Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004128.1 Hibiscus syriacus cultivar Beakdansim tig00009033_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: 56598
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:13845 original size:45 final size:45
Alignment explanation
Indices: 13745--13867 Score: 140
Period size: 45 Copynumber: 2.7 Consensus size: 45
13735 ATAATGCATA
* * * *
13745 ATTATGCATTTTCATTTATGGCAATCGTTCATGCCTTTTTATATACT
1 ATTATACATTTT-ATTTATGGC-ATCTTTCATACCTTTTTATACACT
* *
13792 ATTTTACATTTTATTTATGGCATCATTTCATACC-TTTTATACATT
1 ATTATACATTTTATTTATGGCATC-TTTCATACCTTTTTATACACT
*
13837 GTTATACATTTTATTTATGGCATCCTTTCAT
1 ATTATACATTTTATTTATGGCAT-CTTTCAT
13868 GCCCATTATG
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
45 39 0.59
46 17 0.26
47 10 0.15
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.51
Consensus pattern (45 bp):
ATTATACATTTTATTTATGGCATCTTTCATACCTTTTTATACACT
Found at i:13899 original size:45 final size:44
Alignment explanation
Indices: 13786--13892 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 44
13776 TGCCTTTTTA
* **
13786 TATACTAT-TTTACATTTTATTTATGGCATCATTTCATACCTTT
1 TATACAATGTTTACATTTTATTTATGGCATCATTTCATACCCAT
* * *
13829 TATACATTGTTATACATTTTATTTATGGCATCCTTTCATGCCCAT
1 TATACAATGTT-TACATTTTATTTATGGCATCATTTCATACCCAT
13874 TATGA-AATGTTTACATTTT
1 TAT-ACAATGTTTACATTTT
13893 CCTTTATAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
43 6 0.11
44 10 0.19
45 37 0.69
46 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.50
Consensus pattern (44 bp):
TATACAATGTTTACATTTTATTTATGGCATCATTTCATACCCAT
Found at i:13944 original size:2 final size:2
Alignment explanation
Indices: 13937--13963 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13927 ATTGTACATC
13937 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 A
13964 ACACCCCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14483 original size:55 final size:55
Alignment explanation
Indices: 14417--14925 Score: 715
Period size: 55 Copynumber: 9.3 Consensus size: 55
14407 TTTATTAAGA
* * * *
14417 TGCACAAATAGTGCCTATACGG-TATATCATCTACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCATGTACGGTTAT-TCATCAACTCATGATGAATTCCGTGGATT
* **
14472 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGT-GAAA
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* *
14526 TGCACACTTAGTGCATGTACGGTGGTTATTCATCAACTCATAATGAATTCCGTGGATT
1 TGCACACATAGTGCATGTAC---GGTTATTCATCAACTCATGATGAATTCCGTGGATT
* *
14584 TGCACACATAGTGCATGTACGGTTATTCATTAACTCATGATGAATTCCGTGAATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * *
14639 TGCACACATAATGCATGTACGGTTATTCATCAACTCATGACGAATTCCGTGAATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
**
14694 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTATGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * *
14749 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTAGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
*
14804 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * *
