Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003973.1 Hibiscus syriacus cultivar Beakdansim tig00008618_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: 60944
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:118 original size:30 final size:31
Alignment explanation
Indices: 70--143 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 31
60 TTTTTGTGAA
*
70 AGAGA-TGAAGAT-AAAGTAGTGTCTAAAGT
1 AGAGATTGAAGATGAAAGTAGTGTCCAAAGT
99 AGAGATTG-AGATGAAAGTAGTGTCCAAAGT
1 AGAGATTGAAGATGAAAGTAGTGTCCAAAGT
129 A-AGATTTGAAGATGA
1 AGAGA-TTGAAGATGA
144 TGTGCACGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
29 12 0.30
30 22 0.55
31 6 0.15
ACGTcount: A:0.43, C:0.04, G:0.28, T:0.24
Consensus pattern (31 bp):
AGAGATTGAAGATGAAAGTAGTGTCCAAAGT
Found at i:5651 original size:43 final size:41
Alignment explanation
Indices: 5604--5687 Score: 98
Period size: 43 Copynumber: 2.0 Consensus size: 41
5594 TATCTAGCTT
*
5604 AATTTTCAAA-TCAAAGAATTCTTTTTCAAAATTTTTATTTTTC
1 AATTTTCAAACTC-AA-AATACTTTTTCAAAA-TTTTATTTTTC
* *
5647 AATTTTGAAAGCTCCAAATACTTTTTCAAAATTTTATTTTT
1 AATTTTCAAA-CTCAAAATACTTTTTCAAAATTTTATTTTT
5688 GCTTTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
42 10 0.28
43 23 0.64
44 1 0.03
45 2 0.06
ACGTcount: A:0.35, C:0.12, G:0.04, T:0.50
Consensus pattern (41 bp):
AATTTTCAAACTCAAAATACTTTTTCAAAATTTTATTTTTC
Found at i:7645 original size:21 final size:21
Alignment explanation
Indices: 7621--7672 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
7611 TTAAGGGAAT
*
7621 GGATCTATCCTTTTCAT-CAAG
1 GGATCGATCCTTTT-ATACAAG
*
7642 GGATCGATCCTTTTGTACAAG
1 GGATCGATCCTTTTATACAAG
7663 GGATCGATCC
1 GGATCGATCC
7673 AAAAGTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (21 bp):
GGATCGATCCTTTTATACAAG
Found at i:7720 original size:20 final size:20
Alignment explanation
Indices: 7695--7762 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
7685 AATTCAAAGA
7695 ATCGATCTTTTTTCAAGGAG
1 ATCGATCTTTTTTCAAGGAG
* *
7715 ATCGATCATTTGGTT-AAAGAG
1 ATCGATC-TTT-TTTCAAGGAG
* * *
7736 ATCGATCATTTTGCTAGGAG
1 ATCGATCTTTTTTCAAGGAG
*
7756 ATTGATC
1 ATCGATC
7763 ATTTGAGCCA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
19 1 0.03
20 19 0.51
21 15 0.41
22 2 0.05
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (20 bp):
ATCGATCTTTTTTCAAGGAG
Found at i:7740 original size:41 final size:40
Alignment explanation
Indices: 7690--7767 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 40
7680 TTTGGAATTC
* *
7690 AAAGAATCGATCTTTTTTCAAGGAGATCGATCATTTGGTT
1 AAAGAATCGATCATTTTGCAAGGAGATCGATCATTTGGTT
* *
7730 AAAGAGATCGATCATTTTGCTAGGAGATTGATCATTTG
1 AAAGA-ATCGATCATTTTGCAAGGAGATCGATCATTTG
7768 AGCCAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
40 5 0.15
41 28 0.85
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.36
Consensus pattern (40 bp):
AAAGAATCGATCATTTTGCAAGGAGATCGATCATTTGGTT
Found at i:7763 original size:20 final size:21
Alignment explanation
Indices: 7709--7767 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
7699 ATCTTTTTTC
*
7709 AAGGAGATCGATCATTTGGTT
1 AAGGAGATCGATCATTTGGCT
* *
7730 AAAGAGATCGATCATTTTGCT
1 AAGGAGATCGATCATTTGGCT
*
7751 -AGGAGATTGATCATTTG
1 AAGGAGATCGATCATTTG
7768 AGCCAAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (21 bp):
AAGGAGATCGATCATTTGGCT
Found at i:8585 original size:3 final size:3
Alignment explanation
Indices: 8577--8620 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
