Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003797.1 Hibiscus syriacus cultivar Beakdansim tig00008122_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: 95097
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:5603 original size:9 final size:9
Alignment explanation
Indices: 5585--5630 Score: 51
Period size: 8 Copynumber: 5.2 Consensus size: 9
5575 TTAATTAAAT
5585 ATAATATTAA
1 ATAA-ATTAA
*
5595 ATAATTTAA
1 ATAAATTAA
*
5604 AT-ACTTAA
1 ATAAATTAA
5612 ATAAATT-A
1 ATAAATTAA
5620 ATAAATTAA
1 ATAAATTAA
5629 AT
1 AT
5631 GTTAAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
8 15 0.48
9 12 0.39
10 4 0.13
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (9 bp):
ATAAATTAA
Found at i:5613 original size:17 final size:16
Alignment explanation
Indices: 5569--5656 Score: 65
Period size: 17 Copynumber: 5.4 Consensus size: 16
5559 TATATATATA
* *
5569 TAAAAATTAATTAAA-
1 TAAATATTAAATAAAT
*
5584 TATAATATTAAATAATT
1 TA-AATATTAAATAAAT
5601 TAAATACTTAAATAAAT
1 TAAATA-TTAAATAAAT
* *
5618 TAATAAATTAAAT--GT
1 TAA-ATATTAAATAAAT
5633 TAAATATTAAATATAAT
1 TAAATATTAAATA-AAT
*
5650 AAAATAT
1 TAAATAT
5657 ACCTTAAACA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
14 8 0.14
15 6 0.11
16 14 0.25
17 27 0.47
18 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (16 bp):
TAAATATTAAATAAAT
Found at i:5637 original size:7 final size:7
Alignment explanation
Indices: 5578--5646 Score: 52
Period size: 7 Copynumber: 9.3 Consensus size: 7
5568 ATAAAAATTA
5578 ATTAAAT
1 ATTAAAT
5585 A-T-AAT
1 ATTAAAT
5590 ATTAAAT
1 ATTAAAT
5597 AATTTAAAT
1 -A-TTAAAT
5606 ACTTAAAT
1 A-TTAAAT
*
5614 AAATTAATAA
1 --ATTAA-AT
5624 ATTAAAT
1 ATTAAAT
*
5631 GTTAAAT
1 ATTAAAT
5638 ATTAAAT
1 ATTAAAT
5645 AT
1 AT
5647 AATAAAATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
5 4 0.08
6 2 0.04
7 19 0.38
8 13 0.26
9 10 0.20
10 2 0.04
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (7 bp):
ATTAAAT
Found at i:7202 original size:11 final size:11
Alignment explanation
Indices: 7186--7218 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
7176 ATTTTCATTT
7186 TATTATTATTA
1 TATTATTATTA
7197 TATTATTA-TA
1 TATTATTATTA
7207 TATATATTATTA
1 TAT-TATTATTA
7219 AATAAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.25
11 13 0.65
12 2 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTATTATTA
Found at i:7204 original size:14 final size:14
Alignment explanation
Indices: 7185--7218 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
7175 CATTTTCATT
7185 TTATTAT-TATTATA
1 TTATTATATA-TATA
7199 TTATTATATATATA
1 TTATTATATATATA
7213 TTATTA
1 TTATTA
7219 AATAAAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTATATATATA
Found at i:7577 original size:20 final size:19
Alignment explanation
Indices: 7552--7642 Score: 62
Period size: 19 Copynumber: 4.7 Consensus size: 19
7542 TTCTTTTTAT
7552 ATATATATAAAATTAATTAA
1 ATATATATAAAA-TAATTAA
* *
7572 ATATATATTAAATATTTAA
1 ATATATATAAAATAATTAA
* *
7591 ATACTTAAATAAATTAA-TAA
1 ATA--TATATAAAATAATTAA
* * *
7611 ATTAAATGTTAAAT-ATTAA
1 A-TATATATAAAATAATTAA
7630 ATATA-ATAAAATA
1 ATATATATAAAATA
7643 TACCTTAAAC
Statistics
Matches: 52, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
17 5 0.10
18 4 0.08
19 18 0.35
20 15 0.29
21 10 0.19
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (19 bp):
ATATATATAAAATAATTAA
