Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005720.1 Hibiscus syriacus cultivar Beakdansim tig00013372_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: 92739
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2228 original size:19 final size:19
Alignment explanation
Indices: 2192--2230 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2182 TTTTAAAAAA
*
2192 TATTAAAAATATATTAAAT
1 TATTAAAAATATACTAAAT
2211 TATTAAAAATA-ACCTAAAT
1 TATTAAAAATATA-CTAAAT
2230 T
1 T
2231 TTTATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
TATTAAAAATATACTAAAT
Found at i:8805 original size:14 final size:14
Alignment explanation
Indices: 8773--8799 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8763 ATAATATATA
8773 AATTATAATTTGAT
1 AATTATAATTTGAT
8787 AATTATAATTTGA
1 AATTATAATTTGA
8800 ATATTACTTT
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:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
AATTATAATTTGAT
Found at i:9392 original size:19 final size:18
Alignment explanation
Indices: 9368--9413 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
9358 ATTATTTTTT
9368 AATAATTTTGATTATAAAA
1 AATAATTTT-ATTATAAAA
*
9387 AATAATATTTATTTTAAAA
1 AATAAT-TTTATTATAAAA
9406 AATCAATT
1 AAT-AATT
9414 CATTGACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
AATAATTTTATTATAAAA
Found at i:9570 original size:23 final size:23
Alignment explanation
Indices: 9551--9602 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 23
9541 CTAATATTCA
9551 AATT-ATAATATATATTATATTAT
1 AATTAATAATATATA-TATATTAT
*
9574 AATTAATGATATATATATATTAT
1 AATTAATAATATATATATATTAT
9597 ATATTA
1 A-ATTA
9603 TAGTTAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
AATTAATAATATATATATATTAT
Found at i:13913 original size:40 final size:40
Alignment explanation
Indices: 13797--13922 Score: 137
Period size: 40 Copynumber: 3.1 Consensus size: 40
13787 TTCCAGTAAG
* * *
13797 TGTTGTTATGCATTTTAATTTGCTGCTTGGAAGAATATAT
1 TGTTATTATGCATTTTAATTTGTTGCTTGGAAGAATGTAT
* * * *
13837 TGTAATTATACATTTTAAATTGCTT-CTTGGAAGAATGTTT
1 TGTTATTATGCATTTTAATTTG-TTGCTTGGAAGAATGTAT
* ** *
13877 TGTTATTATGCATTTTTATTTGTTGCTTGGTTGAATGTGT
1 TGTTATTATGCATTTTAATTTGTTGCTTGGAAGAATGTAT
13917 TGTTAT
1 TGTTAT
13923 GTTCGGTGAT
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
39 2 0.03
40 67 0.96
41 1 0.01
ACGTcount: A:0.23, C:0.06, G:0.19, T:0.52
Consensus pattern (40 bp):
TGTTATTATGCATTTTAATTTGTTGCTTGGAAGAATGTAT
Found at i:15469 original size:20 final size:21
Alignment explanation
Indices: 15431--15469 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
15421 TATTCCTTTT
*
15431 TATTCTATTTTTTCAAATAAG
1 TATTCTATTTTATCAAATAAG
*
15452 TATT-TATTTTATCTAATA
1 TATTCTATTTTATCAAATA
15470 CAAATATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (21 bp):
TATTCTATTTTATCAAATAAG
Found at i:15477 original size:18 final size:19
Alignment explanation
Indices: 15456--15496 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
15446 AATAAGTATT
*
15456 TATTTTATCTA-ATACAAA
1 TATTTTATATATATACAAA
*
15474 TA-TTTATATATATACATA
1 TATTTTATATATATACAAA
15492 TATTT
1 TATTT
15497 AGGACAGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 7 0.37
18 10 0.53
19 2 0.11
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTTATATATATACAAA
Found at i:22058 original size:20 final size:20
Alignment explanation
Indices: 22033--22071 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
22023 AATTTAAAAA
22033 ACTTTCAATTTAATCATTCG
1 ACTTTCAATTTAATCATTCG
22053 ACTTTCAATTTAATCATTC
1 ACTTTCAATTTAATCATTC
22072 ATGTTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.46
