Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004207.1 Hibiscus syriacus cultivar Beakdansim tig00009212_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: 68940
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7445 original size:20 final size:20
Alignment explanation
Indices: 7420--7614 Score: 149
Period size: 20 Copynumber: 9.7 Consensus size: 20
7410 GATTTTCCAT
**
7420 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGAA
**
7440 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATCCGA-A
* * *
7460 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGAATCCGAA
* * *
7480 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATCCG-AA
* *
7501 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
* * * *
7521 AATCACAACGAGAATACGTA
1 AATCGCAACGCGAATCCGAA
* * *
7541 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGAA
* *
7561 AATCGCAACGAGAATACGTAA
1 AATCGCAACGCGAATCCG-AA
* *
7582 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
7602 AATCGCAACGCGA
1 AATCGCAACGCGA
7615 TTTTTAAAGC
Statistics
Matches: 136, Mismatches: 35, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
19 1 0.01
20 100 0.74
21 35 0.26
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGAA
Found at i:7510 original size:81 final size:81
Alignment explanation
Indices: 7420--7614 Score: 250
Period size: 81 Copynumber: 2.4 Consensus size: 81
7410 GATTTTCCAT
* ** * * *
7420 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCG-ATTCTG-ACTAT
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTA-TCTGTA-AAT
* *
7483 CGCAACGAGTATCCGTAA
64 CGCAACGAGAATACGTAA
* * * *
7501 AATCGCAACGCGTATCCGTAAATCACAACGAGAATACGTAAATCGCAACGCGTATCTGTAAATCG
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCTGTAAATCG
7566 CAACGAGAATACGTAA
66 CAACGAGAATACGTAA
7582 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
7615 TTTTTAAAGC
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
81 96 0.98
82 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (81 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCTGTAAATCG
CAACGAGAATACGTAA
Found at i:7512 original size:41 final size:41
Alignment explanation
Indices: 7420--7611 Score: 223
Period size: 40 Copynumber: 4.7 Consensus size: 41
7410 GATTTTCCAT
* * * * *
7420 AATCGCAACGCGAATATGAAAATCGCAACGCG-A-ACATATA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA-A
* * *
7460 AATCGCAACGCG-ATTCTG-ACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGTA-TCTGTA-AATCGCAACGAGAATACGTAA
* *
7501 AATCGCAACGCGTATCCGTAAATCACAACGAGAATACGT-A
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAA
7541 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAA
*
7582 AATCGCAACGCGTATCCGTAAATCGCAACG
1 AATCGCAACGCGTATCTGTAAATCGCAACG
7612 CGATTTTTAA
Statistics
Matches: 132, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
39 2 0.02
40 63 0.48
41 62 0.47
42 5 0.04
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (41 bp):
AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAA
Found at i:7602 original size:61 final size:59
Alignment explanation
Indices: 7420--7613 Score: 178
Period size: 61 Copynumber: 3.2 Consensus size: 59
7410 GATTTTCCAT
* * * * *
7420 AATCGCAACGCGAATATGAAAATCGCAACGCGA-ACATATAAATCGCAACGCGATTC-TGA
1 AATCGCAACGCGTATCTGTAAATCGCAACGCGATACGTA-AAATCGCAACGCGATACGT-A
* * * * * *
7479 CTATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGT-AAATCACAACGAGAATACGTA
1 -AATCGCAACGCGTATCTGT-AAATCGCAACGCG-ATACGTAAAATCGCAACGCG-ATACGTA
* *
7541 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCTGTAAATCGCAACGCG-ATACGTAAAATCGCAACGCG-ATACGTA
7602 AATCGCAACGCG
1 AATCGCAACGCG
7614 ATTTTTAAAG
Statistics
Matches: 107, Mismatches: 21, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
60 30 0.28
61 69 0.64
62 5 0.05