Found at i:7624 original size:7 final size:7
Alignment explanation
Indices: 7576--7633 Score: 53
Period size: 7 Copynumber: 7.6 Consensus size: 7
7566 AATTAAATAT
7576 ATATTAA
1 ATATTAA
7583 ATATTTAA
1 ATA-TTAA
7591 ATACTTAA
1 ATA-TTAA
7599 ATAAATTAA
1 AT--ATTAA
*
7608 TAAATTAA
1 -ATATTAA
*
7616 ATGTTAA
1 ATATTAA
7623 ATATTAA
1 ATATTAA
7630 ATAT
1 ATAT
7634 AATAAAATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
7 18 0.43
8 18 0.43
9 4 0.10
10 2 0.05
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (7 bp):
ATATTAA
Found at i:16406 original size:20 final size:20
Alignment explanation
Indices: 16381--16423 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
16371 AATCTTCTAA
*
16381 GTTCCCCTAATCCACTTTTT
1 GTTCCCCTAATCCACTTCTT
16401 GTTCCCCTAATCCACTTCTT
1 GTTCCCCTAATCCACTTCTT
16421 GTT
1 GTT
16424 GGCCCTTGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.35, G:0.07, T:0.44
Consensus pattern (20 bp):
GTTCCCCTAATCCACTTCTT
Found at i:28384 original size:126 final size:126
Alignment explanation
Indices: 28134--28501 Score: 415
Period size: 126 Copynumber: 2.8 Consensus size: 126
28124 TTAATATACA
* *
28134 TAAATAAGATATTTACTTATTTAGAAATATCAGAAAAGGGCTTCTAGGTACCTTAAGACAGCTCT
1 TAAATAAGATATTTATTTATTTAAAAATATCAGAAAAGGGCTTCTAGGTACCTTAAGACAGCTCT
* *
28199 TTTCTTCGATATTAAAAAAATAAAATAAATAACTAAAAACATTTTCTTAAAAAA-TAAAA-A-T
66 TTTCTTTGATATT--AAAAATAAAATAAAT-ACTAAAAACATTTTCTTAAAAAACAAAAATATT
*
28260 TAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGCTTCTAGGTGA-CTTAAGACAGCTC
1 TAAATAAGATATTTATTTATTTAAAAATATCAGAAAAGGGCTTCTAGGT-ACCTTAAGACAGCTC
28324 TTTTCTTTGATATTAAAAAT-AAATAAATA-TAAAAACATTTTTCTTAAGATAATAACAAAAAAA
65 TTTTCTTTGATATTAAAAATAAAATAAATACTAAAAACA-TTTTCTT-A-A-AA-AAC----AAA
28387 AATTATTT
121 AA-TA-TT
* *
28395 TAATACAGTAAGATATTTATTTATTTAAAAATATCAGAAAAGGGCTTCTAGGTACCCTAAGACAT
1 T-A-A-A-TAAGATATTTATTTATTTAAAAATATCAGAAAAGGGCTTCTAGGTACCTTAAGACAG
* * *
28460 CTATTTCCTTTGATATTAATAAATAAAAATAAATATTAAAAA
62 CTCTTTTCTTTGATATTAA-AAAT-AAAATAAATACTAAAAA
28502 TGTAATAAAA
Statistics
Matches: 208, Mismatches: 10, Indels: 31
0.84 0.04 0.12
Matches are distributed among these distances:
121 8 0.04
122 8 0.04
123 9 0.04
124 7 0.03
125 2 0.01
126 74 0.36
127 1 0.00
131 4 0.02
133 1 0.00
135 2 0.01
136 1 0.00
137 1 0.00
138 2 0.01
139 69 0.33
140 4 0.02
142 9 0.04
143 6 0.03
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.35
Consensus pattern (126 bp):
TAAATAAGATATTTATTTATTTAAAAATATCAGAAAAGGGCTTCTAGGTACCTTAAGACAGCTCT
TTTCTTTGATATTAAAAATAAAATAAATACTAAAAACATTTTCTTAAAAAACAAAAATATT
Found at i:28724 original size:11 final size:11
Alignment explanation
Indices: 28650--28737 Score: 58
Period size: 11 Copynumber: 7.8 Consensus size: 11
28640 TAATATATAT
*
28650 TAATAAAAATA
1 TAATTAAAATA
*
28661 AAATTAATAATA
1 TAATTAA-AATA
28673 CTAATT-AAA-A
1 -TAATTAAAATA
28683 T-ATTAAACATA
1 TAATTAAA-ATA
28694 TAAAATTAAAATA
1 T--AATTAAAATA
*
28707 TATTTAAACA-A
1 TAATTAAA-ATA
28718 TAATTAAAATA
1 TAATTAAAATA
*
28729 AAATTAAAA
1 TAATTAAAA
28738 CTAAATATAA
Statistics
Matches: 61, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
8 3 0.05
9 3 0.05
10 3 0.05
11 32 0.52
12 6 0.10
13 8 0.13
14 6 0.10
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (11 bp):
TAATTAAAATA
Found at i:28730 original size:33 final size:32
Alignment explanation
