Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000768.1 Hibiscus syriacus cultivar Beakdansim tig00001493_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: 101610
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4653 original size:16 final size:16
Alignment explanation
Indices: 4611--4655 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
4601 AGAATCAGTA
*
4611 AAAGAAACAGTACAAT
1 AAAGAAATAGTACAAT
* *
4627 AAGAAAAATAGTATAAT
1 AA-AGAAATAGTACAAT
4644 AAAGAAATAGTA
1 AAAGAAATAGTA
4656 AGGTGAAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.64, C:0.04, G:0.13, T:0.18
Consensus pattern (16 bp):
AAAGAAATAGTACAAT
Found at i:20014 original size:21 final size:24
Alignment explanation
Indices: 19990--20034 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 24
19980 TCTGGCTAAT
19990 GGATCAATCC-TTTT-T-GAAAAG
1 GGATCAATCCATTTTCTGGAAAAG
*
20011 GGATCGATCCATTTTCTGGAAAAG
1 GGATCAATCCATTTTCTGGAAAAG
20035 TGTAGAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 4 0.20
23 1 0.05
24 6 0.30
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (24 bp):
GGATCAATCCATTTTCTGGAAAAG
Found at i:22945 original size:19 final size:19
Alignment explanation
Indices: 22921--22971 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
22911 AATAGCCTGA
22921 TGCATCGATGCATGGCTTG
1 TGCATCGATGCATGGCTTG
*
22940 TGCATCGATGCATTGCTTG
1 TGCATCGATGCATGGCTTG
22959 TGCATCGATGCAT
1 TGCATCGATGCAT
22972 CAAATGCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (19 bp):
TGCATCGATGCATGGCTTG
Found at i:23025 original size:19 final size:19
Alignment explanation
Indices: 23001--23051 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
22991 GAAAATATTC
23001 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
23020 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
23039 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
23052 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:23050 original size:83 final size:83
Alignment explanation
Indices: 22876--23051 Score: 196
Period size: 83 Copynumber: 2.1 Consensus size: 83
22866 GCACCAAGTG
* * ***
22876 TGCATCGATGCATGAAATGCATTAGATGTTTGAAAAATAGCCTGATGCATCGATGCATGGCTTGT
1 TGCATCGATGCATCAAATGCATTAGATGTTTGAAAAATAGCCAGATGCATCGATGCATGGAGAGT
***
22941 GCATCGATGCATTGCTTG
66 GCATCGATGCATTGCGAA
* **
22959 TGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATCAAATGCATTAGATG-TTTGAAAAATAGCCAGA-TGCATCGATGCATGGAGA
*
23023 GTGCATCGGTGCA-TG-GAA
64 GTGCATCGATGCATTGCGAA
23041 TGCATTCGATG
1 TGCA-TCGATG
23052 TTCAATTAAT
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
82 4 0.05
83 43 0.55
84 31 0.40
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (83 bp):
TGCATCGATGCATCAAATGCATTAGATGTTTGAAAAATAGCCAGATGCATCGATGCATGGAGAGT
GCATCGATGCATTGCGAA
Found at i:29549 original size:22 final size:21
Alignment explanation
Indices: 29507--29546 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29497 GAGTTTGTTT
*
29507 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
29528 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
29547 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:31539 original size:64 final size:63
Alignment explanation
Indices: 31471--31651 Score: 227
Period size: 64 Copynumber: 2.8 Consensus size: 63
31461 TTGGAACACT
* ***
31471 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
* * **
31535 TGATGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * *
31599 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
31652 CAATTAATTC
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
64 55 0.54
65 46 0.46
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:31623 original size:19 final size:19
Alignment explanation
Indices: 31599--31649 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
