Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005134.1 Hibiscus syriacus cultivar Beakdansim tig00011558_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: 97707
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:5871 original size:22 final size:21
Alignment explanation
Indices: 5820--5871 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 21
5810 AAAAATCAGC
*
5820 AAAAAAAAGTCAAGCACTCTA
1 AAAAAAAAGTCAAGCACTCCA
5841 AAAAGAAAAGTCAAGCACTCCA
1 AAAA-AAAAGTCAAGCACTCCA
5863 AAAGAAAAA
1 AAA-AAAAA
5872 AACAAAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 4 0.14
22 23 0.82
23 1 0.04
ACGTcount: A:0.62, C:0.17, G:0.12, T:0.10
Consensus pattern (21 bp):
AAAAAAAAGTCAAGCACTCCA
Found at i:10513 original size:24 final size:25
Alignment explanation
Indices: 10478--10532 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
10468 ACTTGGAGCC
*
10478 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
10502 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
10526 TCAAGTG
1 TCAAGTG
10533 GCATAACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:16474 original size:14 final size:14
Alignment explanation
Indices: 16455--16497 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
16445 ATAAGATACT
* *
16455 ATCTATTCATCATC
1 ATCTATCCATCACC
16469 ATCTATCCATCACC
1 ATCTATCCATCACC
*
16483 ATC-CTCCATCACC
1 ATCTATCCATCACC
16496 AT
1 AT
16498 TCACGCCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.28, C:0.40, G:0.00, T:0.33
Consensus pattern (14 bp):
ATCTATCCATCACC
Found at i:18595 original size:22 final size:22
Alignment explanation
Indices: 18569--18610 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
18559 TATTTATAGT
18569 TATGAAGATGA-TATTATGAATG
1 TATGAAG-TGATTATTATGAATG
*
18591 TATGAAGTTATTATTATGAA
1 TATGAAGTGATTATTATGAA
18611 CCACATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40
Consensus pattern (22 bp):
TATGAAGTGATTATTATGAATG
Found at i:19531 original size:15 final size:15
Alignment explanation
Indices: 19511--19564 Score: 108
Period size: 15 Copynumber: 3.6 Consensus size: 15
19501 CATTTCTTTC
19511 CATTTCCTTACTTAT
1 CATTTCCTTACTTAT
19526 CATTTCCTTACTTAT
1 CATTTCCTTACTTAT
19541 CATTTCCTTACTTAT
1 CATTTCCTTACTTAT
19556 CATTTCCTT
1 CATTTCCTT
19565 TCTTCTTCCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.19, C:0.28, G:0.00, T:0.54
Consensus pattern (15 bp):
CATTTCCTTACTTAT
Found at i:28764 original size:19 final size:20
Alignment explanation
Indices: 28723--28773 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
28713 GAAACCCCTT
*
28723 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
28743 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
28762 TGAAGATACATG
1 TGAAAATACATG
28774 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:31695 original size:11 final size:10
Alignment explanation
Indices: 31644--31695 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
31634 CTTTGAATTC
*
31644 TTTTCTTTTC
1 TTTTCTTTTT
31654 TTTTCTTCTTT
1 TTTTCTT-TTT
*
31665 TCTTCTTCTTT
1 TTTTCTT-TTT
*
31676 TTGTCTTTTT
1 TTTTCTTTTT
*
31686 CTTTCTTTTT
1 TTTTCTTTTT
31696 GCACTCCAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:31696 original size:18 final size:18
Alignment explanation
Indices: 31642--31696 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
31632 GGCTTTGAAT
31642 TCTTTTCTTTTCTTTTCT-
1 TCTTTTCTTTTCTTTT-TG
31660 TCTTTTCTTCTTCTTTTTG
1 TCTTTTCTT-TTCTTTTTG
31679 TCTTTT-TCTTTCTTTTTG
1 TCTTTTCT-TTTCTTTTTG
31697 CACTCCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 20 0.59
19 14 0.41
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (18 bp):
TCTTTTCTTTTCTTTTTG
Found at i:32442 original size:19 final size:20
Alignment explanation
Indices: 32401--32451 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
32391 GAAACCCCTT