Indices: 28650--28737 Score: 90
Period size: 33 Copynumber: 2.6 Consensus size: 32
28640 TAATATATAT
*
28650 TAATAAAAATAAAATTAATAATACTAATTAAAA
1 TAATTAAAATAAAATTAA-AATACTAATTAAAA
*
28683 T-ATTAAACATATAAAATTAAAATA-TATTTAAACAA
1 TAATT-AA-A-ATAAAATTAAAATACTAATT-AA-AA
28718 TAATTAAAATAAAATTAAAA
1 TAATTAAAATAAAATTAAAA
28738 CTAAATATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
32 2 0.04
33 19 0.40
34 8 0.17
35 15 0.32
36 3 0.06
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (32 bp):
TAATTAAAATAAAATTAAAATACTAATTAAAA
Found at i:30235 original size:3 final size:3
Alignment explanation
Indices: 30227--30276 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
30217 ATATATATAT
** *
30227 TAA TAA TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TTAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
30273 TAA T
1 TAA T
30277 TTTAATGAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:30567 original size:76 final size:77
Alignment explanation
Indices: 30436--30831 Score: 633
Period size: 76 Copynumber: 5.2 Consensus size: 77
30426 GGTCTTATGA
* *
30436 ATGACCCTG-AGGGTTTGAAAACGTCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCCTGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
* *
30500 TAGGACTTACAG
66 AAGGGCTTACAG
* *
30512 ATGACCCTG-AGGCTTTGAGAACATCAAAAAGCTCCCGAAGGCTTTTTGGAGACATCATGCACTG
1 ATGACCCTGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
* *
30576 CAGGACTTACAG
66 AAGGGCTTACAG
* *
30588 ATGACCTTGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTAGAAACATCATGCACTG
1 ATGACCCTGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
30653 AAGGGCTTACAG
66 AAGGGCTTACAG
* *
30665 ATGACCC-GAAGGTTTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCCTGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
30729 AAGGGCTTACAG
66 AAGGGCTTACAG
*
30741 ATGA-CCTGAAGGTTTTGAAAACATCAAAAAGC-CCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCCTGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
30804 AAGGGCTTACAG
66 AAGGGCTTACAG
30816 ATGACCC-GAAGGCTTT
1 ATGACCCTGAAGGCTTT
30832 TTGGAAACAT
Statistics
Matches: 300, Mismatches: 17, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
75 56 0.19
76 176 0.59
77 68 0.23
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (77 bp):
ATGACCCTGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
AAGGGCTTACAG
Found at i:30727 original size:153 final size:152
Alignment explanation
Indices: 30436--30843 Score: 633
Period size: 153 Copynumber: 2.7 Consensus size: 152
30426 GGTCTTATGA
* *
30436 ATGACCCTG-AGGGTTTGAAAACGTCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGA-CCTGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
* * * * *
30500 TAGGACTTACAGATGACCCTG-AGGCTTTGAGAACATCAAAAAGCTCCCGAAGGCTTTTTGGAGA
65 AAGGGCTTACAGATGACCC-GAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAA
*
30564 CATCATGCACTGCAGGACTTACAG
129 CATCATGCACTGAAGGACTTACAG
*
30588 ATGACCTTGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTAGAAACATCATGCACTG
1 ATGACC-TGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
*
30653 AAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTTGGAAAC
65 AAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAAC
*
30718 ATCATGCACTGAAGGGCTTACAG
130 ATCATGCACTGAAGGACTTACAG
*
