Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005118.1 Hibiscus syriacus cultivar Beakdansim tig00011505_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: 57386
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1180 original size:52 final size:52
Alignment explanation
Indices: 1101--1205 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
1091 TAAACGCCAT
*
1101 GCCCACATTGATCTTGATGATATCCAACAACGATTTAGTCCACTTGTGTTTTC
1 GCCCACATTGATCTTGATGATATCCAACAACGATTTAGTCCA-TTGTGTATTC
1154 GCCCACATTGATC-TGATGATATCCAACAACGATTTAGTCCATTGTGTATTC
1 GCCCACATTGATCTTGATGATATCCAACAACGATTTAGTCCATTGTGTATTC
1205 G
1 G
1206 ATTTGTTATA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 10 0.20
52 28 0.55
53 13 0.25
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (52 bp):
GCCCACATTGATCTTGATGATATCCAACAACGATTTAGTCCATTGTGTATTC
Found at i:2253 original size:18 final size:17
Alignment explanation
Indices: 2230--2275 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
2220 TGTTTACAAG
2230 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
* *
2248 GGAATTAGAATCTGTCA
1 GGAATTGGAATCTGTAA
2265 GGAA-TGGAATC
1 GGAATTGGAATC
2276 CAATTCCAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 6 0.24
17 5 0.20
18 14 0.56
ACGTcount: A:0.35, C:0.09, G:0.30, T:0.26
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:2870 original size:37 final size:38
Alignment explanation
Indices: 2800--2871 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
2790 AACCTGAACC
*
2800 CGACCCGAATATCACGCTTAAAAAAACCCGACCCGGCT
1 CGACCCGAATATCACACTTAAAAAAACCCGACCCGGCT
2838 CGACCCGAATATCACACTT-AAAAAACCCGACCCG
1 CGACCCGAATATCACACTTAAAAAAACCCGACCCG
2872 AACAAAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.36, C:0.38, G:0.14, T:0.12
Consensus pattern (38 bp):
CGACCCGAATATCACACTTAAAAAAACCCGACCCGGCT
Found at i:3312 original size:14 final size:14
Alignment explanation
Indices: 3293--3321 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3283 CATCCATTCT
3293 TGGATGGAATTCAG
1 TGGATGGAATTCAG
3307 TGGATGGAATTCAG
1 TGGATGGAATTCAG
3321 T
1 T
3322 TTCCCTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.34, T:0.31
Consensus pattern (14 bp):
TGGATGGAATTCAG
Found at i:12673 original size:20 final size:21
Alignment explanation
Indices: 12628--12674 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
12618 AGACAACGAT
12628 GCTTGAAAGAACTCAAATATG
1 GCTTGAAAGAACTCAAATATG
* *
12649 TCTTGAAAGAACT-AAATTTG
1 GCTTGAAAGAACTCAAATATG
12669 GCTTGA
1 GCTTGA
12675 TCATTCTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (21 bp):
GCTTGAAAGAACTCAAATATG
Found at i:17431 original size:23 final size:23
Alignment explanation
Indices: 17379--17441 Score: 89
Period size: 21 Copynumber: 2.9 Consensus size: 23
17369 AAACTATATA
17379 ATATATTATA--TTTTCAAAATC
1 ATATATTATATGTTTTCAAAATC
*
17400 ATATA--ATATGTTTTCAAAATT
1 ATATATTATATGTTTTCAAAATC
17421 ATATATTATATGTTTTCAAAA
1 ATATATTATATGTTTTCAAAA
17442 ATACGTTTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 3 0.08
21 20 0.54
23 14 0.38
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (23 bp):
ATATATTATATGTTTTCAAAATC
Found at i:17476 original size:40 final size:39
Alignment explanation
Indices: 17415--17559 Score: 129
Period size: 40 Copynumber: 3.7 Consensus size: 39
17405 ATATGTTTTC
* *
17415 AAAATTATATATTATATGTTTTCAAAAATAC-GTTTTCA
1 AAAACTATATATTATATGTTTTCAAAAATACAGTTTTAA
* * * *
17453 AAGACTATATTATATATATGTTTTAAAAAAAACAATTTTTAA
1 AAAACTATA-TAT-TATATGTTTTCAAAAATAC-AGTTTTAA
*
17495 GAAAACTATATATTATATGTTTTC-AAAAT-CGTGTTTTAA