14859 T--ACACACAGTGCTTATGT--GGTTATTCATCAACTCATGATGAATTTCGTTGATT
1 TGCACACATAGTGC--ATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
14912 TGCACACATAGTGC
1 TGCACACATAGTGC
14926 CTATTTGGTA
Statistics
Matches: 410, Mismatches: 35, Indels: 18
0.89 0.08 0.04
Matches are distributed among these distances:
53 44 0.11
54 21 0.05
55 293 0.71
56 3 0.01
57 28 0.07
58 21 0.05
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (55 bp):
TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
Found at i:15358 original size:20 final size:20
Alignment explanation
Indices: 15333--15388 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 20
15323 CGATGTTGCC
*
15333 TGGTATTGATACCCTTACCA
1 TGGTATTGATACCCATACCA
* *
15353 TGGTATCGATACTACCATACTA
1 TGGTATTGATAC--CCATACCA
*
15375 TGGTACTGATACCC
1 TGGTATTGATACCC
15389 CTTCAGGTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 13 0.45
22 16 0.55
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (20 bp):
TGGTATTGATACCCATACCA
Found at i:15431 original size:94 final size:95
Alignment explanation
Indices: 15240--15462 Score: 297
Period size: 94 Copynumber: 2.4 Consensus size: 95
15230 AAGTTCAATA
* * * * * **
15240 GTATCGATACTAC-TACCGTGGTACCGATACTTCTATACTATGGTACTGATACCCCCTTTTGGTA
1 GTATCGATAC-CCTTACCATGGTATCGATACTACCATACTATGGTACTGATACCCCCTTCAGGTA
* * *
15304 TTGATACCCATTTTAGGTTCGATGTTGCCTG
65 TCGATACCAATTTTAGATTCGATGTTGCCTG
*
15335 GTATTGATACCCTTACCATGGTATCGATACTACCATACTATGGTACTGATA-CCCCTTCAGGTAT
1 GTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACTGATACCCCCTTCAGGTAT
* **
15399 CGATACTAATTTTAGATTCGATGTTTTCTG
66 CGATACCAATTTTAGATTCGATGTTGCCTG
15429 GTATCGATACCCTTACCATGGTATCGATACTACC
1 GTATCGATACCCTTACCATGGTATCGATACTACC
15463 TCGTTGGTAT
Statistics
Matches: 112, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
94 69 0.62
95 43 0.38
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (95 bp):
GTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACTGATACCCCCTTCAGGTAT
CGATACCAATTTTAGATTCGATGTTGCCTG
Found at i:18047 original size:41 final size:41
Alignment explanation
Indices: 17986--18066 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
17976 CCAACGGTGT
**
17986 TGAACATTGATACATGAATGTACCAAAGCTGAACTGATAAC
1 TGAACATTGATACACAAATGTACCAAAGCTGAACTGATAAC
18027 TGAACATTGATACACAAATGTACCAAAGCTGAACTGATAA
1 TGAACATTGATACACAAATGTACCAAAGCTGAACTGATAA
18067 GTACTCACTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.23
Consensus pattern (41 bp):
TGAACATTGATACACAAATGTACCAAAGCTGAACTGATAAC
Found at i:18185 original size:18 final size:18
Alignment explanation
Indices: 18162--18196 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
18152 ATTAATATGT
18162 ATCTGATAACTGTAAATC
1 ATCTGATAACTGTAAATC
18180 ATCTGATAACTGTAAAT
1 ATCTGATAACTGTAAAT
18197 ATTTAGAATT
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:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (18 bp):
ATCTGATAACTGTAAATC
Found at i:29704 original size:15 final size:15
Alignment explanation