30741 ATGACCTGAAGGTTTTGAAAACATCAAAAAGC-CCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCTGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
30805 AGGGCTTACAGATGACCCGAAGGCTTTTTGGAAACATCA
66 AGGGCTTACAGATGACCCGAAGG--TTTTGAAAACATCA
30844 TGCACTGAAG
Statistics
Matches: 237, Mismatches: 14, Indels: 9
0.91 0.05 0.03
Matches are distributed among these distances:
151 56 0.24
152 32 0.14
153 149 0.63
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (152 bp):
ATGACCTGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACA
TCATGCACTGAAGGACTTACAG
Found at i:30824 original size:47 final size:47
Alignment explanation
Indices: 30773--30865 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
30763 ATCAAAAAGC
*
30773 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
30820 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
30866 TGGGAAATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.24
Consensus pattern (47 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:31570 original size:22 final size:22
Alignment explanation
Indices: 31545--31599 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
31535 CATAAAGTTT
*
31545 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
31567 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
31589 TCATCTTTGAA
1 TCATCTTTGAA
31600 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:34008 original size:114 final size:114
Alignment explanation
Indices: 33808--34033 Score: 371
Period size: 114 Copynumber: 2.0 Consensus size: 114
33798 GATCATGCAG
* * *
33808 TTCATCTTTTAATTCCAATGATTGGTTCTGGAGTTCCTACCGAACCAAATCAGATAACTCAAAGA
1 TTCATCTTTTAAATCCAATGATTGGTTCTGGAGTTCATACCAAACCAAATCAGATAACTCAAAGA
* *
33873 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTTTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* * *
33922 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTTAAATCCAATGATTGGTTCTGGAGTTCATACCAAACCAAATCAGATAACTCAAAGA
*
33987 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
34034 CATGGCACTT
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTTAAATCCAATGATTGGTTCTGGAGTTCATACCAAACCAAATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:40844 original size:16 final size:15
Alignment explanation
Indices: 40809--40862 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
40799 ATTCTTGAAT
*
40809 ATAATAAATA-AATA
1 ATAATAAAAATAATA
40823 A-AATAAAAATAATA
1 ATAATAAAAATAATA
40837 ATATATAAAAATAATA
1 ATA-ATAAAAATAATA
40853 AGTAATAAAA
1 A-TAATAAAA
40863 GATTTGAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
13 7 0.20
14 6 0.17
15 1 0.03
16 19 0.54
17 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (15 bp):
ATAATAAAAATAATA
Found at i:41556 original size:124 final size:128
Alignment explanation
Indices: 41374--41740 Score: 426
Period size: 124 Copynumber: 2.8 Consensus size: 128
41364 TTAATATACA
* *
41374 TAAATAAGATATTTACTTATTTAGAAATATCAGAAAAGGGCTTCTAGGTACCTTAAGACAGCTCT
1 TAAATGAGATATTTATTTATTTA-AAATATCAGAAAAGGGCTTCTAGGTACCTTAAGACAGCTCT
* *
41439 TTTCTTCGATATTAAAAAATAAAATAAATAACTAAAAACA-TTTTC-T-TAA-AA-AATAAAAAT
65 TTTCTTTGATATTAAAAAATAAAATAAATAA-TAAAAACATTTTTCTTATAATAACAAAAAAAAT
* *
41499 TAAATGAGATATTTATTTATTTAAAATATCAAAAAATGGCTTCTAGGTGA-CTTAAGACAGCTCT
1 TAAATGAGATATTTATTTATTTAAAATATCAGAAAAGGGCTTCTAGGT-ACCTTAAGACAGCTCT
41563 TTTCTTTGATATTAAAAAA-ATAAATAAAT-ATAAAAACATTTTTCTTAAGATAATAACAAAAAA
