Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007469.1 Hibiscus syriacus cultivar Beakdansim tig00020516_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: 73070
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:49 original size:21 final size:21
Alignment explanation
Indices: 23--63 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13 ATGATTTAGT
*
23 AATGATTTGATAATCATTATA
1 AATGATTTGATAATAATTATA
*
44 AATGATTTTATAATAATTAT
1 AATGATTTGATAATAATTAT
64 TTAGTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (21 bp):
AATGATTTGATAATAATTATA
Found at i:109 original size:14 final size:14
Alignment explanation
Indices: 90--116 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
80 ATTTTTATAA
90 TAATGATTTAATAC
1 TAATGATTTAATAC
104 TAATGATTTAATA
1 TAATGATTTAATA
117 ATTATTACTA
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:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (14 bp):
TAATGATTTAATAC
Found at i:141 original size:38 final size:37
Alignment explanation
Indices: 72--143 Score: 90
Period size: 38 Copynumber: 1.9 Consensus size: 37
62 ATTTAGTTAT
* * **
72 ATTTAGTAATTTTTATAATAATGATTTAATACTAATG
1 ATTTAATAATTATTATAATAATGATAGAATACTAATG
*
109 ATTTAATAATTATTACTAATAATTATAGAATACTA
1 ATTTAATAATTATTA-TAATAATGATAGAATACTA
144 CAAATGAGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 13 0.45
38 16 0.55
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (37 bp):
ATTTAATAATTATTATAATAATGATAGAATACTAATG
Found at i:306 original size:23 final size:21
Alignment explanation
Indices: 266--335 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 21
256 GATTTATTGT
*
266 TAATATTTAAATATTTGATAC
1 TAATATTTAAATACTTGATAC
287 TAATGATTTAAAATACTTGATTTAC
1 TAAT-ATTT-AAATACTTGA--TAC
* *
312 TAAATATTTAATTATTTGATAC
1 T-AATATTTAAATACTTGATAC
334 TA
1 TA
336 GTAATGATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
21 5 0.12
22 8 0.20
23 9 0.22
24 8 0.20
25 8 0.20
26 3 0.07
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (21 bp):
TAATATTTAAATACTTGATAC
Found at i:345 original size:17 final size:17
Alignment explanation
Indices: 320--352 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
310 ACTAAATATT
*
320 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
337 TAATGATTTGATACTA
1 TAATGATTTGATACTA
353 AAATCATTGT
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:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:2680 original size:40 final size:40
Alignment explanation
Indices: 2635--2754 Score: 107
Period size: 42 Copynumber: 2.9 Consensus size: 40
2625 AAATATAACT
2635 TAACTATTTAACTACAAACTAATTAAATAATTTTTTTATATAA
1 TAACTATTTAAC-ACAAACTAATTAAATAA-TTTTTTATAT-A
* * *
2678 CTAACTATTACAAAACAAACTAATT-AATTATTTTTTAACTATA
1 -TAACTATT-TAACACAAACTAATTAAATAATTTTTT-A-TATA
** * *
2721 TAACTATCAAACATATACTAATTAAATAATTTTT
1 TAACTATTTAACACAAACTAATTAAATAATTTTT
2755 AATTTATGTA
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
41 11 0.17
42 22 0.35
43 6 0.10
44 22 0.35
45 2 0.03