31589 GAAAATATTC
31599 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
31618 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
31637 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
31650 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:31691 original size:65 final size:63
Alignment explanation
Indices: 31493--31700 Score: 226
Period size: 65 Copynumber: 3.2 Consensus size: 63
31483 GCACCAAGTG
* *
31493 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCGATGCATGGATTG-
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGGA-TGA
*
31557 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA-G
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGATG
31620 A
63 A
* * * * *
31621 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGTACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGA-T
31685 GA
62 GA
*
31687 TGCATCGGTGCATG
1 TGCATCGATGCATG
31701 CCTTTGAATA
Statistics
Matches: 125, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
63 10 0.08
64 45 0.36
65 66 0.53
66 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (63 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGATGA
Found at i:32843 original size:94 final size:94
Alignment explanation
Indices: 32689--32876 Score: 358
Period size: 94 Copynumber: 2.0 Consensus size: 94
32679 CGCTCTTCTG
* *
32689 TATTATAATTACGCTACAACACTTTCACTAATGGAACAAAATTATTTTTGAAGCATTTTCATATC
1 TATTATAATTACGCTACAACACTTTCACTAATGGAACAAAATTAATTTTGAAGCATTTTCACATC
32754 ACTAGCCAAGATCTTAATCGATTCTTCCT
66 ACTAGCCAAGATCTTAATCGATTCTTCCT
32783 TATTATAATTACGCTACAACACTTTCACTAATGGAACAAAATTAATTTTGAAGCATTTTCACATC
1 TATTATAATTACGCTACAACACTTTCACTAATGGAACAAAATTAATTTTGAAGCATTTTCACATC
32848 ACTAGCCAAGATCTTAATCGATTCTTCCT
66 ACTAGCCAAGATCTTAATCGATTCTTCCT
32877 CATACGAAAG
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.36
Consensus pattern (94 bp):
TATTATAATTACGCTACAACACTTTCACTAATGGAACAAAATTAATTTTGAAGCATTTTCACATC
ACTAGCCAAGATCTTAATCGATTCTTCCT
Found at i:40211 original size:22 final size:23
Alignment explanation
Indices: 40174--40304 Score: 149
Period size: 23 Copynumber: 5.7 Consensus size: 23
40164 TTAGTGTAGA
* * *
40174 GGGAATCGATACCCCCCTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
40197 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
40220 GGAAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
* *
40243 GGGAACTGAATCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
* *
40266 GGGAACCGGA-T-CCCCTCTGTAG
1 GGGAACC-GATTCCCCCTTTGAAG
* *
40288 GGGAATCGATACCCCCT
1 GGGAACCGATTCCCCCT
40305 GGGGTTCTGG
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
21 2 0.02
22 15 0.16
23 74 0.80
24 2 0.02
ACGTcount: A:0.24, C:0.31, G:0.26, T:0.20
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:41885 original size:18 final size:19
Alignment explanation
Indices: 41859--41906 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
41849 GATGACTCCG
* *
41859 ACGATGAACCAGAAC-AGC
1 ACGAGGAACAAGAACGAGC
41877 ACGAGGAACAAGAACGAGC
1 ACGAGGAACAAGAACGAGC
41896 A-GAGGAACAAG
1 ACGAGGAACAAG
41907 CACAGCCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.48, C:0.21, G:0.29, T:0.02
Consensus pattern (19 bp):
ACGAGGAACAAGAACGAGC
Found at i:54186 original size:16 final size:16
Alignment explanation
Indices: 54165--54195 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
54155 AATGATGATT
54165 ATACTAGTTGGCATGC
1 ATACTAGTTGGCATGC
54181 ATACTAGTTGGCATG
1 ATACTAGTTGGCATG
54196 TATAATAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (16 bp):
ATACTAGTTGGCATGC
Found at i:58461 original size:16 final size:16
Alignment explanation
Indices: 58440--58470 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
58430 AATGATGATT
58440 ATACTAGTTGGCATGC
1 ATACTAGTTGGCATGC
58456 ATACTAGTTGGCATG
1 ATACTAGTTGGCATG