65 TTTCTTTGATATTAAAAAATA-AAATAAATAATAAAAACATTTTTCTT---ATAATAACAAAAAA
41626 AAT
126 AAT
41629 TATTTTAATACAGTAAGATATTTATTTATTTAAAAATATCAGAAAAGGGCTTCTAGGTACCTTAA
1 TA----AAT---G--AGATATTTATTTATTT-AAAATATCAGAAAAGGGCTTCTAGGTACCTTAA
* * * *
41694 GACATCTCTTTCCTTTGATATTAATAAATAAAAATAAATATTAAAAA
56 GACAGCTCTTTTCTTTGATATTAAAAAAT-AAAATAAATAATAAAAA
41741 TGTAATAAAA
Statistics
Matches: 206, Mismatches: 12, Indels: 31
0.83 0.05 0.12
Matches are distributed among these distances:
122 8 0.04
123 7 0.03
124 64 0.31
125 22 0.11
128 3 0.01
129 2 0.01
130 10 0.05
134 3 0.01
137 1 0.00
139 17 0.08
140 54 0.26
141 8 0.04
142 7 0.03
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.35
Consensus pattern (128 bp):
TAAATGAGATATTTATTTATTTAAAATATCAGAAAAGGGCTTCTAGGTACCTTAAGACAGCTCTT
TTCTTTGATATTAAAAAATAAAATAAATAATAAAAACATTTTTCTTATAATAACAAAAAAAAT
Found at i:41920 original size:23 final size:24
Alignment explanation
Indices: 41876--41922 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
41866 AAAATTAATC
*
41876 AAATAATATATATTAATAAAAATA
1 AAATAATATATACTAATAAAAATA
*
41900 AAATAATA-ATACTAATTAAAATA
1 AAATAATATATACTAATAAAAATA
41923 TTAAACATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
AAATAATATATACTAATAAAAATA
Found at i:43462 original size:2 final size:2
Alignment explanation
Indices: 43455--43503 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
43445 TGGGCTTGTA
43455 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
43497 AT AT AT A
1 AT AT AT A
43504 ATAATAATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43509 original size:3 final size:3
Alignment explanation
Indices: 43501--43548 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
43491 ATATATATAT
* * *
43501 ATA ATA ATA ATA ATA ATA ATT TTA ATA ATA ATA ATA ATTA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
43547 AT
1 AT
43549 TTTAATGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:44678 original size:2 final size:2
Alignment explanation
Indices: 44673--44778 Score: 58
Period size: 2 Copynumber: 52.5 Consensus size: 2
44663 TATAGGTATG
* * * *
44673 TA TA TA AA TA TA TA TC TA TA TC TA TA TA TA TA TA -A AA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * *
44715 TA TA -A GTA TA TA TG TA TG TA TGA TG CA TA TA -A GTA TA TA CA
1 TA TA TA -TA TA TA TA TA TA TA T-A TA TA TA TA TA -TA TA TA TA
44756 TA -A GTA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA T
44779 CATTAAACAT
Statistics
Matches: 78, Mismatches: 17, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
1 4 0.05
2 68 0.87
3 6 0.08
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (2 bp):
TA
Found at i:50558 original size:32 final size:31
Alignment explanation
Indices: 50513--50590 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 31
50503 TGATTATCGA
* * * *
50513 ATCGGTTGTTTTTTTATTCGAATTAATATCAG
1 ATCGATTGATTTTTTAGTCG-ATAAATATCAG
* ** *
50545 ATCGATTGGTTTTTGGGTCGGTAAATATCAG
1 ATCGATTGATTTTTTAGTCGATAAATATCAG
50576 ATCGATTGATTTTTT
1 ATCGATTGATTTTTT
50591 GTTTGGCTCA
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 22 0.59
32 15 0.41
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.47
Consensus pattern (31 bp):
ATCGATTGATTTTTTAGTCGATAAATATCAG
Found at i:51306 original size:32 final size:33
Alignment explanation
Indices: 51265--51372 Score: 107
