Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007137.1 Hibiscus syriacus cultivar Beakdansim tig00018669_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: 68405
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2667 original size:15 final size:15
Alignment explanation
Indices: 2647--2676 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2637 CTAGATTTTT
2647 AAATTCTAAAGAAAA
1 AAATTCTAAAGAAAA
2662 AAATTCTAAAGAAAA
1 AAATTCTAAAGAAAA
2677 CAATATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (15 bp):
AAATTCTAAAGAAAA
Found at i:11920 original size:19 final size:18
Alignment explanation
Indices: 11882--11920 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
11872 GTTCATTCAC
* *
11882 TTAAAATTTATAACTTCG
1 TTAAAATTTATAAATCCG
11900 TTAAAATTTTATAAATCCG
1 TTAAAA-TTTATAAATCCG
11919 TT
1 TT
11921 CCCCCAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.46
Consensus pattern (18 bp):
TTAAAATTTATAAATCCG
Found at i:13976 original size:30 final size:31
Alignment explanation
Indices: 13921--14000 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
13911 ATCATCGAGC
* * *
13921 TTAACGAGCAACTAATCGAGCAAC-AAGTTTT
1 TTAACGAGC-ACGAATCGAGAAACAAAATTTT
*
13952 TTAACGAGCACGATTCGAGAAACAAAATTTT
1 TTAACGAGCACGAATCGAGAAACAAAATTTT
* *
13983 TTAACGAACACGAGTCGA
1 TTAACGAGCACGAATCGA
14001 CCATTGTCTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 11 0.26
31 31 0.74
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (31 bp):
TTAACGAGCACGAATCGAGAAACAAAATTTT
Found at i:15702 original size:15 final size:15
Alignment explanation
Indices: 15678--15712 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
15668 GTAGCAGTTT
*
15678 AAAACGTATTTTTCA
1 AAAACATATTTTTCA
15693 AAAACATATTTTTCA
1 AAAACATATTTTTCA
15708 AAAAC
1 AAAAC
15713 TATAGTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (15 bp):
AAAACATATTTTTCA
Found at i:15982 original size:66 final size:66
Alignment explanation
Indices: 15853--15982 Score: 179
Period size: 66 Copynumber: 2.0 Consensus size: 66
15843 TAGGTCCATA
* * * * **
15853 AGGAATTACCAGTCGATGTTGAACCTATACAAGGAATTACCAACATCGACTGAACCTGTCAGAGA
1 AGGAATTACCAGTCGATGCTGAACATATACAAAGAATTACCAACAACGACTGAACCTACCAGAGA
15918 T
66 T
* * *
15919 AGGAATTACCAGTCGGTGCTGAACATATACAAAGAATTACCAGCAACGATTGAACCTACCAGAG
1 AGGAATTACCAGTCGATGCTGAACATATACAAAGAATTACCAACAACGACTGAACCTACCAGAG
15983 TCTTCATACC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (66 bp):
AGGAATTACCAGTCGATGCTGAACATATACAAAGAATTACCAACAACGACTGAACCTACCAGAGA
T
Found at i:17826 original size:22 final size:22
Alignment explanation
Indices: 17800--17844 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
17790 AAAGTCAACG
* * *
17800 GTCAACGGTCTGACCGGTCAAA
1 GTCAACAGTCAGACCAGTCAAA
17822 GTCAACAGTCAGACCAGTCAAA
1 GTCAACAGTCAGACCAGTCAAA
17844 G
1 G
17845 GGTTGACTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (22 bp):
GTCAACAGTCAGACCAGTCAAA
Found at i:18685 original size:2 final size:2
Alignment explanation
Indices: 18671--18721 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
18661 TTGAGGTGTG
*
18671 AT AT AT CT A- 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
18712 AT AT AT AT AT
1 AT AT AT AT AT
18722 TAAATGTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19480 original size:17 final size:18
Alignment explanation