58471 TATAATAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (16 bp):
ATACTAGTTGGCATGC
Found at i:62732 original size:16 final size:16
Alignment explanation
Indices: 62711--62741 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
62701 AATGATGATT
62711 ATACTAGTTGGCATGC
1 ATACTAGTTGGCATGC
62727 ATACTAGTTGGCATG
1 ATACTAGTTGGCATG
62742 TATAATAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (16 bp):
ATACTAGTTGGCATGC
Found at i:68485 original size:16 final size:17
Alignment explanation
Indices: 68444--68485 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
68434 CCTTTCGTGC
68444 AAAACCCACAAGTTATTA
1 AAAACCCACAAGTTA-TA
*
68462 ACAACCCACAAGTTA-A
1 AAAACCCACAAGTTATA
68478 AAAACCCA
1 AAAACCCA
68486 AATATTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
18 14 0.64
ACGTcount: A:0.52, C:0.29, G:0.05, T:0.14
Consensus pattern (17 bp):
AAAACCCACAAGTTATA
Found at i:68666 original size:17 final size:17
Alignment explanation
Indices: 68644--68681 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
68634 AAAGATTTAT
68644 AATTCGTTCTTGATTCG
1 AATTCGTTCTTGATTCG
*
68661 AATTCGTTCTTGATTTG
1 AATTCGTTCTTGATTCG
68678 AATT
1 AATT
68682 TGATGGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.50
Consensus pattern (17 bp):
AATTCGTTCTTGATTCG
Found at i:73226 original size:15 final size:16
Alignment explanation
Indices: 73199--73233 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
73189 GCTTTCAAAA
73199 TTGAAAAATGAAAATT
1 TTGAAAAATGAAAATT
*
73215 TTGAAAAA-GAAATTT
1 TTGAAAAATGAAAATT
73230 TTGA
1 TTGA
73234 TTTGAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (16 bp):
TTGAAAAATGAAAATT
Found at i:73645 original size:8 final size:9
Alignment explanation
Indices: 73615--73647 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
73605 TTTTATGCAA
73615 TTATATGAT
1 TTATATGAT
*
73624 TTGTATGAT
1 TTATATGAT
73633 TTATATG-T
1 TTATATGAT
73641 TTATATG
1 TTATATG
73648 CATGATTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (9 bp):
TTATATGAT
Found at i:80815 original size:22 final size:22
Alignment explanation
Indices: 80790--80849 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
80780 GAATCGATAA
80790 CCCCCTTGAAGGGGAACCAATT
1 CCCCCTTGAAGGGGAACCAATT
**
80812 CCCCCTTTGAAGGGGAACTGATT
1 CCCCC-TTGAAGGGGAACCAATT
*
80835 CCCCC-TGTAGGGGAA
1 CCCCCTTGAAGGGGAA
80850 TCGATAACCC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.26
22 5 0.15
23 20 0.59
ACGTcount: A:0.23, C:0.30, G:0.27, T:0.20
Consensus pattern (22 bp):
CCCCCTTGAAGGGGAACCAATT
Found at i:82471 original size:18 final size:18
Alignment explanation
Indices: 82436--82474 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
82426 AGAGCAGCAC
*
82436 GAGGAACAAGCACCTCCA
1 GAGGAACAACCACCTCCA
* *
82454 GAGGAACAACCTCGTCCA
1 GAGGAACAACCACCTCCA
82472 GAG
1 GAG
82475 TATCAAATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.31, G:0.26, T:0.08
Consensus pattern (18 bp):
GAGGAACAACCACCTCCA
Found at i:83094 original size:49 final size:49
Alignment explanation
Indices: 83045--83148 Score: 178
Period size: 49 Copynumber: 2.2 Consensus size: 49
83035 GAACAAAAAG
83045 GGGGAG-AAATGTTAAAAGCATTTTAAAGAGGAGTAGTGTTAGAGTAAA
1 GGGGAGTAAATGTTAAAAGCATTTTAAAGAGGAGTAGTGTTAGAGTAAA
*
83093 GGGGAGTAAATGTTAAAAGCGTTTTAAAGAGGAGTAGTGTTAGAGT-AA
1 GGGGAGTAAATGTTAAAAGCATTTTAAAGAGGAGTAGTGTTAGAGTAAA
83141 -GGGAGTAA
1 GGGGAGTAA
83149 TTTCAAAACT
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
47 8 0.15
48 8 0.15
49 38 0.70
ACGTcount: A:0.39, C:0.02, G:0.34, T:0.25
Consensus pattern (49 bp):
GGGGAGTAAATGTTAAAAGCATTTTAAAGAGGAGTAGTGTTAGAGTAAA
Found at i:83590 original size:75 final size:76
Alignment explanation
Indices: 83465--83633 Score: 250
Period size: 75 Copynumber: 2.2 Consensus size: 76
83455 TCCAGAGGGA