Period size: 32 Copynumber: 3.3 Consensus size: 33
51255 TCTTCCTTTT
*
51265 GGTTCGGGTTAATTTCCGTTCAG-ATTGCTTTCA
1 GGTTCGGGTTAAATTCCGTTC-GTATTGCTTTCA
*
51298 GGTT-GGGTTAAATTCGGTTCGTATTGCTTTC-
1 GGTTCGGGTTAAATTCCGTTCGTATTGCTTTCA
* * * *
51329 GGATCGGGTTAAAATCCGATTTGTATTTCTTTC-
1 GGTTCGGGTTAAATTCCG-TTCGTATTGCTTTCA
*
51362 GATTCGGGTTA
1 GGTTCGGGTTA
51373 CTTTCGGTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
31 4 0.06
32 34 0.54
33 25 0.40
ACGTcount: A:0.17, C:0.15, G:0.26, T:0.43
Consensus pattern (33 bp):
GGTTCGGGTTAAATTCCGTTCGTATTGCTTTCA
Found at i:52091 original size:24 final size:24
Alignment explanation
Indices: 52045--52093 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
52035 ATGAATTATT
*
52045 TAATTTTACATCGGCTAAGATTTTA
1 TAATTTTACATC-GCTAAAATTTTA
52070 TAATTTTACACTC-CTAAAATTTTA
1 TAATTTTACA-TCGCTAAAATTTTA
52094 ATATAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
25 10 0.45
26 2 0.09
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (24 bp):
TAATTTTACATCGCTAAAATTTTA
Found at i:63307 original size:16 final size:17
Alignment explanation
Indices: 63288--63319 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
63278 TATTACCATA
63288 ATATTAT-TTTTATATT
1 ATATTATATTTTATATT
63304 ATATTATATTTTATAT
1 ATATTATATTTTATAT
63320 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:63723 original size:17 final size:18
Alignment explanation
Indices: 63678--63724 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
63668 TGTTTATGAG
*
63678 GGAATTGGAATCTGTGAA
1 GGAATTAGAATCTGTGAA
* * *
63696 GAAATTTGAATCTGT-CA
1 GGAATTAGAATCTGTGAA
63713 GGAATTAGAATC
1 GGAATTAGAATC
63725 CAATTCCATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.30
Consensus pattern (18 bp):
GGAATTAGAATCTGTGAA
Found at i:64103 original size:62 final size:61
Alignment explanation
Indices: 63994--64111 Score: 141
Period size: 62 Copynumber: 1.9 Consensus size: 61
63984 ACTTAAAAAA
* * *
63994 ACCCGACCCGACTCGACCCGAATATCACACTTAACAAACCTGACCGAACAAAATAAAGTTTC
1 ACCCGACCCGACCCGACCCGAATATCACAATTAACAAACCCGACCGAA-AAAATAAAGTTTC
* * *
64056 ACCCGACCCGACCCGACCCGAATAT-ATGAATT-AGAAACCCGACCCGAAATAATAAA
1 ACCCGACCCGACCCGACCCGAATATCA-CAATTAACAAACCCGA-CCGAAAAAATAAA
64112 AAAATATTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
61 16 0.33
62 32 0.67
ACGTcount: A:0.40, C:0.33, G:0.13, T:0.14
Consensus pattern (61 bp):
ACCCGACCCGACCCGACCCGAATATCACAATTAACAAACCCGACCGAAAAAATAAAGTTTC
Found at i:65251 original size:75 final size:73
Alignment explanation
Indices: 65115--65402 Score: 227
Period size: 75 Copynumber: 3.9 Consensus size: 73
65105 ATATATACAT
* *
65115 ATTTTGAAACTACGTATATAATATATAGTTTTT--AATAGTTTTT-AAAAC-TATATAATATATA
1 ATTTTGAAAATA--TATATAATATATAATTTTTAAAATA-TTTTTGAAAACATATAT-ATATATA
65176 GTTTAAAAAAAAC
62 GTTT-AAAAAAAC
65189 ATTTTAGAAAATATATATAATATATAATTTTTAAAATCATTTTTGAAAACATATATAT-TATAGT
1 ATTTT-GAAAATATATATAATATATAATTTTTAAAAT-ATTTTTGAAAACATATATATATATAGT
**
65253 TT-TGAAAAC
64 TTAAAAAAAC
* * * * *
65262 ATTTTTTTGAAAACATATATATTATATAGTTTTTGAAGATATTTTTGAAACCATATATATTATAT
1 A---TTTTGAAAATATATATAATATATAATTTTT-AAAATATTTTTGAAAACATATATA-TATAT
** *
65327 AGTTTTTAAAACC
61 AGTTTAAAAAAAC
* * **
65340 ATTTTGAAAACT-TATATAATAAAT-AGTTTTAAAATCA-TTTTG-AAATTTATATAATATATAG
1 ATTTTGAAAA-TATATATAATATATAATTTTTAAAAT-ATTTTTGAAAACATATAT-ATATATAG
65401 TT
63 TT
65403 GAAATTTTTT