Indices: 29651--29712 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
29641 GACCACGAGC
* *
29651 CGAGTCGAGATGAGA
1 CGAGCCGAGACGAGA
* * *
29666 CGAGCCGAGCCGTGC
1 CGAGCCGAGACGAGA
* *
29681 CGTGCCGAGCCGAGA
1 CGAGCCGAGACGAGA
*
29696 CGAGACGAGACGAGA
1 CGAGCCGAGACGAGA
29711 CG
1 CG
29713 GACGGCGACG
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.26, C:0.27, G:0.40, T:0.06
Consensus pattern (15 bp):
CGAGCCGAGACGAGA
Found at i:29712 original size:10 final size:10
Alignment explanation
Indices: 29645--29709 Score: 58
Period size: 10 Copynumber: 6.5 Consensus size: 10
29635 GACCATGACC
29645 ACGAGCCGAG
1 ACGAGCCGAG
* **
29655 TCGAGATGAG
1 ACGAGCCGAG
29665 ACGAGCCGAG
1 ACGAGCCGAG
* * *
29675 CCGTGCCGTG
1 ACGAGCCGAG
*
29685 CCGAGCCGAG
1 ACGAGCCGAG
*
29695 ACGAGACGAG
1 ACGAGCCGAG
29705 ACGAG
1 ACGAG
29710 ACGGACGGCG
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 42 1.00
ACGTcount: A:0.26, C:0.28, G:0.40, T:0.06
Consensus pattern (10 bp):
ACGAGCCGAG
Found at i:31161 original size:218 final size:216
Alignment explanation
Indices: 30783--31219 Score: 840
Period size: 218 Copynumber: 2.0 Consensus size: 216
30773 TTCTGACTTA
30783 AACCTTTGGTAAGTGGATCTGCTAGGTTCCTTTCCGACTTCACATACTCTAAAGAGAGCACTCCA
1 AACCTTTGGTAAGTGGATCTGCTAGGTTCCTTTCCGACTTCACATACTCTAAAGAGAGCACTCCA
30848 TTCTTTATTAAGTGTCTAACAAATTCATGTCTTATGCGAATGTGTCTTTTCTTACCATTGTAAGC
66 TTCTTTATTAAGTGTCTAACAAATTCATGTCTTATGCGAATGTGTCTTTTCTTACCATTGTAAGC
30913 TTGGTTCTTAGCCACACATATCACAGCTTGTGAATCACACAATAATGAAACCGGAGGAGTCGGTC
131 TTGGTTCTTAGCCACACATATCACAGCTTGTGAATCACACAAT-ATGAAACCGGAGGAGTCGGTC
30978 TTCCCCACAACGGAATATCTGCT
195 TTCCCCACAACGGAATAT-TGCT
31001 AACCTTTGGTAAGTGGATCTGCTAGGTTCCTTTCCGACTTCACATACTCTAAAGAGAGCACTCCA
1 AACCTTTGGTAAGTGGATCTGCTAGGTTCCTTTCCGACTTCACATACTCTAAAGAGAGCACTCCA
31066 TTCTTTATTAAGTGTCTAACAAAATTCATGTCTTATGCGAATGTGT-TTTTCTTACCATTGTAAG
66 TTCTTTATTAAGTGTCTAAC-AAATTCATGTCTTATGCGAATGTGTCTTTTCTTACCATTGTAAG
31130 CTTGGTTCTTAGCCACACATATCACAGCTTGTGAATCACACAATATGAAACCGGAGGAGTCGGTC
130 CTTGGTTCTTAGCCACACATATCACAGCTTGTGAATCACACAATATGAAACCGGAGGAGTCGGTC
31195 TTCCCCACAACGGAATATTGCT
195 TTCCCCACAACGGAATATTGCT
31217 AAC
1 AAC
31220 AAGCTTCTGA
Statistics
Matches: 218, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
216 7 0.03
217 39 0.18
218 147 0.67
219 25 0.11
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32
Consensus pattern (216 bp):
AACCTTTGGTAAGTGGATCTGCTAGGTTCCTTTCCGACTTCACATACTCTAAAGAGAGCACTCCA
TTCTTTATTAAGTGTCTAACAAATTCATGTCTTATGCGAATGTGTCTTTTCTTACCATTGTAAGC
TTGGTTCTTAGCCACACATATCACAGCTTGTGAATCACACAATATGAAACCGGAGGAGTCGGTCT
TCCCCACAACGGAATATTGCT
Found at i:44123 original size:36 final size:36
Alignment explanation
Indices: 44020--44168 Score: 176
Period size: 36 Copynumber: 4.2 Consensus size: 36
44010 TTAAACCAAA
* * * *
44020 CAACAATGGAACATCTTCATCCAAGACCAACCCGAG
1 CAACAATGCACCATCTTCACCCAAGACCAAACCGAG
* * *
44056 CAATAATGCACCA-CGTTCA-CCAAGGCTAAACCGAG
1 CAACAATGCACCATC-TTCACCCAAGACCAAACCGAG
*
44091 CAACAATGCACCATCTTCCCCCAAGACCAAACCGAG
1 CAACAATGCACCATCTTCACCCAAGACCAAACCGAG