1 -AAAACTATATATTATATGTTTTCAAAAATAC-AGTTTTAA
**
17534 AAAAC--TATATTATAAATTTTCAAAAA
1 AAAACTATATATTATATGTTTTCAAAAA
17560 CTATATATAT
Statistics
Matches: 87, Mismatches: 14, Indels: 13
0.76 0.12 0.11
Matches are distributed among these distances:
36 14 0.16
37 4 0.05
38 12 0.14
39 10 0.11
40 21 0.24
41 10 0.11
42 8 0.09
43 8 0.09
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (39 bp):
AAAACTATATATTATATGTTTTCAAAAATACAGTTTTAA
Found at i:18147 original size:14 final size:14
Alignment explanation
Indices: 18130--18171 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
18120 TTATACAAAC
*
18130 ATTTTTAAACAATA
1 ATTTTTAAAAAATA
**
18144 ATTTCAAAAAAATA
1 ATTTTTAAAAAATA
18158 ATTTTTAAAAAATA
1 ATTTTTAAAAAATA
18172 TACGAAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTTTTAAAAAATA
Found at i:28935 original size:42 final size:41
Alignment explanation
Indices: 28888--28984 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 41
28878 ATATTTTAAG
* * *
28888 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATGAAA
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGAT-AAA
** * *
28930 TCCTTCGGGTTATCTGTAAGCCTTTAGAGCAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
* *
28971 TCATTTGGGCCATC
1 TCCTTCGGGCCATC
28985 CATAAAACCT
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
41 12 0.27
42 32 0.73
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
Found at i:29166 original size:42 final size:42
Alignment explanation
Indices: 29104--29193 Score: 153
Period size: 42 Copynumber: 2.1 Consensus size: 42
29094 ACTTAGTAAG
* *
29104 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
*
29146 TCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
29188 TCCTTC
1 TCCTTC
29194 GGGTAATTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (42 bp):
TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
Found at i:29207 original size:42 final size:42
Alignment explanation
Indices: 29104--29314 Score: 141
Period size: 42 Copynumber: 5.1 Consensus size: 42
29094 ACTTAGTAAG
* * * *
29104 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCAGGCAATCAGTAAGTCTTTCGAGCATGATGATTAAA
*
29146 TCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCAGGCAATCAGTAAGTCTTTCGAGCATGATGATTAAA
* * ** * * * * *
29188 TCCTTCGGGTAATTTGTAAG-CCTTC-ACCGAAGA-GTAGTGAAG
1 TCCTTCAGGCAATCAGTAAGTCTTTCGAGC-ATGATG-A-TTAAA
*** *
29230 TAAATC---C-ATCAGTAAGTCTTTCGAGCATGATGATGAAA
1 TCCTTCAGGCAATCAGTAAGTCTTTCGAGCATGATGATTAAA
* * * *
29268 TCCTTCAGGCCATCAGTAAGTCGTTCGGGCAAGATGA-TAAA
1 TCCTTCAGGCAATCAGTAAGTCTTTCGAGCATGATGATTAAA
29309 TCCTTC
1 TCCTTC
29315 GTGTCATCCA
Statistics
Matches: 129, Mismatches: 30, Indels: 21
0.72 0.17 0.12
Matches are distributed among these distances:
38 14 0.11
39 8 0.06
40 6 0.05
41 18 0.14
42 83 0.64
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (42 bp):
TCCTTCAGGCAATCAGTAAGTCTTTCGAGCATGATGATTAAA
Found at i:29329 original size:41 final size:42
Alignment explanation
Indices: 29235--29337 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
29225 TGAAGTAAAT
* * *
29235 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCAGG
1 CCATCAGTAAGTCCTTCGGGCAAGATGATGAAATCCTTCAGG
*
29277 CCATCAGTAAGTCGTTCGGGCAAGATGAT-AAATCCTTC-GTG
1 CCATCAGTAAGTCCTTCGGGCAAGATGATGAAATCCTTCAG-G
*
29318 TCATCCA-TAAGTCCTTCGGG
1 CCAT-CAGTAAGTCCTTCGGG
29338 TAGGATGTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
40 1 0.02
41 25 0.46
42 28 0.52
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.28
Consensus pattern (42 bp):