Statistics
Matches: 178, Mismatches: 20, Indels: 34
0.77 0.09 0.15
Matches are distributed among these distances:
72 16 0.09
73 34 0.19
74 10 0.06
75 82 0.46
76 17 0.10
77 13 0.07
78 6 0.03
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (73 bp):
ATTTTGAAAATATATATAATATATAATTTTTAAAATATTTTTGAAAACATATATATATATAGTTT
AAAAAAAC
Found at i:65390 original size:35 final size:32
Alignment explanation
Indices: 65129--65543 Score: 180
Period size: 35 Copynumber: 11.9 Consensus size: 32
65119 TGAAACTACG
* ** *
65129 TATATAATATATAGTTTTTAATAGTTTTTAAAA
1 TATATAATATATAG-TTTTAAAACATTTTGAAA
*
65162 CTATATAATATATAGTTTAAAAAAAACATTTTAGAAAATA
1 -TATATAATATATAGTTT---TAAAACATTTT-G--AA-A
*
65202 TATATAATATATAATTTTTAAAATCATTTTTGAAA
1 TATATAATATAT-AGTTTTAAAA-CA-TTTTGAAA
*
65237 -ACATATATATTATAGTTTTGAAAACATTTTTTTGAAAACA
1 TATATA-ATA-TATAGTTTT-AAAACA---TTTTG--AA-A
* * *
65277 TATATATTATATAGTTTTTGAAGATATTTTTGAAACCA
1 TATATAATATATAG-TTTT-AAAACA-TTTTG-AA--A
*
65315 TATATATTATATAGTTTTTAAAACCATTTTGAAAA
1 TATATAATATATAG-TTTTAAAA-CATTTTG-AAA
*
65350 CTTATATAATAAATAGTTTTAAAATCATTTTGAAA
1 --TATATAATATATAGTTTTAAAA-CATTTTGAAA
* ***
65385 TTTATATAATATATAG-TTGAAATTTTTTTTTGAAA
1 --TATATAATATATAGTTTTAAA--ACATTTTGAAA
* *
65420 CATAT-A-ATATAGTTTTAAAACGTTTTTGAAA
1 TATATAATATATAGTTTTAAAAC-ATTTTGAAA
* *
65451 -ACTATAACATATAGTTTTAAAACATTTTTAAAA
1 TA-TATAATATATAGTTTTAAAACA-TTTTGAAA
* * *
65484 TTATATAGTATATGGTTTTGAAAATATTTTTG-AA
1 -TATATAATATATAGTTTT-AAAACA-TTTTGAAA
65518 -ATAT-ATATATAGTTTTAAAACATTTT
1 TATATAATATATAGTTTTAAAACATTTT
65544 TATATGTAGT
Statistics
Matches: 308, Mismatches: 38, Indels: 75
0.73 0.09 0.18
Matches are distributed among these distances:
29 4 0.01
30 6 0.02
31 28 0.09
32 11 0.04
33 29 0.09
34 38 0.12
35 48 0.16
36 31 0.10
37 36 0.12
38 31 0.10
39 25 0.08
40 17 0.06
41 4 0.01
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (32 bp):
TATATAATATATAGTTTTAAAACATTTTGAAA
Found at i:65579 original size:18 final size:19
Alignment explanation
Indices: 65556--65600 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
65546 TATGTAGTAT
*
65556 TTTATTTTTTATTT-CTTG
1 TTTATTTTTTATTTACTCG
*
65574 TTTA-TTATTATTTACTCG
1 TTTATTTTTTATTTACTCG
65592 TTT-TTTTTT
1 TTTATTTTTT
65601 TTTTTTAGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTATTTTTTATTTACTCG
Found at i:74708 original size:43 final size:43
Alignment explanation
Indices: 74661--74755 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 43
74651 TTTATCAGAA
*
74661 AAACGCCGCAGTAGG-GATTGAGATTTAGCGGCGTTTTACTTAC
1 AAACGCCGCAGTAGGTG-TCGAGATTTAGCGGCGTTTTACTTAC
* * * *
74704 AAACGCTGCAGTAGGTGTCGATATTTTGCGGCGTTTTTCTTAC
1 AAACGCCGCAGTAGGTGTCGAGATTTAGCGGCGTTTTACTTAC
74747 AAACGCCGC
1 AAACGCCGC
74756 TAAATGTTGG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 44 0.98
44 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.29
Consensus pattern (43 bp):
AAACGCCGCAGTAGGTGTCGAGATTTAGCGGCGTTTTACTTAC
Found at i:75149 original size:21 final size:21
Alignment explanation
Indices: 75107--75171 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
75097 TGATATGTTG
* * *
75107 CCGCTGCTTCTTTCTCTACTT
1 CCGCTGCTGCTCTCTCTGCTT
*
75128 CCGCTGTTGCTCTGC-CTGCTT
1 CCGCTGCTGCTCT-CTCTGCTT
75149 CCGCTGCTGCTCTCTCTGCTT
1 CCGCTGCTGCTCTCTCTGCTT
75170 CC
1 CC
75172 CTTGCTTCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.03