Indices: 19458--19499 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
19448 TAATAGTGAG
*
19458 TTATTATAAATT-TGTTT
1 TTATTATAAATTATATTT
19475 TTATTAT-AATTATATTT
1 TTATTATAAATTATATTT
19492 TTATTATA
1 TTATTATA
19500 GTTTAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTATTATAAATTATATTT
Found at i:42380 original size:30 final size:31
Alignment explanation
Indices: 42345--42412 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 31
42335 ATTTTAATCG
* *
42345 AATTTAGGAA-TAAATTAATATTTTATTTAA
1 AATTTAGGAATTAAATTAATATTCTATATAA
*
42375 AATTTA-AAATTAAATTAATATTCTATATAA
1 AATTTAGGAATTAAATTAATATTCTATATAA
42405 AATTTAGG
1 AATTTAGG
42413 GGACAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 2 0.06
30 30 0.94
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (31 bp):
AATTTAGGAATTAAATTAATATTCTATATAA
Found at i:48336 original size:3 final size:3
Alignment explanation
Indices: 48328--48372 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
48318 TTTGTAAATC
* * *
48328 AAT AAT AAT AAT AGT AAT AAT AAT AAT -AT AAC GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
48373 TTATTTTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:48841 original size:133 final size:135
Alignment explanation
Indices: 48583--48864 Score: 424
Period size: 133 Copynumber: 2.1 Consensus size: 135
48573 GGTGACTCGA
* * *
48583 CTCCTACGTGATGAGGATATCTGGTCGGGGGATGACACTGCTCATACGTGATGAAGAGTTCTTGG
1 CTCCTACGTGATGAAGAGATCTGGTCGGGGGATGACACGGCTCATACGTGATGAAGAGTTCTTGG
* * * *
48648 CCATCTTTAGGAAGGGTGATAACTCAATTCCTGCGTGATGAGGACGGCTGGTTATCTATGGTTGA
66 CCATCTTTAGGAAGGGTGATAACTCAATTCCTACATGATGAGGACGACTGATTATCTATGGTTGA
48713 CACAG
131 CACAG
* * *
48718 CTCCTACGTGATGAAGAGATTTGGTTGGTGGATGACACGGCTCATACGTGATGAAGAGTTC-T-G
1 CTCCTACGTGATGAAGAGATCTGGTCGGGGGATGACACGGCTCATACGTGATGAAGAGTTCTTGG
* * *
48781 TCATCTTTAGGAAGGGTGATAACTCAGTTCTTACATGATGAGGACGACTGATTATCTATGGTTGA
66 CCATCTTTAGGAAGGGTGATAACTCAATTCCTACATGATGAGGACGACTGATTATCTATGGTTGA
*
48846 CACGG
131 CACAG
48851 CTCCTACGTGATGA
1 CTCCTACGTGATGA
48865 GGATGGCTGT
Statistics
Matches: 133, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
133 77 0.58
134 1 0.01
135 55 0.41
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (135 bp):
CTCCTACGTGATGAAGAGATCTGGTCGGGGGATGACACGGCTCATACGTGATGAAGAGTTCTTGG
CCATCTTTAGGAAGGGTGATAACTCAATTCCTACATGATGAGGACGACTGATTATCTATGGTTGA
CACAG
Found at i:48926 original size:28 final size:28
Alignment explanation
Indices: 48893--48955 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
48883 AGGGATAAGA
** * *
48893 GTTTCAAGGGAAACCGACTCAAAGATTT
1 GTTTCAAAAGAAACCAACCCAAAGATTT
*
48921 GTTTCAAAAGAAACCAACCCAAATATTT
1 GTTTCAAAAGAAACCAACCCAAAGATTT
48949 GTTTCAA
1 GTTTCAA
48956 CAAACTCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (28 bp):
GTTTCAAAAGAAACCAACCCAAAGATTT
Found at i:49096 original size:66 final size:63
Alignment explanation
Indices: 48985--49167 Score: 197
Period size: 66 Copynumber: 2.8 Consensus size: 63
48975 TTTTAAAAGC
* *
48985 AACTGTCTCAAAAGAGACAAAATTCGTTTAAAGGGAAACGACTCAAAGATGACGTTT-AAAGGGA
1 AACTGTCTCAAAAGAGACAAAATT-GTTTTAAGGGAAACGTCTCAAAGATGACGTTTCAAA-GGA
** * ** *
49049 AACTGTCTCAAGCGAGACAAAACTTGTTTTTAAGGGAAATGTTCTCAAAGATTGGTGTTTCATAG
1 AACTGTCTCAAAAGAGACAAAA-TTG-TTTTAAGGGAAACG-TCTCAAAGA-TGACGTTTCAAAG
49114 GA
62 GA
* *
49116 AACTGTCTCAAATGAGACAAAATTCATTTTAAGGGAAACGATCTCAAAGATG
