Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003786.1 Hibiscus syriacus cultivar Beakdansim tig00008104_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: 57934
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:3322 original size:14 final size:14
Alignment explanation
Indices: 3300--3342 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3290 CACATCATTC
3300 ATCATATAAATCAT
1 ATCATATAAATCAT
* *
3314 ATGATATAATTCAT
1 ATCATATAAATCAT
*
3328 ATCATA-AAAGCAT
1 ATCATATAAATCAT
3341 AT
1 AT
3343 ACTTTACATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.35
Consensus pattern (14 bp):
ATCATATAAATCAT
Found at i:4177 original size:24 final size:20
Alignment explanation
Indices: 4120--4182 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 20
4110 TTTCCCTTGA
*
4120 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
4140 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
4163 ATGTGCATCGATGCACTCCT
1 A-GTGCATCGATGCA-TCCT
4183 TAGCATCGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 14 0.40
21 1 0.03
22 1 0.03
23 4 0.11
24 14 0.40
25 1 0.03
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:4183 original size:24 final size:22
Alignment explanation
Indices: 4120--4184 Score: 71
Period size: 24 Copynumber: 2.9 Consensus size: 22
4110 TTTCCCTTGA
*
4120 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATCCTTAAC
*
4140 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CCTTAAC
4163 ATGTGCATCGATGCACTCCTTA
1 A-GTGCATCGATGCA-TCCTTA
4185 GCATCGATGC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 14 0.38
21 1 0.03
22 1 0.03
23 3 0.08
24 17 0.46
25 1 0.03
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATCCTTAAC
Found at i:6234 original size:11 final size:10
Alignment explanation
Indices: 6201--6246 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
6191 TTAGCTTTAT
6201 ATTTTTATTG
1 ATTTTTATTG
* *
6211 AATTTTAAT-
1 ATTTTTATTG
6220 -TTTTTATTG
1 ATTTTTATTG
6229 CATTTTTATTG
1 -ATTTTTATTG
6240 ATTTTTA
1 ATTTTTA
6247 AAAAAGTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
8 6 0.21
10 14 0.48
11 9 0.31
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (10 bp):
ATTTTTATTG
Found at i:6373 original size:316 final size:311
Alignment explanation
Indices: 5903--6980 Score: 1328
Period size: 316 Copynumber: 3.4 Consensus size: 311
5893 TATATTATTT
* * * * *
5903 TTTTTTATTGCATTTTATTGATTTTTTTTAAAAAATTACTAATAATTTATTTGATCTATCATTTG
1 TTTTTTATTGCATTTTATTGA--TTTTTAAAAAAATGAATAATAATTCATTTGATCTATCAATTG
*
5968 TAATT-AAAGTTTATTTTAATAATTTTTATTTTTAAACAATTAATATTAAAAGT-TAAAACATTA
64 TAATTAAAAGTTTATTTTAAT-ATTTTTATTTTTAAACAATTAATATTAAAAGTCAAAAACATTA
* * * *
6031 TAAATTTTTTTAAAAAATAAAAAAATATTAAAACAAACTTTTAAATAATTTAACAATAGTTAATA
128 TTAA-TTTTTT-AAAAATATAAAAATATTAAAATAAACTTTTAAATATTTTAACAATAGTTAATA
6096 ATGTTTATTTCATTTTTAATAAAATTAGAATTTAATATTT-TTTTATATTTTTTAATTAATATTA
191 ATGTTTATTT-ATTTTTAATAAAATTA-AATTTAATATTTATTTTATATTTTTTAA-TAATATTA
6160 TAATAATATTTTAAATAAAGAGGTGATATTTTTAGCTTTATATTTTTATTGAATTTTAA
253 TAATAATATTTTAAATAAAGAGGTGATATTTTTAGCTTTATATTTTTATTGAATTTTAA
*
6219 TTTTTTATTGCATTTTTATTGATTTTTAAAAAAGTGAATAATAATTCATTTGATCTATCAATTGT
1 TTTTTTATTGCA-TTTTATTGATTTTTAAAAAAATGAATAATAATTCATTTGATCTATCAATTGT
6284 AATT-AAAGTTTA-TTTAATATTTTATATTTTTAAACAATTAATATTAAAAGTCAACAAACATTA
