Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003775.1 Hibiscus syriacus cultivar Beakdansim tig00008084_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: 91023
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:9122 original size:18 final size:18
Alignment explanation
Indices: 9099--9157 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
9089 GAAAATATTT
9099 TTTAATAAATATTAATTC
1 TTTAATAAATATTAATTC
*
9117 TTTAATGATAA-A-TACTT-
1 TTTAAT-A-AATATTAATTC
**
9134 TTTAATAAATATTAGGTC
1 TTTAATAAATATTAATTC
9152 TTTAAT
1 TTTAAT
9158 GATAAATACT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
15 2 0.06
16 2 0.06
17 9 0.27
18 16 0.48
19 2 0.06
20 2 0.06
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (18 bp):
TTTAATAAATATTAATTC
Found at i:9137 original size:35 final size:35
Alignment explanation
Indices: 9091--9168 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 35
9081 AGGTTTTTGA
* *
9091 AAATATTTTTTAATAAATATTAATTCTTTAATGAT
1 AAATACTTTTTAATAAATATTAAGTCTTTAATGAT
*
9126 AAATACTTTTTAATAAATATTAGGTCTTTAATGAT
1 AAATACTTTTTAATAAATATTAAGTCTTTAATGAT
9161 AAATACTT
1 AAATACTT
9169 GATTAGCAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (35 bp):
AAATACTTTTTAATAAATATTAAGTCTTTAATGAT
Found at i:11809 original size:2 final size:2
Alignment explanation
Indices: 11802--11840 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
11792 TTTGTCAATT
11802 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11841 TCTGCTGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27428 original size:55 final size:55
Alignment explanation
Indices: 27360--27606 Score: 300
Period size: 55 Copynumber: 4.5 Consensus size: 55
27350 CCAGAATTTA
* ** * *
27360 GATTGAAGCACAGAGGTGCTCAGTCATAGTTGGCTGCACAGAGGTGTCAGTCCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTC
* *
27415 GATTGAAGTACAGAGGTGCTCAATCA-TCTTAGCTACACAGAGGTGTCAGCTCC-C
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAG-TCCTC
** * * * *
27469 GGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTC
1 GATTGAAGCACAGAGGTGCTCAATCA---TTTTTAGCTACACAGAGGTGTCAGTCCTC
* * *
27527 GATTGAAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAGTTCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTC
27582 GATTGAAGCACAGAGGTGCTCAATC
1 GATTGAAGCACAGAGGTGCTCAATC
27607 GTTAATTCTA
Statistics
Matches: 165, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
54 42 0.25
55 77 0.47
57 2 0.01
58 44 0.27
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (55 bp):
GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTC
Found at i:27538 original size:27 final size:28
Alignment explanation
Indices: 27339--27603 Score: 119
Period size: 27 Copynumber: 9.5 Consensus size: 28
27329 TCATTCCAAT
*
27339 GCACAGAGGTGC-CAGAATT-TAGATTGAA
1 GCACAGAGGTGCTCAG--TTCTCGATTGAA
* **
27367 GCACAGAGGTGCTCAG-TCATAG-TTGGCT
1 GCACAGAGGTGCTCAGTTC-TCGATT-GAA
*
27395 GCACAGAGGTG-TCAGTCCTCGATTGAA
1 GCACAGAGGTGCTCAGTTCTCGATTGAA
* * *
27422 GTACAGAGGTGCTCA-ATCATC--TTAGCTA