63 3 0.03
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (59 bp):
AATCGCAACGCGTATCTGTAAATCGCAACGCGATACGTAAAATCGCAACGCGATACGTA
Found at i:8235 original size:21 final size:20
Alignment explanation
Indices: 8174--8249 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
8164 TTCTAAACTT
8174 AAAATCGCAAC-ATGAAAATG
1 AAAATCGCAACGA-GAAAATG
8194 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGA-GAAAATG
**
8214 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGA-AAATG
8235 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
8250 TAATCGCAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
20 30 0.61
21 19 0.39
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGAGAAAATG
Found at i:8303 original size:19 final size:19
Alignment explanation
Indices: 8281--8417 Score: 96
Period size: 20 Copynumber: 7.6 Consensus size: 19
8271 ATCGCATTGT
8281 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
* *
8300 GA--TTC---TCTCTTTGC
1 GATTTTCATTTCGCGTTGC
* *
8314 GATTTTAATTTCACGTTGC
1 GATTTTCATTTCGCGTTGC
*
8333 GA--TTC-TAT--CGTTGC
1 GATTTTCATTTCGCGTTGC
*
8347 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCGTTGC
**
8366 GATAGTCATTTCCGCGTTGC
1 GATTTTCATTT-CGCGTTGC
* *
8386 GATTTTCATTCTCTCATTGC
1 GATTTTCATT-TCGCGTTGC
8406 GATTTTCATTTC
1 GATTTTCATTTC
8418 AACCAAAAGA
Statistics
Matches: 90, Mismatches: 16, Indels: 24
0.69 0.12 0.18
Matches are distributed among these distances:
14 17 0.19
16 7 0.08
17 7 0.08
19 27 0.30
20 31 0.34
21 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
GATTTTCATTTCGCGTTGC
Found at i:8325 original size:33 final size:33
Alignment explanation
Indices: 8281--8368 Score: 131
Period size: 33 Copynumber: 2.7 Consensus size: 33
8271 ATCGCATTGT
* *
8281 GATTTTCATTTCGCGTTGCGATTCTCTCTTTGC
1 GATTTTCATTTCGCGTTGCGATTCTATCGTTGC
* *
8314 GATTTTAATTTCACGTTGCGATTCTATCGTTGC
1 GATTTTCATTTCGCGTTGCGATTCTATCGTTGC
*
8347 GATTTTCATTTCGCATTGCGAT
1 GATTTTCATTTCGCGTTGCGAT
8369 AGTCATTTCC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (33 bp):
GATTTTCATTTCGCGTTGCGATTCTATCGTTGC
Found at i:8387 original size:20 final size:19
Alignment explanation
Indices: 8341--8388 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
8331 GCGATTCTAT
**
8341 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
8360 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
8380 CGTTGCGAT
1 CGTTGCGAT
8389 TTTCATTCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:8415 original size:40 final size:39
Alignment explanation
Indices: 8341--8417 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 39
8331 GCGATTCTAT
8341 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
* **
8380 CGTTGCGATTTTCATTCTCTCATTGCGATTTTCATTTC
1 CGTTGCGATTTTCATT-TCGCATTGCGATAGTCATTTC
8418 AACCAAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 16 0.47
40 18 0.53
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (39 bp):
CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
Found at i:10455 original size:42 final size:42
Alignment explanation
Indices: 10377--10465 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
10367 GACTCGCCTG
* * * *
10377 TCATCCCTCAAGAGTCCACTCCTATCGTTGATGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
10419 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
10461 TCATC
1 TCATC
10466 GTTGAAGAGG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.20, C:0.38, G:0.17, T:0.25
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:11867 original size:14 final size:14
Alignment explanation
Indices: 11848--11883 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
11838 ATTGTTTAAT
11848 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
11862 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
11876 TGATTTGT
1 TGATTTGT
11884 TTAATTGATG