21 35 0.95
22 1 0.03
ACGTcount: A:0.02, C:0.42, G:0.17, T:0.40
Consensus pattern (21 bp):
CCGCTGCTGCTCTCTCTGCTT
Found at i:80308 original size:23 final size:23
Alignment explanation
Indices: 80275--80365 Score: 119
Period size: 23 Copynumber: 4.0 Consensus size: 23
80265 ATTATTATAT
*
80275 GGCACTACGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
*
80298 GGCACTCCGGTGCAATTTTACGC
1 GGCACTCCGGTGCAATTCTACGC
* *
80321 GGTACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
* * *
80344 GGCACTTCAGTGCAATTATACG
1 GGCACTCCGGTGCAATTCTACG
80366 ATTTGTGGTG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.26
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:86511 original size:63 final size:62
Alignment explanation
Indices: 86444--86595 Score: 189
Period size: 63 Copynumber: 2.4 Consensus size: 62
86434 GAAGGTGTAC
86444 CGATGCACATGAAGTGCATCGATGCACCCCATTAAATACAAACATCGAAT-GCCATCGATGCAT
1 CGATGCACATGAAGTGCATCGATGCACCCCATTAAATAC-AACATCGAATAG-CATCGATGCAT
* * * * **
86507 CGATGCATAAGGAGTGCATCGATGCACCCCATTAAATACAACATCGAATAGGATTTATGCAT
1 CGATGCACATGAAGTGCATCGATGCACCCCATTAAATACAACATCGAATAGCATCGATGCAT
** *
86569 CGATGCATGGTGTAGTGCATCGATGCA
1 CGATGCA-CATGAAGTGCATCGATGCA
86596 TACCTCCATT
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
62 25 0.32
63 52 0.68
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (62 bp):
CGATGCACATGAAGTGCATCGATGCACCCCATTAAATACAACATCGAATAGCATCGATGCAT
Found at i:87216 original size:23 final size:23
Alignment explanation
Indices: 87190--87244 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
87180 ATGGCATTAC
87190 GGTGCAATTCTACGCGGCACTCT
1 GGTGCAATTCTACGCGGCACTCT
* *
87213 GGTGCAATTCTACGTGGCACTTT
1 GGTGCAATTCTACGCGGCACTCT
*
87236 GGTGTAATT
1 GGTGCAATT
87245 ATACAAGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (23 bp):
GGTGCAATTCTACGCGGCACTCT
Found at i:93505 original size:40 final size:40
Alignment explanation
Indices: 93451--93551 Score: 123
Period size: 41 Copynumber: 2.5 Consensus size: 40
93441 CGTTTATACA
93451 AAAAACGCCACTATTGATTA-CACTATTATGGCGTTTGTCT
1 AAAAACG-CACTATTGATTAGCACTATTATGGCGTTTGTCT
* * * * *
93491 AAAAATGTCACTATTGATTAGTACTATTGTTGTGTTTGTCT
1 AAAAACG-CACTATTGATTAGCACTATTATGGCGTTTGTCT
93532 AAAAACGCAACTATTGATTA
1 AAAAACGC-ACTATTGATTA
93552 TATTATTGCG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 19 0.37
41 33 0.63
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (40 bp):
AAAAACGCACTATTGATTAGCACTATTATGGCGTTTGTCT
Found at i:94096 original size:30 final size:31
Alignment explanation
Indices: 94060--94120 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
94050 ATCAAAATTT
94060 CCCAAG-AAATTGCATCCAAACTCTCCACTA
1 CCCAAGAAAATTGCATCCAAACTCTCCACTA
*
94090 CCCAAGAAAATTGTATCCAAACTCTCCACTA
1 CCCAAGAAAATTGCATCCAAACTCTCCACTA
94121 AGTTCCTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 6 0.21
31 23 0.79
ACGTcount: A:0.38, C:0.34, G:0.07, T:0.21
Consensus pattern (31 bp):
CCCAAGAAAATTGCATCCAAACTCTCCACTA
Found at i:94782 original size:20 final size:20
Alignment explanation
Indices: 94757--94794 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
94747 TTTGGTTCAC
*
94757 AGAATGTACGATTACCAGTG
1 AGAATGTAAGATTACCAGTG
94777 AGAATGTAAGATTACCAG
1 AGAATGTAAGATTACCAG
94795 GAATAGGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGTAAGATTACCAGTG
Done.