Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002562.1 Hibiscus syriacus cultivar Beakdansim tig00005201_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: 67914
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:1492 original size:30 final size:30
Alignment explanation
Indices: 1449--1514 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
1439 ATAAGCCTTA
* * *
1449 GAAAAATTTGGGGATC-ATTATGTAATTTTT
1 GAAAAATTGGGGGACCAATTA-GTAATTTTG
*
1479 GAAAAGTTGGGGGACCAAATTAGTAATTTTG
1 GAAAAATTGGGGGACC-AATTAGTAATTTTG
1510 GAAAA
1 GAAAA
1515 TTATGTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
30 13 0.43
31 13 0.43
32 4 0.13
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (30 bp):
GAAAAATTGGGGGACCAATTAGTAATTTTG
Found at i:6825 original size:64 final size:64
Alignment explanation
Indices: 6757--6977 Score: 206
Period size: 64 Copynumber: 3.5 Consensus size: 64
6747 TTGTTTGAAG
** * ** *
6757 GTGCATCGATGCATTGGTAGTGCATTGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAAGAAA-ACATCGAATGCAATT
*
6820 T
64 A
*
6821 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAAACATCGAATGCAATTA
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTA
* * * * * *
6885 GTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCAGT-ATAATACAACATCGAATACATTTT
1 GTGCATCGATGCATAA-GTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCA-ATT
6948 A
64 A
* *
6949 -TGCA-C--CGCATTAGTAGTGCATCGATGCAT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCAT
6978 ACCTTCATTA
Statistics
Matches: 134, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
59 2 0.01
60 18 0.13
62 1 0.01
63 20 0.15
64 86 0.64
65 7 0.05
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTA
Found at i:7841 original size:103 final size:103
Alignment explanation
Indices: 7715--7937 Score: 428
Period size: 103 Copynumber: 2.2 Consensus size: 103
7705 GTCGAGGGTC
7715 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
7780 TTGATCCCTAATATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAATATATGTATATGATTCTTAAGGAGTGA
*
7818 TATGTGGTTCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
7883 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAATATATGTATATGATTCTTAAGGAGTGA
7921 TATGTGGTCCTTCGGGA
1 TATGTGGTCCTTCGGGA
7938 CATTATTATA
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
103 117 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAATATATGTATATGATTCTTAAGGAGTGA
Found at i:7979 original size:23 final size:23
Alignment explanation
Indices: 7949--8011 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
7939 ATTATTATAT
*
7949 GGCACTCCGGTACAATTCTACAC
1 GGCACTCCGGTGCAATTCTACAC
**
7972 GGCACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACAC
*
7995 GGCACTTCGGTGCAATT
1 GGCACTCCGGTGCAATT
8012 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.25
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACAC
Found at i:12513 original size:64 final size:64
Alignment explanation
Indices: 12445--12589 Score: 186
Period size: 64 Copynumber: 2.3 Consensus size: 64
12435 TTGTTTGAAG
** **
12445 GTGCATCGATGAATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATT
1 GTGCATCGATGAATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATT
*
12508 T
64 A
* *
12509 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTA
1 GTGCATCGATGAATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTA
*
12573 GTGCATCGATGCATAAG
1 GTGCATCGATGAATAAG
12590 GCATGCATCG
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
64 66 0.92
65 6 0.08
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGAATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTA
Found at i:13589 original size:103 final size:103
Alignment explanation
Indices: 13356--13574 Score: 429
Period size: 103 Copynumber: 2.1 Consensus size: 103
13346 GTCGAGGGTC
13356 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
13421 TTGATCCCTAGTATATGTATATGATTCTTAAAGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAAGAGTGA
13459 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
13524 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAAGAGTGA
13562 TATGTGGTCCTTC
1 TATGTGGTCCTTC
13575 AGGACATTAT
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAAGAGTGA
Found at i:13624 original size:23 final size:23
Alignment explanation
