Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008824.1 Hibiscus syriacus cultivar Beakdansim tig00111996_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: 4603428
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 19
Found at i:4486328 original size:5 final size:5
Alignment explanation
Indices: 4486318--4486369 Score: 65
Period size: 5 Copynumber: 10.8 Consensus size: 5
4486308 GTATGAGTCT
*
4486318 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT- TGTT- TTTTC TTCTTC -TTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC
4486366 TTTT
1 TTTT
4486370 TCTATTTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
4 9 0.21
5 30 0.71
6 3 0.07
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:4486336 original size:16 final size:16
Alignment explanation
Indices: 4486315--4486372 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
4486305 GATGTATGAG
4486315 TCTTTTTCTTTTCTTT
1 TCTTTTTCTTTTCTTT
4486331 TC-TTTTCTTTTCTTTT
1 TCTTTTTCTTTTC-TTT
*
4486347 TGTTTTTTCTTCTTC-TT
1 T-CTTTTTCTT-TTCTTT
4486364 TCTTTTTCT
1 TCTTTTTCT
4486373 ATTTTTGTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
15 10 0.28
16 13 0.36
17 3 0.08
18 7 0.19
19 3 0.08
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (16 bp):
TCTTTTTCTTTTCTTT
Found at i:4486372 original size:10 final size:9
Alignment explanation
Indices: 4486317--4486378 Score: 54
Period size: 10 Copynumber: 6.3 Consensus size: 9
4486307 TGTATGAGTC
4486317 TTTTTCTTT
1 TTTTTCTTT
4486326 TCTTTTCTTT
1 T-TTTTCTTT
4486336 TCTTTTCTTT
1 T-TTTTCTTT
4486346 TTGTTT-TTT
1 TT-TTTCTTT
*
4486355 CTTCTTCTTT
1 -TTTTTCTTT
4486365 CTTTTTCTATT
1 -TTTTTCT-TT
4486376 TTT
1 TTT
4486379 GTTGCTTTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
9 7 0.15
10 37 0.80
11 2 0.04
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:4486377 original size:23 final size:23
Alignment explanation
Indices: 4486328--4486377 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
4486318 TTTTCTTTTC
* *
4486328 TTTTCTTTTCTTTTCTTTTTGTT
1 TTTTCTTTTCTTTTCTTTTTCTA
4486351 TTTTCTTCTTC-TTTCTTTTTCTA
1 TTTTCTT-TTCTTTTCTTTTTCTA
4486374 TTTT
1 TTTT
4486378 TGTTGCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (23 bp):
TTTTCTTTTCTTTTCTTTTTCTA
Found at i:4486629 original size:15 final size:16
Alignment explanation
Indices: 4486586--4486631 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
4486576 TATGAAATAA
*
4486586 GAAATGGAAGAAGAATG
1 GAAATGG-AGAAGAAAG
*
4486603 GAAAT-GATAAGAAAG
1 GAAATGGAGAAGAAAG
4486618 GAAATGGA-AAGAAA
1 GAAATGGAGAAGAAA
4486632 TGATATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 18 0.69
16 3 0.12
17 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.30, T:0.11
Consensus pattern (16 bp):
GAAATGGAGAAGAAAG
Found at i:4493306 original size:6 final size:6
Alignment explanation
Indices: 4493295--4493319 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4493285 TGTAGGAGTC
4493295 TTTTCT TTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT T
4493320 CTTTTTGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:4493547 original size:14 final size:14
Alignment explanation
Indices: 4493528--4493562 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
4493518 AAGAATAATT
4493528 AAGAATGGAAATGG
1 AAGAATGGAAATGG
*
4493542 AAGAATTGAAATGG
1 AAGAATGGAAATGG
4493556 ATAGAAT
1 A-AGAAT
4493563 AATTATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.29, T:0.20
Consensus pattern (14 bp):
AAGAATGGAAATGG
Found at i:4497935 original size:30 final size:31
Alignment explanation
Indices: 4497896--4497955 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
4497886 TCATGCTTCC
**
4497896 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
4497927 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
4497956 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:4499002 original size:24 final size:24
Alignment explanation
Indices: 4498974--4499030 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