* * *
44127 CAACAATGCACCATCTTCACCAAAGACCAAACCTAA
1 CAACAATGCACCATCTTCACCCAAGACCAAACCGAG
44163 CAACAA
1 CAACAA
44169 CACATACTAC
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
35 29 0.30
36 67 0.70
ACGTcount: A:0.40, C:0.36, G:0.11, T:0.13
Consensus pattern (36 bp):
CAACAATGCACCATCTTCACCCAAGACCAAACCGAG
Found at i:44127 original size:71 final size:71
Alignment explanation
Indices: 44011--44168 Score: 192
Period size: 71 Copynumber: 2.2 Consensus size: 71
44001 ATCGTTAAAT
* * * *
44011 TAAACCAAACAACAATGGAACATCTTCATCCAAGACCAACCCGAGCAATAATGCACCA-CGTTCA
1 TAAACCAAACAACAATGCAACATCTTCACCCAAGACCAAACCGAGCAACAATGCACCATC-TTCA
44075 CCAAGGC
65 CCAAGGC
* * * *
44082 TAAACCGAGCAACAATGCACCATCTTCCCCCAAGACCAAACCGAGCAACAATGCACCATCTTCAC
1 TAAACCAAACAACAATGCAACATCTTCACCCAAGACCAAACCGAGCAACAATGCACCATCTTCAC
*
44147 CAAAGAC
66 C-AAGGC
* *
44154 CAAACCTAACAACAA
1 TAAACCAAACAACAA
44169 CACATACTAC
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
71 56 0.77
72 17 0.23
ACGTcount: A:0.42, C:0.35, G:0.11, T:0.13
Consensus pattern (71 bp):
TAAACCAAACAACAATGCAACATCTTCACCCAAGACCAAACCGAGCAACAATGCACCATCTTCAC
CAAGGC
Found at i:44331 original size:42 final size:42
Alignment explanation
Indices: 44283--44441 Score: 150
Period size: 41 Copynumber: 3.9 Consensus size: 42
44273 CAAAATGGTA
*
44283 ACTTTAGCGGCATTTTTATACAAAACGTCGCGATAGAGTAGT
1 ACTTTAGCGGCATTTTTATACAAAACGTCGCAATAGAGTAGT
* * *
44325 ACTTTAGCGGCATTTGTATA-AAAATGTCGTAATAGAGT--T
1 ACTTTAGCGGCATTTTTATACAAAACGTCGCAATAGAGTAGT
* * *
44364 CATCTATAGTGGCATTTTTCA-AC-AAACGCCGCAATAGAGTAGT
1 -A-CTTTAGCGGCATTTTT-ATACAAAACGTCGCAATAGAGTAGT
* * * *
44407 ACTTTAGCAGCGTTTTTATA-GAAACGCCGCAATAG
1 ACTTTAGCGGCATTTTTATACAAAACGTCGCAATAG
44442 GTTCATCCAT
Statistics
Matches: 95, Mismatches: 14, Indels: 17
0.75 0.11 0.13
Matches are distributed among these distances:
39 1 0.01
40 2 0.02
41 70 0.74
42 21 0.22
43 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (42 bp):
ACTTTAGCGGCATTTTTATACAAAACGTCGCAATAGAGTAGT
Found at i:44505 original size:162 final size:164
Alignment explanation
Indices: 44319--44618 Score: 408
Period size: 162 Copynumber: 1.8 Consensus size: 164
44309 GTCGCGATAG
44319 AGTAGTACTTTAGCGGCATTTGTATAAAAATGTCGTAATAGAGTTCATCTATAGTGGCATTTT-T
1 AGTAGTACTTTAGCGGCATTTGTATAAAAATGTCGTAATAGAGTTCATCTATAGTGGCATTTTAT
* * * *
44383 CAACAAACGCCGCAATAGAGTAGTACTTTAGCAG-CGTTTTTATAGAAACGCCGCAATA-GGTTC
66 CAACAAACGCCACAAAAGAGTAGTACTTTAG-AGACGTTTTTATACAAACGCCACAATAGGGTTC
44446 ATCCATAGTTGTGTTTCTCAACAAATGTCATGACA
130 ATCCATAGTTGTGTTTCTCAACAAATGTCATGACA
** * * * *
44481 AGTAGTACTTTAGCGGTGTTTGTATAAAAATGTCGTAATAGGGTTTATTTATAGTGGCGTTTTAT
1 AGTAGTACTTTAGCGGCATTTGTATAAAAATGTCGTAATAGAGTTCATCTATAGTGGCATTTTAT
* * * * * * *
44546 CGATAAATGCCATAAAAGAGTAGTACTTTAGTGATGTTTTTATACAAATGCCACAATAGGGTTCA
66 CAACAAACGCCACAAAAGAGTAGTACTTTAGAGACGTTTTTATACAAACGCCACAATAGGGTTCA
*
44611 TCTATAGT
131 TCCATAGT
44619 GGCATTTTTT
Statistics
Matches: 117, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
162 58 0.50
163 46 0.39
164 13 0.11