8567 GTCACTATGA
8577 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
8621 ATGACATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:8671 original size:17 final size:17
Alignment explanation
Indices: 8640--8672 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
8630 TTATATATTA
8640 TTAAATATAAAAATAAT
1 TTAAATATAAAAATAAT
8657 TTAAA-ATAAATAATAA
1 TTAAATATAAA-AATAA
8673 AATATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAATATAAAAATAAT
Found at i:9023 original size:9 final size:8
Alignment explanation
Indices: 9001--9025 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
8991 TGTTTATCTA
9001 TTAAAAAT
1 TTAAAAAT
9009 TTAAAAAT
1 TTAAAAAT
9017 TTAAAAAT
1 TTAAAAAT
9025 T
1 T
9026 CAATGATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TTAAAAAT
Found at i:9549 original size:10 final size:10
Alignment explanation
Indices: 9534--9621 Score: 50
Period size: 10 Copynumber: 8.1 Consensus size: 10
9524 CATTTAAATG
9534 ATAAACGAAC
1 ATAAACGAAC
*
9544 ATAAACGTAC
1 ATAAACGAAC
* *
9554 GTAAATGAAC
1 ATAAACGAAC
* *
9564 ACAAACGAATGAAT
1 ATAAAC----GAAC
9578 ATAAACGAAC
1 ATAAACGAAC
9588 ATAAACGAACAC
1 ATAAACG-A-AC
*
9600 AATAAACAAAC
1 -ATAAACGAAC
*
9611 ATAAACTAAC
1 ATAAACGAAC
9621 A
1 A
9622 ACACAAACAC
Statistics
Matches: 59, Mismatches: 12, Indels: 14
0.69 0.14 0.16
Matches are distributed among these distances:
10 39 0.66
11 3 0.05
12 3 0.05
13 6 0.10
14 8 0.14
ACGTcount: A:0.59, C:0.18, G:0.09, T:0.14
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:9611 original size:23 final size:23
Alignment explanation
Indices: 9578--9621 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
9568 ACGAATGAAT
*
9578 ATAAACGAACATAAACGAACACA
1 ATAAACAAACATAAACGAACACA
*
9601 ATAAACAAACATAAACTAACA
1 ATAAACAAACATAAACGAACA
9622 ACACAAACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.20, G:0.05, T:0.11
Consensus pattern (23 bp):
ATAAACAAACATAAACGAACACA
Found at i:9629 original size:23 final size:23
Alignment explanation
Indices: 9580--9630 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
9570 GAATGAATAT
* *
9580 AAACGAACATAAACGAACACAAT
1 AAACAAACATAAACGAACACAAC
*
9603 AAACAAACATAAACTAACA-ACAC
1 AAACAAACATAAACGAACACA-AC
9626 AAACA
1 AAACA
9631 CAAAAAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.65, C:0.24, G:0.04, T:0.08
Consensus pattern (23 bp):
AAACAAACATAAACGAACACAAC
Found at i:17798 original size:18 final size:19
Alignment explanation
Indices: 17762--17798 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
17752 CACGGAATGT
17762 AAGATTACCAGTAGGAATAA
1 AAGATTACCAG-AGGAATAA
17782 AAGATTACCAG-GGAATA
1 AAGATTACCAGAGGAATA
17799 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGAGGAATAA
Found at i:18545 original size:23 final size:23
Alignment explanation
Indices: 18484--18536 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
18474 TGCTAACTGT
* **
18484 TTCAACAAAACAGTGTTGAATGA
1 TTCAGCAAAACAGTACTGAATGA
18507 TTCAGCAAAACAGTACTGAATGA
1 TTCAGCAAAACAGTACTGAATGA
18530 TTCAGCA
1 TTCAGCA
18537 CATAAGTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (23 bp):
TTCAGCAAAACAGTACTGAATGA
Found at i:18634 original size:73 final size:73
Alignment explanation
Indices: 18515--18660 Score: 265
Period size: 73 Copynumber: 2.0 Consensus size: 73
18505 GATTCAGCAA
* * *
18515 AACAGTACTGAATGATTCAGCACATAAGTACATTTTGAATGATTCAGAGCCACTATCAAATAGCA