Consensus pattern (20 bp):
ACTTTCAATTTAATCATTCG
Found at i:22649 original size:21 final size:24
Alignment explanation
Indices: 22625--22669 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
22615 TATTTGATAA
22625 TTGTTG-TAATT-CG-TAATTATT
1 TTGTTGATAATTACGATAATTATT
22646 TTGTTGATTAATTACGATAATTAT
1 TTGTTGA-TAATTACGATAATTAT
22670 AGCAGGAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.30
23 5 0.25
24 2 0.10
25 7 0.35
ACGTcount: A:0.29, C:0.04, G:0.13, T:0.53
Consensus pattern (24 bp):
TTGTTGATAATTACGATAATTATT
Found at i:23027 original size:40 final size:42
Alignment explanation
Indices: 22981--23071 Score: 104
Period size: 40 Copynumber: 2.3 Consensus size: 42
22971 TTATTAATAA
*
22981 ACAATAAAAACTAATA-AGTTAACTAAT-CTATTATTTTTAAT
1 ACAATAAAAACTAATATA-TTAACTAATAATATTATTTTTAAT
*
23022 A-AAT-AAAA-TAATATTATTAATTAATAATATTATTTTTAAT
1 ACAATAAAAACTAATA-TATTAACTAATAATATTATTTTTAAT
23062 ACAA-AAAAAC
1 ACAATAAAAAC
23072 CCAACCCTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
38 5 0.12
39 12 0.29
40 18 0.43
41 7 0.17
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (42 bp):
ACAATAAAAACTAATATATTAACTAATAATATTATTTTTAAT
Found at i:23036 original size:21 final size:19
Alignment explanation
Indices: 23012--23062 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
23002 ACTAATCTAT
23012 TATTTTTAATAAATAAAATAA
1 TATTTTTAATAAAT--AATAA
* * *
23033 TATTATTAATTAATAATAT
1 TATTTTTAATAAATAATAA
23052 TATTTTTAATA
1 TATTTTTAATA
23063 CAAAAAAACC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 13 0.52
21 12 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTTTAATAAATAATAA
Found at i:23315 original size:31 final size:31
Alignment explanation
Indices: 23280--23338 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
23270 TCGAATTACA
23280 TAGTCCAACATCAAAACATAATTAAAAATAT
1 TAGTCCAACATCAAAACATAATTAAAAATAT
* * *
23311 TAGTCTAACATCCATACATAATTAAAAA
1 TAGTCCAACATCAAAACATAATTAAAAA
23339 ATGTCATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.53, C:0.17, G:0.03, T:0.27
Consensus pattern (31 bp):
TAGTCCAACATCAAAACATAATTAAAAATAT
Found at i:23522 original size:66 final size:68
Alignment explanation
Indices: 23420--23552 Score: 243
Period size: 66 Copynumber: 2.0 Consensus size: 68
23410 TTGAAAAAAA
23420 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAA-T-ACCAAATAGGTAGTTTACCCTA
1 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
23483 AAT
66 AAT
*
23486 AATAATTGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
1 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
23551 AA
66 AA
23553 AAAAACTCTA
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
66 39 0.61
67 1 0.02
68 24 0.38
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (68 bp):
AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
AAT
Found at i:27882 original size:21 final size:21
Alignment explanation
Indices: 27856--27898 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27846 TTTCTGGGTT
* *
27856 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
27877 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
27898 A
1 A
27899 CGAATATGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:27973 original size:67 final size:66
Alignment explanation
Indices: 27878--28026 Score: 217
Period size: 67 Copynumber: 2.2 Consensus size: 66
27868 ACCCATTCAA
* * *
27878 GGGGAACCGATACCCCTTCAACGAATATGACTTCCAGAATGCTAGAGGGGAATCGGTACCCCCAG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATA-CCCCAG
27943 GG
65 GG
* * * *
27945 GGGGAACCGATACCCCCTCATCGTATATGAATTCCAGATTGCTTGAGGGGAATCGATACCCCAGG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCAGG
