Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005361.1 Hibiscus syriacus cultivar Beakdansim tig00012177_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: 62547
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:675 original size:23 final size:23
Alignment explanation
Indices: 645--724 Score: 96
Period size: 23 Copynumber: 3.6 Consensus size: 23
635 ACACTTAACA
645 GTGCATCGATGCATCCATTGAAT
1 GTGCATCGATGCATCCATTGAAT
*
668 GTGCATCGATACAT-CA-TGAA-
1 GTGCATCGATGCATCCATTGAAT
*
688 GATGCACCGATGCACTCC-TTGAAT
1 G-TGCATCGATGCA-TCCATTGAAT
712 GTGCATCGATGCA
1 GTGCATCGATGCA
725 AAAGGACATG
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
20 1 0.02
21 14 0.29
22 3 0.06
23 29 0.60
24 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCATCCATTGAAT
Found at i:2307 original size:21 final size:21
Alignment explanation
Indices: 2265--2308 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2255 ACTCCGGGAG
* *
2265 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
2286 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
2307 CT
1 CT
2309 CATTCGGCAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:3365 original size:46 final size:45
Alignment explanation
Indices: 3308--3414 Score: 144
Period size: 45 Copynumber: 2.4 Consensus size: 45
3298 TGCACATACT
* *
3308 ATGCATCGATGCACTCAGGGT-TTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAAGCTATTT-TG-AAACATCGAATGCATTTG
* * *
3354 ATGCATGGATGCACACAAGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAAGCTATTTTGAAACATCGAATGCATTTG
3399 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
3415 TTAGTGCACC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 31 0.58
46 19 0.36
47 3 0.06
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (45 bp):
ATGCATCGATGCACTCAAGCTATTTTGAAACATCGAATGCATTTG
Found at i:4289 original size:19 final size:19
Alignment explanation
Indices: 4265--4318 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
4255 GAATGTAGTT
4265 CATGCATCGATGCACTCTC
1 CATGCATCGATGCACTCTC
4284 CATGCATCGATGCACTCTC
1 CATGCATCGATGCACTCTC
4303 CATGCATCGATGCACT
1 CATGCATCGATGCACT
4319 GTGCATCGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.22, C:0.35, G:0.17, T:0.26
Consensus pattern (19 bp):
CATGCATCGATGCACTCTC
Found at i:4325 original size:15 final size:15
Alignment explanation
Indices: 4305--4333 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4295 GCACTCTCCA
4305 TGCATCGATGCACTG
1 TGCATCGATGCACTG
4320 TGCATCGATGCACT
1 TGCATCGATGCACT
4334 CAGGTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.28
Consensus pattern (15 bp):
TGCATCGATGCACTG
Found at i:4440 original size:64 final size:65
Alignment explanation
Indices: 4322--4444 Score: 187
Period size: 64 Copynumber: 1.9 Consensus size: 65
4312 ATGCACTGTG
* *
4322 CATCGATGCACTCAGGTTTTTATGAAAACATCGAATGTATTTGATGCATCGATGCACAAGACATA
1 CATCGATGCACTCAGGTATTTATGAAAACATCGAATGCATTTGATGCATCGATGCACAAGACATA
* *
4387 CATCGATGCACTCAGGCTATTT-TG-AAACATCGAATGCATTTTATGCATTGATGCACAA
1 CATCGATGCACTCAGG-TATTTATGAAAACATCGAATGCATTTGATGCATCGATGCACAA
4445 TTAGTGCACC
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