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (164 bp):
AGTAGTACTTTAGCGGCATTTGTATAAAAATGTCGTAATAGAGTTCATCTATAGTGGCATTTTAT
CAACAAACGCCACAAAAGAGTAGTACTTTAGAGACGTTTTTATACAAACGCCACAATAGGGTTCA
TCCATAGTTGTGTTTCTCAACAAATGTCATGACA
Found at i:44522 original size:80 final size:81
Alignment explanation
Indices: 44317--44663 Score: 246
Period size: 83 Copynumber: 4.2 Consensus size: 81
44307 ACGTCGCGAT
* * *
44317 AGAGTAGTACTTTAGCGGCATTTGTATAAAAATGTCGTAATAGAGTTCATCTATAGTGGCATTTT
1 AGAGTAGTACTTTAGCGGCGTTTGTATAAAAATGTCGTAATAG-GTTCATCCATAGTGGCATTTC
* *
44382 TCAACAAACGCCGCAAT
65 TCAACAAACGCCACAAC
* * * * * * * **
44399 AGAGTAGTACTTTAGCAGCGTTTTTATAGAAACGCCGCAATAGGTTCATCCATAGTTGTGTTTCT
1 AGAGTAGTACTTTAGCGGCGTTTGTATAAAAATGTCGTAATAGGTTCATCCATAGTGGCATTTCT
* * **
44464 CAACAAATGTCATGAC
66 CAACAAACGCCACAAC
* * ** *
44480 A-AGTAGTACTTTAGCGGTGTTTGTATAAAAATGTCGTAATAGGGTTTATTTATAGTGGCGTTTT
1 AGAGTAGTACTTTAGCGGCGTTTGTATAAAAATGTCGTAATA-GGTTCATCCATAGTGGC-ATTT
* * * * * *
44544 ATCGATAAATGCCATAAA
64 CTCAACAAACGCCACAAC
* ** * * * ** *
44562 AGAGTAGTACTTTAGTGATGTTTTTATACAAATGCCACAATAGGGTTCATCTATAGTGGCATTTT
1 AGAGTAGTACTTTAGCGGCGTTTGTATAAAAATGTCGTAATA-GGTTCATCCATAGTGGCA-TTT
* * **
44627 TTCAACGAACGCTGCAAC
64 CTCAACAAACGCCACAAC
* *
44645 AGAATAGTTCTTTAGCGGC
1 AGAGTAGTACTTTAGCGGC
44664 CTTTTTTTAC
Statistics
Matches: 200, Mismatches: 61, Indels: 7
0.75 0.23 0.03
Matches are distributed among these distances:
80 33 0.17
81 40 0.20
82 52 0.26
83 75 0.38
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (81 bp):
AGAGTAGTACTTTAGCGGCGTTTGTATAAAAATGTCGTAATAGGTTCATCCATAGTGGCATTTCT
CAACAAACGCCACAAC
Found at i:44841 original size:18 final size:17
Alignment explanation
Indices: 44805--44846 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
44795 GTCGATCTCC
*
44805 CCTTTTATTTTCCCTAA
1 CCTTTTCTTTTCCCTAA
*
44822 CCTTTTCTTCTTCTCTAA
1 CCTTTTCTT-TTCCCTAA
44840 CCTTTTC
1 CCTTTTC
44847 GGTCCCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.12, C:0.33, G:0.00, T:0.55
Consensus pattern (17 bp):
CCTTTTCTTTTCCCTAA
Found at i:46527 original size:13 final size:13
Alignment explanation
Indices: 46509--46536 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
46499 AATGGTGATC
46509 CTCTTTTATTATA
1 CTCTTTTATTATA
46522 CTCTTTTATTATA
1 CTCTTTTATTATA
46535 CT
1 CT
46537 AAACTGAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (13 bp):
CTCTTTTATTATA
Found at i:48081 original size:39 final size:38
Alignment explanation
Indices: 48005--48081 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 38
47995 AGGTAATTAG
* *
48005 CGGCGTTTTCTTAAAACGACGCTATAGATCTTGACCTT
1 CGGCGTTTTCTTAAAACGACGCTATAGAACTTAACCTT
* *
48043 CGGCGTTTTCCTTAAAAACG-TGCTATTGAACTTAACCTT
1 CGGCGTTTT-CTT-AAAACGACGCTATAGAACTTAACCTT
48082 TTGCGGCGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 9 0.27
39 18 0.55
40 6 0.18
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (38 bp):
CGGCGTTTTCTTAAAACGACGCTATAGAACTTAACCTT
Found at i:48331 original size:24 final size:24
Alignment explanation