4498964 GAACTTGGAG
*
4498974 CTTCAA-TGATCACAACTTTTTGCA
1 CTTCAAGTGA-CACAACTTTTTGAA
* *
4498998 CTTCAAGTGACATATCTTTTTGAA
1 CTTCAAGTGACACAACTTTTTGAA
4499022 CTTCAAGTG
1 CTTCAAGTG
4499031 GCATAACTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 26 0.90
25 3 0.10
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (24 bp):
CTTCAAGTGACACAACTTTTTGAA
Found at i:4499035 original size:24 final size:24
Alignment explanation
Indices: 4498989--4499035 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
4498979 ATGATCACAA
*
4498989 CTTTTTGCACTTCAAGTGACATAT
1 CTTTTTGAACTTCAAGTGACATAT
*
4499013 CTTTTTGAACTTCAAGTGGCATA
1 CTTTTTGAACTTCAAGTGACATA
4499036 ACTGTTGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (24 bp):
CTTTTTGAACTTCAAGTGACATAT
Found at i:4499046 original size:24 final size:24
Alignment explanation
Indices: 4498997--4499051 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
4498987 AACTTTTTGC
* * *
4498997 ACTTCAAGTGACATATCTTTTTGA
1 ACTTCAAGTGACATAACTGTTGGA
*
4499021 ACTTCAAGTGGCATAACTGTTGGA
1 ACTTCAAGTGACATAACTGTTGGA
*
4499045 ACGTCAA
1 ACTTCAA
4499052 AGGACATGTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (24 bp):
ACTTCAAGTGACATAACTGTTGGA
Found at i:4501115 original size:19 final size:20
Alignment explanation
Indices: 4501068--4501123 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
4501058 GAAACCCCTT
**
4501068 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
4501088 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
* *
4501107 TGAAGATACATGCTTTT
1 TGAAAATACATGATTTT
4501124 GGCCGAATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:4502056 original size:30 final size:31
Alignment explanation
Indices: 4502017--4502076 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
4502007 ACATGCTTCC
**
4502017 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
4502048 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
4502077 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:4504563 original size:51 final size:49
Alignment explanation
Indices: 4504508--4504613 Score: 133
Period size: 49 Copynumber: 2.1 Consensus size: 49
4504498 GTGCTGGAAT
**
4504508 GAATGCATTATAATATAATGAGTTGA-CGTGCATGTGTGCATCAACTAAAAC
1 GAATGCATTAT-A-ATAATGAACT-ACCGTGCATGTGTGCATCAACTAAAAC
* * *
4504559 GAATGTATTATAATAGTGAACTACCGTGCATGTGTGCATCAACTAAAAT
1 GAATGCATTATAATAATGAACTACCGTGCATGTGTGCATCAACTAAAAC
4504608 GAATGC
1 GAATGC
4504614 CATGTGTGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
48 1 0.02
49 36 0.75
50 1 0.02
51 10 0.21
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (49 bp):
GAATGCATTATAATAATGAACTACCGTGCATGTGTGCATCAACTAAAAC
Found at i:4504681 original size:51 final size:53
Alignment explanation
Indices: 4504619--4504725 Score: 164
Period size: 56 Copynumber: 2.0 Consensus size: 53
4504609 AATGCCATGT
*
4504619 GTGAATT-A-AAAATAAATGATATCATGCTATTTGAATGTGAATGCACGTGAA
1 GTGAATTAAGAAAATAAATGATACCATGCTATTTGAATGTGAATGCACGTGAA
4504670 GTGAATTAAAAAGAAAATAAATGATACCATGCTATTTGAATGTGAATGCACGTGAA
1 GTGAATT---AAGAAAATAAATGATACCATGCTATTTGAATGTGAATGCACGTGAA
4504726 TGACATAATG
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
51 7 0.14
55 1 0.02
56 42 0.84
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.29
Consensus pattern (53 bp):
GTGAATTAAGAAAATAAATGATACCATGCTATTTGAATGTGAATGCACGTGAA
Found at i:4511676 original size:15 final size:15
Alignment explanation
Indices: 4511640--4511669 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4511630 GTGCTTCAAC
4511640 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
4511654 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
4511669 T
1 T
4511670 CTTTTTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:4517105 original size:86 final size:86
Alignment explanation
Indices: 4517000--4517171 Score: 344
Period size: 86 Copynumber: 2.0 Consensus size: 86
4516990 TGTCTCCACT