1 GCACAGAGGTGCTCAGTTC-TCGATT-G-AA
* * **
27450 -CACAGAGGTG-TCAGCTCCCGGCTGAA
1 GCACAGAGGTGCTCAGTTCTCGATTGAA
*** *
27476 GCACAGAGGTGCTCAG-TCATTTTTTTTAA
1 GCACAGAGGTGCTCAGTTC--TCGATTGAA
27505 CTGCACAGAGGTG-TCAGTTCTCGATTGAA
1 --GCACAGAGGTGCTCAGTTCTCGATTGAA
* * ** *
27534 GCACAGAGGTGCTCA-ATCACTTTTGGCTA
1 GCACAGAGGTGCTCAGTTCTCGATT-G-AA
27563 -CACAGAGGTG-TCAGTTCTCGATTGAA
1 GCACAGAGGTGCTCAGTTCTCGATTGAA
27589 GCACAGAGGTGCTCA
1 GCACAGAGGTGCTCA
27604 ATCGTTAATT
Statistics
Matches: 176, Mismatches: 35, Indels: 52
0.67 0.13 0.20
Matches are distributed among these distances:
26 9 0.05
27 75 0.43
28 63 0.36
29 12 0.07
30 4 0.02
31 13 0.07
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (28 bp):
GCACAGAGGTGCTCAGTTCTCGATTGAA
Found at i:27622 original size:55 final size:55
Alignment explanation
Indices: 27306--27624 Score: 266
Period size: 55 Copynumber: 5.8 Consensus size: 55
27296 CTTGATTTTA
* * * *
27306 GATTGTAGCACAAAGGTGCTCAATCATTCCAA---T-GCACAGAGGTGCCAGAATT-TA
1 GATTGAAGCACAGAGGTGCTCAATCATT--AATTCTAGCACAGAGGTGTCAG--TTCTC
* * *
27360 GATTGAAGCACAGAGGTGCTCAGTCA-TAGTTGGCT-GCACAGAGGTGTCAGTCCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTAATT--CTAGCACAGAGGTGTCAGTTCTC
* * * * *
27415 GATTGAAGTACAGAGGTGCTCAATCATCTTA-GCTA-CACAGAGGTGTCAGCTCCC
1 GATTGAAGCACAGAGGTGCTCAATCAT-TAATTCTAGCACAGAGGTGTCAGTTCTC
** * ** *
27469 GGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTAATTCT-A--GCACAGAGGTGTCAGTTCTC
27527 GATTGAAGCACAGAGGTGCTCAATCACTT--TTGGCTA-CACAGAGGTGTCAGTTCTC
1 GATTGAAGCACAGAGGTGCTCAATCA-TTAATT--CTAGCACAGAGGTGTCAGTTCTC
*
27582 GATTGAAGCACAGAGGTGCTCAATCGTTAATTCTAGCACAGAG
1 GATTGAAGCACAGAGGTGCTCAATCATTAATTCTAGCACAGAG
27625 ATGCTATGGA
Statistics
Matches: 216, Mismatches: 29, Indels: 39
0.76 0.10 0.14
Matches are distributed among these distances:
51 1 0.00
53 3 0.01
54 71 0.33
55 77 0.36
56 17 0.08
57 3 0.01
58 41 0.19
59 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (55 bp):
GATTGAAGCACAGAGGTGCTCAATCATTAATTCTAGCACAGAGGTGTCAGTTCTC
Found at i:27857 original size:81 final size:81
Alignment explanation
Indices: 27722--27879 Score: 271
Period size: 81 Copynumber: 2.0 Consensus size: 81
27712 GCGAGTTACA
*
27722 AAGAATGGTTCGCACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGTTA
1 AAGAATGGTTCGCACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
* *
27787 CTGAGCCGGTTGCACC
66 CCGAGCCAGTTGCACC
* *
27803 AAGAATGGTTCGCACACGAAATGGCGGATCGACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
1 AAGAATGGTTCGCACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
27868 CCGAGCCAGTTG
66 CCGAGCCAGTTG
27880 TGCAAGAGAC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.16
Consensus pattern (81 bp):
AAGAATGGTTCGCACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
CCGAGCCAGTTGCACC
Found at i:51005 original size:61 final size:61
Alignment explanation
Indices: 50930--51236 Score: 510
Period size: 61 Copynumber: 5.0 Consensus size: 61
50920 AAACACACAA