28010 G
66 G
*
28011 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
28027 ATGAGAAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
66 23 0.31
67 51 0.69
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (66 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCAGG
G
Found at i:28362 original size:29 final size:29
Alignment explanation
Indices: 28328--28399 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
28318 CATATTATGA
**
28328 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
* *
28357 TACATGACATGAATTCATCTTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
28386 TACATGACATGAAT
1 TACATGACATGAAT
28400 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:28454 original size:30 final size:31
Alignment explanation
Indices: 28414--28472 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
28404 AGAAAAGTTC
*
28414 TATGCACTATGTGATAAAAGTATGTAAATGA
1 TATGCACTATGTGATAAAAGTATGGAAATGA
* *
28445 TATGC-CTATGTGTTAAAGGTATGGAAAT
1 TATGCACTATGTGATAAAAGTATGGAAAT
28473 ACTATGTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (31 bp):
TATGCACTATGTGATAAAAGTATGGAAATGA
Found at i:28765 original size:22 final size:22
Alignment explanation
Indices: 28692--28757 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
28682 TTATGGACAT
28692 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
28714 AATTCTAC-GGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
28735 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
28757 A
1 A
28758 TTTATACGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.49
22 22 0.51
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:34792 original size:21 final size:21
Alignment explanation
Indices: 34766--34808 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34756 TTTCTGGGTT
* *
34766 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
34787 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
34808 A
1 A
34809 CGAATATGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:34883 original size:67 final size:66
Alignment explanation
Indices: 34788--34937 Score: 219
Period size: 67 Copynumber: 2.3 Consensus size: 66
34778 ACCCATTCAA
* * *
34788 GGGGAACCGATACCCCTTCAACGAATATGACTTCCAGAATGCTAGAGGGGAATCGGTACCCCCAG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATA-CCCCAG
34853 GG
65 GG
* * * *
34855 GGGGAACCGATACCCCCTCATCGTATATGAATTCCAGATTGCTTGAGGGGAATCGATACCCCAGG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCAGG
34920 G
66 G
*
34921 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
34938 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
66 24 0.32
67 51 0.68
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (66 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCAGG
G
Found at i:35272 original size:29 final size:29
Alignment explanation
Indices: 35238--35309 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
35228 CATATTATGA
**
35238 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
* *
35267 TACATGACATGAATTCATCTTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
35296 TACATGACATGAAT
1 TACATGACATGAAT
35310 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:35364 original size:30 final size:31
Alignment explanation
Indices: 35324--35382 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
35314 AGAAAAGTTC
*
35324 TATGCACTATGTGATAAAAGTATGTAAATGA
1 TATGCACTATGTGATAAAAGTATGGAAATGA
* *
35355 TATGC-CTATGTGTTAAAGGTATGGAAAT
1 TATGCACTATGTGATAAAAGTATGGAAAT
35383 ACTATGTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (31 bp):
TATGCACTATGTGATAAAAGTATGGAAATGA