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:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:12012 original size:19 final size:19
Alignment explanation
Indices: 11990--12048 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
11980 AAAAATGACT
11990 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
12009 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
12023 ATCGCAATGCGAAATTAAA
1 ATCGCAATGCGAAATGAAA
12042 ATCGCAA
1 ATCGCAA
12049 CAACAAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.50
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:12032 original size:33 final size:32
Alignment explanation
Indices: 11990--12083 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 32
11980 AAAAATGACT
* *
11990 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAT-AAAATCGCAACGACAAA
*
12023 ATCGCAATGCGAAATTAAAATCGCAACAACAAA
1 ATCGCAATGCGAAA-TAAAATCGCAACGACAAA
* *
12056 ATCACAACGCGAAACTAAAATCGCAACG
1 ATCGCAATGCGAAA-TAAAATCGCAACG
12084 CGAAACTAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
33 52 0.98
34 1 0.02
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (32 bp):
ATCGCAATGCGAAATAAAATCGCAACGACAAA
Found at i:12105 original size:19 final size:19
Alignment explanation
Indices: 12022--12098 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
12012 GCAACGAGAG
* *
12022 AATCGCAATGCGAAATTAA
1 AATCGCAACGCGAAACTAA
12041 AATCGCAA--C--AAC-AA
1 AATCGCAACGCGAAACTAA
*
12055 AATCACAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
12074 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
12093 ATTCGC
1 AATCGC
12099 GTTGCGATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
14 9 0.18
15 2 0.04
16 1 0.02
17 1 0.02
18 3 0.06
19 33 0.67
ACGTcount: A:0.48, C:0.25, G:0.13, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:12168 original size:33 final size:33
Alignment explanation
Indices: 12098--12254 Score: 239
Period size: 33 Copynumber: 4.8 Consensus size: 33
12088 ACTAAATTCG
*
12098 CGTTGCGATTTTCATTTCG---TGCAATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* *
12128 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
12161 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* *
12194 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
12227 CGTTGCGATTTTCATTTCACATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
12255 AGTCATTTCC
Statistics
Matches: 115, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
30 19 0.17
33 96 0.83
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:12187 original size:19 final size:19
Alignment explanation
Indices: 12130--12308 Score: 119
Period size: 19 Copynumber: 10.4 Consensus size: 19
12120 AATTCCCTCG
12130 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
12149 TTGTGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
12163 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
**
12182 TTGCGA--TTC-CCTCG--
1 TTGCGATTTTCATTTCGCA
12196 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
12215 TTGTGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
12229 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCGCA
** *
12248 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
12268 TTGCGATTTTCA-----CA
1 TTGCGATTTTCATTTCGCA
12282 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
12301 TTGCGATT
1 TTGCGATT
12309 CTCTCATTGC
Statistics
Matches: 119, Mismatches: 20, Indels: 42
0.66 0.11 0.23
Matches are distributed among these distances:
14 29 0.24
16 20 0.17
17 19 0.16
19 39 0.33
20 12 0.10
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:12205 original size:66 final size:66
Alignment explanation
Indices: 12098--12254 Score: 275
Period size: 66 Copynumber: 2.4 Consensus size: 66
12088 ACTAAATTCG
*