CCATCAGTAAGTCCTTCGGGCAAGATGATGAAATCCTTCAGG
Found at i:29334 original size:122 final size:122
Alignment explanation
Indices: 29113--29334 Score: 329
Period size: 122 Copynumber: 1.8 Consensus size: 122
29103 GTCCTTCGGG
* * * *
29113 CCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGCAT
1 CCATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTCAGGCCATCAGTAAGTCGTTCGAGCAA
***
29178 GATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGTAAAT
66 GATGATTAAATCCTTCGGGTAATCCATAAGCCTTCACCGAAGAGTAGTGAAGTAAAT
* *
29235 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCAGGCCATCAGTAAGTCGTTCGGGCAA
1 CCATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTCAGGCCATCAGTAAGTCGTTCGAGCAA
* *
29300 GATGA-TAAATCCTTCGTGTCATCCATAAGTCCTTC
66 GATGATTAAATCCTTCGGGTAATCCATAAG-CCTTC
29335 GGGTAGGATG
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
121 19 0.22
122 69 0.78
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (122 bp):
CCATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTCAGGCCATCAGTAAGTCGTTCGAGCAA
GATGATTAAATCCTTCGGGTAATCCATAAGCCTTCACCGAAGAGTAGTGAAGTAAAT
Found at i:29845 original size:53 final size:53
Alignment explanation
Indices: 29756--29965 Score: 233
Period size: 53 Copynumber: 3.9 Consensus size: 53
29746 AGAATTACAC
* * * *
29756 CAGAAAATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGGACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
*
29809 CAGACGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* * * * ***
29862 CAGAAGATTATTCAAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCCGTTTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* * * * * *
29915 TAGAAGATTGTTTGAGTTCCTTAATCCCTG-AGAAATAGGGAGTGGACCCGT
1 CAGAAGATTGTTCGAGTT-C-TACTCCCTGAAGAAAGAGGGAGCGAACCCGT
29966 CATTTGAAGA
Statistics
Matches: 134, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
53 107 0.80
54 19 0.14
55 8 0.06
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
Found at i:32942 original size:20 final size:19
Alignment explanation
Indices: 32903--32944 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
32893 TTTCCTCGAT
32903 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
32922 ATTAAAATAATTAATATATA
1 ATTAAAA-AATAAATAAATA
32942 ATT
1 ATT
32945 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:33055 original size:120 final size:120
Alignment explanation
Indices: 32838--33055 Score: 280
Period size: 120 Copynumber: 1.8 Consensus size: 120
32828 TAAATAAAAC
* * * * *
32838 ATTTATTTATTTAGAAATATTAGAAAAGGACTTCTAGGTGCCTTAAGACAGCTCTTTTCCTCGAT
1 ATTTATTTATTTAAAAATATTAGAAAAGGACATCCAGGTGCCTTAAGACAGCTCCTTTCCTCAAT
*
32903 ATTAAAAAATAAATAAATAATTAAAATAATTAATATATAATTTATAAAATAGGAT
66 ATTAAAAAATAAATAAATAATTAAAAAAATTAATATATAATTTATAAAATAGGAT
* ** * *
32958 ATTTATTTATTTAAAAATATTAGAAAATGGACATCCAGTTGTTTTAAGACTGC-CCTTT-CTTAA
1 ATTTATTTATTTAAAAATATTAGAAAA-GGACATCCAGGTGCCTTAAGACAGCTCCTTTCCTCAA
*
33021 TATTGAAAAATAAATAAAT-ATTAAAACAAGATTAA
65 TATTAAAAAATAAATAAATAATTAAAA-AA-ATTAA
33056 AATAAGTTAA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
118 7 0.08
119 22 0.27
120 35 0.42
121 19 0.23
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.37
Consensus pattern (120 bp):
ATTTATTTATTTAAAAATATTAGAAAAGGACATCCAGGTGCCTTAAGACAGCTCCTTTCCTCAAT
ATTAAAAAATAAATAAATAATTAAAAAAATTAATATATAATTTATAAAATAGGAT
Found at i:33096 original size:20 final size:18
Alignment explanation
Indices: 33073--33112 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
33063 TAAAAGTAAT
*
33073 TAAAATAAGATTTTAATAAA
1 TAAAATAA-ATATT-ATAAA
33093 TAAAATAAATATTATAAA