64 31 0.58
65 18 0.34
66 4 0.08
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (65 bp):
CATCGATGCACTCAGGTATTTATGAAAACATCGAATGCATTTGATGCATCGATGCACAAGACATA
Found at i:4540 original size:21 final size:21
Alignment explanation
Indices: 4516--4567 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
4506 CACTTGATGC
*
4516 ACCGATGTACCTTGTGTATGT
1 ACCGATGCACCTTGTGTATGT
*
4537 ACCGATGCACCTTGTGTATGC
1 ACCGATGCACCTTGTGTATGT
*
4558 ATCGATGCAC
1 ACCGATGCAC
4568 TGACGCTCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (21 bp):
ACCGATGCACCTTGTGTATGT
Found at i:11440 original size:6 final size:6
Alignment explanation
Indices: 11423--11464 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
11413 TTGAGGTGGG
* * *
11423 GCTACG GCTACA GCTACA ACTACA GCTACA ACTACA GCTACA
1 GCTACA GCTACA GCTACA GCTACA GCTACA GCTACA GCTACA
11465 CTCTGATACC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.36, C:0.33, G:0.14, T:0.17
Consensus pattern (6 bp):
GCTACA
Found at i:11445 original size:12 final size:12
Alignment explanation
Indices: 11430--11464 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
11420 GGGGCTACGG
11430 CTACAGCTACAA
1 CTACAGCTACAA
11442 CTACAGCTACAA
1 CTACAGCTACAA
11454 CTACAGCTACA
1 CTACAGCTACA
11465 CTCTGATACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.40, C:0.34, G:0.09, T:0.17
Consensus pattern (12 bp):
CTACAGCTACAA
Found at i:15619 original size:3 final size:3
Alignment explanation
Indices: 15613--15679 Score: 95
Period size: 3 Copynumber: 23.3 Consensus size: 3
15603 ATTAGTAATA
*
15613 ATT ATT ATT A-T ATT GTT ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
15659 ATT ATT A-T ATT ATT AAT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
15680 CATTTACATT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 6 0.11
3 51 0.89
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:15633 original size:14 final size:14
Alignment explanation
Indices: 15613--15679 Score: 98
Period size: 14 Copynumber: 4.7 Consensus size: 14
15603 ATTAGTAATA
15613 ATTATTATTATATT
1 ATTATTATTATATT
* *
15627 GTTATTATTTTATT
1 ATTATTATTATATT
15641 ATTATTATTATTATT
1 ATTATTATTA-TATT
15656 ATTATTATTATATT
1 ATTATTATTATATT
*
15670 ATTAATATTA
1 ATTATTATTA
15680 CATTTACATT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 33 0.70
15 14 0.30
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (14 bp):
ATTATTATTATATT
Found at i:15952 original size:18 final size:18
Alignment explanation
Indices: 15925--15959 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15915 ACATCAGCTG
*
15925 CCAACACCAGCTTAGCCA
1 CCAACACCAGCTCAGCCA
*
15943 CCAACGCCAGCTCAGCC
1 CCAACACCAGCTCAGCC
15960 GCCACTCAAG
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:0.29, C:0.49, G:0.14, T:0.09
Consensus pattern (18 bp):
CCAACACCAGCTCAGCCA
Found at i:16953 original size:5 final size:5
Alignment explanation
Indices: 16943--16968 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16933 GCAAGTTATG
16943 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
