Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002088.1 Hibiscus syriacus cultivar Beakdansim tig00004260_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: 75954
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:14420 original size:20 final size:20
Alignment explanation
Indices: 14395--14434 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
14385 ACCTTTCATC
14395 ATTTGAGCTACTTCTCATGT
1 ATTTGAGCTACTTCTCATGT
14415 ATTTGAGCTACTTCTCATGT
1 ATTTGAGCTACTTCTCATGT
14435 GCTTGAGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTTGAGCTACTTCTCATGT
Found at i:14440 original size:20 final size:20
Alignment explanation
Indices: 14397--14443 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
14387 CTTTCATCAT
*
14397 TTGAGCTACTTCTCATGTAT
1 TTGAGCTACTTCTCATGTAC
*
14417 TTGAGCTACTTCTCATGTGC
1 TTGAGCTACTTCTCATGTAC
14437 TTGAGCT
1 TTGAGCT
14444 GAAGATAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (20 bp):
TTGAGCTACTTCTCATGTAC
Found at i:14961 original size:33 final size:33
Alignment explanation
Indices: 14919--14987 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
14909 GTTGATGAAT
*
14919 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* *
14952 GAAGGATGATGTTATTGGCGTGATATGGTAATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
14985 GAA
1 GAA
14988 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.33, C:0.01, G:0.35, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:15028 original size:36 final size:36
Alignment explanation
Indices: 14958--15070 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
14948 AATGGAAGGA
* * *
14958 TGATGTTATTGGCGTGAT-ATGGTAATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
14993 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
15029 TGATGATATAGGCGTCATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
15065 TGATGA
1 TGATGA
15071 AAATAGTATC
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 16 0.23
36 54 0.77
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:18981 original size:23 final size:21
Alignment explanation
Indices: 18937--18982 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
18927 TGTAGGAGTC
* *
18937 TTTTTCTTTTCTTTTTGTTTT
1 TTTTTCTTTTCTTGTTGCTTT
18958 TTTTTCTTCTTTCTTGTTGCTTT
1 TTTTTC-T-TTTCTTGTTGCTTT
18981 TT
1 TT
18983 GTTGTAGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 1 0.05
23 14 0.67
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (21 bp):
TTTTTCTTTTCTTGTTGCTTT
Found at i:19357 original size:33 final size:33
Alignment explanation
Indices: 19320--19388 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
19310 CTTGTTGAAT
*
19320 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* *
19353 GAAGGATGATGTTATTGGCGTGATATGGTAATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
19386 GAA
1 GAA
19389 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.33, C:0.01, G:0.35, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:19411 original size:11 final size:12
Alignment explanation
Indices: 19388--19441 Score: 53
Period size: 11 Copynumber: 4.6 Consensus size: 12
19378 TGGTAATGGA
19388 ATAT-GGTGATG
1 ATATAGGTGATG
19399 ATATAGGTG-TG
1 ATATAGGTGATG
19410 ATA-ATGGTGATGG
1 ATATA-GGTGAT-G
19423 ACTAT-GGTGATG
1 A-TATAGGTGATG
19435 ATATAGG
1 ATATAGG
19442 CGTGATAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
10 1 0.03
11 16 0.44
12 9 0.25
13 8 0.22
14 2 0.06
ACGTcount: A:0.30, C:0.02, G:0.35, T:0.33
Consensus pattern (12 bp):
ATATAGGTGATG
Found at i:19429 original size:36 final size:36
Alignment explanation
Indices: 19359--19471 Score: 147
Period size: 36 Copynumber: 3.2 Consensus size: 36
19349 AATGGAAGGA
* * *
19359 TGATGTTATTGGCGTGAT-ATGGTAATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
19394 TGATGATATAGGTGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
19430 TGATGATATAGGCGTGATAATGGAGATGGATTATGA
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
19466 TGATGA
1 TGATGA
19472 AAATAGTATC
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 15 0.22
36 53 0.78
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.34
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:19431 original size:13 final size:12
Alignment explanation
Indices: 19374--19438 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
19364 TTATTGGCGT
*
19374 GATATGGTAATG
1 GATATGGTGATG
19386 GAATATGGTGAT-
1 G-ATATGGTGATG
19398 GATATAGGTG-T-
1 GATAT-GGTGATG
19409 GATAATGGTGATG
1 GAT-ATGGTGATG
19422 GACTATGGTGAT-
1 GA-TATGGTGATG
19434 GATAT
1 GATAT
19439 AGGCGTGATA
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
11 15 0.33
12 11 0.24
13 19 0.41
14 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.34, T:0.34
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:25168 original size:36 final size:36
Alignment explanation
Indices: 25115--25227 Score: 138
Period size: 36 Copynumber: 3.2 Consensus size: 36
25105 GATACTATTT
* * *