4517000 TAATCATCAATTTGAAGGAACGTGAGTATTACCTGGCCATGAAGAGTTGTCTCCATTTTACACCG
1 TAATCATCAATTTGAAGGAACGTGAGTATTACCTGGCCATGAAGAGTTGTCTCCATTTTACACCG
4517065 AATCATCACTTGAATTCATGG
66 AATCATCACTTGAATTCATGG
4517086 TAATCATCAATTTGAAGGAACGTGAGTATTACCTGGCCATGAAGAGTTGTCTCCATTTTACACCG
1 TAATCATCAATTTGAAGGAACGTGAGTATTACCTGGCCATGAAGAGTTGTCTCCATTTTACACCG
4517151 AATCATCACTTGAATTCATGG
66 AATCATCACTTGAATTCATGG
4517172 AGAATTATGA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (86 bp):
TAATCATCAATTTGAAGGAACGTGAGTATTACCTGGCCATGAAGAGTTGTCTCCATTTTACACCG
AATCATCACTTGAATTCATGG
Found at i:4521400 original size:11 final size:11
Alignment explanation
Indices: 4521384--4521408 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4521374 AATACAAAAA
4521384 GAAGTGCAAGT
1 GAAGTGCAAGT
4521395 GAAGTGCAAGT
1 GAAGTGCAAGT
4521406 GAA
1 GAA
4521409 AGAAAAACAA
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:0.36, T:0.16
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:4529186 original size:19 final size:20
Alignment explanation
Indices: 4529162--4529201 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
4529152 TATCCTTTCT
4529162 TTATTTCATTTT-ATT-CTTA
1 TTATTT-ATTTTCATTACTTA
4529181 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
4529201 T
1 T
4529202 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:4536568 original size:15 final size:17
Alignment explanation
Indices: 4536537--4536578 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
4536527 GTAAGAAAAG
4536537 ATGAAATAATAAAG-AA
1 ATGAAATAATAAAGAAA
*
4536553 ATGAAATAGT-AAGAAA
1 ATGAAATAATAAAGAAA
4536569 ATGAAGATAA
1 ATGAA-ATAA
4536579 CTTACAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 3 0.14
16 16 0.73
17 3 0.14
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (17 bp):
ATGAAATAATAAAGAAA
Found at i:4542919 original size:19 final size:20
Alignment explanation
Indices: 4542872--4542922 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
4542862 GAAACCCCTT
**
4542872 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
4542892 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
4542911 TGAAGATACATG
1 TGAAAATACATG
4542923 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:4543837 original size:30 final size:31
Alignment explanation
Indices: 4543798--4543857 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
4543788 TAATGCTTCC
**
4543798 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
4543829 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
4543858 TACAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:4544918 original size:24 final size:24
Alignment explanation
Indices: 4544891--4544972 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 24
4544881 ATGATCACAA
*
4544891 CTTTTGGCACTTCAAGTGACATAT
1 CTTTTGGAACTTCAAGTGACATAT
* * *
4544915 CTTTTTGAACTTCAAGTGGCATAA
1 CTTTTGGAACTTCAAGTGACATAT
* * *
4544939 CTGTTGGAACGTCAAAG-GACATGT
1 CTTTTGGAACTTC-AAGTGACATAT
*
4544963 CTTGTGGAAC
1 CTTTTGGAAC
4544973 ACCGAAGGTC
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
24 42 0.93
25 3 0.07
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (24 bp):
CTTTTGGAACTTCAAGTGACATAT
Found at i:4547971 original size:30 final size:31
Alignment explanation
Indices: 4547932--4547991 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
4547922 TCATGCTTTC
**
4547932 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
4547963 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
4547992 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:4549038 original size:24 final size:24
Alignment explanation
Indices: 4549010--4549066 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
4549000 GAACTTGGAG
*
4549010 CTTCAA-TGATCACAACTTTTTGCA
1 CTTCAAGTGA-CACAACTTTTTGAA
* *
4549034 CTTCAAGTGACATATCTTTTTGAA
1 CTTCAAGTGACACAACTTTTTGAA
4549058 CTTCAAGTG
1 CTTCAAGTG
4549067 GCATAACTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 26 0.90
25 3 0.10
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (24 bp):