* *
83465 ACCGATTCCCCCTGAATGGTTTGGCTCTGAGAAAAACATAATGCTTAGAGGGAACCGATTCCCCC
1 ACCGATTCCCCCTGAATGGTTTGGCTCTGAGAAAAACAGAATGCTCAGAGGGAACCGATTCCCCC
83530 CCAA-GGGGGT
66 CCAAGGGGGGT
* * **
83540 ACCGATTCCCCCTGAATGGTTTGGCTCTGAGAAAAATAGAATGCTCAGAGGGTATTGATTCCCCC
1 ACCGATTCCCCCTGAATGGTTTGGCTCTGAGAAAAACAGAATGCTCAGAGGGAACCGATTCCCCC
83605 CCAAGGGGGGGGGT
66 CCAA---GGGGGGT
83619 ACCGATTCCCCCTGA
1 ACCGATTCCCCCTGA
83634 TCAACTGTCG
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
75 63 0.75
79 21 0.25
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.22
Consensus pattern (76 bp):
ACCGATTCCCCCTGAATGGTTTGGCTCTGAGAAAAACAGAATGCTCAGAGGGAACCGATTCCCCC
CCAAGGGGGGT
Found at i:85362 original size:49 final size:49
Alignment explanation
Indices: 85031--85354 Score: 301
Period size: 50 Copynumber: 6.5 Consensus size: 49
85021 AGGTCTTAAT
* * ** * * * *
85031 GATTGACTCCTCTACACGAGAAATTCAGGCTGAAGACAACAATACTGAAG
1 GATTGACTCCTCTACATGAGAAAGTCAGTTTG-AGATAACATTACTAAAA
* * * *
85081 GATTGACTCCTCTACACGAGAAAGTCAGGTTGAGGATGACATTACTAAAT
1 GATTGACTCCTCTACATGAGAAAGTCAGTTTGA-GATAACATTACTAAAA
* * * * *
85131 GATTGGCTCCTCTATACGAGAAAGTCAGTTTGAAGATAACACTACTAAAT
1 GATTGACTCCTCTACATGAGAAAGTCAGTTTG-AGATAACATTACTAAAA
* * * * * *
85181 GATTAACTCCTCTATATGATAAAGTCATTTTAGGGATAACATTACTGAAA
1 GATTGACTCCTCTACATGAGAAAGTCAGTTT-GAGATAACATTACTAAAA
* * *
85231 GATT-AGC-CCTCTACATGAGAAAGTCATGTTTAAGATAAAATTACTGAAA
1 GATTGA-CTCCTCTACATGAGAAAGTCA-GTTTGAGATAACATTACTAAAA
* * * * *
85280 GTTTGACTCATCTACATCAAAAAGTCAGTTTGAGATAATATTACTAAAA
1 GATTGACTCCTCTACATGAGAAAGTCAGTTTGAGATAACATTACTAAAA
85329 GATTGACTCCTCTACATGAGAAAGTC
1 GATTGACTCCTCTACATGAGAAAGTC
85355 GGGTTGAGGA
Statistics
Matches: 229, Mismatches: 38, Indels: 15
0.81 0.13 0.05
Matches are distributed among these distances:
49 79 0.34
50 148 0.65
51 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (49 bp):
GATTGACTCCTCTACATGAGAAAGTCAGTTTGAGATAACATTACTAAAA
Found at i:90248 original size:21 final size:21
Alignment explanation
Indices: 90214--90253 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
90204 AATAAACACA
*
90214 ATACAAATGTGAAAAACAAAG
1 ATACAAATGCGAAAAACAAAG
* *
90235 ATACAAGTGCGAAATACAA
1 ATACAAATGCGAAAAACAA
90254 GGATGCAGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.12, G:0.15, T:0.15
Consensus pattern (21 bp):
ATACAAATGCGAAAAACAAAG
Found at i:92493 original size:23 final size:21
Alignment explanation
Indices: 92467--92509 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
92457 TAGATTTTTA
*
92467 GACTTTGTTATATTTAGGTATTT
1 GACTTTG-GATATTT-GGTATTT
92490 GACTTTGGATATTTGGTATT
1 GACTTTGGATATTTGGTATT
92510 ATAAACCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.53
Consensus pattern (21 bp):
GACTTTGGATATTTGGTATTT
Found at i:96447 original size:19 final size:19
Alignment explanation
Indices: 96420--96474 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
96410 CCTGATTCTA
*
96420 CATGAGATTATATCCCCTG
1 CATGGGATTATATCCCCTG
** *
96439 CATGGGATTATATGTCATG
1 CATGGGATTATATCCCCTG
96458 CATGGGATTATATCCCC
1 CATGGGATTATATCCCC
96475 ATCTTGATTC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (19 bp):
CATGGGATTATATCCCCTG
Found at i:96530 original size:29 final size:29
Alignment explanation
Indices: 96456--96544 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 29
96446 TTATATGTCA
*
96456 TGCATGGGATTATATCCCCATCTTGATTC
1 TGCATGGGATTATATCTCCATCTTGATTC
* *
96485 TGCATAGGATT-TGATCTCTATAC-TGATTC
1 TGCATGGGATTAT-ATCTCCAT-CTTGATTC
* *
96514 TGCATGGGATTATATCTCCTTCATGATTC
1 TGCATGGGATTATATCTCCATCTTGATTC
96543 TG
1 TG
96545 TATGTGATCC
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
28 2 0.04
29 46 0.92
30 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.40
Consensus pattern (29 bp):
TGCATGGGATTATATCTCCATCTTGATTC
Done.