65 AATTAAAAGTTTATTTTAATATTTT-TATTTTTAAACAATTAATATTAAAAGTCAA-AAACATTA
* *
6347 TTAATAATTTTTAAAAATATAAAAATATTAAAATAAACTTTTAAATTTTTTAACAACAGTTAATA
128 TTAAT--TTTTTAAAAATATAAAAATATTAAAATAAACTTTTAAATATTTTAACAATAGTTAATA
* *
6412 ATGTTT-TTTGATTTTTAATAAAATTAAAATTTAATATTTATTTAATAATTTTTAA-AATTAATT
191 ATGTTTATTT-ATTTTTAATAAAATT-AAATTTAATATTTATTTTATATTTTTTAATAA-T-ATT
* * * *
6475 ATTAAGAATA-TTTAAATAAATAGGTGATATTTTTTATCTTTTTATTATTTTTAATGAATTTT-A
252 A-TAATAATATTTTAAATAAAGAGGTGATA-TTTTTAGC--TTTA-TATTTTTATTGAATTTTAA
* * *
6538 TTTTTTATTACATTTTTATTGA-TTTTAAAAAAATAAATAATAATTCATTTGATTTAT-AATTGT
1 TTTTTTATTGCA-TTTTATTGATTTTTAAAAAAATGAATAATAATTCATTTGATCTATCAATTGT
* *
6601 AATTAAAAGTTTGTTTTAATATTTTATATTTTTAAACAATT-ATATT-AAA-TCAATAACATTAT
65 AATTAAAAGTTTATTTTAATATTTT-TATTTTTAAACAATTAATATTAAAAGTCAAAAACATTAT
* *
6663 TAATTGTTTAAAAATATAAAAATATT-AAATAAACTTTTAAA-ATTTTTAATAATAGTTTAAT-A
129 TAATTTTTTAAAAATATAAAAATATTAAAATAAACTTTTAAATA-TTTTAACAATAG-TTAATAA
** * *
6725 TAATTATTTATTTTTAAT-AAATTATATTTAATATTTATTTTATTTTTTTTAAATAATATTATAA
192 TGTTTATTTATTTTTAATAAAATTAAATTTAATATTTATTTTATATTTTTT-AATAATATTAT-A
6789 ATAATATTTTAAATAAAGAGGTGATATTTTTAGCTTTATATTCTCTTTATTGAATTTTATTAAAT
255 ATAATATTTTAAATAAAGAGGTGATATTTTTAGCTTTATA-T-T-TTTATTG----------AAT
6854 TTTAA
307 TTTAA
* * * *
6859 TTTTTTATTGTATTTTATTGATTTTTGAAAAAAAAAGAATAATAATTCATTTAATATATCAATTG
1 TTTTTTATTGCATTTTATTGATTTTT--AAAAAAATGAATAATAATTCATTTGATCTATCAATTG
6924 TAATTAAAAGTTTATTTTAATATTTTTATATTTTAAACAATTAATATTAAAAGTCAA
64 TAATTAAAAGTTTATTTTAATATTTTTAT-TTTTAAACAATTAATATTAAAAGTCAA
6981 TACATTTAAA
Statistics
Matches: 669, Mismatches: 47, Indels: 81
0.84 0.06 0.10
Matches are distributed among these distances:
307 2 0.00
308 5 0.01
309 2 0.00
310 46 0.07
311 26 0.04
312 40 0.06
313 34 0.05
314 35 0.05
315 94 0.14
316 117 0.17
317 41 0.06
318 44 0.07
319 53 0.08
320 31 0.05
321 15 0.02
323 30 0.04
324 42 0.06
325 5 0.01
326 3 0.00
327 4 0.01
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (311 bp):
TTTTTTATTGCATTTTATTGATTTTTAAAAAAATGAATAATAATTCATTTGATCTATCAATTGTA
ATTAAAAGTTTATTTTAATATTTTTATTTTTAAACAATTAATATTAAAAGTCAAAAACATTATTA
ATTTTTTAAAAATATAAAAATATTAAAATAAACTTTTAAATATTTTAACAATAGTTAATAATGTT
TATTTATTTTTAATAAAATTAAATTTAATATTTATTTTATATTTTTTAATAATATTATAATAATA
TTTTAAATAAAGAGGTGATATTTTTAGCTTTATATTTTTATTGAATTTTAA
Found at i:6543 original size:27 final size:26
Alignment explanation
Indices: 6506--6564 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
6496 AGGTGATATT
6506 TTTTATCTTTTTATT-ATTTTTAATGAA
1 TTTTA-CTTTTTATTAATTTTTAATG-A
* *
6533 TTTTATTTTTTATTACATTTTTATTGA
1 TTTTACTTTTTATTA-ATTTTTAATGA
6560 TTTTA
1 TTTTA
6565 AAAAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 8 0.29
27 11 0.39
28 9 0.32
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.69
Consensus pattern (26 bp):
TTTTACTTTTTATTAATTTTTAATGA
Found at i:6778 original size:32 final size:32
Alignment explanation
Indices: 6705--6797 Score: 93
Period size: 32 Copynumber: 2.9 Consensus size: 32
6695 ACTTTTAAAA
6705 TTTTT-AATAATAGTTTAATATAATTATTTATTT
1 TTTTTAAATAATA-TTTAATAT-ATTATTTATTT
** *
6738 TTAATAAATTATATTTAATAT-TTATTTTATTT
1 TTTTTAAATAATATTTAATATATTA-TTTATTT
*
6770 TTTTTAAATAATATTATAA-ATAATATTT
1 TTTTTAAATAATATT-TAATATATTATTT
6798 TAAATAAAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
31 3 0.06
32 24 0.49
33 16 0.33