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (40 bp):
TAACTATTTAACACAAACTAATTAAATAATTTTTTATATA
Found at i:2686 original size:44 final size:43
Alignment explanation
Indices: 2626--2754 Score: 129
Period size: 44 Copynumber: 3.0 Consensus size: 43
2616 TCAACAAACA
2626 AATATAACTTAACTATTTAACTACAAACTAATTAAATAATTTTTT
1 AATATAAC-TAACTATTTAAC-ACAAACTAATTAAATAATTTTTT
* * * *
2671 TATATAACTAACTATTACAAAACAAACTAATT-AATTATTTTTT
1 AATATAACTAACTATT-TAACACAAACTAATTAAATAATTTTTT
** * *
2714 AACTAT-A-TAACTATCAAACATATACTAATTAAATAATTTTT
1 AA-TATAACTAACTATTTAACACAAACTAATTAAATAATTTTT
2755 AATTTATGTA
Statistics
Matches: 70, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
41 11 0.16
42 16 0.23
43 12 0.17
44 22 0.31
45 9 0.13
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (43 bp):
AATATAACTAACTATTTAACACAAACTAATTAAATAATTTTTT
Found at i:2782 original size:41 final size:40
Alignment explanation
Indices: 2650--2782 Score: 99
Period size: 41 Copynumber: 3.2 Consensus size: 40
2640 ATTTAACTAC
* * *
2650 AAACTAATTAAATAATTTTTTTA-TATAACTAACTATTACAAAAC
1 AAACTAATTAAATAA-TTTTTAACTAT-A-TAACTA-TA-AACAT
* *
2694 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
2735 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
2776 AAACTAA
1 AAACTAA
2783 CAATCATATA
Statistics
Matches: 73, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
41 33 0.45
42 12 0.16
43 12 0.16
44 16 0.22
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.41
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:3317 original size:29 final size:29
Alignment explanation
Indices: 3284--3387 Score: 156
Period size: 29 Copynumber: 3.6 Consensus size: 29
3274 TCGTGAGCTA
*
3284 GGACTACATGGCGACCTACTTGGTCGCCG
1 GGACTACATGGCGACCTACTAGGTCGCCG
3313 GGACTACATGGCGACCTA-TAAGGTCGCCG
1 GGACTACATGGCGACCTACT-AGGTCGCCG
* *
3342 GGACTACATGGCGACCTACAAGGTCGCCC
1 GGACTACATGGCGACCTACTAGGTCGCCG
*
3371 AGACTACATGGCGACCT
1 GGACTACATGGCGACCT
3388 CTCCATTGGC
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
28 1 0.01
29 68 0.99
ACGTcount: A:0.23, C:0.31, G:0.29, T:0.17
Consensus pattern (29 bp):
GGACTACATGGCGACCTACTAGGTCGCCG
Found at i:6855 original size:32 final size:32
Alignment explanation
Indices: 6808--6873 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
6798 TTGACTCGAC
6808 CCGATATTAAACCGACCC-AAAATCTAACCGAT
1 CCGATATTAAACCGACCCAAAAATC-AACCGAT
* *
6840 CCGATATTGACCCGACCCAAAAATCAACCGAT
1 CCGATATTAAACCGACCCAAAAATCAACCGAT
6872 CC
1 CC
6874 AATTTTGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 25 0.81
33 6 0.19
ACGTcount: A:0.38, C:0.35, G:0.11, T:0.17
Consensus pattern (32 bp):
CCGATATTAAACCGACCCAAAAATCAACCGAT
Found at i:6869 original size:48 final size:47
Alignment explanation
Indices: 6779--6875 Score: 113
Period size: 48 Copynumber: 2.0 Consensus size: 47
6769 ACCTAAACCA
* * * * *
6779 AAAATCAATCGATCCAATATTGACTCGACCCGATATTAAACCGACCC
1 AAAATCAACCGATCCAATATTGACCCGACCCAAAAATAAACCGACCC
* * *
6826 AAAATCTAACCGATCCGATATTGACCCGACCCAAAAATCAACCGATCC