12098 CGTTGCGATTTTCATTTCG---TGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGTGATTCTC
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGTGATTCTC
12160 T
66 T
12161 CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGTGATTCTC
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGTGATTCTC
12226 T
66 T
*
12227 CGTTGCGATTTTCATTTCACATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
12255 AGTCATTTCC
Statistics
Matches: 89, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
63 19 0.21
66 70 0.79
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (66 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGTGATTCTC
T
Found at i:12279 original size:34 final size:34
Alignment explanation
Indices: 12241--12341 Score: 141
Period size: 34 Copynumber: 3.0 Consensus size: 34
12231 GCGATTTTCA
12241 TTTCACATTGCGATAGTCATTTCCGCGTTGCGAT
1 TTTCACATTGCGATAGTCATTTCCGCGTTGCGAT
** *
12275 TTTCACATTGCGATTTTCATTT-CGCATTGCGAT
1 TTTCACATTGCGATAGTCATTTCCGCGTTGCGAT
* * *
12308 TCTCTCATTGCGATAGTAATTTCCGCGTTGCGAT
1 TTTCACATTGCGATAGTCATTTCCGCGTTGCGAT
12342 AGACATTAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 27 0.47
34 30 0.53
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.41
Consensus pattern (34 bp):
TTTCACATTGCGATAGTCATTTCCGCGTTGCGAT
Found at i:14890 original size:24 final size:24
Alignment explanation
Indices: 14856--14909 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
14846 CTGAAAAATC
14856 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
14880 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
14904 ATCAAA
1 ATCAAA
14910 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:14923 original size:24 final size:24
Alignment explanation
Indices: 14856--14923 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
14846 CTGAAAAATC
* * *
14856 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
14880 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
14904 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
14924 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:15715 original size:18 final size:18
Alignment explanation
Indices: 15692--15736 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
15682 AAAACATTTG
15692 TGTTGCGAAATTAAAACA
1 TGTTGCGAAATTAAAACA
15710 TGTTGCGAAATTAAAACA
1 TGTTGCGAAATTAAAACA
15728 TGTTGCGAA
1 TGTTGCGAA
15737 TTCAGAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (18 bp):
TGTTGCGAAATTAAAACA
Found at i:15818 original size:20 final size:20
Alignment explanation
Indices: 15789--16080 Score: 222
Period size: 20 Copynumber: 14.5 Consensus size: 20
15779 GTCAGAATCT
*
15789 CGTTGTGATTTACAGATTCG
1 CGTTGCGATTTACAGATTCG
* *
15809 CATTGCGATTTAC-GTGTTCG
1 CGTTGCGATTTACAG-ATTCG
*
15829 TGTTGCGATTTAC-GTATTCG
1 CGTTGCGATTTACAG-ATTCG
* *
15849 CATTGCGATTTACAGATACG
1 CGTTGCGATTTACAGATTCG
* *
15869 CATTGCGATTTAC-GTATTCT
1 CGTTGCGATTTACAG-ATTCG
* *
15889 CTTTGCGATTTACAGATACG
1 CGTTGCGATTTACAGATTCG
* *
15909 CATTGCGATTTAC-GTATTCT
1 CGTTGCGATTTACAG-ATTCG
* *
15929 CGTTGCGATTTACAGATACA
1 CGTTGCGATTTACAGATTCG
15949 CGTTGCGATTTTAC-GTATT-G
1 CGTTGCGA-TTTACAG-ATTCG
* *
15969 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTACAGATTCG
* * *
15990 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACAGATTCG
* *
16011 CGTTGCGATAGT-CAGAATCG
1 CGTTGCGAT-TTACAGATTCG
*
16031 CGTTGCGATTTATATG-TTCG
1 CGTTGCGATTTACA-GATTCG
* *
16051 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACAGATTCG
16071 CGTTGCGATT
1 CGTTGCGATT
16081 CTGGAAAATC
Statistics
Matches: 221, Mismatches: 35, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
19 4 0.02
20 176 0.80
21 41 0.19
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTACAGATTCG
Found at i:15875 original size:40 final size:40
Alignment explanation
Indices: 15789--16080 Score: 261
