGAGCAACGAAGTGAATCAAAATTTTCAAGATCTGATCTCCCCTAAAAAGTA-TGGAG-C-
* *
56317 GCCTATT
128 ACATATT
* * *
56324 -TTCTTC---CAAATTTGGTCTTCCTAAAGAGTAGTGAAGCAAATCAAGTTCGATTCAATCTTCC
1 CTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCAAGTTCGATTCAATCTTCC
56385 CTGAAA-AG-AAGCGAAGTGAATCAAAAATTTTCAAGATCTGAT
66 CT-AAAGAGCAA-CGAAGTGAATC-AAAATTTTCAAGATCTGAT
56427 TGCCCAAAAA
Statistics
Matches: 304, Mismatches: 48, Indels: 37
0.78 0.12 0.10
Matches are distributed among these distances:
128 5 0.02
129 15 0.05
130 81 0.27
131 4 0.01
132 66 0.22
133 18 0.06
134 5 0.02
135 9 0.03
136 53 0.17
137 48 0.16
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (134 bp):
CTTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCAAGTTCGATTCAATCTTCC
CTAAAGAGCAACGAAGTGAATCAAAATTTTCAAGATCTGATCTCCCCTAAAAAGTATGGAGCACA
TATT
Found at i:56416 original size:262 final size:265
Alignment explanation
Indices: 55916--56444 Score: 683
Period size: 262 Copynumber: 2.0 Consensus size: 265
55906 GTAGTGGGGA
* * *
55916 AGATCCTTCTTCTTTCAGATTTGATCTTCCTGAAGAGCAGCTAAGCAAATCAAAGTTTGATTCAA
1 AGATCCTTCTTCTTTCAGATTTGATATTCCTGAAGAGCAGCAAAGCAAATCAAAGTTCGATTCAA
* * * *
55981 TCTTCCCTGAAGAGCAACGAAGTGGATCAAAATTTTTCGAGTCTGATCTCCCCTAAAAAGTAATG
66 TCTTCCCTAAAGAGCAACGAAGTGGATCAAAATTTTACAAGTCTGATCTCCCCCAAAAAGTAATG
* * * *
56046 GAGCATATTATTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAACAGTGAAACAAATCAAGTTCA
131 GAGCAGACTATTCTTCTTC--TCAAATTTGGTCTTCCTAAAGAACAGTGAAACAAATCAAGTTCA
* * *
56111 ATTCAATTTTACCTAAAGAAAAACAAAGTGAATCAATAATTTTCAAGATATGATTACCTGAAAAA
194 ATTCAATCTTACCTAAAGAAAAACAAAGTGAATCAAAAATTTTCAAGATATGATTACC-CAAAAA
56176 -GTGGAAC
258 GGTGGAAC
* *
56183 AGATTCTTCTTCTTTCAGATTTGGTATTCCTGAAGAGCAGCAAAGCAAATC-AAGTTCGATTCAA
1 AGATCCTTCTTCTTTCAGATTTGATATTCCTGAAGAGCAGCAAAGCAAATCAAAGTTCGATTCAA
* * * *
56247 TCTTCCTTAAAGAGCAACGAAGTGGATCAAAA-TTTACAAGTTTGATCTCCCCCAAAGAGTAGTG
66 TCTTCCCTAAAGAGCAACGAAGTGGATCAAAATTTTACAAGTCTGATCTCCCCCAAAAAGTAATG
* * ** * *
56311 GAGTCGGCCTATT-TTCTTC-CAAATTTGGTCTTCCTAAAGAGTAGTGAAGCAAATCAAGTTCGA
131 GAG-CAGACTATTCTTCTTCTCAAATTTGGTCTTCCTAAAGAACAGTGAAACAAATCAAGTTCAA
* * * * * *
56374 TTCAATCTTCCCTGAAA-AGAAGCGAAGTGAATCAAAAATTTTCAAGATCTGATTGCCCAAAAAG
195 TTCAATCTTACCT-AAAGAAAAACAAAGTGAATCAAAAATTTTCAAGATATGATTACCCAAAAAG
56438 GTGGAAC
259 GTGGAAC
56445 GAATCAAGTC
Statistics
Matches: 227, Mismatches: 32, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
261 5 0.02
262 90 0.40
263 3 0.01
265 35 0.15
266 47 0.21
267 47 0.21
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (265 bp):
AGATCCTTCTTCTTTCAGATTTGATATTCCTGAAGAGCAGCAAAGCAAATCAAAGTTCGATTCAA
TCTTCCCTAAAGAGCAACGAAGTGGATCAAAATTTTACAAGTCTGATCTCCCCCAAAAAGTAATG
GAGCAGACTATTCTTCTTCTCAAATTTGGTCTTCCTAAAGAACAGTGAAACAAATCAAGTTCAAT
