Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000590.1 Hibiscus syriacus cultivar Beakdansim tig00001146_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: 55515
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:87 original size:18 final size:18
Alignment explanation
Indices: 64--104 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
54 AGAACGATTA
*
64 ATTTTAAT-AAATATTATT
1 ATTTTAATAAAATATCA-T
82 ATTTT-ATAAAATATCAT
1 ATTTTAATAAAATATCAT
99 ATTTTA
1 ATTTTA
105 CCCCTAAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTAATAAAATATCAT
Found at i:9245 original size:21 final size:22
Alignment explanation
Indices: 9220--9270 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
9210 GTAGTGAGAG
*
9220 TGAGGAAGAGATTGCAGAGC-C
1 TGAGGAAGACATTGCAGAGCAC
9241 TGAGGAAGACATTGCAGAGCAC
1 TGAGGAAGACATTGCAGAGCAC
9263 -GAGGAAGA
1 TGAGGAAGA
9271 AAAACATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.37, C:0.14, G:0.37, T:0.12
Consensus pattern (22 bp):
TGAGGAAGACATTGCAGAGCAC
Found at i:20360 original size:22 final size:22
Alignment explanation
Indices: 20335--20377 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
20325 AATGGGGAAG
*
20335 AAAAAATGTTAA-TTTTATTTA
1 AAAAAAAGTTAACTTTTATTTA
*
20356 AAAAAAAGTTAACTTTTTTTTA
1 AAAAAAAGTTAACTTTTATTTA
20378 TAACTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
AAAAAAAGTTAACTTTTATTTA
Found at i:21302 original size:18 final size:20
Alignment explanation
Indices: 21273--21327 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 20
21263 GATTAAAAGT
* *
21273 ATAATATTATTTTACTAAT-
1 ATAATTTTATTTTAATAATG
21292 AT-ATTTTATTTTAATAATG
1 ATAATTTTATTTTAATAATG
*
21311 ATAATTTTGTTTTAATA
1 ATAATTTTATTTTAATA
21328 GTTTATGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 14 0.45
19 4 0.13
20 13 0.42
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
ATAATTTTATTTTAATAATG
Found at i:21323 original size:20 final size:18
Alignment explanation
Indices: 21279--21327 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
21269 AAGTATAATA
*
21279 TTATTTTACTAATATATT
1 TTATTTTAATAATATATT
21297 TTATTTTAATAATGATAATT
1 TTATTTTAATAAT-AT-ATT
*
21317 TTGTTTTAATA
1 TTATTTTAATA
21328 GTTTATGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 12 0.44
19 2 0.07
20 13 0.48
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (18 bp):
TTATTTTAATAATATATT
Found at i:27657 original size:16 final size:16
Alignment explanation
Indices: 27636--27667 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
27626 AAATATATCC
27636 AGTGCTTCTGTTGAAG
1 AGTGCTTCTGTTGAAG
27652 AGTGCTTCTGTTGAAG
1 AGTGCTTCTGTTGAAG
27668 CAAAATGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.31, T:0.38
Consensus pattern (16 bp):
AGTGCTTCTGTTGAAG
Found at i:28567 original size:3 final size:3
Alignment explanation
Indices: 28556--28616 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
28546 TTTTTTTCCG
** * *
28556 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TCA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28601 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
28617 CAAATTTTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 4 0.08
3 41 0.85
4 3 0.06