Period size: 40 Copynumber: 7.2 Consensus size: 40
15779 GTCAGAATCT
* * *
15789 CGTTGTGATTTACAG-ATTCGCATTGCGATTTAC-GTGTTCG
1 CGTTGCGATTTAC-GTATTCGCATTGCGATTTACAG-ATACG
*
15829 TGTTGCGATTTACGTATTCGCATTGCGATTTACAGATACG
1 CGTTGCGATTTACGTATTCGCATTGCGATTTACAGATACG
* * *
15869 CATTGCGATTTACGTATTCTCTTTGCGATTTACAGATACG
1 CGTTGCGATTTACGTATTCGCATTGCGATTTACAGATACG
* * * *
15909 CATTGCGATTTACGTATTCTCGTTGCGATTTACAGATACA
1 CGTTGCGATTTACGTATTCGCATTGCGATTTACAGATACG
* *
15949 CGTTGCGATTTTACGTATT-GTCGTTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCG-CATTGCGATTTACAGATACG
* * * * *
15990 CGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATCG
1 CGTTGCGA-TTTACGTATTCGCATTGCGAT-TTACAGATA-CG
** * * * * *
16031 CGTTGCGATTTATATGTTCGCGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGTATTCGCATTGCGATTTACAGATACG
16071 CGTTGCGATT
1 CGTTGCGATT
16081 CTGGAAAATC
Statistics
Matches: 215, Mismatches: 28, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
39 2 0.01
40 144 0.67
41 68 0.32
42 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCGCATTGCGATTTACAGATACG
Found at i:15974 original size:41 final size:40
Alignment explanation
Indices: 15830--16080 Score: 290
Period size: 40 Copynumber: 6.2 Consensus size: 40
15820 ACGTGTTCGT
* *
15830 GTTGCGATTTACGTATTCGCATTGCGATTTACAGATACGC
1 GTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGC
* *
15870 ATTGCGATTTACGTATTCTCTTTGCGATTTACAGATACGC
1 GTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGC
* *
15910 ATTGCGATTTACGTATTCTCGTTGCGATTTACAGATACAC
1 GTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGC
* *
15950 GTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGC
1 GTTGCGA-TTTACGTATTCTCGTTGCGATTTACAGATACGC
* * *
15991 GTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATCGC
1 GTTGCGA-TTTACGTATTCTCGTTGCGAT-TTACAGATA-CGC
** * * * * *
16032 GTTGCGATTTATATGTTCGCGTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGC
16072 GTTGCGATT
1 GTTGCGATT
16081 CTGGAAAATC
Statistics
Matches: 183, Mismatches: 23, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
39 1 0.01
40 112 0.61
41 69 0.38
42 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (40 bp):
GTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGC
Found at i:17918 original size:17 final size:17
Alignment explanation
Indices: 17896--17944 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
17886 TTTTAAGATT
17896 TTATATTTGATTCAAAA
1 TTATATTTGATTCAAAA
**
17913 TTATATTTGATTTTAAA
1 TTATATTTGATTCAAAA
17930 TTATATTTGATTCAA
1 TTATATTTGATTCAA
17945 TTATTCGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (17 bp):
TTATATTTGATTCAAAA
Found at i:19281 original size:21 final size:21
Alignment explanation
Indices: 19257--19309 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
19247 GGTAGTGAAT
19257 CTAGCTAGGTAAG-AGAGGTAG
1 CTAGCTAGGTAAGTA-AGGTAG
*
19278 CTAGCTAGGT-AGTTAAGTTAG
1 CTAGCTAGGTAAG-TAAGGTAG
19299 CTAGCTAGGTA
1 CTAGCTAGGTA
19310 CCTAGTGTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.07
21 25 0.89
22 1 0.04
ACGTcount: A:0.30, C:0.11, G:0.32, T:0.26
Consensus pattern (21 bp):
CTAGCTAGGTAAGTAAGGTAG
Found at i:19416 original size:21 final size:21
Alignment explanation
Indices: 19378--19423 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
19368 CTACTCGAAC
*
19378 TTCAGCTCCTCTCTAGCTAGA
1 TTCAGCTCCTATCTAGCTAGA
*
19399 TTCAGCTCCATATC-AGCTAGG
1 TTCAGCTCC-TATCTAGCTAGA
19420 TTCA
1 TTCA
19424 ACTGCTTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (21 bp):
TTCAGCTCCTATCTAGCTAGA
Found at i:26031 original size:24 final size:24
Alignment explanation
Indices: 26004--26065 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
25994 CGTTCGTGAA
*
26004 CGTTCGGTTATGTTCGTTTATATG
1 CGTTCAGTTATGTTCGTTTATATG
* *
26028 CGTTTAGTTATGTTCGTTTATGTG