1 TAAAATAAATATTATAAA
33111 TA
1 TA
33113 TATATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 4 0.21
20 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
TAAAATAAATATTATAAA
Found at i:34520 original size:3 final size:3
Alignment explanation
Indices: 34512--34582 Score: 53
Period size: 3 Copynumber: 25.0 Consensus size: 3
34502 GGCCTGTTTG
* * *
34512 TAA TAA TAA TAA TTA T-T TAT TTAA TAA TAA TAA T-A TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
* *
34555 TAA TAT TAA -AA CAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34583 ATAAAACAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
2 9 0.16
3 46 0.81
4 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:34556 original size:13 final size:14
Alignment explanation
Indices: 34533--34586 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 14
34523 ATTATTTATT
34533 TAATAATAATAATA
1 TAATAATAATAATA
34547 TAAT-ATAATAATA
1 TAATAATAATAATA
* *
34560 T--TAA-AACAAAA
1 TAATAATAATAATA
34571 TAATAATAATAA-A
1 TAATAATAATAATA
34584 TAA
1 TAA
34587 AACAAATGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
11 7 0.21
12 1 0.03
13 17 0.52
14 8 0.24
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:34556 original size:16 final size:16
Alignment explanation
Indices: 34535--34579 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
34525 TATTTATTTA
* *
34535 ATAATAATAATATAAT
1 ATAATAATAATAAAAC
*
34551 ATAATAATATTAAAAC
1 ATAATAATAATAAAAC
*
34567 AAAATAATAATAA
1 ATAATAATAATAA
34580 TAAATAAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAATAATAATAAAAC
Found at i:34593 original size:22 final size:24
Alignment explanation
Indices: 34546--34592 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
34536 TAATAATAAT
34546 ATAATATAATAATATTAAAACAAA
1 ATAATATAATAATATTAAAACAAA
34570 ATAATAATAATAA-A-TAAAACAAA
1 ATAAT-ATAATAATATTAAAACAAA
34593 TGAAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.41
24 6 0.27
25 7 0.32
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (24 bp):
ATAATATAATAATATTAAAACAAA
Found at i:35170 original size:113 final size:112
Alignment explanation
Indices: 35044--36361 Score: 1851
Period size: 113 Copynumber: 11.7 Consensus size: 112
35034 GAATTCGAGC
* * * *
35044 AACAAGTTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTTATTATTAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
** * *
35109 GCCCTGGCAATGCTTG-TCCATCGAATGATAAATTCAAGCGAAAAGTTG
66 TACCTGGAAATGC-TGATCCATCGAATGATGAATTCAAGC-AAAAGTTG
35157 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* *
35222 GACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
66 TACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGC-AAAAGTTG
*
35270 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
** * **
35335 TTTC-AGAAATATTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
66 TACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGC-AAAAGTTG
35382 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * *
35447 GACCTGGTAGTGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
66 TACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGC-AAAAGTTG
35495 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
** * *
35560 TTTC-AGAAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
66 TACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGC-AAAAGTTG
*
35607 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * *
35672 GACCTGGTAAA-GTTGATCCATC-AAGTGATGAATTCGAGCAAAAAGTTG
66 TACCTGG-AAATGCTGATCCATCGAA-TGATGAATTCAAGC-AAAAGTTG
* *