CTTCAAGTGACACAACTTTTTGAA
Found at i:4549071 original size:24 final size:24
Alignment explanation
Indices: 4549025--4549071 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
4549015 ATGATCACAA
*
4549025 CTTTTTGCACTTCAAGTGACATAT
1 CTTTTTGAACTTCAAGTGACATAT
*
4549049 CTTTTTGAACTTCAAGTGGCATA
1 CTTTTTGAACTTCAAGTGACATA
4549072 ACTGTTGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (24 bp):
CTTTTTGAACTTCAAGTGACATAT
Found at i:4549082 original size:24 final size:24
Alignment explanation
Indices: 4549033--4549087 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
4549023 AACTTTTTGC
* * *
4549033 ACTTCAAGTGACATATCTTTTTGA
1 ACTTCAAGTGACATAACTGTTGGA
*
4549057 ACTTCAAGTGGCATAACTGTTGGA
1 ACTTCAAGTGACATAACTGTTGGA
*
4549081 ACGTCAA
1 ACTTCAA
4549088 AGGACATGTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (24 bp):
ACTTCAAGTGACATAACTGTTGGA
Found at i:4551152 original size:19 final size:20
Alignment explanation
Indices: 4551105--4551155 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
4551095 GAAACCCCTT
**
4551105 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
4551125 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
4551144 TGAAGATACATG
1 TGAAAATACATG
4551156 CTCTTGGTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:4551544 original size:10 final size:10
Alignment explanation
Indices: 4551524--4551555 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
4551514 GTCTTCTCAG
4551524 CTCCTCAGCTA
1 CTCC-CAGCTA
4551535 CTCCCAGCTA
1 CTCCCAGCTA
4551545 CTCCCAGCTA
1 CTCCCAGCTA
4551555 C
1 C
4551556 CTTTAGTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 17 0.81
11 4 0.19
ACGTcount: A:0.19, C:0.50, G:0.09, T:0.22
Consensus pattern (10 bp):
CTCCCAGCTA
Found at i:4554707 original size:51 final size:53
Alignment explanation
Indices: 4554645--4554751 Score: 164
Period size: 56 Copynumber: 2.0 Consensus size: 53
4554635 AATGCCATGT
*
4554645 GTGAATT-A-AAAATAAATGATATCATGCTATTTGAATGTGAATGCACGTGAA
1 GTGAATTAAGAAAATAAATGATACCATGCTATTTGAATGTGAATGCACGTGAA
4554696 GTGAATTAAAAAGAAAATAAATGATACCATGCTATTTGAATGTGAATGCACGTGAA
1 GTGAATT---AAGAAAATAAATGATACCATGCTATTTGAATGTGAATGCACGTGAA
4554752 TGACATAATG
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
51 7 0.14
55 1 0.02
56 42 0.84
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.29
Consensus pattern (53 bp):
GTGAATTAAGAAAATAAATGATACCATGCTATTTGAATGTGAATGCACGTGAA
Found at i:4560685 original size:24 final size:25
Alignment explanation
Indices: 4560649--4560696 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
4560639 CACCATGATC
* * *
4560649 TGCATTTTGTTCAGTTTCTTCATCT
1 TGCATTGTGTTCAGGTTCCTCATCT
4560674 TGCATTGT-TTCAGGTTCCTCATC
1 TGCATTGTGTTCAGGTTCCTCATC
4560697 AAAAATTGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.12, C:0.23, G:0.15, T:0.50
Consensus pattern (25 bp):
TGCATTGTGTTCAGGTTCCTCATCT
Found at i:4562212 original size:5 final size:5
Alignment explanation
Indices: 4562198--4562227 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
4562188 GTGCTTCAAC
4562198 TTTC- TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
4562228 CTTTTTGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:4570616 original size:17 final size:17
Alignment explanation
Indices: 4570586--4570633 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
4570576 TTTGAATTTC
* *
4570586 TTTTTTTTTTTTTTG-A
1 TTTTTCTTTCTTTTGTA
*
4570602 TTTTTCTCTTCTTTTGTC
1 TTTTTCT-TTCTTTTGTA
4570620 TTTTTCTTTCTTTT
1 TTTTTCTTTCTTTT
4570634 TGCACTCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 6 0.22
17 14 0.52
18 7 0.26
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.81
Consensus pattern (17 bp):
TTTTTCTTTCTTTTGTA
Found at i:4575148 original size:5 final size:5
Alignment explanation
Indices: 4575138--4575162 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4575128 CTCTTTTGAA
4575138 TTTCT TTTCT TTTCT TTTCT TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT
4575163 GATTTTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:4575171 original size:19 final size:18
Alignment explanation
Indices: 4575147--4575197 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
4575137 ATTTCTTTTC
4575147 TTTTCTTTTCTTTTCTGAT
1 TTTTCTTTTCTTTTCT-AT
* * *
4575166 TTTTCTCTTCTTTTGTCT
1 TTTTCTTTTCTTTTCTAT
4575184 TTTTCTTTTGCTTT
1 TTTTCTTTT-CTTT
4575198 GCACGTCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.02, C:0.18, G:0.06, T:0.75
Consensus pattern (18 bp):
TTTTCTTTTCTTTTCTAT
Found at i:4576755 original size:2 final size:2
Alignment explanation
Indices: 4576744--4576783 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
4576734 TAACTATAGG
4576744 TA TA -A TA TA TA TA TA 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 TA TA TA TA TA TA TA TA T
4576784 CTATCTTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4585797 original size:19 final size:20
Alignment explanation
Indices: 4585750--4585800 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
4585740 GAAACCCCTT
**
4585750 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
4585770 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
4585789 TGAAGATACATG
1 TGAAAATACATG
4585801 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:4587356 original size:21 final size:22
Alignment explanation
Indices: 4587331--4587382 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
4587321 AAAGATCATG
4587331 TCCTTTGA-TTGAAGAGTCACA
1 TCCTTTGATTTGAAGAGTCACA
* *
4587352 TCCTTAGATTCTTGAAGAGTCACG
1 TCCTTTGA-T-TTGAAGAGTCACA
4587376 TCCTTTG
1 TCCTTTG
4587383 GCTCCTTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 7 0.28
24 18 0.72
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (22 bp):
TCCTTTGATTTGAAGAGTCACA
Found at i:4589008 original size:14 final size:15
Alignment explanation
Indices: 4588978--4589023 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 15
4588968 TTTTGCTTCA
4588978 CTTTTTCTTTTC-TT
1 CTTTTTCTTTTCTTT
*
4588992 -TTTTT-TATTC-TT
1 CTTTTTCTTTTCTTT
4589004 CTTTTTCTTTTCTTT
1 CTTTTTCTTTTCTTT
4589019 CTTTT
1 CTTTT
4589024 GCACTCCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 6 0.22
13 10 0.37
14 4 0.15
15 7 0.26
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (15 bp):
CTTTTTCTTTTCTTT
Found at i:4590414 original size:34 final size:36
Alignment explanation
Indices: 4590359--4590425 Score: 102
Period size: 34 Copynumber: 1.9 Consensus size: 36
4590349 ATACAATCTG
*
4590359 TCCATCACTATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
4590395 TCCATCACCA-TA-CACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
4590426 ACTTATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 18 0.62
35 2 0.07
36 9 0.31
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:4590893 original size:14 final size:15
Alignment explanation
Indices: 4590862--4590903 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
4590852 TTTGGAGTGC
4590862 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
4590877 AAAAG-AAGAATAA-A
1 AAAAGAAAGAA-AAGA
*
4590891 AAAACAAAGAAAA
1 AAAAGAAAGAAAA
4590904 AGTGAAGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:4596081 original size:35 final size:36
Alignment explanation
Indices: 4596025--4596092 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
4596015 ATACAATCTG
4596025 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
4596061 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
4596093 ACTTATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:4597285 original size:19 final size:20
Alignment explanation
Indices: 4597238--4597288 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
4597228 GAAACCCCTT
**
4597238 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
4597258 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
4597277 TGAAGATACATG
1 TGAAAATACATG
4597289 CTCTTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Done.