Indices: 13590--13652 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
13580 ATTATTGTAT
*
13590 GGCACTCTGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
*
13613 GGCACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
*
13636 GGCACTTCGGTGCAATT
1 GGCACTCCGGTGCAATT
13653 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.17, C:0.29, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:16690 original size:20 final size:21
Alignment explanation
Indices: 16646--16691 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
16636 AATAGAGTCA
* *
16646 ATACCATGGTATGGTAGTATTG
1 ATACCATGGTAAGG-AGTATCG
16668 ATACCATGGTAAGG-GTATCG
1 ATACCATGGTAAGGAGTATCG
16688 ATAC
1 ATAC
16692 TATTGAGCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
22 13 0.59
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.30
Consensus pattern (21 bp):
ATACCATGGTAAGGAGTATCG
Found at i:17683 original size:81 final size:81
Alignment explanation
Indices: 17187--17668 Score: 777
Period size: 81 Copynumber: 6.0 Consensus size: 81
17177 TGAATAATTA
* * *
17187 TTTGAGTAAAAGATTAATGGCCTAGCTGTGTATTTGACAGAAATGTGTCAATTATGGCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
17252 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* *
17268 TTTGAGTGAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
*
17333 TGAAAGGTTAAATACT
66 TGAAAGGTTAAATACC
* * * *
17349 TTTTAGTAAAATATTAATGGCCTAGCTGTGCATTTGACAGAAAGATGTCAATTATGCCAATTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
*
17414 TGAAAGGTTAAATACA
66 TGAAAGGTTAAATACC
*
17430 TTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
17495 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* *
17511 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTATCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
17576 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* * * *
17592 TTTGAGTAAAATATTAATGGCCTAGATGTGCATTTGACAAAAAGGTGTCAATTATGTCAG-TAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
* *
17656 TGAATGATTAAAT
66 TGAAAGGTTAAAT
17669 GCTTGTGGGA
Statistics
Matches: 371, Mismatches: 30, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
80 15 0.04
81 356 0.96
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (81 bp):
TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
TGAAAGGTTAAATACC
Found at i:20130 original size:2 final size:2
Alignment explanation
Indices: 20125--20155 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20115 TAATGTCATA
20125 AT AT 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 AT AT A
20156 ACTTTTCTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22587 original size:81 final size:81
Alignment explanation
Indices: 22485--23451 Score: 1432
Period size: 81 Copynumber: 12.0 Consensus size: 81
22475 GAATAATTAA
* *
22485 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGGCAGTTAGAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
22550 GAAAGGTTAAATACCT
66 GAAAGGTTAAATACCT
*
22566 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
*
22631 GAAAGGTTAAATACTT
66 GAAAGGTTAAATACCT
* * * * * *
22647 TTTAGTAAAATATTAATGGCCTAGCTATGCATTTGACAGAAAGATGTCAATTATGTCAATTAGAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
* *
22712 AAAAGGTTAAATACAT
66 GAAAGGTTAAATACCT
* * *
22728 TTGAGTAAAATATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAG
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
* *
22793 GAAATGTTAAATATCT
66 GAAAGGTTAAATACCT
* * * * ** *
22809 TTGAGTAAAAGATTAATGTCCTAGTTGTGCATTTGACAGAAAGGTGTCGATTATTCCTTTTAAAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
*
22874 GAAAAGTTAAATACCT
66 GAAAGGTTAAATACCT
* * * * * *
22890 TAGAGT-AAAGATTAATGGCCTAGTTGTGAATTTGACATAAAGGTTTCAATTATGCCAATTAGAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
22954 GAAAGGTTAAATACCT
66 GAAAGGTTAAATACCT
* *
22970 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGATGTCAATTATGCCAATTAGAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
23035 GAAAGGTTAAATACCT
66 GAAAGGTTAAATACCT
*
23051 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
*
23116 GAAACGTTAAATACCT
66 GAAAGGTTAAATACCT
* * *
23132 ATGAGTAAAATATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
*
23197 GAAAGTTTAAATACCT
66 GAAAGGTTAAATACCT
* * *
23213 TTGAGTAAAAGATTAATGGCCTAGCAGTGCATTTGACAGAAATGTGTCAATTATGTCAGTTAGAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