16969 GCACAACTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:22331 original size:153 final size:153
Alignment explanation
Indices: 22053--22398 Score: 647
Period size: 153 Copynumber: 2.3 Consensus size: 153
22043 TAAGGGTGTT
*
22053 TTTCATTCGAAAACAAATTCTGTCTCCCTTGAGATATTTTTCCACAAATTTTGAGAAGTTTAAAA
1 TTTCATTCGAAAACAAATTCTGTCTCGCTTGAGATATTTTTCCACAAATTTTGAGAAGTTTAAAA
22118 CAAATTTTTGTCTCTCTTGAGACAATTTCTTTTGGAAAATCATTGATTTTGTTTCTTTTGAAATA
66 CAAATTTTTGTCTCTCTTGAGACAATTTCTTTTGGAAAATCATTGATTTTGTTTCTTTTGAAATA
*
22183 AAATTTTGTCTCATTTGAGATAG
131 AAATTTTGTCTCATTTGAGACAG
*
22206 TTTCATTCGAAAACAAATTCTGTCTCGCATGAGATATTTTTCCACAAATTTTGAGAAGTTTAAAA
1 TTTCATTCGAAAACAAATTCTGTCTCGCTTGAGATATTTTTCCACAAATTTTGAGAAGTTTAAAA
*
22271 CAAATTTTTGTCTCTCTTGAGACAATTTCTTTTGGAAAATCTTTGATTTTGTTTCTTTTGAAATA
66 CAAATTTTTGTCTCTCTTGAGACAATTTCTTTTGGAAAATCATTGATTTTGTTTCTTTTGAAATA
22336 AAATTTTGTCTCATTTGAGACAG
131 AAATTTTGTCTCATTTGAGACAG
*
22359 TTTCATTCGAAAACAAATTTTGTCTCGCTTGAGATATTTT
1 TTTCATTCGAAAACAAATTCTGTCTCGCTTGAGATATTTT
22399 CCCTTTGAGA
Statistics
Matches: 187, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
153 187 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.44
Consensus pattern (153 bp):
TTTCATTCGAAAACAAATTCTGTCTCGCTTGAGATATTTTTCCACAAATTTTGAGAAGTTTAAAA
CAAATTTTTGTCTCTCTTGAGACAATTTCTTTTGGAAAATCATTGATTTTGTTTCTTTTGAAATA
AAATTTTGTCTCATTTGAGACAG
Found at i:22511 original size:34 final size:34
Alignment explanation
Indices: 22447--22566 Score: 177
Period size: 36 Copynumber: 3.4 Consensus size: 34
22437 ACAAAGTTGA
* *
22447 TCTCACTTGAGACAATTAATTTAAAAACAAATTTTG
1 TCTCGCTTGAGACAATT--TCTAAAAACAAATTTTG
22483 TCTCGCTTGAGACAATTTCTAAAAACAAATTTTG
1 TCTCGCTTGAGACAATTTCTAAAAACAAATTTTG
*
22517 TTTCGCTTGAGACAATTTCTATCAAAACAAATTTTG
1 TCTCGCTTGAGACAATTTCTA--AAAACAAATTTTG
22553 TCTCGCTTGAGACA
1 TCTCGCTTGAGACA
22567 TTTTTTTTCT
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
34 36 0.46
36 42 0.54
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (34 bp):
TCTCGCTTGAGACAATTTCTAAAAACAAATTTTG
Found at i:23001 original size:30 final size:30
Alignment explanation
Indices: 22965--23053 Score: 126
Period size: 30 Copynumber: 3.0 Consensus size: 30
22955 ACAAACCATC
22965 ATCTTTGAGTTGTTTCTTTTGAAACAAAGA
1 ATCTTTGAGTTGTTTCTTTTGAAACAAAGA
** *
22995 ATCTTTGAGTCATTTCTTTTGAAACCAA-A
1 ATCTTTGAGTTGTTTCTTTTGAAACAAAGA
*
23024 ATCTTTGAGTTTGTTTCTTTTGAAATAAAG
1 ATCTTTGAG-TTGTTTCTTTTGAAACAAAG
23054 TTTTGTCTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 10 0.20
30 40 0.80
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (30 bp):
ATCTTTGAGTTGTTTCTTTTGAAACAAAGA
Found at i:23268 original size:29 final size:29
Alignment explanation
Indices: 23221--23327 Score: 90
Period size: 29 Copynumber: 3.5 Consensus size: 29
23211 CCTTTGAGAT
*
23221 TGTTTCTTTTGAGA-AAAATCCTTGAGTC
1 TGTTTCTTTTGAAACAAAATCCTTGAGTC
*
23249 TGTTTCTTTGGAAACAAAATTTACAATCTTTGAGTC
1 TGTTTCTTTTGAAACAAAA--T-C---C-TTGAGTC
** *
23285 TGTTTCTTTTGAAACATCATCTTTGAGTC
1 TGTTTCTTTTGAAACAAAATCCTTGAGTC
*
23314 GGTTTCTTTTGAAA
1 TGTTTCTTTTGAAA
23328 TCATTATCCC
Statistics
Matches: 64, Mismatches: 7, Indels: 15
0.74 0.08 0.17