1 CGTTCAGTTATGTTCGTTTATATG
*
26052 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
26066 TAACCTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.13, C:0.11, G:0.23, T:0.53
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATATG
Found at i:27585 original size:10 final size:10
Alignment explanation
Indices: 27570--27644 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
27560 GGGTCTCCAA
27570 CGTTTATGTT
1 CGTTTATGTT
27580 CGTTTATGTT
1 CGTTTATGTT
27590 CG----TGTT
1 CGTTTATGTT
*
27596 CATTTATGTT
1 CGTTTATGTT
*
27606 CGTGTT-CGTTT
1 CGT-TTATG-TT
* *
27617 ATGTTTGTGTT
1 -CGTTTATGTT
27628 CGTTTATGTT
1 CGTTTATGTT
27638 CGTTTAT
1 CGTTTAT
27645 TTATTAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.10
10 34 0.68
11 8 0.16
12 3 0.06
ACGTcount: A:0.09, C:0.11, G:0.21, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:27601 original size:16 final size:16
Alignment explanation
Indices: 27576--27640 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
27566 CCAACGTTTA
27576 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
27592 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
27608 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
27624 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
27640 T
1 T
27641 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:27731 original size:16 final size:16
Alignment explanation
Indices: 27710--27741 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
27700 AAAAAAATTT
27710 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
27726 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
27742 CTTATTTATT
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:0.06, C:0.12, G:0.25, T:0.56
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:32144 original size:37 final size:37
Alignment explanation
Indices: 32094--32168 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
32084 AAATATGGAA
* *
32094 TACAAATTCAAACTCTGTAAGGCTTTAATTGATGTTG
1 TACAAATTCAAACTCTGCAAGGCTTTAACTGATGTTG
32131 TACAAATTCAAACTCTGCAAGGCTTTAACTGATGTTG
1 TACAAATTCAAACTCTGCAAGGCTTTAACTGATGTTG
32168 T
1 T
32169 CTTCAACTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (37 bp):
TACAAATTCAAACTCTGCAAGGCTTTAACTGATGTTG
Found at i:58092 original size:29 final size:30
Alignment explanation
Indices: 58051--58115 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
58041 TATAAATAAT
*
58051 AAAACACTATATAACATA-TATTATATTTCC
1 AAAA-ACTATATAACATATTAATATATTTCC
* *
58081 AAAAACTATATAATATATTAATATATTTTC
1 AAAAACTATATAACATATTAATATATTTCC
58111 AAAAA
1 AAAAA
58116 TCGTTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 12 0.39
30 19 0.61
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (30 bp):
AAAAACTATATAACATATTAATATATTTCC
Found at i:58176 original size:22 final size:20
Alignment explanation
Indices: 58148--58190 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
58138 AAAACAATAT
**
58148 TATATATAGGTTTTCAAAAC
1 TATATATATATTTTCAAAAC
58168 TATATATATATTTTCAAAAC
1 TATATATATATTTTCAAAAC
58188 TAT
1 TAT
58191 TTTAAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (20 bp):
TATATATATATTTTCAAAAC
Found at i:58203 original size:29 final size:30
Alignment explanation
Indices: 58158--58261 Score: 111
Period size: 29 Copynumber: 3.3 Consensus size: 30
58148 TATATATAGG
*
58158 TTTTCAAAACTATATATATATTTTCAAAACTA
1 TTTT-AAAAC-ATATATACATTTTCAAAACTA
* *
58190 TTTTAAAAC-TATATACGTTTTCAAAACCA
1 TTTTAAAACATATATACATTTTCAAAACTA
58219 TTTTAAAAAACATATTTATACATTTTCAAAACTA
1 TTTT--AAAACATA--TATACATTTTCAAAACTA
58253 TTTTTAAAA
1 -TTTTAAAA
58262 AAAACTATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
29 21 0.34
31 10 0.16
32 6 0.10
33 4 0.07
34 16 0.26
35 4 0.07
ACGTcount: A:0.44, C:0.12, G:0.01, T:0.42
Consensus pattern (30 bp):