50930 ATTTAAATTTATAAAAAGATAATATTATTAATTTTAAAAATTATATATTTAAGCTTGTTTT
1 ATTTAAATTTATAAAAAGATAATATTATTAATTTTAAAAATTATATATTTAAGCTTGTTTT
*
50991 ATTTAAATTTATAAAAAGATAGTATTATTAATTTTAAAAATTATATATTTAAGCTTGTTTT
1 ATTTAAATTTATAAAAAGATAATATTATTAATTTTAAAAATTATATATTTAAGCTTGTTTT
* * *
51052 ATTTAAACTTATAAAAAATATAATATTATTAATTTTAAAAATTATATATTTAATCTTGTTTT
1 ATTTAAATTTAT-AAAAAGATAATATTATTAATTTTAAAAATTATATATTTAAGCTTGTTTT
* *
51114 ATTTAAATTTATAAAAA-ACAATATTATTAATTTTAAAAATTAAATATTTAAGCTTGTTTT
1 ATTTAAATTTATAAAAAGATAATATTATTAATTTTAAAAATTATATATTTAAGCTTGTTTT
* *
51174 ATTTAAATTTATAAAAAGATAATATTATTAATTTTTAAAAA-TATATATTTAAACTTGTCTT
1 ATTTAAATTTATAAAAAGATAATATTATTAA-TTTTAAAAATTATATATTTAAGCTTGTTTT
51235 AT
1 AT
51237 AATAAACTTA
Statistics
Matches: 230, Mismatches: 13, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
60 57 0.25
61 107 0.47
62 66 0.29
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.49
Consensus pattern (61 bp):
ATTTAAATTTATAAAAAGATAATATTATTAATTTTAAAAATTATATATTTAAGCTTGTTTT
Found at i:51078 original size:24 final size:22
Alignment explanation
Indices: 51051--51104 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
51041 AAGCTTGTTT
51051 TATTTAAACTTATAAAAAATATAA
1 TATTTAAA-TTATAAAAAATAT-A
* * *
51075 TATTATTAATTTTAAAAATTATA
1 TATT-TAAATTATAAAAAATATA
51098 TATTTAA
1 TATTTAA
51105 TCTTGTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 2 0.08
23 5 0.20
24 15 0.60
25 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTTAAATTATAAAAAATATA
Found at i:52071 original size:41 final size:41
Alignment explanation
Indices: 51963--52122 Score: 261
Period size: 41 Copynumber: 3.9 Consensus size: 41
51953 TTTTGGACAT
* *
51963 GTGTAGAGTA--TATCTTATAAAAACTAGGGTACCTTTTTA
1 GTGTAGAGTACCTCTCTTATAAAAACTAGGGTACCTTTCTA
*
52002 GTGTAGAGGTAACTCTCTTATAAAAACTAGGGTACCTTTCTA
1 GTGTAGA-GTACCTCTCTTATAAAAACTAGGGTACCTTTCTA
52044 GTGTAGAGTACCTCTCTTATAAAAACTAGGGTACCTTTCTA
1 GTGTAGAGTACCTCTCTTATAAAAACTAGGGTACCTTTCTA
*
52085 GTGTAGAGTACCTCTCTTATAAAAACTAGGGAACCTTT
1 GTGTAGAGTACCTCTCTTATAAAAACTAGGGTACCTTT
52123 TTACTGTTTT
Statistics
Matches: 114, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
39 7 0.06
40 3 0.03
41 70 0.61
42 34 0.30
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (41 bp):
GTGTAGAGTACCTCTCTTATAAAAACTAGGGTACCTTTCTA
Found at i:61827 original size:22 final size:22
Alignment explanation
Indices: 61802--61843 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
61792 ATCTATGTTG
61802 TTTTGTA-TCGTAATACTATAAT
1 TTTTGTATTCGTAAT-CTATAAT
61824 TTTTGTATTCGTAATCTATA
1 TTTTGTATTCGTAATCTATA
61844 TGGTACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (22 bp):
TTTTGTATTCGTAATCTATAAT
Found at i:62280 original size:4 final size:4
Alignment explanation
Indices: 62271--62295 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
62261 TTGGACGCCA
62271 ATGC ATGC ATGC ATGC ATGC ATGC A
1 ATGC ATGC ATGC ATGC ATGC ATGC A
62296 CTGATTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (4 bp):
ATGC