1 AAAATC-AACCGATCCAATATTGACCCGACCCAAAAATAAACCGACCC
6874 AA
1 AA
6876 TTTTGATCCA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
47 6 0.15
48 35 0.85
ACGTcount: A:0.40, C:0.31, G:0.10, T:0.19
Consensus pattern (47 bp):
AAAATCAACCGATCCAATATTGACCCGACCCAAAAATAAACCGACCC
Found at i:12530 original size:19 final size:19
Alignment explanation
Indices: 12506--12549 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
12496 AAAGTCCAAT
12506 GGAGCATATGAGAACATGA
1 GGAGCATATGAGAACATGA
12525 GGAGCATATGAGAACATGA
1 GGAGCATATGAGAACATGA
12544 GGAGCA
1 GGAGCA
12550 GATTTATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.41, C:0.11, G:0.34, T:0.14
Consensus pattern (19 bp):
GGAGCATATGAGAACATGA
Found at i:24070 original size:21 final size:19
Alignment explanation
Indices: 24042--24087 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
24032 TCATTGAATC
24042 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
24062 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
24081 ACTTAGT
1 A-TTAGT
24088 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:25978 original size:2 final size:2
Alignment explanation
Indices: 25973--26035 Score: 99
Period size: 2 Copynumber: 31.5 Consensus size: 2
25963 CATATATGTT
*
25973 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* *
26015 TG TA TG TG TG TG CG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG T
26036 ATGTATGTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.03, C:0.02, G:0.46, T:0.49
Consensus pattern (2 bp):
TG
Found at i:26302 original size:46 final size:45
Alignment explanation
Indices: 26223--26321 Score: 110
Period size: 46 Copynumber: 2.2 Consensus size: 45
26213 CGAAGTGCCA
* * * *
26223 CGTAGAAATGTCCTGAATAACCATATAGTATTGTCCCGAAGGACCG
1 CGTAGAAATGTCCCGAAGAACCATATAG-ATTGTCACAAAGGACCG
* *
26269 CGTAGAAATGTCCCGAAGAACCACGTATA-ATTGTTACAAAGGATCG
1 CGTAGAAATGTCCCGAAGAACCA--TATAGATTGTCACAAAGGACCG
26315 CGTAGAA
1 CGTAGAA
26322 CCCTCGACTC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
46 41 0.91
48 4 0.09
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (45 bp):
CGTAGAAATGTCCCGAAGAACCATATAGATTGTCACAAAGGACCG
Found at i:26450 original size:45 final size:45
Alignment explanation
Indices: 26393--26504 Score: 136
Period size: 45 Copynumber: 2.5 Consensus size: 45
26383 ACCATTTACA
* *
26393 CATT-TCACATAGCTTGTATCACATAGACATATAATCACAATGCT
1 CATTGTCACATAGCTTATATCACATAGACATATAATCACAAAGCT
* *** * *
26437 CATTGTCACATAGCTTACATCACATTTTCATGTAATCACAAAGGT
1 CATTGTCACATAGCTTATATCACATAGACATATAATCACAAAGCT
*
26482 CAATGTCACATAGCTTATATCAC
1 CATTGTCACATAGCTTATATCAC
26505 CCTTTCATGT
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
44 4 0.07
45 53 0.93
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (45 bp):
CATTGTCACATAGCTTATATCACATAGACATATAATCACAAAGCT
Found at i:26511 original size:45 final size:45
Alignment explanation
Indices: 26424--26540 Score: 144
Period size: 45 Copynumber: 2.6 Consensus size: 45
26414 CATAGACATA
* * * *