*
23278 GAAAGGTTAAATACTT
66 GAAAGGTTAAATACCT
* * * * * *
23294 TTTAGTAAAATATTAATGGCCTAGCTATGCATTTGACAGAAAGATGTCAATTATGTCAATTAGAT
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
* **
23359 AAAAGGTTAAATAGAT
66 GAAAGGTTAAATACCT
* *
23375 TTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAG
1 TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
*
23440 GAAAGATTAAAT
66 GAAAGGTTAAAT
23452 GTTTGTGGGG
Statistics
Matches: 799, Mismatches: 86, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
80 69 0.09
81 730 0.91
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (81 bp):
TTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
GAAAGGTTAAATACCT
Found at i:24259 original size:19 final size:20
Alignment explanation
Indices: 24216--24261 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
24206 TACTATGCTG
*
24216 GAAATTAATGTTAGAATGTT
1 GAAATTGATGTTAGAATGTT
*
24236 GAAATTGATGTTATAATG-T
1 GAAATTGATGTTAGAATGTT
24255 GAAATTG
1 GAAATTG
24262 GGTCATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.39, C:0.00, G:0.22, T:0.39
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Found at i:27200 original size:14 final size:15
Alignment explanation
Indices: 27181--27213 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
27171 AACATAATTC
*
27181 TAATTCT-TATAATA
1 TAATTCTATAAAATA
27195 TAATTCTATAAAATA
1 TAATTCTATAAAATA
27210 TAAT
1 TAAT
27214 CAATACGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATTCTATAAAATA
Found at i:33858 original size:18 final size:18
Alignment explanation
Indices: 33835--33869 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
33825 GATGTTACGT
33835 TAACCATTTCAAAATTTG
1 TAACCATTTCAAAATTTG
33853 TAACCATTTCAAAATTT
1 TAACCATTTCAAAATTT
33870 TCTTGTACAA
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:0.17, G:0.03, T:0.40
Consensus pattern (18 bp):
TAACCATTTCAAAATTTG
Found at i:40592 original size:25 final size:25
Alignment explanation
Indices: 40558--40615 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
40548 TTGTCTGTAC
40558 TAATCTCTCTCCGGAAGCCATCGAA
1 TAATCTCTCTCCGGAAGCCATCGAA
*
40583 TAATCTCTCTCCGGAGGCCATCGAA
1 TAATCTCTCTCCGGAAGCCATCGAA
40608 TAATCTCT
1 TAATCTCT
40616 AATAAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.28
Consensus pattern (25 bp):
TAATCTCTCTCCGGAAGCCATCGAA
Found at i:48438 original size:12 final size:12
Alignment explanation
Indices: 48417--48442 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
48407 TTGAGGAATA
48417 GGAGGAGGATTT
1 GGAGGAGGATTT
48429 GGAGGAGGATTT
1 GGAGGAGGATTT
48441 GG
1 GG
48443 TTGTCGACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.54, T:0.23
Consensus pattern (12 bp):
GGAGGAGGATTT
Found at i:52881 original size:20 final size:20
Alignment explanation
Indices: 52856--52894 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
52846 GAAGTTTTAA
52856 GATCATCAATTT-TCTTTGAT
1 GATCATC-ATTTATCTTTGAT
52876 GATCATCATTTATCTTTGA
1 GATCATCATTTATCTTTGA
52895 AAGTAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
GATCATCATTTATCTTTGAT
Found at i:58113 original size:12 final size:12
Alignment explanation
Indices: 58096--58121 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58086 AAAACCCTGC
58096 TAGAACTCACAG
1 TAGAACTCACAG
58108 TAGAACTCACAG
1 TAGAACTCACAG
58120 TA
1 TA
58122 ACTGACTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.19
Consensus pattern (12 bp):
TAGAACTCACAG
Found at i:60095 original size:13 final size:13
Alignment explanation
Indices: 60085--60141 Score: 87
Period size: 13 Copynumber: 4.4 Consensus size: 13
60075 TCTATGACGT
60085 GCATTTATGACAC
1 GCATTTATGACAC
60098 GCATTTATGACAC
1 GCATTTATGACAC
*
60111 ACATTTATGACAC
1 GCATTTATGACAC
* *
60124 TCATTTATGACGC
1 GCATTTATGACAC
60137 GCATT
1 GCATT
60142 GAGCGTCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (13 bp):
GCATTTATGACAC
Found at i:60107 original size:26 final size:26
Alignment explanation
Indices: 60077--60141 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
60067 GTCATAAATC
*
60077 TATGACGTGCATTTATGACACGCATT
1 TATGACGCGCATTTATGACACGCATT
* * *
60103 TATGACACACATTTATGACACTCATT
1 TATGACGCGCATTTATGACACGCATT
60129 TATGACGCGCATT
1 TATGACGCGCATT
60142 GAGCGTCATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (26 bp):
TATGACGCGCATTTATGACACGCATT
Done.