TCAATCTTACCTAAAGAAAAACAAAGTGAATCAAAAATTTTCAAGATATGATTACCCAAAAAGGT
GGAAC
Found at i:56433 original size:132 final size:132
Alignment explanation
Indices: 55922--56435 Score: 485
Period size: 132 Copynumber: 3.9 Consensus size: 132
55912 GGGAAGATCC
* * *
55922 TTCTTCTTTCAGATTTGATCTTCCTGAAGAGCAGCT-AAGCAAATCAAAGTTTGATTCAATCTTC
1 TTCTTCTTCCAGATTTGGTCTTCCTGAAGAGCAG-TGAAGCAAATC-AAGTTCGATTCAATCTTC
* * * *
55986 CCTG-AAGAGCAACGAAGTGGATCAAAATTTTTCGAGTCTGATCTCCCCTAAAAAGTAATGGAGC
64 CCTGAAAGAGCAACGAAGTGAATCAAAAATTTTCAAGTCTGATCTCCCC--AAAAGTAGTGGAGC
*
56050 ATATTA
127 AGATTA
* * * *
56056 TTCTTCTTCTTTCAGATTTGGTCTTCCTGAAGAACAGTGAAACAAATCAAGTTCAATTCAATTTT
1 TTCTTCTTC---CAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCAAGTTCGATTCAATCTT
* ** * * * ** *
56121 ACCT-AAAGAAAAACAAAGTGAATCAATAATTTTCAAGATATGAT-TACCTGAAAA--AGTGGAA
63 CCCTGAAAGAGCAACGAAGTGAATCAAAAATTTTCAAG-TCTGATCT-CCCCAAAAGTAGTGGAG
*
56182 CAGATTC
126 CAGATTA
* * **
56189 TTCTTCTTTCAGATTTGGTATTCCTGAAGAGCAGCAAAGCAAATCAAGTTCGATTCAATCTT-CC
1 TTCTTCTTCCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCAAGTTCGATTCAATCTTCCC
* * * * *
56253 TTAAAGAGCAACGAAGTGGATC-AAAATTTACAAGTTTGATCTCCCCCAAAGAGTAGTGGAGTCG
66 TGAAAGAGCAACGAAGTGAATCAAAAATTTTCAAGTCTGATCT-CCCCAAA-AGTAGTGGAG-CA
**
56317 GCCTA
128 GATTA
* * *
56322 TT-TTCTTCCAAATTTGGTCTTCCTAAAGAGTAGTGAAGCAAATCAAGTTCGATTCAATCTTCCC
1 TTCTTCTTCCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCAAGTTCGATTCAATCTTCCC
*
56386 TGAAA-AG-AAGCGAAGTGAATCAAAAATTTTCAAGATCTGAT-TGCCCAAAA
66 TGAAAGAGCAA-CGAAGTGAATCAAAAATTTTCAAG-TCTGATCTCCCCAAAA
56436 AGGTGGAACG
Statistics
Matches: 306, Mismatches: 57, Indels: 37
0.76 0.14 0.09
Matches are distributed among these distances:
128 5 0.02
129 19 0.06
130 63 0.21
131 3 0.01
132 76 0.25
133 41 0.13
134 13 0.04
135 4 0.01
136 44 0.14
137 38 0.12
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (132 bp):
TTCTTCTTCCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCAAGTTCGATTCAATCTTCCC
TGAAAGAGCAACGAAGTGAATCAAAAATTTTCAAGTCTGATCTCCCCAAAAGTAGTGGAGCAGAT
TA
Found at i:56818 original size:2 final size:2
Alignment explanation
Indices: 56811--56860 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
56801 TCAATATGGA
* * *
56811 AT AT AT AT GT AT AA AT AT AA 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
56853 AT AT AT AT
1 AT AT AT AT
56861 GAAAAAACAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:57992 original size:50 final size:52
Alignment explanation
Indices: 57922--58059 Score: 163
Period size: 59 Copynumber: 2.6 Consensus size: 52
57912 CACACTCCAA
* *
57922 TTTGTCTTTTCATCGCGACTAGGAGGGTT-GG-TTAGAGTCATATTATCGAG
1 TTTGTCTTTTCATTGCGACTAGGAGGGTTAGGATTAGAGCCATATTATCGAG
* *
57972 TTTGCCTTTTCATTGTGACTAGGAGGGTTCGATAGGACACTTAGAGCCATATTATCGAG