34 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (32 bp):
TTTTTAAATAATATTTAATATATTATTTATTT
Found at i:6791 original size:12 final size:12
Alignment explanation
Indices: 6774--6804 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6764 TTATTTTTTT
6774 TAAATAATATTA
1 TAAATAATATTA
*
6786 TAAATAATATTT
1 TAAATAATATTA
6798 TAAATAA
1 TAAATAA
6805 AGAGGTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAAATAATATTA
Found at i:6794 original size:37 final size:36
Alignment explanation
Indices: 6728--6797 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
6718 TTTAATATAA
**
6728 TTATTTATTTTTAATAAATTATATTTAATATTTATT
1 TTATTTATTTTTAATAAATTATAAATAATATTTATT
6764 TTATTT-TTTTTAAATAATATTATAAATAATATTT
1 TTATTTATTTTT-AATAA-ATTATAAATAATATTT
6798 TAAATAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 5 0.17
36 11 0.37
37 14 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (36 bp):
TTATTTATTTTTAATAAATTATAAATAATATTTATT
Found at i:7891 original size:318 final size:313
Alignment explanation
Indices: 7343--8071 Score: 1024
Period size: 319 Copynumber: 2.3 Consensus size: 313
7333 AAAATGATGA
* * *
7343 AATAATTCATTTGATCTATCAATTGTAATTAAAAGTTTATTTAATAATTTTATTTTTTAAACAAT
1 AATAATTCATTTGATCTATCAATTGTAATTAAAAGTTTTTTTAATATTTTTATATTTTAAACAA-
* *
7408 TAATATTAAAAGTCGAAAAATATTATTAATTGTTTAAAAATATAAAAAATATTAAAACAAACTTT
65 TAATATTAAAAGTC-AATAACATTATTAATTGTTTAAAAATATAAAAAATATTAAAACAAACTTT
* *
7473 TAAATTTTTTAACAACAATTAATAATGTTTATTCATTTTTAATAAATTAGAATTAATATTTATTT
129 TAAATTTTTTAACAACAA-TAATAATATTTATT-ATTTTTAATAAATTAAAATTAATATTTATTT
* * *
7538 TATAGTTTTTAAAATAATATTATAAATGAATTTTAAATAAATAGGTGATATTTTTTAGCTTTATA
192 TATAGTTTTTAAAATAATATTATAAATAAATTTTAAATAAAGAGATGATATTTTTTAGCTTTATA
*
7603 -TTATTTATTGAATTTTAATTTTTTATTACATTTTTATTGATTTTTTTAAAAATGTGAAT
257 TTTATTTATTGAATTTTAATTTTTTATTACATTTTTATT-A-TTTTTGAAAAA-GTGAAT
* *
7662 AATAATTCATTTAATCTATTAATTGTAATTAAAAGTTTGTTTTAATATTTTTATATTTTAAACAA
1 AATAATTCATTTGATCTATCAATTGTAATTAAAAGTTT-TTTTAATATTTTTATATTTTAAACAA
*
7727 TAATATTAAAAGTCAATAACATTATTAATTGTTTAAAAATATAAAAAATATTAAAATAAACTTTT
65 TAATATTAAAAGTCAATAACATTATTAATTGTTTAAAAATATAAAAAATATTAAAACAAACTTTT
*
7792 AAATTTTTTTAACAAC-A-AATAATATTTGTT-TTTTTAATAAAATTAAAATTTAATATTTATTT
130 AAA-TTTTTTAACAACAATAATAATATTTATTATTTTTAAT-AAATTAAAA-TTAATATTTATTT
*
7854 TATATTTTTTAAAATTAATATTATAAATAATATTTTAAATAAAGAGATGATATTTTTTAGCTTTA
192 TATAGTTTTTAAAA-TAATATTATAAATAA-ATTTTAAATAAAGAGATGATATTTTTTAGCTTTA
* * **
7919 TATTCTTTTTTTATTGAATTTTATTTTTTTATTGTATTTTTATTATTTTTGAAAAAGTGAAT
255 TA---TTTATTTATTGAATTTTAATTTTTTATTACATTTTTATTATTTTTGAAAAAGTGAAT
* *
7981 AATAATTCATTTGATATATCAATTGTAATTAAAAATTTATTTTAA-ATTTTTATATTTTTAAA-A
1 AATAATTCATTTGATCTATCAATTGTAATTAAAAGTTT-TTTTAATATTTTTATA-TTTTAAACA
*
8044 A-ATTATTAAAAGTCAATAAACATT-TTAA
64 ATAATATTAAAAGTCAAT-AACATTATTAA
8072 AAAATATCAC
Statistics
Matches: 372, Mismatches: 26, Indels: 26
0.88 0.06 0.06
Matches are distributed among these distances:
314 8 0.02
315 8 0.02
316 37 0.10
317 33 0.09
318 103 0.28
319 115 0.31
320 33 0.09
321 1 0.00
322 34 0.09
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (313 bp):
AATAATTCATTTGATCTATCAATTGTAATTAAAAGTTTTTTTAATATTTTTATATTTTAAACAAT
AATATTAAAAGTCAATAACATTATTAATTGTTTAAAAATATAAAAAATATTAAAACAAACTTTTA
AATTTTTTAACAACAATAATAATATTTATTATTTTTAATAAATTAAAATTAATATTTATTTTATA