Matches are distributed among these distances:
28 12 0.19
29 24 0.38
31 1 0.02
32 1 0.02
33 1 0.02
34 1 0.02
35 1 0.02
36 23 0.36
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (29 bp):
TGTTTCTTTTGAAACAAAATCCTTGAGTC
Found at i:23595 original size:135 final size:135
Alignment explanation
Indices: 23336--23696 Score: 494
Period size: 135 Copynumber: 2.7 Consensus size: 135
23326 AATCATTATC
* * * *
23336 CCTAAAGATGGCC-ATAACTCTTCATCACGTATGAGCAGTGTCATCTCCTGACCAGATCTCTTCA
1 CCTAAAGATGACCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTCCTCA
** * *
23400 TCAATTAGGAGTCGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCA
66 TCACGTAGGAGTCGTGTCACCCATAGATAACCAGCAGTCCTCATCGCGTAGGAACCGAGTTATCA
23465 CCCTT
131 CCCTT
* * *
23470 CCTAAAGATGTCCAAGAACTCTTCATCACGTATGAGCCA-TGTCATCCCCTGACCATACCTCCTC
1 CCTAAAGATGACCAAGAACTCTTCATCACGTATGAG-CAGTGTCATCCCCTGACCAGATCTCCTC
* * * *
23534 ATCACGTAGGAGTCGTGTCACCTATAGATAACCAGTAGTCCTCATTGCGTAGGAACTGAGTTATC
65 ATCACGTAGGAGTCGTGTCACCCATAGATAACCAGCAGTCCTCATCGCGTAGGAACCGAGTTATC
23599 ACCCTT
130 ACCCTT
* * *
23605 CATAAAGATGACCAAGAACTCTTCATCACGTATGAGAAGTGTCAT-CCCTCGACCAGATTTCCTC
1 CCTAAAGATGACCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCT-GACCAGATCTCCTC
** *
23669 ATCACGTAGGAACCGTGTCACCCTTAGA
65 ATCACGTAGGAGTCGTGTCACCCATAGA
23697 CGACCCAAAC
Statistics
Matches: 199, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
134 17 0.09
135 180 0.90
136 2 0.01
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (135 bp):
CCTAAAGATGACCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTCCTCA
TCACGTAGGAGTCGTGTCACCCATAGATAACCAGCAGTCCTCATCGCGTAGGAACCGAGTTATCA
CCCTT
Found at i:23901 original size:3 final size:3
Alignment explanation
Indices: 23895--23943 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
23885 ATTAGTAATA
* *
23895 ATT ATT ATT A-T ATT ATT ATT ATT -TC ATT ATT ATT ATT -CT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
23940 ATT A
1 ATT A
23944 ATTTTATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:23911 original size:11 final size:11
Alignment explanation
Indices: 23895--23953 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
23885 ATTAGTAATA
23895 ATTATTATTAT
1 ATTATTATTAT
23906 ATTATTATTAT
1 ATTATTATTAT
23917 -TTCATTATTATT
1 ATT-ATTATTA-T
23929 ATTCTATTATTAT
1 A-T-TATTATTAT
*
23942 -TAATT-TTAT
1 ATTATTATTAT
23951 ATT
1 ATT
23954 TACATTTTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
9 4 0.10
10 6 0.15
11 19 0.47
12 1 0.03
13 1 0.03
14 8 0.20
15 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATTATTAT
Found at i:23914 original size:14 final size:13
Alignment explanation
Indices: 23895--23943 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 13
23885 ATTAGTAATA
23895 ATTATTATTATATT
1 ATTATTATT-TATT
23909 ATTATTATTTCATT
1 ATTATTATTT-ATT
23923 ATTATTATTCTATT
1 ATTATTATT-TATT
23937 ATTATTA
1 ATTATTA
23944 ATTTTATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 1 0.03
14 31 0.94
15 1 0.03
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTATTATTTATT
Found at i:23953 original size:14 final size:15