1 TTTGTCTTTTCATTGCGACTAGGAGGG-T---TAGG--A-TTAGAGCCATATTATCGAG
58031 TTTGTCTTTTCATTGCGACTAGGAGGGTT
1 TTTGTCTTTTCATTGCGACTAGGAGGGTT
58060 CGATAGGACA
Statistics
Matches: 73, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
50 24 0.33
51 1 0.01
54 1 0.01
55 3 0.04
58 1 0.01
59 43 0.59
ACGTcount: A:0.20, C:0.15, G:0.27, T:0.38
Consensus pattern (52 bp):
TTTGTCTTTTCATTGCGACTAGGAGGGTTAGGATTAGAGCCATATTATCGAG
Found at i:58045 original size:59 final size:59
Alignment explanation
Indices: 57953--58072 Score: 213
Period size: 59 Copynumber: 2.0 Consensus size: 59
57943 GGAGGGTTGG
* *
57953 TTAGAGTCATATTATCGAGTTTGCCTTTTCATTGTGACTAGGAGGGTTCGATAGGACAC
1 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCGATAGGACAC
*
58012 TTAGAGCCATATTATCGAGTTTGTCTTTTCATTGCGACTAGGAGGGTTCGATAGGACAC
1 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCGATAGGACAC
58071 TT
1 TT
58073 TTCCATTTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (59 bp):
TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCGATAGGACAC
Found at i:60148 original size:21 final size:21
Alignment explanation
Indices: 60108--60149 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
60098 ACAGAGAACA
*
60108 TTACCAAGGTACTTCATCCTC
1 TTACCAAGGTACGTCATCCTC
60129 TTACCAAGGTA-GTCATTCCTC
1 TTACCAAGGTACGTCA-TCCTC
60150 ATCTTCTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.33
Consensus pattern (21 bp):
TTACCAAGGTACGTCATCCTC
Found at i:62163 original size:50 final size:50
Alignment explanation
Indices: 62099--62219 Score: 215
Period size: 50 Copynumber: 2.4 Consensus size: 50
62089 AGGATTAGAT
*
62099 TTATTATTTTATTAGAAATTAAGGTTGAGTTAAAACATTAATTTTAGTTA
1 TTATTATTTTATTAGGAATTAAGGTTGAGTTAAAACATTAATTTTAGTTA
* *
62149 TTATTATTTTATTAGGAATTAAGGTTGAGTTAAAATATTATTTTTAGTTA
1 TTATTATTTTATTAGGAATTAAGGTTGAGTTAAAACATTAATTTTAGTTA
62199 TTATTATTTTATTAGGAATTA
1 TTATTATTTTATTAGGAATTA
62220 GAGTTAAGAC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 68 1.00
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.51
Consensus pattern (50 bp):
TTATTATTTTATTAGGAATTAAGGTTGAGTTAAAACATTAATTTTAGTTA
Found at i:62580 original size:59 final size:59
Alignment explanation
Indices: 62488--62601 Score: 201
Period size: 59 Copynumber: 1.9 Consensus size: 59
62478 TGGTTATAGT
* *
62488 CATATTATCGAGTTTTCCTTTTCATTGCGACTAGGAGTGTTCGATAGGACACTTAGAGC
1 CATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCGATAGGACACTTAGAGC
*
62547 CATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTTGATAGGACACTTA
1 CATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCGATAGGACACTTA
62602 TCCATCTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.36
Consensus pattern (59 bp):
CATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCGATAGGACACTTAGAGC
Done.