25115 TCATCACCATAATCCATCTCCATTATCATGCCTATA
1 TCATCACCATAACCCATCACCATTATCACGCCTATA
*
25151 TCATCACCATAGCCCATCACCATTATCACGCCTATA
1 TCATCACCATAACCCATCACCATTATCACGCCTATA
** * *
25187 TCATCACCATATTCCATTACCA-TATCACGCCAATA
1 TCATCACCATAACCCATCACCATTATCACGCCTATA
*
25222 ACATCA
1 TCATCA
25228 TCCTTCCATT
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 17 0.25
36 51 0.75
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAACCCATCACCATTATCACGCCTATA
Found at i:25240 original size:33 final size:33
Alignment explanation
Indices: 25198--25266 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
25188 CATCACCATA
*
25198 TTCCATTACCATATCA-CGCCAATAACATCATCC
1 TTCCATTACCATATCATCACCAATAA-ATCATCC
* *
25231 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATTACCATATCATCACCAATAAATCATCC
25264 TTC
1 TTC
25267 ATTCATCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.30, C:0.35, G:0.01, T:0.33
Consensus pattern (33 bp):
TTCCATTACCATATCATCACCAATAAATCATCC
Found at i:25652 original size:20 final size:20
Alignment explanation
Indices: 25615--25653 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
25605 AACAAAAAGC
*
25615 AACAAGAAAGAAGAAAAAAA
1 AACAAGAAAGAAAAAAAAAA
25635 AACAA-AAAGAAAAGAAAAA
1 AACAAGAAAGAAAA-AAAAA
25654 GACTCCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (20 bp):
AACAAGAAAGAAAAAAAAAA
Found at i:29582 original size:36 final size:36
Alignment explanation
Indices: 29530--29642 Score: 158
Period size: 36 Copynumber: 3.2 Consensus size: 36
29520 GATACTATTT
29530 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCTCCATTATCACGCCTATA
* *
29566 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCTCCATTATCACGCCTATA
* *
29602 TCATCACCATATTCCAT-TACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCT-CCATTATCACGCCTATA
*
29637 ACATCA
1 TCATCA
29643 TCCTTCCATT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
35 17 0.24
36 53 0.76
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCTCCATTATCACGCCTATA
Found at i:29655 original size:33 final size:33
Alignment explanation
Indices: 29578--29681 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
29568 ATCACCATAG
* * *
29578 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATTACCA-TATCACGCCAATAACATCATCC---T
29614 TCCATTACCATATCACGCCAATAACATCATCCT
1 TCCATTACCATATCACGCCAATAACATCATCCT
* * *
29647 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATTACCATATCA-CGCCAATAACATCATCCT
29680 TC
1 TC
29682 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 25 0.42
34 7 0.12
35 17 0.28
36 11 0.18
ACGTcount: A:0.31, C:0.36, G:0.02, T:0.32
Consensus pattern (33 bp):
TCCATTACCATATCACGCCAATAACATCATCCT
Found at i:33517 original size:18 final size:18
Alignment explanation
Indices: 33490--33524 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33480 CGTTGTCATA
33490 TAAATAGTAAAGAATGTG
1 TAAATAGTAAAGAATGTG
* *
33508 TAAATGGTAAAGTATGT
1 TAAATAGTAAAGAATGT
33525 CTTGTAGCCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (18 bp):
TAAATAGTAAAGAATGTG
Found at i:36477 original size:13 final size:11
Alignment explanation
Indices: 36436--36520 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
36426 ACAATCTGTC
36436 CATCACCATTAT
1 CATCACCA-TAT
*
36448 CA-CGCCTATAT
1 CATCACC-ATAT
36459 CATCACCATAGT
1 CATCACCATA-T
36471 CCATCACCATTAT
1 -CATCACCA-TAT
*
36484 CACTC-CTATAT
1 CA-TCACCATAT
36495 CATCACCATATT
1 CATCACCATA-T
36507 CCATCACCATAT
1 -CATCACCATAT
36519 CA
1 CA
36521 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
10 2 0.03
11 22 0.37
12 13 0.22
13 21 0.35
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.02, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:36480 original size:36 final size:36
Alignment explanation
Indices: 36433--36537 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
36423 GATACAATCT
36433 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
36469 GTCCATCACCATTATCACTCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
36505 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
36538 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.36, G:0.04, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:37021 original size:14 final size:15
Alignment explanation
Indices: 36987--37033 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
36977 AATTTGGAGT
36987 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
37002 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
37016 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
37033 G
1 G
37034 TGAAGCAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:40450 original size:13 final size:11
Alignment explanation
Indices: 40409--40493 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
40399 ACAATCTGTC
40409 CATCACCATTAT
1 CATCACCA-TAT
*
40421 CA-CGCCTATAT
1 CATCACC-ATAT
40432 CATCACCATAGT
1 CATCACCATA-T
40444 CCATCACCATTAT
1 -CATCACCA-TAT
*
40457 CA-CGCCTATAT
1 CATCACC-ATAT
40468 CATCACCATATT
1 CATCACCATA-T
40480 CCATCACCATAT