*
32401 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
32421 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
32440 TGAAGATACATG
1 TGAAAATACATG
32452 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:35708 original size:36 final size:35
Alignment explanation
Indices: 35615--35725 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
35605 TTGGTGGTTA
* * *
35615 TATAGGCGTGAAATGGTGATAGAAGATGGTAAGGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTAATGT
* * * * *
35650 TATAGTCTTGCAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTAATGT
35685 TATAGGCGTGAAAATGGTGATGGAAGATGGTAATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTAATGT
35721 T-TAGG
1 TATAGG
35726 TAGTATCTTA
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
35 39 0.63
36 23 0.37
ACGTcount: A:0.32, C:0.04, G:0.35, T:0.29
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTAATGT
Found at i:38189 original size:19 final size:20
Alignment explanation
Indices: 38148--38198 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
38138 GAAACCCCTT
*
38148 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
38168 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
38187 TGAAGATACATG
1 TGAAAATACATG
38199 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:42370 original size:19 final size:20
Alignment explanation
Indices: 42329--42379 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
42319 GAAACCCCTT
*
42329 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
42349 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
42368 TGAAGATACATG
1 TGAAAATACATG
42380 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:45865 original size:8 final size:8
Alignment explanation
Indices: 45854--45878 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
45844 GAGAAAAATC
45854 AGAAAAGA
1 AGAAAAGA
45862 AGAAAAGA
1 AGAAAAGA
45870 AGAAAAGA
1 AGAAAAGA
45878 A
1 A
45879 AAGAATAAGA
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:61811 original size:33 final size:32
Alignment explanation
Indices: 61749--61812 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
61739 GCAAAAATTA
*
61749 AAGAAAGAAATGATTAAAATAGAATATGAAAG
1 AAGAAAGAAATGATTAAAAAAGAATATGAAAG
61781 AAGAAAGGAAATGA-TAAGAAAAGGAA-ATGAAA
1 AAGAAA-GAAATGATTAA-AAAA-GAATATGAAA
61813 TGGATAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 9 0.32
33 16 0.57
34 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.14
Consensus pattern (32 bp):
AAGAAAGAAATGATTAAAAAAGAATATGAAAG
Found at i:61812 original size:21 final size:21
Alignment explanation
Indices: 61783--61822 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
61773 TATGAAAGAA
61783 GAAAGGAAAT-GATAAGAAAAG
1 GAAAGGAAATGGAT-AGAAAAG
*
61804 GAAATGAAATGGATAGAAA
1 GAAAGGAAATGGATAGAAA
61823 TGTTATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (21 bp):
GAAAGGAAATGGATAGAAAAG
Found at i:65025 original size:19 final size:20
Alignment explanation
Indices: 65001--65051 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
64991 CGGCCAAGAG
* *
65001 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
65020 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
*
65040 CCTGTATTTTCA
1 CATGTATTTTCA
65052 AAGGGGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:65445 original size:22 final size:21
Alignment explanation
Indices: 65404--65447 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
65394 CACCATCTCC
*
65404 ACTTCATCATCAACATCATCA
1 ACTTCATCATCAACACCATCA
*
65425 ACTTCATCCATCAAGACCATCA
1 ACTTCAT-CATCAACACCATCA
65447 A
1 A
65448 TTCCGCATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.39, C:0.34, G:0.02, T:0.25
Consensus pattern (21 bp):
ACTTCATCATCAACACCATCA
Found at i:65774 original size:17 final size:17
Alignment explanation