Indices: 48285--48334 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
48275 ATCAACAATT
* **
48285 CACCATCTCCATCCAAGTTTAAAC
1 CACCACCTCCATCCAAGGCTAAAC
*
48309 CACCACCTCCATCCAGGGCTAAAC
1 CACCACCTCCATCCAAGGCTAAAC
48333 CA
1 CA
48335 AGCATTAATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.42, G:0.08, T:0.18
Consensus pattern (24 bp):
CACCACCTCCATCCAAGGCTAAAC
Found at i:51600 original size:15 final size:16
Alignment explanation
Indices: 51575--51605 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
51565 TGAGAAAATT
51575 TTAATTTTAATTTTAA
1 TTAATTTTAATTTTAA
51591 TTAA-TTTAATTTTAA
1 TTAATTTTAATTTTAA
51606 AATAACGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATTTTAATTTTAA
Found at i:52146 original size:36 final size:36
Alignment explanation
Indices: 52097--52184 Score: 140
Period size: 36 Copynumber: 2.4 Consensus size: 36
52087 ACGTAAAACT
* * *
52097 AAACCAAGAAACAATGGACCATCTTCATCCAAGACC
1 AAACCGAGCAACAATGGACCATCTTCATCAAAGACC
52133 AAACCGAGCAACAATGGACCATCTTCATCAAAGACC
1 AAACCGAGCAACAATGGACCATCTTCATCAAAGACC
*
52169 AAATCGAGCAACAATG
1 AAACCGAGCAACAATG
52185 CAGGATCTAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.44, C:0.28, G:0.14, T:0.14
Consensus pattern (36 bp):
AAACCGAGCAACAATGGACCATCTTCATCAAAGACC
Found at i:52248 original size:36 final size:35
Alignment explanation
Indices: 52198--52319 Score: 136
Period size: 36 Copynumber: 3.4 Consensus size: 35
52188 GATCTACGCT
* *
52198 CAAGGCTGAACCAAGCAGCAATGCACCACCTCGATC
1 CAAGGCTAAACCAAGCA-CAATGCACCACCTCCATC
* * * *
52234 CAACGCTAACCCAAGCAACAATCCACCACCTCCATT
1 CAAGGCTAAACCAAGC-ACAATGCACCACCTCCATC
* * *
52270 AAAGGTTAAACCAAGCACTAATGCACCATCTCCATC
1 CAAGGCTAAACCAAGCAC-AATGCACCACCTCCATC
52306 CAAGGCTAAACCAA
1 CAAGGCTAAACCAA
52320 TCATTAATCG
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
35 2 0.03
36 66 0.96
37 1 0.01
ACGTcount: A:0.38, C:0.36, G:0.12, T:0.14
Consensus pattern (35 bp):
CAAGGCTAAACCAAGCACAATGCACCACCTCCATC
Found at i:52334 original size:36 final size:36
Alignment explanation
Indices: 52199--52336 Score: 95
Period size: 36 Copynumber: 3.8 Consensus size: 36
52189 ATCTACGCTC
* * * *
52199 AAGGCTGAACCAAGCAGC-AAT-GCACCACCTCGATCC
1 AAGGCTAAACCAAGCA-CTAATCG-ACCATCTCCATCA
* * * * *
52235 AACGCTAACCCAAGCAAC-AATCCACCACCTCCATTA
1 AAGGCTAAACCAAGC-ACTAATCGACCATCTCCATCA
* *
52271 AAGGTTAAACCAAGCACTAAT-GCACCATCTCCATCC
1 AAGGCTAAACCAAGCACTAATCG-ACCATCTCCATCA
* *
52307 AAGGCTAAACCAATCATTAATCGACCATCT
1 AAGGCTAAACCAAGCACTAATCGACCATCT
52337 GAAGCTCCAT
Statistics
Matches: 80, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
35 2 0.03
36 76 0.95
37 2 0.03
ACGTcount: A:0.37, C:0.35, G:0.12, T:0.17
Consensus pattern (36 bp):
AAGGCTAAACCAAGCACTAATCGACCATCTCCATCA
Found at i:55106 original size:5 final size:5
Alignment explanation
Indices: 55098--55123 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
55088 GGGGCCTTCT
55098 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
55124 GTGATAAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Done.