26424 TAATCACAATGCTCATTGTCACATAGCTTACATCACATTTTCATG
1 TAATCACAAAGATCAATGTCACATAGCTTACATCACACTTTCATG
* * *
26469 TAATCACAAAGGTCAATGTCACATAGCTTATATCACCCTTTCATG
1 TAATCACAAAGATCAATGTCACATAGCTTACATCACACTTTCATG
* * *
26514 TAATCACATAGATCAATATCATATAGC
1 TAATCACAAAGATCAATGTCACATAGC
26541 ACAAAATATA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.32
Consensus pattern (45 bp):
TAATCACAAAGATCAATGTCACATAGCTTACATCACACTTTCATG
Found at i:37695 original size:24 final size:24
Alignment explanation
Indices: 37668--37713 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
37658 ACGTATAAAT
* *
37668 TGCACCAAAGTGCCGCGTAGAATA
1 TGCACCAAAGTACCACGTAGAATA
*
37692 TGCACCGAAGTACCACGTAGAA
1 TGCACCAAAGTACCACGTAGAA
37714 ATGTCCCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (24 bp):
TGCACCAAAGTACCACGTAGAATA
Found at i:37729 original size:23 final size:22
Alignment explanation
Indices: 37683--37782 Score: 67
Period size: 23 Copynumber: 4.3 Consensus size: 22
37673 CAAAGTGCCG
37683 CGTAGAATATG-CACCGAAGTACCA
1 CGTAGAA-ATGTC-CCGAAG-ACCA
37707 CGTAGAAATGTCCCGAAGAACCA
1 CGTAGAAATGTCCCGAAG-ACCA
* * * * *
37730 CATAGTATTGTCCCAAATGACCG
1 CGTAGAAATGTCCCGAA-GACCA
* *
37753 CTTAGAAATGTCCCAAATGACCA
1 CGTAGAAATGTCCCGAA-GACCA
*
37776 TGTAGAA
1 CGTAGAA
37783 TTATCCTAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
23 53 0.85
24 9 0.15
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (22 bp):
CGTAGAAATGTCCCGAAGACCA
Found at i:37957 original size:45 final size:45
Alignment explanation
Indices: 37908--38007 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 45
37898 CATACACATA
* *
37908 TAATCACATAGCTCATTGTCACATA-TCTTACATCACATTTTCATG
1 TAATCACATAGCTCAATGCCACATAGT-TTACATCACATTTTCATG
* * *
37953 TAATCAC-TAAGGTCAATGCCACATAGTTTATATCACCTTTTCATG
1 TAATCACAT-AGCTCAATGCCACATAGTTTACATCACATTTTCATG
37998 TAATCACATA
1 TAATCACATA
38008 TATCAATATC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
44 1 0.02
45 44 0.94
46 2 0.04
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (45 bp):
TAATCACATAGCTCAATGCCACATAGTTTACATCACATTTTCATG
Found at i:50238 original size:56 final size:56
Alignment explanation
Indices: 50145--50576 Score: 264
Period size: 54 Copynumber: 7.8 Consensus size: 56
50135 ATGGAAAATA
* * * * *
50145 CACAGAGGTGCTAGCTTAATGATTGATGCACACAGGTGCTCAATCGTTTC-TTAATG
1 CACAGAGGTGCCAG-TTAAAGATTGATACACAGAGGTGCTCAATCATTTCTTTAATG
* *
50201 CATAGAGGTGCCAGTTCAAAGATTGATACACAGAGGTGCTCAATCATCTCTTTAATG
1 CACAGAGGTGCCAGTT-AAAGATTGATACACAGAGGTGCTCAATCATTTCTTTAATG
* * **
50258 CACAGAGGTGCAAGTTCAAATATTGATGTACAGAGGTGCTCAATCATTTCTTTAATG
1 CACAGAGGTGCCAGTT-AAAGATTGATACACAGAGGTGCTCAATCATTTCTTTAATG
* * ** * *
50315 CA-AAAGGTGTCAGGTTTTAGATT-ACAGCACAGAGGTGCTCAATCA--TCTTAAATG
1 CACAGAGGTGCCA-GTTAAAGATTGATA-CACAGAGGTGCTCAATCATTTCTTTAATG
* ** * * *
50369 CACAGAGGTGCCAAATTTTAGATTGA-AGCACGGAGGTGCTCAATCA--TC-CTAAAG
1 CACAGAGGTGCC-AGTTAAAGATTGATA-CACAGAGGTGCTCAATCATTTCTTTAATG
* *** * * **
50423 CACAGAGGTGCTAGATGCTAGATTTAAACACAGAGGTGCTCAATCA--TCCCTAA-G