GTTTTTAAAATAATATTATAAATAAATTTTAAATAAAGAGATGATATTTTTTAGCTTTATATTTA
TTTATTGAATTTTAATTTTTTATTACATTTTTATTATTTTTGAAAAAGTGAAT
Found at i:7946 original size:19 final size:19
Alignment explanation
Indices: 7924--7968 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
7914 CTTTATATTC
7924 TTTTTTTATTG-AATTTTA
1 TTTTTTTATTGTAATTTTA
*
7942 TTTTTTTATTGTATTTTTA
1 TTTTTTTATTGTAATTTTA
7961 TTATTTTT
1 TT-TTTTT
7969 GAAAAAGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 11 0.46
19 8 0.33
20 5 0.21
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (19 bp):
TTTTTTTATTGTAATTTTA
Found at i:8306 original size:18 final size:19
Alignment explanation
Indices: 8280--8321 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
8270 ACAAAAGTGT
*
8280 TAAATTGATAAAT-AAAGA
1 TAAAATGATAAATGAAAGA
* *
8298 TAAAATGATATATGACAGA
1 TAAAATGATAAATGAAAGA
8317 TAAAA
1 TAAAA
8322 AAAAATTGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.60, C:0.02, G:0.12, T:0.26
Consensus pattern (19 bp):
TAAAATGATAAATGAAAGA
Found at i:27602 original size:37 final size:37
Alignment explanation
Indices: 27560--27686 Score: 119
Period size: 37 Copynumber: 3.6 Consensus size: 37
27550 CTTTTGAAAA
27560 AAATAATAA-CTAAGTGACCAAATAGGTAGTTTAACCT
1 AAATAATAATC-AAGTGACCAAATAGGTAGTTTAACCT
* * *
27597 AAATAATAATCGAGTGACCTAAACA--TA----AA-TT
1 AAATAATAATCAAGTGACC-AAATAGGTAGTTTAACCT
* *
27628 AGATAATATAT-AAGTGACCAAATAGGTAGTTTACCCT
1 AAATAATA-ATCAAGTGACCAAATAGGTAGTTTAACCT
27665 AAATAATAATCAAGTGACCAAA
1 AAATAATAATCAAGTGACCAAA
27687 ACATAAATTA
Statistics
Matches: 70, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
30 4 0.06
31 15 0.21
32 6 0.09
36 5 0.07
37 35 0.50
38 5 0.07
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (37 bp):
AAATAATAATCAAGTGACCAAATAGGTAGTTTAACCT
Found at i:27644 original size:31 final size:31
Alignment explanation
Indices: 27609--27717 Score: 78
Period size: 31 Copynumber: 3.4 Consensus size: 31
27599 ATAATAATCG
*
27609 AGTGACCTAAACATAAATTAGATAATATATA
1 AGTGACCTAAACATAAATTACATAATATATA
* ** *
27640 AGTGACC-AAATAGGTAGTTTACCCTAAATAATAATCA
1 AGTGACCTAAACA--TAAATTA-CAT-AAT-AT-AT-A
* *
27677 AGTGACCAAAACATAAATTATATAATATATA
1 AGTGACCTAAACATAAATTACATAATATATA
27708 AGTGA-CTAAA
1 AGTGACCTAAA
27718 TAGGTAGTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 17
0.68 0.13 0.20
Matches are distributed among these distances:
30 8 0.14
31 13 0.22
32 7 0.12
33 3 0.05
34 6 0.10
35 3 0.05
36 7 0.12
37 8 0.14
38 4 0.07
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.28
Consensus pattern (31 bp):
AGTGACCTAAACATAAATTACATAATATATA
Found at i:27671 original size:68 final size:68
Alignment explanation
Indices: 27560--27803 Score: 366
Period size: 68 Copynumber: 3.6 Consensus size: 68
27550 CTTTTGAAAA
*
27560 AAATAATA-ACTAAGTGACCAAATAGGTAGTTTAACCTAAATAATAATCGAGTGACCTAAACATA
1 AAATAATATA-TAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGTGACCTAAACATA
27624 AATT
65 AATT
* * *
27628 AGATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCAAGTGACCAAAACATAA
1 AAATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGTGACCTAAACATAA
27693 ATT
66 ATT
* * * * *
27696 ATATAATATATAAGTGACTAAATAGGTAGTTTACCCTAAATAAAAATTGAGCGA-CTAAAACATA
1 AAATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGTGACCT-AAACATA
27760 AATT
65 AATT
*
27764 AAATAATATATAAGTGACCAAATATGTAGTTTACCCTAAA