1 AACAGTACTAAATGATTCAGCACATAAGTACATTTTGAATGATTCAGAGCCACTATCAAACAACA
18580 TGTTACAT
66 TGTTACAT
18588 AACAGTACTAAATGATTCAGCACATAAGTACATTTTGAATGATTCAGAGCCACTATCAAACAACA
1 AACAGTACTAAATGATTCAGCACATAAGTACATTTTGAATGATTCAGAGCCACTATCAAACAACA
18653 TGTTACAT
66 TGTTACAT
18661 TCAGAGCTAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (73 bp):
AACAGTACTAAATGATTCAGCACATAAGTACATTTTGAATGATTCAGAGCCACTATCAAACAACA
TGTTACAT
Found at i:18799 original size:30 final size:28
Alignment explanation
Indices: 18763--18818 Score: 94
Period size: 30 Copynumber: 1.9 Consensus size: 28
18753 TCTTAGTATC
18763 ATTAAGTTTGATTTAATTTTAGAAATTTAA
1 ATTAAGTTTGATTTAA-TTTA-AAATTTAA
18793 ATTAAGTTTGATTTAATTTAAAATTT
1 ATTAAGTTTGATTTAATTTAAAATTT
18819 TATAACTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 6 0.23
29 4 0.15
30 16 0.62
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (28 bp):
ATTAAGTTTGATTTAATTTAAAATTTAA
Found at i:19886 original size:40 final size:34
Alignment explanation
Indices: 19798--19872 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 34
19788 TAATTAATAC
*
19798 TTAAGTTAATTTTATGTATTTTTATTTTCAACAT
1 TTAAGTTAATTTTATGTATATTTATTTTCAACAT
19832 TTAAGTTAATTTTATGTATATTTATTTTCAACAT
1 TTAAGTTAATTTTATGTATATTTATTTTCAACAT
*
19866 TTTAGTT
1 TTAAGTT
19873 TATATATCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.59
Consensus pattern (34 bp):
TTAAGTTAATTTTATGTATATTTATTTTCAACAT
Found at i:19888 original size:36 final size:34
Alignment explanation
Indices: 19798--19891 Score: 107
Period size: 34 Copynumber: 2.7 Consensus size: 34
19788 TAATTAATAC
* * *
19798 TTAAGTTAATTTTATGTATTTTTATTTTCAACAT
1 TTAAGTTAATATCATGTATATTTATTTTCAACAT
* *
19832 TTAAGTTAATTTTATGTATATTTATTTTCAACAT
1 TTAAGTTAATATCATGTATATTTATTTTCAACAT
* *
19866 TTTAGTTTATATATCATTTATATTTA
1 TTAAG-TTA-ATATCATGTATATTTA
19892 AGAATAAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
34 37 0.70
35 3 0.06
36 13 0.25
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (34 bp):
TTAAGTTAATATCATGTATATTTATTTTCAACAT
Found at i:21060 original size:23 final size:23
Alignment explanation
Indices: 20997--21064 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
20987 AACAAATTTG
* *
20997 CCTTTATGACATATTTTCGTCTA
1 CCTTTATAACATATTTTCTTCTA
* ***
21020 TCTTTA-AGACACGCTTTCTTCTA
1 CCTTTATA-ACATATTTTCTTCTA
21043 CCTTTATAACATATTTTCTTCT
1 CCTTTATAACATATTTTCTTCT
21065 GTTTTTTGGC
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.22, C:0.24, G:0.06, T:0.49
Consensus pattern (23 bp):
CCTTTATAACATATTTTCTTCTA
Found at i:23977 original size:20 final size:21
Alignment explanation
Indices: 23952--23991 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
23942 AGAGAATCGA
23952 TAAATATTAACTTTT-GATAT
1 TAAATATTAACTTTTAGATAT
23972 TAAATATTAACTTTTAGATA
1 TAAATATTAACTTTTAGATA
23992 AATATATGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (21 bp):
TAAATATTAACTTTTAGATAT
Found at i:23998 original size:20 final size:19
Alignment explanation
Indices: 23951--23996 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
23941 AAGAGAATCG
23951 ATAAATATTAACTTTTGAT
1 ATAAATATTAACTTTTGAT
*
23970 ATTAAATATTAACTTTT-AG
1 A-TAAATATTAACTTTTGAT
23989 ATAAATAT
1 ATAAATAT
23997 ATGTCGATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 7 0.28
19 3 0.12
20 15 0.60
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (19 bp):
ATAAATATTAACTTTTGAT
Found at i:30558 original size:15 final size:15
Alignment explanation