1 -CATCACCATAT
40492 CA
1 CA
40494 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:40453 original size:36 final size:36
Alignment explanation
Indices: 40406--40510 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
40396 GATACAATCT
40406 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
40442 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
40478 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
40511 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:44814 original size:90 final size:91
Alignment explanation
Indices: 44698--44879 Score: 267
Period size: 90 Copynumber: 2.0 Consensus size: 91
44688 GAGAAATGAT
* *
44698 GCTTGGCCGAATAGGGAGAGAGCTCTTCATATTGGCGCCTAAATAAACCACATGCAAGGCACAT-
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATATTGGCACCTAAATAAACCACATGCAAGGCACATG
*
44762 GGGGCTGTTCACATGCAAAACACATG
66 GGGGCTGGTCACATGCAAAACACATG
* * * *
44788 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATATTGGCACCTAAATAAACCACATGCAAGGCACATG
* **
44853 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGGTCACATGCAAAACACATG
44879 G
1 G
44880 GTGTTCTAGG
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 58 0.72
91 23 0.28
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATATTGGCACCTAAATAAACCACATGCAAGGCACATG
GGGGCTGGTCACATGCAAAACACATG
Found at i:55964 original size:20 final size:20
Alignment explanation
Indices: 55939--55987 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
55929 GATGAAGTAT
55939 GGTAATGGAAGTAGAATGAA
1 GGTAATGGAAGTAGAATGAA
55959 GGTAATGGAAGTAGAATGAA
1 GGTAATGGAAGTAGAATGAA
55979 GGTAATGGA
1 GGTAATGGA
55988 GATGAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (20 bp):
GGTAATGGAAGTAGAATGAA
Found at i:57168 original size:30 final size:31
Alignment explanation
Indices: 57116--57175 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
57106 CTTAGCTTTA
**
57116 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
57146 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
57176 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:63957 original size:19 final size:20
Alignment explanation
Indices: 63933--63983 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
63923 CGGCCAAGAG
* *
63933 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
63952 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
63972 CATGTATTTTCA
1 CATGTATTTTCA
63984 AAGAGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:64730 original size:8 final size:8
Alignment explanation
Indices: 64685--64743 Score: 57
Period size: 8 Copynumber: 6.9 Consensus size: 8
64675 TTGGAGTGCA
64685 AAAAGAAAG
1 AAAAG-AAG
64694 AAAAGACA-
1 AAAAGA-AG
64702 AAAAGAAG
1 AAAAGAAG
*
64710 AGAAAAATCAG
1 A-AAAGA--AG
64721 AAAAGAAG
1 AAAAGAAG
64729 AAAAGAAG
1 AAAAGAAG
64737 AAAAGAA
1 AAAAGAA
64744 AAGAAAAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
7 1 0.02
8 25 0.58
9 10 0.23
10 4 0.09
11 3 0.07
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (8 bp):
AAAAGAAG
Found at i:64753 original size:27 final size:26
Alignment explanation
Indices: 64685--64750 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
64675 TTGGAGTGCA
64685 AAAAG-AAAGAAAAGACAAAAAGAAG
1 AAAAGAAAAGAAAAGACAAAAAGAAG
*
64710 AGAAA-AATCAGAAAAGA-AGAAAAGAAG
1 A-AAAGAA-AAGAAAAGACA-AAAAGAAG
64737 AAAAGAAAAGAAAA
1 AAAAGAAAAGAAAA
64751 AGAGAAGTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
25 1 0.03
26 14 0.41
27 19 0.56
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.02
Consensus pattern (26 bp):
AAAAGAAAAGAAAAGACAAAAAGAAG
Found at i:67166 original size:30 final size:31
Alignment explanation
Indices: 67114--67173 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
67104 CTTAGCTTTA
**
67114 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
67144 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
67174 GGCAACATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:68102 original size:19 final size:20
Alignment explanation
Indices: 68078--68128 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
68068 CGGCCAAGAG
* *
68078 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
68097 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
68117 CATGTATTTTCA
1 CATGTATTTTCA
68129 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:75507 original size:36 final size:36
Alignment explanation
Indices: 75452--75561 Score: 168
Period size: 36 Copynumber: 3.1 Consensus size: 36
75442 TTAGAAGATA
*
75452 CATATGTCCATCACCATTATCACGCCTAAATCATCAC
1 CATA-GTCCATCACCATTATCACGCCTATATCATCAC
*
75489 CATAGTCCATCACTATTATCACGCCTATATCATCAC
1 CATAGTCCATCACCATTATCACGCCTATATCATCAC
* *
75525 CATATTCCATCACCA-TATCACGCCTATATTATCAC
1 CATAGTCCATCACCATTATCACGCCTATATCATCAC
75560 CA
1 CA
75562 CTTATAAATT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 21 0.31
36 43 0.63
37 4 0.06
ACGTcount: A:0.32, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
CATAGTCCATCACCATTATCACGCCTATATCATCAC
Done.