1 AAATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAA
27804 AAAACTTCCC
Statistics
Matches: 160, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
67 1 0.01
68 158 0.99
69 1 0.01
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.28
Consensus pattern (68 bp):
AAATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGTGACCTAAACATAA
ATT
Found at i:36632 original size:19 final size:19
Alignment explanation
Indices: 36589--36633 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
36579 GGGCTTGAAC
36589 TTCATTAAAAAAGTTTAAA
1 TTCATTAAAAAAGTTTAAA
*
36608 TGTCATTTAAAAA-TTTAAAA
1 T-TCATTAAAAAAGTTT-AAA
36628 TTCATT
1 TTCATT
36634 GTTCATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (19 bp):
TTCATTAAAAAAGTTTAAA
Found at i:43812 original size:41 final size:41
Alignment explanation
Indices: 43767--43887 Score: 197
Period size: 41 Copynumber: 3.0 Consensus size: 41
43757 AATGACCAAC
* *
43767 AAAATCGCAATGCGATTTTCCATTTCGCGTTGAGATAGTTG
1 AAAATCGCATTGCGATTTTCCATTTCGCGTTGCGATAGTTG
* *
43808 AAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTT
1 AAAATCGCATTGCGATTTTCCATTTCGCGTTGCGATAGTTG
*
43849 AAAATCGCATTGCGATTTTTCATTTCGCGTTGCGATAGT
1 AAAATCGCATTGCGATTTTCCATTTCGCGTTGCGATAGT
43888 CTACAGTTGT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.37
Consensus pattern (41 bp):
AAAATCGCATTGCGATTTTCCATTTCGCGTTGCGATAGTTG
Found at i:43837 original size:20 final size:20
Alignment explanation
Indices: 43777--43884 Score: 83
Period size: 20 Copynumber: 5.3 Consensus size: 20
43767 AAAATCGCAA
43777 TGCGATTTTCCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
* * ** **
43797 TGAGATAGTTGAAAATCGCGT
1 TGCGAT-TTTCCATTTCGCGT
43818 TGCGATTTTCCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
* ** *
43838 TGCGATAGTTT-AAAATCGCAT
1 TGCGAT--TTTCCATTTCGCGT
*
43859 TGCGATTTTTCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
43879 TGCGAT
1 TGCGAT
43885 AGTCTACAGT
Statistics
Matches: 64, Mismatches: 20, Indels: 8
0.70 0.22 0.09
Matches are distributed among these distances:
19 3 0.05
20 32 0.50
21 26 0.41
22 3 0.05
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (20 bp):
TGCGATTTTCCATTTCGCGT
Found at i:43910 original size:41 final size:40
Alignment explanation
Indices: 43767--43933 Score: 185
Period size: 41 Copynumber: 4.1 Consensus size: 40
43757 AATGACCAAC
** *
43767 AAAATCGCAATGCGATTTTCCATTTCGCGTTGAGATAGTT
1 AAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTT
43807 GAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTT
1 -AAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAG-TT
* *
43849 AAAATCGCATTGCGATTTTTCATTTCGCGTTGCGATAGTCT
1 AAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-T
* * * * *
43890 ACAGTTGTCGTTGCGATTTTCCAAATT--CGTTGTGATAGTT
1 AAAATCG-CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTT
43930 AAAA
1 AAAA
43934 AAAAAGATTT
Statistics
Matches: 108, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
40 4 0.04
41 87 0.81
42 14 0.13
43 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (40 bp):
AAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTT
Found at i:43921 original size:82 final size:81
Alignment explanation
Indices: 43767--43934 Score: 205
Period size: 82 Copynumber: 2.0 Consensus size: 81
43757 AATGACCAAC
*