1 AACTGTCTCAAAAGAGACAAAATT-GTTTTAAGGGAAACG-TCTCAAAGATG
49168 TTTGTCGTGT
Statistics
Matches: 100, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
64 21 0.21
65 16 0.16
66 32 0.32
67 29 0.29
68 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (63 bp):
AACTGTCTCAAAAGAGACAAAATTGTTTTAAGGGAAACGTCTCAAAGATGACGTTTCAAAGGA
Found at i:49459 original size:28 final size:26
Alignment explanation
Indices: 49426--49496 Score: 97
Period size: 26 Copynumber: 2.6 Consensus size: 26
49416 CCTCAGAGAT
*
49426 GATTTTGTTAAGAGAAACAAACTCAAA
1 GATTTT-TCAAGAGAAACAAACTCAAA
*
49453 GATTTTTCAAAAGAAACAAACTCAAA
1 GATTTTTCAAGAGAAACAAACTCAAA
49479 GATTTATTTCAAGAGAAA
1 GA-TT-TTTCAAGAGAAA
49497 TTGTCTCAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 20 0.51
27 8 0.21
28 11 0.28
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.27
Consensus pattern (26 bp):
GATTTTTCAAGAGAAACAAACTCAAA
Found at i:49612 original size:29 final size:29
Alignment explanation
Indices: 49579--49686 Score: 123
Period size: 28 Copynumber: 3.7 Consensus size: 29
49569 GAGAGACACA
* *
49579 ATTTTGTTTCCAAAGAAATAGACTCAAAG
1 ATTTTGTTTCAAAAGAAACAGACTCAAAG
49608 ATTTTTTTTGTTTCAAAAGAAACA-ACTCAAAG
1 A----TTTTGTTTCAAAAGAAACAGACTCAAAG
*
49640 ATTTT-TATTCAAAAGGAACAGACTCAAAG
1 ATTTTGT-TTCAAAAGAAACAGACTCAAAG
49669 A-TTTGTTTCAAAAGAAAC
1 ATTTTGTTTCAAAAGAAAC
49687 TGTTTCGATA
Statistics
Matches: 68, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
27 1 0.01
28 30 0.44
29 11 0.16
32 9 0.13
33 17 0.25
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (29 bp):
ATTTTGTTTCAAAAGAAACAGACTCAAAG
Found at i:49613 original size:63 final size:63
Alignment explanation
Indices: 49456--49614 Score: 205
Period size: 64 Copynumber: 2.5 Consensus size: 63
49446 ACTCAAAGAT
*
49456 TTTTCAAAAGAAACAAACTCAAAGATTTATTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTCA
1 TTTTC-AAAGAAACAAACTCAAAGATTT-TTTCAAAAGAAATTGTCTCAAGAGAGACAAAATTCA
* * *
49521 TTTT-AAGAGAAACAAACTCAAAGATTTTTTCAAAAGAAATTGTCTTAAGAGAGACACAATT-T
1 TTTTCAA-AGAAACAAACTCAAAGATTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAATTCA
* *
49583 TGTTTCCAAAGAAATAGACTCAAAGATTTTTT
1 T-TTT-CAAAGAAACAAACTCAAAGATTTTTT
49615 TTGTTTCAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
62 1 0.01
63 36 0.43
64 41 0.49
65 6 0.07
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.30
Consensus pattern (63 bp):
TTTTCAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAATTCA
Found at i:49641 original size:32 final size:33
Alignment explanation
Indices: 49580--49672 Score: 115
Period size: 33 Copynumber: 3.0 Consensus size: 33
49570 AGAGACACAA
* *
49580 TTTTGTTTCCAAAGAAATAGACTCAAAGATTTT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGATTTT
49613 TTTTGTTTCAAAAGAAACA-ACTCAAAGA---T
1 TTTTGTTTCAAAAGAAACAGACTCAAAGATTTT
* *
49642 TTTT-ATTCAAAAGGAACAGACTCAAAGATTT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGATTT
49673 GTTTCAAAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
28 12 0.23
29 14 0.27
32 9 0.17
33 17 0.33
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
TTTTGTTTCAAAAGAAACAGACTCAAAGATTTT
Found at i:50018 original size:105 final size:105
Alignment explanation
Indices: 49804--50105 Score: 383
Period size: 105 Copynumber: 2.9 Consensus size: 105
49794 CGGTTTTGAA
* * * * * *