Indices: 65746--65795 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 17
65736 AATTGGAGTG
65746 CAAAAAGAAAGAAAAAGA-
1 CAAAAAG-AAGAAAAA-AT
65764 CAAAAAGAAGAAAAAAT
1 CAAAAAGAAGAAAAAAT
65781 CAGAAAAGAAGAAAA
1 CA-AAAAGAAGAAAA
65796 GAAAAGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.03
17 10 0.33
18 19 0.63
ACGTcount: A:0.76, C:0.06, G:0.16, T:0.02
Consensus pattern (17 bp):
CAAAAAGAAGAAAAAAT
Found at i:65800 original size:21 final size:19
Alignment explanation
Indices: 65746--65800 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 19
65736 AATTGGAGTG
65746 CAAAAAG-AAAGAAAAAGA
1 CAAAAAGAAAAGAAAAAGA
65764 CAAAAAGAAGAA-AAAATCAGA
1 CAAAAAGAA-AAGAAAA--AGA
65785 -AAAGAAGAAAAGAAAA
1 CAAA-AAGAAAAGAAAA
65801 GAAATTCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
18 7 0.23
19 5 0.16
20 7 0.23
21 12 0.39
ACGTcount: A:0.76, C:0.05, G:0.16, T:0.02
Consensus pattern (19 bp):
CAAAAAGAAAAGAAAAAGA
Found at i:65803 original size:18 final size:18
Alignment explanation
Indices: 65766--65804 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
65756 GAAAAAGACA
*
65766 AAAAGAAGAAAAAATCAG
1 AAAAGAAGAAAAAATAAG
65784 AAAAGAAGAAAAGAA-AAG
1 AAAAGAAGAAAA-AATAAG
65802 AAA
1 AAA
65805 TTCAAAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (18 bp):
AAAAGAAGAAAAAATAAG
Found at i:69156 original size:19 final size:20
Alignment explanation
Indices: 69132--69182 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
69122 CGGCCAAGAG
* *
69132 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
69151 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
*
69171 CCTGTATTTTCA
1 CATGTATTTTCA
69183 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:69576 original size:22 final size:21
Alignment explanation
Indices: 69535--69578 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
69525 CACCATCTCC
*
69535 ACTTCATCATCAACATCATCA
1 ACTTCATCATCAACACCATCA
*
69556 ACTTCATCCATCAAGACCATCA
1 ACTTCAT-CATCAACACCATCA
69578 A
1 A
69579 TTCCGCAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.39, C:0.34, G:0.02, T:0.25
Consensus pattern (21 bp):
ACTTCATCATCAACACCATCA
Found at i:75345 original size:22 final size:21
Alignment explanation
Indices: 75317--75362 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
75307 AAAATAAATT
*
75317 AAAACCTTATCAG-AACACTCAC
1 AAAACCTCA-CAGTAACACTC-C
75339 AAAACCTCACAGTAACACTCC
1 AAAACCTCACAGTAACACTCC
75360 AAA
1 AAA
75363 GAAATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.48, C:0.33, G:0.04, T:0.15
Consensus pattern (21 bp):
AAAACCTCACAGTAACACTCC
Found at i:76114 original size:16 final size:15
Alignment explanation
Indices: 76095--76133 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
76085 TTTGATAATT
76095 AAGAAATGAAAATGGA
1 AAGAAATG-AAATGGA
*
76111 AAGAATTGAAATGGA
1 AAGAAATGAAATGGA
76126 AAGAAATG
1 AAGAAATG
76134 TTATCAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (15 bp):
AAGAAATGAAATGGA
Found at i:76368 original size:34 final size:33
Alignment explanation
Indices: 76279--76381 Score: 134
Period size: 35 Copynumber: 3.0 Consensus size: 33
76269 GGTGGTTATA
* * *
76279 TAGGCGTGAAATGGTGATAGAAGATGGTAAGGAT
1 TAGGCGTGAAATGGTGATGGAAGATGGTGATG-T
* *
76313 ATAGGCGTGCAATGGTAATGGAAGATGGTGATGT
1 -TAGGCGTGAAATGGTGATGGAAGATGGTGATGT
76347 TAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
1 TAGGCGTG-AAATGGTGATGGAAGATGGTGATGT
76381 T
1 T
76382 TAGGTAGTAT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
33 8 0.13
34 25 0.42
35 27 0.45
ACGTcount: A:0.31, C:0.04, G:0.39, T:0.26
Consensus pattern (33 bp):
TAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:79901 original size:19 final size:20
Alignment explanation
Indices: 79854--79903 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
79844 GAAACCCATT
**
79854 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