43767 AAAATCGCAATGCGATTTTCCATTTCGCGTTGAGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 AAAATCGCAATGCGATTTTCCATTTCGCGTTGAGATAGTTGAAAATCGCGTTGCGATTTTCCAAT
*
43832 TCGCGTTGCGATAGTTT
66 TC-CGTTGCGATAGTTA
* * * * * *
43849 AAAATCGCATTGCGATTTTTCATTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCA
1 AAAATCGCAATGCGATTTTCCATTTCGCGTTGAGATAGT-TGAAAATCG-CGTTGCGATTTTCC-
*
43913 AATT-CGTTGTGATAGTTA
63 AATTCCGTTGCGATAGTTA
43931 AAAA
1 AAAA
43935 AAAAGATTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
82 56 0.76
83 15 0.20
84 3 0.04
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (81 bp):
AAAATCGCAATGCGATTTTCCATTTCGCGTTGAGATAGTTGAAAATCGCGTTGCGATTTTCCAAT
TCCGTTGCGATAGTTA
Found at i:44038 original size:5 final size:6
Alignment explanation
Indices: 44006--44041 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
43996 AACACGTATT
44006 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG AC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG AC
44042 GACGGACGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 9 0.30
6 21 0.70
ACGTcount: A:0.31, C:0.53, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:44704 original size:20 final size:20
Alignment explanation
Indices: 44681--44835 Score: 157
Period size: 20 Copynumber: 7.6 Consensus size: 20
44671 CAATGCAACT
44681 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** * ** *
44701 ATCGCAATTCGAATTTCAACT
1 ATCGCAACGCGAAATGGAA-A
44722 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** *
44742 ATCGCAACGCGAATTTCAACT
1 ATCGCAACGCGAAATGGAA-A
44763 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** *
44783 ATCGCAACGCGAATTTCAACT
1 ATCGCAACGCGAAATGGAA-A
44804 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
44824 ATCGCAACGCGA
1 ATCGCAACGCGA
44836 TTTTCAACTA
Statistics
Matches: 104, Mismatches: 28, Indels: 6
0.75 0.20 0.04
Matches are distributed among these distances:
20 58 0.56
21 46 0.44
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:44725 original size:41 final size:41
Alignment explanation
Indices: 44659--44949 Score: 363
Period size: 41 Copynumber: 7.0 Consensus size: 41
44649 TATCAACTGG
*
44659 AAATCGCAACGAC-AA-TGCAACTATCGCAACGCGAAATGGA
1 AAATCGCAACG-CGAATTTCAACTATCGCAACGCGAAATGGA
**
44699 AAATCGCAATTCGAATTTCAACTATCGCAACGCGAAATGGA
1 AAATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGA
44740 AAATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGA
1 AAATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGA
44781 AAATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGA
1 AAATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGA
* * * *
44822 AAATCGCAACGCGATTTTCAACTATCGTAACGCGAATTTGCA
1 AAATCGCAACGCGAATTTCAACTATCGCAACGCGAA-ATGGA
* * *
44864 ATAGT-GGAGATCGCGTTGCGATTTCAACTATCGCAACGCGAAATGGA
1 A-AATCGCA-A-CGC---G-AATTTCAACTATCGCAACGCGAAATGGA
* * *
44911 AAAACGCAACGCGATTTTCAACTATCGCAATGCGAAATG
1 AAATCGCAACGCGAATTTCAACTATCGCAACGCGAAATG
44950 CAACGTGAAT
Statistics
Matches: 218, Mismatches: 22, Indels: 21
0.84 0.08 0.08
Matches are distributed among these distances:
39 1 0.00
40 11 0.05
41 161 0.74
42 7 0.03
43 3 0.01
44 3 0.01
45 3 0.01
46 2 0.01
47 7 0.03
48 20 0.09
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (41 bp):
AAATCGCAACGCGAATTTCAACTATCGCAACGCGAAATGGA
Found at i:44727 original size:21 final size:21
Alignment explanation