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:36457 original size:36 final size:35
Alignment explanation
Indices: 36369--36467 Score: 128
Period size: 36 Copynumber: 2.8 Consensus size: 35
36359 AGTTTCCTTC
*
36369 GAAAACAAATTTTGTCTCGCTTGAGAC-AGTTCTT
1 GAAAACAAATTTTGTCTCGCTTGAGACAAGTTATT
* * *
36403 GAAAAACAAATTTTGTCTCACTTAAGACAATTTATCT
1 G-AAAACAAATTTTGTCTCGCTTGAGACAAGTTAT-T
*
36440 GAAAACAAATTTCGTCTCGCTTGAGACA
1 GAAAACAAATTTTGTCTCGCTTGAGACA
36468 TTTTTCCTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
34 1 0.02
35 24 0.44
36 28 0.51
37 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (35 bp):
GAAAACAAATTTTGTCTCGCTTGAGACAAGTTATT
Found at i:36561 original size:106 final size:105
Alignment explanation
Indices: 36441--36726 Score: 436
Period size: 106 Copynumber: 2.7 Consensus size: 105
36431 AATTTATCTG
36441 AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGCTTCACT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGCTTCACT
36506 TGAAACAAAATTAATCTCACTTGAGATTGTTGTTT-TTAAAA
66 TGAAACAAAATTAATCTCACTTGAGATTGTTGTTTATT--AA
*
36547 AAAACAAATTTCGTCTCGCTTGAGACATTTTTTCCTTTGA-AAACAAATTTTGAATTTGCTTCAC
1 AAAACAAATTTCGTCTCGCTTGAGACA-TTTTTCCTTTGAGATACAAATTTTGAATTTGCTTCAC
**
36611 TTGAAACAAAATTAATCTCACTTGAGATTGTTGTTTATTTC
65 TTGAAACAAAATTAATCTCACTTGAGATTGTTGTTTATTAA
* * * * *
36652 AAAACAAATTTCGTCTCGCTTGAGACATTTTTTCTATGAGATACAAA-TTTAAATTTG-TTGTAT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGCTT-CAC
36715 TTGAAACAAAAT
65 TTGAAACAAAAT
36727 AAACACCTTT
Statistics
Matches: 167, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
103 2 0.01
104 32 0.19
105 33 0.20
106 86 0.51
107 14 0.08
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.40
Consensus pattern (105 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGCTTCACT
TGAAACAAAATTAATCTCACTTGAGATTGTTGTTTATTAA
Found at i:37050 original size:95 final size:93
Alignment explanation
Indices: 36951--37128 Score: 207
Period size: 94 Copynumber: 1.9 Consensus size: 93
36941 ACATTTTAGA
* ** *
36951 TCGTTTCTATTAAAACAAATTTTGTTTCCCTTGAGGCAGTTTCTCTATAAATACAA-A-ATCTTT
1 TCGTTTCCATTAAAACAAATTTTCATT--CTTGAGACAGTTTCTCT-TAAA-ACAAGACATCTTT
*
37014 GAGGTTGTTTCTCTTAAAAAACCATCTTTGAG
62 GAGGTTGTTTCTCTGAAAAAACCATCTTTGAG
* * * *
37046 TCGTTTCCCTTGAAACGAATTTTCATTCTTGAGACATTTTCTCTTAAAACAAGATCATCTTTGAG
1 TCGTTTCCATTAAAACAAATTTTCATTCTTGAGACAGTTTCTCTTAAAACAAGA-CATCTTTGAG
*
37111 TTTGTTTCTCTGAAAAAA
65 GTTGTTTCTCTGAAAAAA
37129 AATGTTTTAT
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
91 4 0.06
92 5 0.07
93 15 0.21
94 25 0.36
95 21 0.30
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (93 bp):
TCGTTTCCATTAAAACAAATTTTCATTCTTGAGACAGTTTCTCTTAAAACAAGACATCTTTGAGG
TTGTTTCTCTGAAAAAACCATCTTTGAG
Found at i:37313 original size:36 final size:36
Alignment explanation
Indices: 37240--37314 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
37230 AACAAACATC
*
37240 TTTGAGATCATTTCCCTTTAAACGAATTTTGTCTCA
1 TTTGAGATCATTTCCCTTTAAACGAATTTTGACTCA
* *
37276 TTTGAGA-CAGTTTTCCTTTAAAC-AATCTTTGAGTCA
1 TTTGAGATCA-TTTCCCTTTAAACGAAT-TTTGACTCA
37312 TTT
1 TTT
37315 CTTTTGAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 5 0.15
36 29 0.85
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.45