1 CACAGAGGTGCCAG-TTAAAGATTGATACACAGAGGTGCTCAATCATTTCTTTAATG
* *** ** * *
50477 CACAGAGATGCCAGATCCTAGATTGAGGCACAGAGGTGCTCAGT-AATT-TTTAACTG
1 CACAGAGGTGCCAG-TTAAAGATTGATACACAGAGGTGCTCAATCATTTCTTTAA-TG
* *** *
50533 CACAGAGGTGTCAGTTTTCGATTGA-AGCATAGAGGTGCTCAATC
1 CACAGAGGTGCCAGTTAAAGATTGATA-CACAGAGGTGCTCAATC
50577 TTTAATTCAA
Statistics
Matches: 307, Mismatches: 53, Indels: 32
0.78 0.14 0.08
Matches are distributed among these distances:
53 2 0.01
54 92 0.30
55 68 0.22
56 83 0.27
57 62 0.20
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (56 bp):
CACAGAGGTGCCAGTTAAAGATTGATACACAGAGGTGCTCAATCATTTCTTTAATG
Found at i:50265 original size:29 final size:29
Alignment explanation
Indices: 50229--50379 Score: 86
Period size: 28 Copynumber: 5.4 Consensus size: 29
50219 AAGATTGATA
*
50229 CACAGAGGTGCTCAATCATCTCTTTAATG
1 CACAGAGGTGCTCAATCATATCTTTAATG
* * *
50258 CACAGAGGTG--CAAGTTCAAAT-ATTGATG
1 CACAGAGGTGCTCAA--TCATATCTTTAATG
* *
50286 TACAGAGGTGCTCAATCATTTCTTTAATG
1 CACAGAGGTGCTCAATCATATCTTTAATG
* * ** **
50315 CA-AAAGGTG-TCAGGTTTTA-GATTACA-G
1 CACAGAGGTGCTCA-ATCATATCTTTA-ATG
*
50342 CACAGAGGTGCTCAATC--ATCTTAAATG
1 CACAGAGGTGCTCAATCATATCTTTAATG
50369 CACAGAGGTGC
1 CACAGAGGTGC
50380 CAAATTTTAG
Statistics
Matches: 88, Mismatches: 23, Indels: 24
0.65 0.17 0.18
Matches are distributed among these distances:
26 2 0.02
27 26 0.30
28 34 0.39
29 23 0.26
30 3 0.03
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (29 bp):
CACAGAGGTGCTCAATCATATCTTTAATG
Found at i:50346 original size:113 final size:111
Alignment explanation
Indices: 50140--50415 Score: 285
Period size: 113 Copynumber: 2.5 Consensus size: 111
50130 ATAGTATGGA
* * *
50140 AAATACACAGAGGTGCTAGCTTAATGATTGATGCACACAGGTGCTCAATCGTTTCTTAATGCATA
1 AAATGCACAGAGGTGCAAGCTTAATGATTGATGCACACAGGTGCTCAATCATTTCTTAATGCATA
* *
50205 GAGGTGCCAGTTCAAAGATTGATACACAGAGGTGCTCAATCATCTCTT
66 AAGGTGCCAGTTCAAAGATTGACACACAGAGGTGCTCAATCA--TCTT
* * *
50253 TAATGCACAGAGGTGCAAG-TTCAAAT-ATTGATGTACAGAGGTGCTCAATCATTTCTTTAATGC
1 AAATGCACAGAGGTGCAAGCTT--AATGATTGATGCACACAGGTGCTCAATCATTTC-TTAATGC
* **
50316 A-AAAGGTGTCAGGTT-TTAGATT-ACAGCACAGAGGTGCTCAATCATCTT
63 ATAAAGGTGCCA-GTTCAAAGATTGACA-CACAGAGGTGCTCAATCATCTT
** * * **
50364 AAATGCACAGAGGTGCCAAATTTTA-GATTGAAGCACGGAGGTGCTCAATCAT
1 AAATGCACAGAGGTG-CAAGCTTAATGATTGATGCACACAGGTGCTCAATCAT
50416 CCTAAAGCAC
Statistics
Matches: 138, Mismatches: 17, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
111 42 0.30
112 7 0.05
113 75 0.54
114 14 0.10
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (111 bp):
AAATGCACAGAGGTGCAAGCTTAATGATTGATGCACACAGGTGCTCAATCATTTCTTAATGCATA
AAGGTGCCAGTTCAAAGATTGACACACAGAGGTGCTCAATCATCTT
Found at i:54669 original size:2 final size:2
Alignment explanation
Indices: 54662--54699 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
54652 TAACAACGTG
54662 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
54700 GTTTGTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Done.