49804 AATCTCAAGTGAGATTAATTTTGTTTCAAATAAAACAACTTTGAAATTTGTAT-TCT-GAGGGAA
1 AATCTCAAGTGAGATTAATTTTGTTTCAAATGAAGCAAATTCGAAATTTGTATCT-TAAAGGAAA
* * *
49867 AATGTCTCAAGTGAGACGAAATTTGTTTTGAAATAAACAAC
65 AATGTCTCAAGCGAGAAGAAATTTGTTTTGAAAGAAACAAC
** *
49908 AATCTCAAGTGAGATTAATTTTGTTTCATTTGAAGCAAATTCGAAATTTATATCTTAAAGGAAAA
1 AATCTCAAGTGAGATTAATTTTGTTTCAAATGAAGCAAATTCGAAATTTGTATCTTAAAGGAAAA
* *
49973 ATATCTCAAGCAAGAAGAAATTTGTTTTGAAAGAAACAAC
66 ATGTCTCAAGCGAGAAGAAATTTGTTTTGAAAGAAACAAC
* * * * **
50013 AATCTCAAGTGAGATTAATTTTGTTTTAAGTGAGGCAAATTCAAAATTTGTATCACAAAGGAAAA
1 AATCTCAAGTGAGATTAATTTTGTTTCAAATGAAGCAAATTCGAAATTTGTATCTTAAAGGAAAA
* *
50078 ATGTCTCAAGCGAGATGAAGTTTGTTTT
66 ATGTCTCAAGCGAGAAGAAATTTGTTTT
50106 AAGATAAATT
Statistics
Matches: 170, Mismatches: 26, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
104 47 0.28
105 123 0.72
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (105 bp):
AATCTCAAGTGAGATTAATTTTGTTTCAAATGAAGCAAATTCGAAATTTGTATCTTAAAGGAAAA
ATGTCTCAAGCGAGAAGAAATTTGTTTTGAAAGAAACAAC
Found at i:50503 original size:16 final size:16
Alignment explanation
Indices: 50464--50497 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
50454 TGTAACATGT
*
50464 ATGTATGTGTTGATGC
1 ATGTATGTATTGATGC
50480 ATGTATGTATTGATGC
1 ATGTATGTATTGATGC
50496 AT
1 AT
50498 TGATGTGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44
Consensus pattern (16 bp):
ATGTATGTATTGATGC
Found at i:58168 original size:3 final size:3
Alignment explanation
Indices: 58160--58204 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
58150 AATGTAAATC
* * *
58160 AAT AAT AAT AAT AGT AAT AAT AAT AAT -AT AAC GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
58205 TTATTTAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:59018 original size:13 final size:13
Alignment explanation
Indices: 59000--59038 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
58990 TTTTCTAGTA
59000 ATTTAATTTTTAT
1 ATTTAATTTTTAT
59013 ATTTAATATTTTTAT
1 ATTT-A-ATTTTTAT
*
59028 ATTCAATTTTT
1 ATTTAATTTTT
59039 GACATATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 10 0.43
14 2 0.09
15 11 0.48
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTAATTTTTAT
Found at i:59025 original size:15 final size:15
Alignment explanation
Indices: 59005--59065 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
58995 TAGTAATTTA
59005 ATTTTTATATTTAAT
1 ATTTTTATATTTAAT
*
59020 ATTTTTATATTCAAT
1 ATTTTTATATTTAAT
*
59035 -TTTTGACATATTTGAAT
1 ATTTT--TATATTT-AAT
*
59052 AATTTTATATTTAA
1 ATTTTTATATTTAA
59066 AATAAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
14 4 0.11
15 16 0.43
16 11 0.30
17 3 0.08
18 3 0.08
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (15 bp):
ATTTTTATATTTAAT
Found at i:59664 original size:6 final size:6
Alignment explanation
Indices: 59653--59683 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
59643 GACACGTATT
59653 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
59684 GACGAGACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:59690 original size:5 final size:5
Alignment explanation
Indices: 59680--59733 Score: 108
Period size: 5 Copynumber: 10.8 Consensus size: 5
59670 GACCACGACC
59680 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG
59730 ACGA
1 ACGA
59734 CGGCGGCGGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 49 1.00