Consensus pattern (36 bp):
TTTGAGATCATTTCCCTTTAAACGAATTTTGACTCA
Found at i:37331 original size:63 final size:62
Alignment explanation
Indices: 37233--37350 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 62
37223 GAAATAAAAC
*
37233 AAACATCTTTGAGATCATTTCCCTTTAAACGAATTTTGTCTCATTTGAGACAGTTTTCCTTT
1 AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTCATTTGAGACAGTTTTCCTTT
* *
37295 AAACAATCTTTGAG-TCATTT-CTTTTGAAACAAAATTTTGTCTCTTTTGAGACAGTT
1 AAAC-ATCTTTGAGATCATTTCCCTTT-AAAC-AAATTTTGTCTCATTTGAGACAGTT
37351 GCTTTTGAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
61 4 0.08
62 14 0.28
63 32 0.64
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (62 bp):
AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTCATTTGAGACAGTTTTCCTTT
Found at i:37500 original size:40 final size:40
Alignment explanation
Indices: 37445--37766 Score: 211
Period size: 40 Copynumber: 7.6 Consensus size: 40
37435 TGGCCAGCCG
*
37445 TCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATC
* * * *
37485 TCCTCATCACGTAGGAGCCGTGTCAACCACAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAG---ACCAGATC
* * *
37527 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGATC
* *
37574 TCTTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATC
* * * * *
37614 TCTTCATCACGTATGAGCCGTGTCA-CCCTAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAG---ACCAGATC
* * *
37655 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGATC
* * **
37702 TCTTCATCACGTATGAGTCGTGTCATTCCCC-GACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCA-TCCCCAGACCAGATC
* *
37742 TCTTCATCACGTAGGAGCCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCA
37767 CCCTTAGATG
Statistics
Matches: 223, Mismatches: 35, Indels: 48
0.73 0.11 0.16
Matches are distributed among these distances:
39 5 0.02
40 85 0.38
41 1 0.00
42 27 0.12
43 37 0.17
44 3 0.01
45 2 0.01
46 59 0.26
47 4 0.02
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.25
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATC
Found at i:37724 original size:46 final size:45
Alignment explanation
Indices: 37531--37714 Score: 179
Period size: 46 Copynumber: 4.2 Consensus size: 45
37521 CCAGCCGTCC
37531 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAACCGTGTTATCACC-TTAGATGGCCAGAACTCT
* * * *
37577 TCATCATGTAGGAACCGTGTCATC-CC-CAGA---CCAGATCTCT
1 TCATCACGTAGGAACCGTGTTATCACCTTAGATGGCCAGAACTCT
* * * ** * *
37617 TCATCACGTATGAGCCGTG---TCACCCTAGATAACCAG-CCGTCC
1 TCATCACGTAGGAACCGTGTTATCACCTTAGATGGCCAGAAC-TCT
37659 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAACCGTGTTATCACC-TTAGATGGCCAGAACTCT
37705 TCATCACGTA
1 TCATCACGTA
37715 TGAGTCGTGT
Statistics
Matches: 110, Mismatches: 17, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
37 2 0.02
38 2 0.02
39 3 0.03
40 25 0.23
41 1 0.01
42 23 0.21
43 3 0.03
45 7 0.06
46 43 0.39
47 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (45 bp):
TCATCACGTAGGAACCGTGTTATCACCTTAGATGGCCAGAACTCT
Found at i:37732 original size:129 final size:128
Alignment explanation
Indices: 37427--37781 Score: 563
Period size: 128 Copynumber: 2.8 Consensus size: 128
37417 AACCATAACT
* * *
37427 CCTTTAGATGGCCAG-CCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTCA
1 CCTTTAGATGGCCAGAAC-TCTTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCA
37491 TCACGTAGGAGCCGTGTCAACCAC-AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC
65 TCACGTAGGAGCCGTGTC-ACC-CTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC
37555 A
128 A
37556 CCTTTAGATGGCCAGAACTCTTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCAT
1 CCTTTAGATGGCCAGAACTCTTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCAT
*
37621 CACGTATGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
66 CACGTAGGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
* * **
37684 CCTTTAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATTCCCC-GACCAGATCTCTTCA
1 CCTTTAGATGGCCAGAACTCTTCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTCA
*
37748 TCACGTAGGAGCCGTGTCACCCTTAGATGACCAG
65 TCACGTAGGAGCCGTGTCACCC-TAGATAACCAG
37782 ACCTCTTCAT
Statistics
Matches: 212, Mismatches: 10, Indels: 8
0.92 0.04 0.03
Matches are distributed among these distances:
127 1 0.00
128 119 0.56
129 91 0.43
130 1 0.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (128 bp):
CCTTTAGATGGCCAGAACTCTTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCAT
CACGTAGGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
Found at i:37798 original size:43 final size:43
Alignment explanation
Indices: 37476--37808 Score: 227
Period size: 43 Copynumber: 7.8 Consensus size: 43
37466 GTCATCCCCA
* * * **
37476 GACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCACAGAT
1 GACCAGACCTCTTCATCACGTAGGAGCCGTGTCACCCTTAGAT
* * * *
37519 AACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGAT
1 GACCAGACC-TCTTCATCACGTAGGAGCCGTG---TCACCCTTAGAT
* * * * *
37565 GGCCAGAACTCTTCATCATGTAGGAACCGTGTCATCCC---CA-
1 GACCAGACCTCTTCATCACGTAGGAGCCGTGTCA-CCCTTAGAT
* *
37605 GACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC-TAGAT
1 GACCAGACCTCTTCATCACGTAGGAGCCGTGTCACCCTTAGAT
* * * *
37647 AACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGAT
1 GACCAGACC-TCTTCATCACGTAGGAGCCGTG---TCACCCTTAGAT
* * * * ****
37693 GGCCAGAACTCTTCATCACGTATGAGTCGTGTCA---TTCCCC
1 GACCAGACCTCTTCATCACGTAGGAGCCGTGTCACCCTTAGAT
*
37733 GACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCCTTAGAT
1 GACCAGACCTCTTCATCACGTAGGAGCCGTGTCACCCTTAGAT
** *
37776 GACCAGACCTCTTCATTGCGTAGGAGCAGTGTC
1 GACCAGACCTCTTCATCACGTAGGAGCCGTGTC
37809 GTCCCCACCA
Statistics
Matches: 223, Mismatches: 49, Indels: 36
0.72 0.16 0.12
Matches are distributed among these distances:
39 3 0.01
40 61 0.27
41 3 0.01
42 25 0.11
43 63 0.28
44 2 0.01
45 5 0.02
46 59 0.26
47 2 0.01
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (43 bp):
GACCAGACCTCTTCATCACGTAGGAGCCGTGTCACCCTTAGAT
Found at i:37985 original size:3 final size:3
Alignment explanation
Indices: 37974--38034 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
37964 TTTTTTTCCG
** * *
37974 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TCA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38019 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
38035 CAAATTTTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 4 0.08
3 41 0.85
4 3 0.06
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:40658 original size:15 final size:15