TTTTAAAACATATATACATTTTCAAAACTA
Found at i:58239 original size:34 final size:31
Alignment explanation
Indices: 58170--58272 Score: 111
Period size: 29 Copynumber: 3.2 Consensus size: 31
58160 TTCAAAACTA
*
58170 TATATATATTTTCAAAACTATTTT--AAAAC
1 TATATACATTTTCAAAACTATTTTAAAAAAC
* *
58199 TATATACGTTTTCAAAACCATTTTAAAAAAC
1 TATATACATTTTCAAAACTATTTTAAAAAAC
58230 ATATTTATACATTTTCAAAACTATTTTTAAAAAAAAC
1 -TA--TATACATTTTCAAAACTA-TTTT--AAAAAAC
58267 TATATA
1 TATATA
58273 TTATATATAC
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
29 21 0.34
31 5 0.08
32 2 0.03
34 20 0.33
35 4 0.07
36 2 0.03
37 7 0.11
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.41
Consensus pattern (31 bp):
TATATACATTTTCAAAACTATTTTAAAAAAC
Found at i:62190 original size:20 final size:21
Alignment explanation
Indices: 62165--62210 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
62155 GAGGGTTTTC
62165 TGTGGTCATTC-GAATAATTA
1 TGTGGTCATTCGGAATAATTA
* *
62185 TGTGGTCTTTCGGGATAATTA
1 TGTGGTCATTCGGAATAATTA
*
62206 GGTGG
1 TGTGG
62211 CACTTTGGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.22, C:0.09, G:0.30, T:0.39
Consensus pattern (21 bp):
TGTGGTCATTCGGAATAATTA
Found at i:62233 original size:23 final size:23
Alignment explanation
Indices: 62207--62291 Score: 115
Period size: 23 Copynumber: 3.8 Consensus size: 23
62197 GGATAATTAG
62207 GTGGCACTTTGGTGCAAACTTAT
1 GTGGCACTTTGGTGCAAACTTAT
*
62230 GTGGCACTTTGGTGCAAACCTAT
1 GTGGCACTTTGGTGCAAACTTAT
62253 GTGGTC-CTTTGG-G-ATAA-TTAT
1 GTGG-CACTTTGGTGCA-AACTTAT
62274 GTGGCACTTTGGTGCAAA
1 GTGGCACTTTGGTGCAAA
62292 TTACGAGCTG
Statistics
Matches: 55, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.02
21 14 0.25
22 6 0.11
23 33 0.60
24 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.34
Consensus pattern (23 bp):
GTGGCACTTTGGTGCAAACTTAT
Found at i:64380 original size:12 final size:12
Alignment explanation
Indices: 64363--64389 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
64353 TGTGAAGAAA
64363 ATTGGTATAATT
1 ATTGGTATAATT
64375 ATTGGTATAATT
1 ATTGGTATAATT
64387 ATT
1 ATT
64390 CCCTTGGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (12 bp):
ATTGGTATAATT
Found at i:68493 original size:23 final size:24
Alignment explanation
Indices: 68457--68523 Score: 91
Period size: 23 Copynumber: 2.8 Consensus size: 24
68447 AGAGTCAGGG
*
68457 TTCTACGCGCTCCTTCGGGATAA-
1 TTCTACGCGGTCCTTCGGGATAAT
* **
68480 TTCTACGTGGTCCTTCAAGATAAT
1 TTCTACGCGGTCCTTCGGGATAAT
68504 TTCTACGCGGTCCTTCGGGA
1 TTCTACGCGGTCCTTCGGGA
68524 CATCTATATG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 19 0.53
24 17 0.47
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.33
Consensus pattern (24 bp):
TTCTACGCGGTCCTTCGGGATAAT
Found at i:68511 original size:47 final size:45
Alignment explanation
Indices: 68457--68544 Score: 122
Period size: 47 Copynumber: 1.9 Consensus size: 45
68447 AGAGTCAGGG
*
68457 TTCTACGCGCTCCTTCGGGATAATTCTACGTGGTCCTTCAAGATAAT
1 TTCTACGCGCTCCTTCGGGA-AA-TCTACATGGTCCTTCAAGATAAT
* * *
68504 TTCTACGCGGTCCTTCGGGACATCTATATGGTCCTTCAAGA
1 TTCTACGCGCTCCTTCGGGAAATCTACATGGTCCTTCAAGA
68545 CATTCTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 17 0.46
46 1 0.03
47 19 0.51
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.33
Consensus pattern (45 bp):
TTCTACGCGCTCCTTCGGGAAATCTACATGGTCCTTCAAGATAAT
Found at i:68536 original size:21 final size:22
Alignment explanation
Indices: 68512--68564 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
68502 ATTTCTACGC
68512 GGTCCTTCGGGACA-TCTATAT
1 GGTCCTTCGGGACATTCTATAT
**
68533 GGTCCTTCAAGACATTCTATAT
1 GGTCCTTCGGGACATTCTATAT
68555 GG-CACTTCGG
1 GGTC-CTTCGG
68565 TGCAATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.32
Consensus pattern (22 bp):
GGTCCTTCGGGACATTCTATAT
Done.