Found at i:62752 original size:87 final size:87
Alignment explanation
Indices: 62606--62781 Score: 289
Period size: 87 Copynumber: 2.0 Consensus size: 87
62596 TTACCGAACA
* *
62606 TGTTGGTAAATCTGGCTAGCAATTGTATCACTTCCAGAGTTTAACAAACTTATCATGACTTGCGT
1 TGTTGGGAAATCTGGCTAGCAATTGTATCACTTCCAGAGTTTAACAAACTTATCATGACTTGCGG
** *
62671 TTGAAATCAGCCTCGTAACCGG
66 ACGAAACCAGCCTCGTAACCGG
*
62693 TGTTGGGAAATCTGGCTAGCAATTGTATCACTTCCAGAGTTTAACAAACTTGTCATGACTTGCGG
1 TGTTGGGAAATCTGGCTAGCAATTGTATCACTTCCAGAGTTTAACAAACTTATCATGACTTGCGG
*
62758 ACGAAACCAGCCTCGTCACCGG
66 ACGAAACCAGCCTCGTAACCGG
62780 TG
1 TG
62782 ATACGGCCAA
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 82 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (87 bp):
TGTTGGGAAATCTGGCTAGCAATTGTATCACTTCCAGAGTTTAACAAACTTATCATGACTTGCGG
ACGAAACCAGCCTCGTAACCGG
Found at i:66084 original size:24 final size:24
Alignment explanation
Indices: 66057--66107 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
66047 AAAATCAAGG
66057 TAAAAGCACACTTCATAGGGACAT
1 TAAAAGCACACTTCATAGGGACAT
66081 TAAAAGCACACTTCATAGGGACAT
1 TAAAAGCACACTTCATAGGGACAT
66105 TAA
1 TAA
66108 TACCTTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (24 bp):
TAAAAGCACACTTCATAGGGACAT
Found at i:67439 original size:18 final size:18
Alignment explanation
Indices: 67416--67450 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
67406 CATCCCTTCG
* *
67416 CTGCTGGGGTTGCTGCGC
1 CTGCTGAGGCTGCTGCGC
67434 CTGCTGAGGCTGCTGCG
1 CTGCTGAGGCTGCTGCG
67451 GTGGCGGCTG
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:0.03, C:0.29, G:0.43, T:0.26
Consensus pattern (18 bp):
CTGCTGAGGCTGCTGCGC
Found at i:67463 original size:3 final size:3
Alignment explanation
Indices: 67457--67514 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
67447 TGCGGTGGCG
* * * * * *
67457 GCT GCT GTT GCT GTT GTT GCT GTT GTT GCT GCT GCT GCT GCT GCT GGT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
*
67505 GTT GCT GCT G
1 GCT GCT GCT G
67515 GTGTTGTTGT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.00, C:0.21, G:0.36, T:0.43
Consensus pattern (3 bp):
GCT
Found at i:67468 original size:6 final size:6
Alignment explanation
Indices: 67459--67541 Score: 58
Period size: 6 Copynumber: 13.8 Consensus size: 6
67449 CGGTGGCGGC
* * * * * * *
67459 TGCTGT TGCTGT TGTTGC TGTTGT TGCTGC TGCTGC TGCTGC TGGTGT
1 TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT
* * * * *
67507 TGCTGC TGGTGT TGTTGT TGTTGT TGCTGC TGCTG
1 TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTG
67542 GGCATGCCTC
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.00, C:0.17, G:0.36, T:0.47
Consensus pattern (6 bp):
TGCTGT
Found at i:67474 original size:9 final size:9
Alignment explanation
Indices: 67457--67529 Score: 65
Period size: 9 Copynumber: 8.1 Consensus size: 9
67447 TGCGGTGGCG
*
67457 GCTGCTGTT
1 GCTGTTGTT
67466 GCTGTTGTT
1 GCTGTTGTT
67475 GCTGTTGTT
1 GCTGTTGTT
* *
67484 GCTGCTGCT
1 GCTGTTGTT
* *
67493 GCTGCTGCT
1 GCTGTTGTT
* *