Indices: 44676--44860 Score: 162
Period size: 21 Copynumber: 9.0 Consensus size: 21
44666 AACGACAATG
* *
44676 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAATTT
* * **
44697 GAA-AATCGCAATTCGAATTT
1 CAACTATCGCAACGCGAATTT
* *
44717 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAATTT
* *
44738 GAA-AATCGCAACGCGAATTT
1 CAACTATCGCAACGCGAATTT
* *
44758 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAATTT
* *
44779 GAA-AATCGCAACGCGAATTT
1 CAACTATCGCAACGCGAATTT
* *
44799 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAATTT
* * *
44820 GAA-AATCGCAACGCGATTTT
1 CAACTATCGCAACGCGAATTT
*
44840 CAACTATCGTAACGCGAATTT
1 CAACTATCGCAACGCGAATTT
44861 GCAATAGTGG
Statistics
Matches: 123, Mismatches: 37, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
20 61 0.50
21 62 0.50
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (21 bp):
CAACTATCGCAACGCGAATTT
Found at i:44904 original size:20 final size:20
Alignment explanation
Indices: 44881--44945 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
44871 AGATCGCGTT
44881 GCGATTTCAACTATCGCAAC
1 GCGATTTCAACTATCGCAAC
* ** * *
44901 GCGAAATGGAA-AAACGCAAC
1 GCG-ATTTCAACTATCGCAAC
*
44921 GCGATTTTCAACTATCGCAAT
1 GCGA-TTTCAACTATCGCAAC
44942 GCGA
1 GCGA
44946 AATGCAACGT
Statistics
Matches: 31, Mismatches: 11, Indels: 5
0.66 0.23 0.11
Matches are distributed among these distances:
19 1 0.03
20 16 0.52
21 14 0.45
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
GCGATTTCAACTATCGCAAC
Found at i:44953 original size:21 final size:21
Alignment explanation
Indices: 44888--44953 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
44878 GTTGCGATTT
44888 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
44909 GAA-AAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
44929 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
44950 CAAC
1 CAAC
44954 GTGAATTTGT
Statistics
Matches: 31, Mismatches: 13, Indels: 2
0.67 0.28 0.04
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.17
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:45135 original size:21 final size:23
Alignment explanation
Indices: 45093--45145 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
45083 ATTTTCTCTA
*
45093 AATTTTAATATTAAAATCAA-TT
1 AATTTAAATATTAAAATCAATTT
45115 AATTTAAAT-TTAAATAT-AATTT
1 AATTTAAATATTAAA-ATCAATTT
45137 AATTATAAA
1 AATT-TAAA
45146 ATAAAAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 7 0.26
22 16 0.59
23 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTTAAATATTAAAATCAATTT
Found at i:48158 original size:4 final size:4
Alignment explanation
Indices: 48149--48184 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
48139 AACAGCATGT
48149 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
48185 AAAGAAGAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:48865 original size:2 final size:2
Alignment explanation
Indices: 48858--48926 Score: 97
Period size: 2 Copynumber: 35.5 Consensus size: 2
48848 TATTTTAGTC
* * *
48858 AT AT AT AT AT GT AT GT AT GT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48899 AT AT AT AT AT AT AT AT A- AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48927 GAAAGATTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
1 2 0.03
2 57 0.97
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Done.