79874 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
79893 TGAAGATACAT
1 TGAAAATACAT
79904 ACTGTTGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:87414 original size:56 final size:54
Alignment explanation
Indices: 87283--87406 Score: 160
Period size: 54 Copynumber: 2.3 Consensus size: 54
87273 AGATTCCCTT
* *
87283 TCGGACTCTTGCACCAATGTCTTAGCAAGCCCGATACTCTATCTTGACTCATTA
1 TCGGACACTTGCACCAATGTCTTAGCAAGCCCGATACTCTATCTTAACTCATTA
* * * *
87337 TCGGACACTTGCACCAATGTCTTGGCAAGCCCGATCCTCTGTCTTAAACCTC-TCTG
1 TCGGACACTTGCACCAATGTCTTAGCAAGCCCGATACTCTATCTT-AA-CTCAT-TA
87393 TCGGACACTTGCAC
1 TCGGACACTTGCAC
87407 TAGTGTCTCG
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
54 41 0.67
55 2 0.03
56 18 0.30
ACGTcount: A:0.22, C:0.32, G:0.17, T:0.29
Consensus pattern (54 bp):
TCGGACACTTGCACCAATGTCTTAGCAAGCCCGATACTCTATCTTAACTCATTA
Found at i:89964 original size:2 final size:2
Alignment explanation
Indices: 89957--90041 Score: 131
Period size: 2 Copynumber: 43.5 Consensus size: 2
89947 AGTTATTTTC
89957 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
*
89999 AT AT AT AT AT AT AT AT AT AT A- AT A- AGT AT AT -T AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
90039 AT A
1 AT A
90042 GTCACAATCT
Statistics
Matches: 77, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
1 3 0.04
2 73 0.95
3 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:91261 original size:22 final size:22
Alignment explanation
Indices: 91233--91275 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
91223 CTTCATTTCA
*
91233 TCATCAACATCATCAACATCCT
1 TCATCAACACCATCAACATCCT
* *
91255 TCATCAAGACCATCATCATCC
1 TCATCAACACCATCAACATCC
91276 CATAATTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.37, G:0.02, T:0.26
Consensus pattern (22 bp):
TCATCAACACCATCAACATCCT
Found at i:91606 original size:18 final size:17
Alignment explanation
Indices: 91578--91635 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
91568 TTGGAGTGCA
91578 AAAAGAAAGAAAAAAAC
1 AAAAGAAAGAAAAAAAC
*
91595 AAAAG-AAGAGAAAAATC
1 AAAAGAAAGA-AAAAAAC
* *
91612 AAAAAAAAAAAAAAAATC
1 AAAAGAAAGAAAAAAA-C
91630 AAAAGA
1 AAAAGA
91636 GAAAACAAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
16 4 0.12
17 20 0.61
18 9 0.27
ACGTcount: A:0.81, C:0.05, G:0.10, T:0.03
Consensus pattern (17 bp):
AAAAGAAAGAAAAAAAC
Found at i:91608 original size:16 final size:18
Alignment explanation
Indices: 91578--91635 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
91568 TTGGAGTGCA
91578 AAAAGAAAGAAAAAAA-C
1 AAAAGAAAGAAAAAAATC
*
91595 AAAAG-AAGAGAAAAATC
1 AAAAGAAAGAAAAAAATC
* *
91612 AAAAAAAAAAAAAAAATC
1 AAAAGAAAGAAAAAAATC
91630 AAAAGA
1 AAAAGA
91636 GAAAACAAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
16 9 0.26
17 10 0.29
18 15 0.44
ACGTcount: A:0.81, C:0.05, G:0.10, T:0.03
Consensus pattern (18 bp):
AAAAGAAAGAAAAAAATC
Found at i:91640 original size:18 final size:18
Alignment explanation
Indices: 91576--91640 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
91566 AATTGGAGTG
*
91576 CAAAA-AGAAAGAAAAAAA
1 CAAAAGAGAAA-AAAAAAT
* *
91594 CAAAAGA-AGAGAAAAAT
1 CAAAAGAGAAAAAAAAAT
* *
91611 CAAAAAAAAAAAAAAAAT
1 CAAAAGAGAAAAAAAAAT
91629 CAAAAGAGAAAA
1 CAAAAGAGAAAA
91641 CAAGCAAGGA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 11 0.30
18 25 0.68
19 1 0.03
ACGTcount: A:0.80, C:0.06, G:0.11, T:0.03
Consensus pattern (18 bp):
CAAAAGAGAAAAAAAAAT
Found at i:96125 original size:16 final size:16
Alignment explanation
Indices: 96106--96144 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
96096 ATTGGAGTGC
96106 AAAAAAAGA-AAAAGAT
1 AAAAAAAGAGAAAA-AT
*
96122 AAAAGAAGAGAAAAAT
1 AAAAAAAGAGAAAAAT
96138 AAAAAAA
1 AAAAAAA
96145 AATCAATAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (16 bp):
AAAAAAAGAGAAAAAT
Done.