Alignment explanation
Indices: 23895--23950 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 15
23885 ATTAGTAATA
*
23895 ATTATT-ATTATATT
1 ATTATTAATTTTATT
*
23909 ATTATT-ATTTCATT
1 ATTATTAATTTTATT
*
23923 ATTATT-ATTCTATT
1 ATTATTAATTTTATT
23937 ATTATTAATTTTAT
1 ATTATTAATTTTAT
23951 ATTTACATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
14 30 0.83
15 6 0.17
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTATTAATTTTATT
Found at i:25233 original size:14 final size:14
Alignment explanation
Indices: 25216--25251 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
25206 GAGCACTTAC
*
25216 ATTTCAGCATTTAT
1 ATTTAAGCATTTAT
25230 ATTTAAGCATTTAT
1 ATTTAAGCATTTAT
25244 ATTTAAGC
1 ATTTAAGC
25252 CACTAGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.47
Consensus pattern (14 bp):
ATTTAAGCATTTAT
Found at i:25761 original size:30 final size:29
Alignment explanation
Indices: 25609--25773 Score: 93
Period size: 30 Copynumber: 5.6 Consensus size: 29
25599 TGAAATTTCA
* * *
25609 TTTTAGTCCTTTAACTTTCTGTTTTTGCTA
1 TTTTAG-CCTCTAAGTTTCTGTTTTTGCTG
* * * **
25639 TTGTAGTCC-CTTATTTTCCTGTTTTCACT-
1 TTTTAG-CCTCTAAGTTT-CTGTTTTTGCTG
*
25668 TTTTAGTCCT-TAGGTTTCTGTTTTGTGCTG
1 TTTTAG-CCTCTAAGTTTCTGTTTT-TGCTG
* ** * *
25698 GTTTAGCCTCTAAGTTTCTGTAATTACTA
1 TTTTAGCCTCTAAGTTTCTGTTTTTGCTG
* *
25727 TTTTAGACCTCTAATTTTCTATTTTTGCTG
1 TTTTAG-CCTCTAAGTTTCTGTTTTTGCTG
*
25757 TTTTAGCTCTTTAAGTT
1 TTTTAGC-CTCTAAGTT
25774 GTTATTATTA
Statistics
Matches: 101, Mismatches: 27, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
28 7 0.07
29 31 0.31
30 63 0.62
ACGTcount: A:0.15, C:0.17, G:0.13, T:0.55
Consensus pattern (29 bp):
TTTTAGCCTCTAAGTTTCTGTTTTTGCTG
Found at i:28885 original size:18 final size:19
Alignment explanation
Indices: 28843--28882 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
28833 TTTGGTTCAC
*
28843 GGAATGGAAGATTATCAGTG
1 GGAATGGAAGATTACCAG-G
*
28863 GGAATGTAAGATTACCAGG
1 GGAATGGAAGATTACCAGG
28882 G
1 G
28883 AATAGGATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.23
Consensus pattern (19 bp):
GGAATGGAAGATTACCAGG
Found at i:29070 original size:39 final size:39
Alignment explanation
Indices: 29026--29113 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 39
29016 TAACAAGTTG
* *
29026 AAAAATATTTATAT-ATTTTCTTTAAAAAATT-TAAATTT
1 AAAAA-ATTTATATAATTTTCTTTAAAAAATTGAAAATAT
* *
29064 AAAAAATTTATATAATTTTTTTTACAAAATTGAAAATAT
1 AAAAAATTTATATAATTTTCTTTAAAAAATTGAAAATAT
29103 AAAAAAGTTTA
1 AAAAAA-TTTA
29114 ATGAAAGGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
37 8 0.19
38 20 0.47
39 11 0.26
40 4 0.09
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (39 bp):
AAAAAATTTATATAATTTTCTTTAAAAAATTGAAAATAT
Found at i:29854 original size:17 final size:18
Alignment explanation
Indices: 29832--29885 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 18
29822 GATAAACTTA
29832 CATTTG-CAGTTCCTCTC
1 CATTTGACAGTTCCTCTC
29849 CATTTGAACCAGTTCCTCTC
1 CATTTG-A-CAGTTCCTCTC
29869 CATTTGAACCAGTTCCT
1 CATTTG-A-CAGTTCCT
29886 TCTAGATCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.18
20 28 0.82