ACGTcount: A:0.41, C:0.20, G:0.39, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:60394 original size:41 final size:41
Alignment explanation
Indices: 60330--60426 Score: 149
Period size: 41 Copynumber: 2.4 Consensus size: 41
60320 TTTACTATAG
60330 ACTATCGCAACGCGAAATAGAAAATCGCAACGACACTGTAC
1 ACTATCGCAACGCGAAATAGAAAATCGCAACGACACTGTAC
* * * * *
60371 ACTACCGCAATGCGAGATGGAAAATCGCAATGACACTGTAC
1 ACTATCGCAACGCGAAATAGAAAATCGCAACGACACTGTAC
60412 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
60427 TTTTCAACTA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.38, C:0.27, G:0.20, T:0.15
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATAGAAAATCGCAACGACACTGTAC
Found at i:60442 original size:62 final size:62
Alignment explanation
Indices: 60371--60582 Score: 230
Period size: 62 Copynumber: 3.3 Consensus size: 62
60361 GACACTGTAC
* * *
60371 ACTACCGCAATGCGAGATGGAAAATCGCAATGACACTGTACACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAATGACACTGTACACTATCGCAACGCGATTTTCA
* * *
60433 ACTATCGCAACGCGAAATGAAAAATCGCAACGATCGCAATGACTGTACACTATCGCAATGCGATT
1 ACTATCGCAACGCGAAATGGAAAATCGC-A--AT-G--A-CACTGTACACTATCGCAACGCGATT
60498 TTCA
59 TTCA
* * * * *
60502 TCTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAGACTATCGCAACGAC-ACTGT-A
1 ACTATCGCAACGCGAAATGGAAAATCGCAATGACACTGTACACTATCGCAACG-CGATTTTCA
60563 GACTATCGCAACGCGAAATG
1 -ACTATCGCAACGCGAAATG
60583 CAACGCGAAT
Statistics
Matches: 126, Mismatches: 15, Indels: 18
0.79 0.09 0.11
Matches are distributed among these distances:
61 1 0.01
62 62 0.49
63 3 0.02
65 3 0.02
66 2 0.02
68 2 0.02
69 53 0.42
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (62 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAATGACACTGTACACTATCGCAACGCGATTTTCA
Found at i:60507 original size:69 final size:70
Alignment explanation
Indices: 60394--60534 Score: 239
Period size: 69 Copynumber: 2.0 Consensus size: 70
60384 GAGATGGAAA
60394 ATCGCAATGACACTGTACACTATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAAATC
1 ATCGCAATGA-ACTGTACACTATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAAATC
60459 GCAACG
65 GCAACG
* * *
60465 ATCGCAATG-ACTGTACACTATCGCAATGCGATTTTCATCTATCGCAACGCGAAATGGAAAATCG
1 ATCGCAATGAACTGTACACTATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAAATCG
60529 CAACG
66 CAACG
60534 A
1 A
60535 CACTGTAGAC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 58 0.87
71 9 0.13
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (70 bp):
ATCGCAATGAACTGTACACTATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAAATCG
CAACG
Found at i:60551 original size:21 final size:21
Alignment explanation
Indices: 60525--60575 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
60515 GAAATGGAAA
60525 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
60546 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
60567 ATCGCAACG
1 ATCGCAACG
60576 CGAAATGCAA
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:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGACACTGTAGACT
Found at i:68007 original size:2 final size:2
Alignment explanation
Indices: 67965--67990 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
67955 TACTTCTTCC
67965 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
67991 TACTGCAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.