Alignment explanation
Indices: 40621--40658 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
40611 CCCTTTTGTC
40621 TTTAAAAATGATTTT
1 TTTAAAAATGATTTT
*
40636 TCTT-AAAATTATTTT
1 T-TTAAAAATGATTTT
40651 TTTAAAAA
1 TTTAAAAA
40659 AAGACGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
14 2 0.10
15 16 0.80
16 2 0.10
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (15 bp):
TTTAAAAATGATTTT
Found at i:46161 original size:12 final size:12
Alignment explanation
Indices: 46146--46184 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
46136 TTCGAATAAA
46146 TTATGTATTTTT
1 TTATGTATTTTT
*
46158 TTATATATTTTT
1 TTATGTATTTTT
*
46170 TTGTGTATATTTT
1 TTATGTAT-TTTT
46183 TT
1 TT
46185 TTATAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 17 0.74
13 6 0.26
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (12 bp):
TTATGTATTTTT
Found at i:47573 original size:23 final size:23
Alignment explanation
Indices: 47538--47707 Score: 195
Period size: 23 Copynumber: 7.5 Consensus size: 23
47528 AGATGAACAA
* * * *
47538 AAGAATAATAAATGGGTTTTTGG
1 AAGAAGAAGAAATGAGTTTATGG
47561 AAGAAGAAGAAATGAGTTTATGG
1 AAGAAGAAGAAATGAGTTTATGG
* *
47584 AAGAAGAAGAAACGAGTTTATGA
1 AAGAAGAAGAAATGAGTTTATGG
*
47607 AAGAAGAA-AAATGGGTTTATGG
1 AAGAAGAAGAAATGAGTTTATGG
* *
47629 AAGAAGAA-ACGATGAGTTAATGG
1 AAGAAGAAGA-AATGAGTTTATGG
47652 AAGAAGAAGAAA--ATGTTTATGG
1 AAGAAGAAGAAATGA-GTTTATGG
* *
47674 AAGAATAAGAAATGTGTTTATGG
1 AAGAAGAAGAAATGAGTTTATGG
47697 AAGAAGAAGAA
1 AAGAAGAAGAA
47708 TGATTCAAAC
Statistics
Matches: 125, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
21 1 0.01
22 38 0.30
23 85 0.68
24 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.28, T:0.22
Consensus pattern (23 bp):
AAGAAGAAGAAATGAGTTTATGG
Found at i:47628 original size:45 final size:44
Alignment explanation
Indices: 47538--47709 Score: 177
Period size: 45 Copynumber: 3.8 Consensus size: 44
47528 AGATGAACAA
* * * *
47538 AAGAATAATAAATGGGTTTTTGGAAGAAGAAGAAATGAGTTTATGG
1 AAGAAGAAGAAATGAGTTTATGGAAGAAGAA-AAATG-GTTTATGG
* *
47584 AAGAAGAAGAAACGAGTTTATGAAAGAAGAAAAATGGGTTTATGG
1 AAGAAGAAGAAATGAGTTTATGGAAGAAGAAAAAT-GGTTTATGG
* *
47629 AAGAAGAA-ACGATGAGTTAATGGAAGAAGAAGAAAAT-GTTTATGG
1 AAGAAGAAGA-AATGAGTTTATGGAAGAAG-A-AAAATGGTTTATGG
* * *
47674 AAGAATAAGAAATGTGTTTATGGAAGAAGAAGAATG
1 AAGAAGAAGAAATGAGTTTATGGAAGAAGAAAAATG
47710 ATTCAAACTG
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 4 0.04
44 2 0.02
45 66 0.63
46 28 0.27
47 5 0.05
ACGTcount: A:0.48, C:0.01, G:0.28, T:0.23
Consensus pattern (44 bp):
AAGAAGAAGAAATGAGTTTATGGAAGAAGAAAAATGGTTTATGG
Found at i:47656 original size:68 final size:68
Alignment explanation
Indices: 47537--47707 Score: 231
Period size: 68 Copynumber: 2.5 Consensus size: 68
47527 CAGATGAACA
* * *
47537 AAAGAATAATAAATGGGTTTTTGGAAGAAGAAGAAATGAGTTTATGGAAGAAGAAGAAACGA-GT
1 AAAGAATAAGAAATGGGTTTATGGAAGAAGAAGAAATGAGTTAATGGAAGAAGAAGAAA--ATGT
47601 TTATG
64 TTATG
* *
47606 AAAGAAGAA-AAATGGGTTTATGGAAGAAGAA-ACGATGAGTTAATGGAAGAAGAAGAAAATGTT
1 AAAGAATAAGAAATGGGTTTATGGAAGAAGAAGA-AATGAGTTAATGGAAGAAGAAGAAAATGTT
47669 TATG
65 TATG
* *
47673 GAAGAATAAGAAATGTGTTTATGGAAGAAGAAGAA
1 AAAGAATAAGAAATGGGTTTATGGAAGAAGAAGAA