Found at i:35675 original size:22 final size:22
Alignment explanation
Indices: 35601--35667 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
35591 TTATGGACAT
35601 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
35623 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
35645 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
35667 A
1 A
35668 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:38513 original size:2 final size:2
Alignment explanation
Indices: 38506--38584 Score: 140
Period size: 2 Copynumber: 39.5 Consensus size: 2
38496 TGGCAATCTA
38506 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
* *
38548 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38585 CCTAATTTTA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44313 original size:2 final size:2
Alignment explanation
Indices: 44306--44340 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
44296 GGCAATCTAA
* *
44306 AT AT AT AT AT AT AT AT AT AT AT AT AA AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44341 CCTAATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:61727 original size:27 final size:26
Alignment explanation
Indices: 61668--61757 Score: 87
Period size: 27 Copynumber: 3.5 Consensus size: 26
61658 ATAATAAAAA
* **
61668 TAAATA-AA-ATACATAATATATTGA
1 TAAATATAATATATATAATATATTTT
*
61692 TAACATATAATATGTAT-ATATATTTTT
1 TAA-ATATAATATATATAATATA-TTTT
*
61719 TAAATTATAACATATATAATATATTTT
1 TAAA-TATAATATATATAATATATTTT
61746 TAAATATAATAT
1 TAAATATAATAT
61758 TCTCTCTCTA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
24 3 0.06
25 3 0.06
26 15 0.28
27 27 0.51
28 5 0.09
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.44
Consensus pattern (26 bp):
TAAATATAATATATATAATATATTTT
Found at i:61827 original size:10 final size:9
Alignment explanation
Indices: 61801--61836 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
61791 TTTCAAAAAC
61801 TATATAATA
1 TATATAATA
61810 TATATAATA
1 TATATAATA
61819 TACTATAATA
1 TA-TATAATA
61829 TATTATAA
1 TA-TATAA
61837 CACCTCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 11 0.44
10 14 0.56
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (9 bp):
TATATAATA
Found at i:62740 original size:20 final size:20
Alignment explanation
Indices: 62717--62754 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
62707 ATTAATATCG
*
62717 GATGCTCGGTATTGATACCA
1 GATGCTCGGTATCGATACCA
*
62737 GATGCTTGGTATCGATAC
1 GATGCTCGGTATCGATAC
62755 TATAGTCTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GATGCTCGGTATCGATACCA
Found at i:63754 original size:51 final size:51
Alignment explanation
Indices: 63678--63775 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
63668 TTGTTACTAG
* * *
63678 AAGATCTTTTAGTAGCTTATAGAGGACTTTACCGATGCTATGTGATACCAA
1 AAGATCATTTAGTAGATTAGAGAGGACTTTACCGATGCTATGTGATACCAA
**
63729 AAGATCATTTAGTAGATTAGAGAGGACTTTATTGATGCTATGTGATA
1 AAGATCATTTAGTAGATTAGAGAGGACTTTACCGATGCTATGTGATA
63776 GTCGGACCCC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (51 bp):
AAGATCATTTAGTAGATTAGAGAGGACTTTACCGATGCTATGTGATACCAA
Found at i:64908 original size:20 final size:20
Alignment explanation
Indices: 64885--64939 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
64875 TATGTTATCA
64885 GTATCGATACTCACCCTTGG
1 GTATCGATACTCACCCTTGG
*
64905 GTATCGATACTGACCCTTGG
1 GTATCGATACTCACCCTTGG
64925 GTATCGATACTCACC
1 GTATCGATACTCACC
64940 ATAAGTATCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (20 bp):
GTATCGATACTCACCCTTGG
Found at i:64949 original size:19 final size:20
Alignment explanation
Indices: 64884--64953 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