35720 AACAAGTTTTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * *
35785 TACCTGGTAATGATGATCCATTGAATGATGAATTCAAACAAAAGGTTG
66 TACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAA-GTTG
* *
35833 AACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTA
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * **
35898 T-CTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTG
66 TAC-CTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAA-GTTG
* *
35946 AACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * ** *
36011 TACCTGGAAATGCTGATCCATC-AAGTAATGGATTTGAGCAAAAGGTTA
66 TACCTGGAAATGCTGATCCATCGAA-TGATGAATTCAAGCAAAA-GTTG
* *
36059 AACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * *
36124 TACCTGGTAATGATGATCCATCGAATGATGAATTCAAACAAAAGGTTG
66 TACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAA-GTTG
* * *
36172 AATAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTA
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * ** *
36237 T-CTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAGCAGAAGGTTG
66 TAC-CTGGAAATGCTGATCCATCGAATGATGAATTCAAGCA-AAAGTTG
* * *
36285 AACAAGCTCTCCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
36350 TACCTGGAAATG
66 TACCTGGAAATG
36362 TTTTAAGAAA
Statistics
Matches: 1093, Mismatches: 97, Indels: 30
0.90 0.08 0.02
Matches are distributed among these distances:
112 221 0.20
113 861 0.79
114 11 0.01
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (112 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
TACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAGTTG
Found at i:39819 original size:114 final size:114
Alignment explanation
Indices: 39619--39838 Score: 350
Period size: 114 Copynumber: 1.9 Consensus size: 114
39609 GATCATGCAG
* * * *
39619 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAGCCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
39684 ATACTTTCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAA
* * *
39733 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTTAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
39798 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTA
39839 CGAGAACATG
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 96 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAA
Found at i:42004 original size:18 final size:18
Alignment explanation
Indices: 41981--42076 Score: 76
Period size: 18 Copynumber: 5.4 Consensus size: 18
41971 TCCCTTTTTC
*
41981 TTTTTCCCTTTTTTTCCT
1 TTTTTCTCTTTTTTTCCT
*
41999 TTTTTCTCATTTTTT-C-
1 TTTTTCTCTTTTTTTCCT
42015 TTTTTCATCTTTTTTTCC-
1 TTTTTC-TCTTTTTTTCCT
* *
42033 TTTTTC-CTTTTTCCTCAT
1 TTTTTCTCTTTTT-TTCCT
*
42051 TTTTTTTCATCTTTTTT-CT
1 TTTTTCTC-T-TTTTTTCCT
42070 TTTTTCT
1 TTTTTCT
42077 TTCTTTGCTA
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
16 12 0.19
17 11 0.18
18 25 0.40
19 8 0.13
20 2 0.03
21 4 0.06
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTCTCTTTTTTTCCT
Found at i:42072 original size:7 final size:7
Alignment explanation
Indices: 41975--42104 Score: 55
Period size: 7 Copynumber: 16.3 Consensus size: 7
41965 ATTTCTTCCC
41975 TTTTTCT
1 TTTTTCT
*
41982 TTTTCCCTT
1 TTTT-TC-T
41991 TTTTTCCTT
1 TTTTT-C-T
42000 TTTTCTCAT
1 TTTT-TC-T
42009 TTTTTCT
1 TTTTTCT
42016 TTTTCATCTT
1 TTTT--TC-T
42026 TTTTTCCT
1 TTTTT-CT
*
42034 TTTTCCT
1 TTTTTCT
*
42041 TTTTCCTCA
1 TTTT--TCT
42050 TTTTT-T
1 TTTTTCT
**
42056 TTCATCT
1 TTTTTCT
42063 TTTTTCT
1 TTTTTCT
42070 TTTTTCT
1 TTTTTCT
42077 TTCTTTGCT
1 TT-TTT-CT
42086 AGATTTTTCT
1 ---TTTTTCT
42096 TTTTTCT
1 TTTTTCT
42103 TT
1 TT
42105 CTTTGCTGGA