47708 TGATTCAAAC
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
66 1 0.01
67 15 0.17
68 65 0.72
69 9 0.10
ACGTcount: A:0.49, C:0.01, G:0.28, T:0.22
Consensus pattern (68 bp):
AAAGAATAAGAAATGGGTTTATGGAAGAAGAAGAAATGAGTTAATGGAAGAAGAAGAAAATGTTT
ATG
Found at i:50659 original size:16 final size:17
Alignment explanation
Indices: 50624--50664 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
50614 ATGTAACAAT
50624 ATATTATAAAAATTTAAA
1 ATATTA-AAAAATTTAAA
50642 AT-TTAAAAAATATT-AA
1 ATATTAAAAAAT-TTAAA
50658 ATATTAA
1 ATATTAA
50665 TTTTATTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.48
17 9 0.43
18 2 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATTAAAAAATTTAAA
Found at i:51152 original size:21 final size:21
Alignment explanation
Indices: 51126--51176 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
51116 CGACCCGAAA
51126 TAATAAAAAATTATTTTTATT
1 TAATAAAAAATTATTTTTATT
51147 TAATAAAAAATTATTTTTATT
1 TAATAAAAAATTATTTTTATT
51168 TAATAAAAA
1 TAATAAAAA
51177 CAGTTAATTG
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATAAAAAATTATTTTTATT
Found at i:51365 original size:267 final size:267
Alignment explanation
Indices: 50876--51423 Score: 768
Period size: 267 Copynumber: 2.0 Consensus size: 267
50866 CGGCCCGAAA
50876 TAATAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATTATATAGAGGAG
1 TAATAAAAAATTATTTTTATTCAATAAAAACAG-GA-TTAATTG-AAAAAAATTATATAGAGGAG
* *
50941 TATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATTTTTTTTGGCCGGGTCGGGTATT
63 TATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTT-G-CGGGTCGGGTATT
* * *
51006 TTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAAACCGACCTGACCCG
126 TTTCACCCTAAACCCGAACTCGACCCGACCCAAATATCACACTT-AAAAAAACCGACCCGACCCA
* *
51071 ACCAAAATAAAGTTTCACCCAACCCGAATATATGAATTAG-AA-ACCCGACCCGAAATAATAAAA
190 ACCAAAATAAAGTTGCACCCAACCCGAATATATAAATTAGAAACACCCGACCCGAAATAATAAAA
*
51134 AATTATTTTTATT
255 AAATATTTTTATT
* *
51147 TAATAAAAAATTATTTTTATTTAATAAAAACA-G-TTAATTG-AAAAAATTATGTATAGAGGGGT
1 TAATAAAAAATTATTTTTATTCAATAAAAACAGGATTAATTGAAAAAAATTA--TATAGAGGAGT
* *
51209 ATTATTGTAATTATTCTTAAATATATAAGGTAAAATTATATATATTTT-CGGGTCTGGTATTTTT
64 ATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTGCGGGTCGGGTATTTTT
* *
51273 CACCCTAAACTCGAACTCGACCCGACCCAAATATCACACTT-AAAAAACCGACCCGACCCAATCA
129 CACCCTAAACCCGAACTCGACCCGACCCAAATATCACACTTAAAAAAACCGACCCGACCCAACCA
51337 AAATAAAGTTGCACCCGACCCGACCCGAATATATAAATTAGAAACCCGACCCGACCCGAAATAAT
194 AAATAAAGTTGCACCC-A----ACCCGAATATATAAATTAGAAA--C-ACCCGACCCGAAATAAT
51402 AAAAAAATATTTTTATT
251 AAAAAAATATTTTTATT
*
51419 CAATA
1 TAATA
51424 TATGAATAAG
Statistics
Matches: 250, Mismatches: 15, Indels: 23
0.87 0.05 0.08
Matches are distributed among these distances:
262 35 0.14
263 1 0.00
264 54 0.22
265 9 0.04
267 80 0.32
268 2 0.01
269 1 0.00
271 31 0.12
272 37 0.15
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (267 bp):
TAATAAAAAATTATTTTTATTCAATAAAAACAGGATTAATTGAAAAAAATTATATAGAGGAGTAT
TATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTGCGGGTCGGGTATTTTTCA
CCCTAAACCCGAACTCGACCCGACCCAAATATCACACTTAAAAAAACCGACCCGACCCAACCAAA
ATAAAGTTGCACCCAACCCGAATATATAAATTAGAAACACCCGACCCGAAATAATAAAAAAATAT
TTTTATT
Done.