64874 CTATGTTATC
64884 AGTATCGATACTCACCCTTG
1 AGTATCGATACTCACCCTTG
* *
64904 GGTATCGATACTGACCCTTG
1 AGTATCGATACTCACCCTTG
* * *
64924 GGTATCGATACTCA-CCATA
1 AGTATCGATACTCACCCTTG
64943 AGTATCGATAC
1 AGTATCGATAC
64954 CAAAAATAGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 13 0.30
20 31 0.70
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTCACCCTTG
Found at i:73567 original size:21 final size:21
Alignment explanation
Indices: 73543--73593 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
73533 CACTGTAGTC
73543 TCTATACCAGATAAACTGGTA
1 TCTATACCAGATAAACTGGTA
73564 TCTATACCAGATAAACTGGTA
1 TCTATACCAGATAAACTGGTA
73585 TCTATACCA
1 TCTATACCA
73594 TCGAAATGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (21 bp):
TCTATACCAGATAAACTGGTA
Found at i:73641 original size:20 final size:20
Alignment explanation
Indices: 73596--73652 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
73586 CTATACCATC
*
73596 GAAATGGTCTTCATACAAGA
1 GAAATTGTCTTCATACAAGA
* *
73616 GGAATTGTCTTCATACCAGA
1 GAAATTGTCTTCATACAAGA
* *
73636 TAAATTGGTATTCATAC
1 GAAATT-GTCTTCATAC
73653 TGAAGATTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 21 0.70
21 9 0.30
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (20 bp):
GAAATTGTCTTCATACAAGA
Found at i:73651 original size:21 final size:21
Alignment explanation
Indices: 73546--73652 Score: 78
Period size: 21 Copynumber: 5.2 Consensus size: 21
73536 TGTAGTCTCT
73546 ATACCAGATAAACTGGTA-TC
1 ATACCAGATAAACTGGTATTC
73566 TATACCAGATAAACTGGTA-TC
1 -ATACCAGATAAACTGGTATTC
*** *
73587 TATACCATCGAAA-TGGTCTTC
1 -ATACCAGATAAACTGGTATTC
* ** * *
73608 ATACAAGAGGAA-TTGTCTTC
1 ATACCAGATAAACTGGTATTC
*
73628 ATACCAGATAAATTGGTATTC
1 ATACCAGATAAACTGGTATTC
73649 ATAC
1 ATAC
73653 TGAAGATTAG
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
20 28 0.40
21 42 0.60
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (21 bp):
ATACCAGATAAACTGGTATTC
Found at i:75047 original size:31 final size:32
Alignment explanation
Indices: 74986--75048 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
74976 AGGTAGAACA
* *
74986 CTTAGTGTTCGAGAGAAAGTATGTGAATGATC
1 CTTAGTGTTCGAGAGAAACTATATGAATGATC
75018 CTTAGTGTTCGAGAGAAACTA-ATGAATGATC
1 CTTAGTGTTCGAGAGAAACTATATGAATGATC
75049 AACGTGAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.30
Consensus pattern (32 bp):
CTTAGTGTTCGAGAGAAACTATATGAATGATC
Found at i:91258 original size:77 final size:76
Alignment explanation
Indices: 91131--91283 Score: 227
Period size: 77 Copynumber: 2.0 Consensus size: 76
91121 CTGTAATTCG
* * * *
91131 ATCTAAACAAAAACCGAATTAATGATGTTATTGGAAAATATAAATTGGAATCACGTATATTCATG
1 ATCTAAACAAAAACCGAATTAATGATGTTACTGGAAAACATAAACTGGAATCACGTATA-TCATA
91196 TGTCATACATTA
65 TGTCATACATTA
* *
91208 ATCTAGACAAAAAACTG-ATTAATGATGTTACTGGAAAACATAAACTGGAATCACGTATATCATA
1 ATCTAAAC-AAAAACCGAATTAATGATGTTACTGGAAAACATAAACTGGAATCACGTATATCATA
91272 TGTCATACATTA
65 TGTCATACATTA
91284 CTCACAAATC
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
76 16 0.23
77 46 0.67
78 7 0.10
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (76 bp):
ATCTAAACAAAAACCGAATTAATGATGTTACTGGAAAACATAAACTGGAATCACGTATATCATAT
GTCATACATTA
Found at i:92678 original size:22 final size:22
Alignment explanation
Indices: 92653--92694 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
92643 CAAAATACAT
92653 AGATAAAATGTACCATAAAGGC
1 AGATAAAATGTACCATAAAGGC
* **
92675 AGATATAATGTGTCATAAAG
1 AGATAAAATGTACCATAAAG
92695 ACATAATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.24
Consensus pattern (22 bp):
AGATAAAATGTACCATAAAGGC
Done.