ACGTcount: A:0.19, C:0.33, G:0.11, T:0.37
Consensus pattern (18 bp):
CATTTGACAGTTCCTCTC
Found at i:29863 original size:20 final size:20
Alignment explanation
Indices: 29838--29885 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
29828 CTTACATTTG
29838 CAGTTCCTCTCCATTTGAAC
1 CAGTTCCTCTCCATTTGAAC
29858 CAGTTCCTCTCCATTTGAAC
1 CAGTTCCTCTCCATTTGAAC
29878 CAGTTCCT
1 CAGTTCCT
29886 TCTAGATCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.19, C:0.35, G:0.10, T:0.35
Consensus pattern (20 bp):
CAGTTCCTCTCCATTTGAAC
Found at i:35724 original size:34 final size:34
Alignment explanation
Indices: 35679--35745 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
35669 AATATGAATT
*
35679 ACAACTTCTCTC-GATCTAACAAGGAGAAAACAATG
1 ACAACTTCTCTCTGA--TAAAAAGGAGAAAACAATG
35714 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAGGAGAAAACAA
35746 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 23 0.79
35 4 0.14
36 2 0.07
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.21
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAGGAGAAAACAATG
Found at i:39586 original size:16 final size:15
Alignment explanation
Indices: 39556--39590 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
39546 ATATATTTAG
*
39556 TATAAATGGTGTATT
1 TATAAATGATGTATT
39571 TATAACATGATGTATT
1 TATAA-ATGATGTATT
39587 TATA
1 TATA
39591 TCTTTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (15 bp):
TATAAATGATGTATT
Found at i:39747 original size:23 final size:20
Alignment explanation
Indices: 39717--39768 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
39707 TCCAAAATGT
39717 TATAATTAATTATAATATAAAA
1 TATAATTAATT-TAA-ATAAAA
*
39739 TATATATTAATTTAAATAAAT
1 TATA-ATTAATTTAAATAAAA
*
39760 TAAAATTAA
1 TATAATTAA
39769 AAATACACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.19
21 8 0.30
22 7 0.26
23 7 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TATAATTAATTTAAATAAAA
Found at i:40613 original size:13 final size:14
Alignment explanation
Indices: 40591--40625 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
40581 ATGAAAGCAT
40591 TTTGATTAATTGAA
1 TTTGATTAATTGAA
40605 TTT-ATTAATTGAA
1 TTTGATTAATTGAA
40618 TTTGATTA
1 TTTGATTA
40626 TTTGTCAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (14 bp):
TTTGATTAATTGAA
Found at i:46476 original size:18 final size:18
Alignment explanation
Indices: 46442--46475 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
46432 AAGGAGCTGA
46442 TTTTTTTAATAAAAAAAC
1 TTTTTTTAATAAAAAAAC
46460 TTTTTTT-ATAAAAAAA
1 TTTTTTTAATAAAAAAA
46476 AATTAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTTTTTAATAAAAAAAC
Found at i:60715 original size:20 final size:20
Alignment explanation
Indices: 60660--60717 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
60650 TCATAATAAT
60660 TTTTATTTATTCACAATTTGTAA
1 TTTT-TTTATT-A-AATTTGTAA
* *
60683 -TTTTTAATATAAATTTTTAA
1 TTTTTTTAT-TAAATTTGTAA
60703 TTTTTTTATTAAATT
1 TTTTTTTATTAAATT
60718 GAAAGGTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
20 14 0.47
21 12 0.40
22 4 0.13
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTTTTATTAAATTTGTAA
Done.