Statistics
Matches: 96, Mismatches: 11, Indels: 32
0.69 0.08 0.23
Matches are distributed among these distances:
6 3 0.03
7 40 0.42
8 12 0.12
9 28 0.29
10 8 0.08
11 3 0.03
12 2 0.02
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.74
Consensus pattern (7 bp):
TTTTTCT
Found at i:42072 original size:17 final size:16
Alignment explanation
Indices: 41975--42076 Score: 66
Period size: 17 Copynumber: 5.9 Consensus size: 16
41965 ATTTCTTCCC
*
41975 TTTTTC-TTTTTCCCTT
1 TTTTTCTTTTTTCTC-T
41991 TTTTTCCTTTTTTCTCAT
1 TTTTT-CTTTTTTCTC-T
42009 TTTTTC-TTTTTCATCTT
1 TTTTTCTTTTTTC-TC-T
*
42026 TTTTTCCTTTTTC-CT
1 TTTTTCTTTTTTCTCT
42041 TTTTCCTCATTTTTTTTCATCT
1 TTTT--TC---TTTTTTC-TCT
42063 TTTTTCTTTTTTCT
1 TTTTTCTTTTTTCT
42077 TTCTTTGCTA
Statistics
Matches: 71, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
15 5 0.07
16 13 0.18
17 20 0.28
18 19 0.27
20 8 0.11
22 6 0.08
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTCTTTTTTCTCT
Found at i:46383 original size:33 final size:33
Alignment explanation
Indices: 46336--46413 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
46326 CACAAGTATA
*
46336 ATATATATATATATGATCAATGATATATGTTTT
1 ATATGTATATATATGATCAATGATATATGTTTT
*
46369 ATATGTATATATATGATCAATGATGTATGTTTT
1 ATATGTATATATATGATCAATGATATATGTTTT
46402 ATATGTATATAT
1 ATATGTATATAT
46414 GTATATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.37, C:0.03, G:0.12, T:0.49
Consensus pattern (33 bp):
ATATGTATATATATGATCAATGATATATGTTTT
Found at i:46462 original size:22 final size:24
Alignment explanation
Indices: 46412--46462 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 24
46402 ATATGTATAT
*
46412 ATGTAT-ATATATGTACATATGCA
1 ATGTATAAAATATGTACATATGCA
*
46435 AT-TATAAAATATGTATA-ATGC-
1 ATGTATAAAATATGTACATATGCA
46456 ATGTATA
1 ATGTATA
46463 TTTATATGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 2 0.08
22 11 0.46
23 11 0.46
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (24 bp):
ATGTATAAAATATGTACATATGCA
Found at i:46505 original size:2 final size:2
Alignment explanation
Indices: 46500--46526 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46490 AGTAAACGAA
46500 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
46527 AAAGAACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47154 original size:2 final size:2
Alignment explanation
Indices: 47147--47184 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
47137 AGCTAACTTT
47147 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47185 CACATATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47237 original size:12 final size:12
Alignment explanation
Indices: 47220--47245 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
47210 TATACTTATG
47220 TATGTATGTATA
1 TATGTATGTATA
47232 TATGTATGTATA
1 TATGTATGTATA
47244 TA
1 TA
47246 CAACCATGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (12 bp):
TATGTATGTATA
Found at i:47821 original size:2 final size:2
Alignment explanation
Indices: 47816--47938 Score: 114
Period size: 2 Copynumber: 62.5 Consensus size: 2
47806 TATATACTTT
* *
47816 TA TA TA TA TA TA TA TA TA CT- TA TA TA TA TA TA TA CTT TT TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA
* * * *
47859 CT- TA TA TA GA TA -A T- TA TG TA CA TA CA TCA TA T- TA TA T- TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
47898 TA 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 TA T
47939 GTACATGCAT
Statistics
Matches: 101, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
1 6 0.06
2 90 0.89
3 5 0.05