Indices: 30538--30577 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
30528 AGACACTTCT
30538 GCAGCGGCTGCTGGA
1 GCAGCGGCTGCTGGA
30553 GCAGCGGCTGCTGGA
1 GCAGCGGCTGCTGGA
*
30568 GCACCGGCTG
1 GCAGCGGCTG
30578 ACAAGGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.12, C:0.30, G:0.45, T:0.12
Consensus pattern (15 bp):
GCAGCGGCTGCTGGA
Found at i:35489 original size:130 final size:130
Alignment explanation
Indices: 35345--35592 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
35335 TATTTATATA
*
35345 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
35410 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATTTGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATTTGCT
35475 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * * *
35540 TTAACACATGATTATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
35593 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATTTGCT
Found at i:35623 original size:130 final size:129
Alignment explanation
Indices: 35359--35623 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
35349 ATTTGGTCCT
* *
35359 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
35424 TGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATTTGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATTAGCTATCAAAGAAGT-CA
*
35489 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATTA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
35554 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAATT-AGCTATCAAAGAAGT
35618 -A
128 CA
35619 AAATT
1 AAATT
35624 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 10 0.09
133 3 0.03
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATTAGCTATCAAAGAAGTCA
Found at i:36921 original size:130 final size:131
Alignment explanation
Indices: 36780--37028 Score: 410
Period size: 131 Copynumber: 1.9 Consensus size: 131
36770 TATTTATATA
*
36780 ATCAATTTGGTCCTAAATTAAAT-AAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGT
1 ATCAATTTGGTCCTAAATTAAATAAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGT
* ** *
36844 GTTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGC
66 GTTAACACATGATCATGACACGTGTCATTGGTGACAAATGTCACCACCTAATTATTTATATATGC
36909 T
131 T
36910 ATCAATTTGGTCCTAAATTAAATAAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGT
1 ATCAATTTGGTCCTAAATTAAATAAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGT
* * * *
36975 GTTAACACATGATCATGATATGTGTTATTGGTGACAAATGTCACCTCCTAATTA
66 GTTAACACATGATCATGACACGTGTCATTGGTGACAAATGTCACCACCTAATTA
37029 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
130 23 0.21
131 86 0.79
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (131 bp):
ATCAATTTGGTCCTAAATTAAATAAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGT
GTTAACACATGATCATGACACGTGTCATTGGTGACAAATGTCACCACCTAATTATTTATATATGC
T
Found at i:37059 original size:131 final size:129
Alignment explanation
Indices: 36794--37059 Score: 293
Period size: 131 Copynumber: 2.0 Consensus size: 129
36784 ATTTGGTCCT
* *
36794 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
** * *** * * **** *
36859 TGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACAAATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
36924 AAATTAAATAAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATC
1 AAATTAAAT-AAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATC
* * * * *
36989 ATGATATGTGTTATTGGTGACAAATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAG
65 ATGACACGTGTCATTGGTGACAAATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAG
37053 T-A
127 TCA
37055 AAATT
1 AAATT
37060 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
130 9 0.08
131 90 0.80
133 8 0.07
134 5 0.04
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACAAATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:37386 original size:28 final size:27
Alignment explanation
Indices: 37355--37417 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
37345 AGTTGATACA
*
37355 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
37383 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
37411 ATATTTT
1 ATATTTT
37418 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:37518 original size:16 final size:18
Alignment explanation
Indices: 37497--37530 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
37487 ATTTCTTATT
37497 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
37513 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
37531 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:37677 original size:21 final size:21
Alignment explanation
Indices: 37653--37695 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
37643 TATTACCTTA
37653 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
37674 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
37695 A
1 A
37696 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:37713 original size:35 final size:35
Alignment explanation
Indices: 37664--37749 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
37654 ATTGAAGTAT
** * *
37664 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
37699 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
37734 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
37750 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:37932 original size:29 final size:29
Alignment explanation
Indices: 37880--37939 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
37870 GCAAACGGAA
* *
37880 TAAATGTTGGGGGACTGTATTGCAAGTTT
1 TAAATGTTGGGGGACTGAAATGCAAGTTT
37909 TAAATGTTGGGGGACCT-AAATGCAAGTTT
1 TAAATGTTGGGGGA-CTGAAATGCAAGTTT
37938 TA
1 TA
37940 GAAATGTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.35
Consensus pattern (29 bp):
TAAATGTTGGGGGACTGAAATGCAAGTTT
Found at i:39080 original size:15 final size:15
Alignment explanation
Indices: 39043--39103 Score: 58
Period size: 14 Copynumber: 4.1 Consensus size: 15
39033 CTTGAATAAG
39043 ATGAAAGAAGAAGAA
1 ATGAAAGAAGAAGAA
39058 ATG-AAGAAGAAG-A
1 ATGAAAGAAGAAGAA
39071 ATGAAGAGAAG-AGAA
1 ATGAA-AGAAGAAGAA
*
39086 GTGGAAAGGAA-AAGAA
1 AT-GAAA-GAAGAAGAA
39102 AT
1 AT
39104 CCACATCTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
13 4 0.11
14 12 0.32
15 11 0.29
16 11 0.29
ACGTcount: A:0.61, C:0.00, G:0.31, T:0.08
Consensus pattern (15 bp):
ATGAAAGAAGAAGAA
Found at i:39085 original size:17 final size:18
Alignment explanation
Indices: 39036--39086 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
39026 ATAGTCACTT
39036 GAAT-AAGATGAA-AGAA
1 GAATGAAGATGAAGAGAA
39052 GAA-GAA-ATGAAGAAGAA
1 GAATGAAGATGAAG-AGAA
39069 GAATGAAGA-GAAGAGAA
1 GAATGAAGATGAAGAGAA
39086 G
1 G
39087 TGGAAAGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
15 5 0.17
16 5 0.17
17 12 0.40
18 7 0.23
19 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.31, T:0.08
Consensus pattern (18 bp):
GAATGAAGATGAAGAGAA
Found at i:40243 original size:13 final size:13