67502 GGTGTTGCT
1 GCTGTTGTT
*
67511 GCTGGTGTT
1 GCTGTTGTT
*
67520 GTTGTTGTT
1 GCTGTTGTT
67529 G
1 G
67530 TTGCTGCTGC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 54 1.00
ACGTcount: A:0.00, C:0.16, G:0.37, T:0.47
Consensus pattern (9 bp):
GCTGTTGTT
Found at i:67489 original size:12 final size:12
Alignment explanation
Indices: 67468--67538 Score: 79
Period size: 12 Copynumber: 5.9 Consensus size: 12
67458 CTGCTGTTGC
* *
67468 TGTTGTTGCTGT
1 TGTTGCTGCTGG
*
67480 TGTTGCTGCTGC
1 TGTTGCTGCTGG
*
67492 TGCTGCTGCTGG
1 TGTTGCTGCTGG
67504 TGTTGCTGCTGG
1 TGTTGCTGCTGG
* * *
67516 TGTTGTTGTTGT
1 TGTTGCTGCTGG
67528 TGTTGCTGCTG
1 TGTTGCTGCTG
67539 CTGGGCATGC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 49 1.00
ACGTcount: A:0.00, C:0.15, G:0.37, T:0.48
Consensus pattern (12 bp):
TGTTGCTGCTGG
Found at i:73936 original size:23 final size:24
Alignment explanation
Indices: 73905--73951 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
73895 TGTTGTTGTG
73905 GTTTATGTTCATTTATGTTCGTTT
1 GTTTATGTTCATTTATGTTCGTTT
* *
73929 GTTT-TGTTTATTTATGTTTGTTT
1 GTTTATGTTCATTTATGTTCGTTT
73952 ACGTTCGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.11, C:0.04, G:0.17, T:0.68
Consensus pattern (24 bp):
GTTTATGTTCATTTATGTTCGTTT
Found at i:73943 original size:33 final size:34
Alignment explanation
Indices: 73906--73976 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 34
73896 GTTGTTGTGG
* * *
73906 TTTATGTTCATTTATGTTCGTTTGTTT-TGTTTA
1 TTTATGTTCATTTACGTTCGTTCGTTTGTGTTCA
**
73939 TTTATGTTTGTTTACGTTCGTTCGTTTGTGTTCA
1 TTTATGTTCATTTACGTTCGTTCGTTTGTGTTCA
73973 TTTA
1 TTTA
73977 CATCCGTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 23 0.72
34 9 0.28
ACGTcount: A:0.11, C:0.08, G:0.17, T:0.63
Consensus pattern (34 bp):
TTTATGTTCATTTACGTTCGTTCGTTTGTGTTCA
Found at i:73976 original size:24 final size:24
Alignment explanation
Indices: 73939--74000 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
73929 GTTTTGTTTA
** * *
73939 TTTATGTTTGTTTACGTTCGTTCG
1 TTTATGTTCATTTACATCCGTTCG
* *
73963 TTTGTGTTCATTTACATCCGTTCT
1 TTTATGTTCATTTACATCCGTTCG
73987 TTTATGTTCATTTA
1 TTTATGTTCATTTA
74001 TTTGTATTCG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.13, C:0.15, G:0.15, T:0.58
Consensus pattern (24 bp):
TTTATGTTCATTTACATCCGTTCG
Found at i:74371 original size:17 final size:16
Alignment explanation
Indices: 74338--74371 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
74328 CTCTTAAAAG
74338 TTTTAAATTATAAATA
1 TTTTAAATTATAAATA
*
74354 TTTTAAATATATATATA
1 TTTTAAAT-TATAAATA
74371 T
1 T
74372 ATATATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAATTATAAATA
Found at i:74454 original size:7 final size:8
Alignment explanation
Indices: 74425--74452 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
74415 GATTTTTCTT
74425 TTTTTAAA
1 TTTTTAAA
74433 TTTTTAAA
1 TTTTTAAA
74441 TTTTTAAA
1 TTTTTAAA
74449 TTTT
1 TTTT
74453 AATCATTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTTTAAA
Done.