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47824 original size:22 final size:22
Alignment explanation
Indices: 47799--47938 Score: 125
Period size: 20 Copynumber: 6.5 Consensus size: 22
47789 TGTAAAAAAA
* *
47799 ATATTTATATATACTTTTATAT
1 ATATATATATATACTTATATAT
47821 ATATATATATATACTTATATAT
1 ATATATATATATACTTATATAT
* *
47843 ATATATACTTTTTATACTTATATAG
1 ATATATA---TATATACTTATATAT
* * *
47868 ATA-AT-TATGTACATACATCAT
1 ATATATATATATACTTATAT-AT
47889 AT-TATAT-TATA--TATATAT
1 ATATATATATATACTTATATAT
47907 ATATATATATATA--TATATAT
1 ATATATATATATACTTATATAT
47927 ATATATATATAT
1 ATATATATATAT
47939 GTACATGCAT
Statistics
Matches: 99, Mismatches: 11, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
18 4 0.04
19 9 0.09
20 32 0.32
21 8 0.08
22 28 0.28
24 2 0.02
25 16 0.16
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (22 bp):
ATATATATATATACTTATATAT
Found at i:48205 original size:18 final size:19
Alignment explanation
Indices: 48166--48211 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
48156 ATCATATAAA
*
48166 AATTAAATTTATAAATTTT
1 AATTAAATTTATAAATTCT
48185 AATT-AATTTATATAA-TCT
1 AATTAAATTTATA-AATTCT
*
48203 AATAAAATT
1 AATTAAATT
48212 ATGTTTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
AATTAAATTTATAAATTCT
Found at i:48259 original size:14 final size:13
Alignment explanation
Indices: 48242--48284 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
48232 TTAATAAAAT
48242 TAATTTAATGATTA
1 TAATTTAA-GATTA
48256 TAA-TTAAGAGTTA
1 TAATTTAAGA-TTA
48269 TAATTTAAGGATTA
1 TAATTTAA-GATTA
48283 TA
1 TA
48285 GTTAATATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 2 0.08
13 10 0.38
14 12 0.46
15 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (13 bp):
TAATTTAAGATTA
Found at i:53061 original size:15 final size:17
Alignment explanation
Indices: 53026--53062 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
53016 AAAATATTTT
*
53026 ATATTATATATTTATTT
1 ATATTATATATTTATTA
53043 ATATTAT-TA-TTATTA
1 ATATTATATATTTATTA
53058 ATATT
1 ATATT
53063 TTTTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 2 0.11
17 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTATATATTTATTA
Found at i:53061 original size:25 final size:25
Alignment explanation
Indices: 53019--53075 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
53009 TTCTACAAAA
53019 ATATT-TTATATTATATATTTATTT
1 ATATTATTATATTATATATTTATTT
*
53043 ATATTATTATTATTA-ATATTTTTTT
1 ATATTATTA-TATTATATATTTATTT
*
53068 TTATTATT
1 ATATTATT
53076 TTTGCATGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 5 0.17
25 19 0.66
26 5 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
ATATTATTATATTATATATTTATTT
Found at i:53590 original size:23 final size:21
Alignment explanation
Indices: 53558--53602 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
53548 TTTTTATTTC
53558 TTTTTACATTGTTATATATATAT
1 TTTTTACATTGTTAT-TA-ATAT
* *
53581 TTTTTTCATTTTTATTAATAT
1 TTTTTACATTGTTATTAATAT
53602 T
1 T
53603 ATTATATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 2 0.10
23 13 0.65
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTTACATTGTTATTAATAT
Found at i:55816 original size:21 final size:21
Alignment explanation
Indices: 55764--55816 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
55754 TTCAGACGAA
55764 GAGGACAAATCAAAGAAGATG
1 GAGGACAAATCAAAGAAGATG
*
55785 GAGGAGAAAATC-AAGCAA-ATG
1 GAGGA-CAAATCAAAG-AAGATG
55806 GAGGACCAAAT
1 GAGGA-CAAAT
55817 GAAGGTAGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.51, C:0.11, G:0.28, T:0.09
Consensus pattern (21 bp):
GAGGACAAATCAAAGAAGATG
Done.