Alignment explanation
Indices: 40225--40257 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
40215 TACATAGGGA
40225 AACTCACTTAGCT
1 AACTCACTTAGCT
40238 AACTCACTTAGCT
1 AACTCACTTAGCT
40251 AACTCAC
1 AACTCAC
40258 ATAACACTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.33, G:0.06, T:0.27
Consensus pattern (13 bp):
AACTCACTTAGCT
Found at i:49321 original size:162 final size:162
Alignment explanation
Indices: 49054--49378 Score: 641
Period size: 162 Copynumber: 2.0 Consensus size: 162
49044 TAATTATGTT
49054 TATATTTTTGTTTATTTAGAGAAATTGAACTCACCCATCTCCTTTCTCCACGTATTTATTTGTTT
1 TATATTTTTGTTTATTTAGAGAAATTGAACTCACCCATCTCCTTTCTCCACGTATTTATTTGTTT
49119 ATTTTACTCATTTCTATCTTCCATAATTTAACTCAATTTTGGGAGACAATATGGCAAAACAACAA
66 ATTTTACTCATTTCTATCTTCCATAATTTAACTCAATTTTGGGAGACAATATGGCAAAACAACAA
49184 ATCTATTACATTCGACATCTCCCTAGTAATTA
131 ATCTATTACATTCGACATCTCCCTAGTAATTA
*
49216 TATATTTTTGTTTATTTAGAGAAATTGAACTCACCCATCTCCTTTCTCCACTTATTTATTTGTTT
1 TATATTTTTGTTTATTTAGAGAAATTGAACTCACCCATCTCCTTTCTCCACGTATTTATTTGTTT
49281 ATTTTACTCATTTCTATCTTCCATAATTTAACTCAATTTTGGGAGACAATATGGCAAAACAACAA
66 ATTTTACTCATTTCTATCTTCCATAATTTAACTCAATTTTGGGAGACAATATGGCAAAACAACAA
49346 ATCTATTACATTCGACATCTCCCTAGTAATTA
131 ATCTATTACATTCGACATCTCCCTAGTAATTA
49378 T
1 T
49379 TTACCTTCTT
Statistics
Matches: 162, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
162 162 1.00
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (162 bp):
TATATTTTTGTTTATTTAGAGAAATTGAACTCACCCATCTCCTTTCTCCACGTATTTATTTGTTT
ATTTTACTCATTTCTATCTTCCATAATTTAACTCAATTTTGGGAGACAATATGGCAAAACAACAA
ATCTATTACATTCGACATCTCCCTAGTAATTA
Found at i:52331 original size:25 final size:25
Alignment explanation
Indices: 52297--52347 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
52287 CTTTTGTGTT
52297 TGTTTGTGATACATGTGATTCACCA
1 TGTTTGTGATACATGTGATTCACCA
52322 TGTTTGTGATACATGTGATTCACCA
1 TGTTTGTGATACATGTGATTCACCA
52347 T
1 T
52348 TCCTCTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.41
Consensus pattern (25 bp):
TGTTTGTGATACATGTGATTCACCA
Found at i:53543 original size:16 final size:17
Alignment explanation
Indices: 53506--53542 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
53496 AAATCATTTG
*
53506 AAAATAATAAAAAAGTC
1 AAAATAATAAAAAAATC
*
53523 AAAATTATAAAAAAATC
1 AAAATAATAAAAAAATC
53540 AAA
1 AAA
53543 TATTTAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (17 bp):
AAAATAATAAAAAAATC
Found at i:53708 original size:27 final size:26
Alignment explanation
Indices: 53652--53723 Score: 76
Period size: 27 Copynumber: 2.8 Consensus size: 26
53642 TTCTAATTTA
* * * *
53652 TTTTATAATTTTTAATTATTTCGAACT
1 TTTTATTATTTTTAAATATTTC-TATT
*
53679 TTTAATTATTTTTAAATATTTCTATT
1 TTTTATTATTTTTAAATATTTCTATT
53705 TTTTA-TATTTTTAAA-ATTT
1 TTTTATTATTTTTAAATATTT
53724 TCAATAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
24 4 0.10
25 10 0.26
26 6 0.15
27 19 0.49
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (26 bp):
TTTTATTATTTTTAAATATTTCTATT
Found at i:58551 original size:21 final size:21
Alignment explanation
Indices: 58525--58564 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
58515 TCTATTGAAA
* *
58525 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGCTGTGGAGTATG
58546 CTCCACCTGCTGTGGAGTA
1 CTCCACCTGCTGTGGAGTA
58565 CTACTTATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.33
Consensus pattern (21 bp):
CTCCACCTGCTGTGGAGTATG
Done.