Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008473.1 Hibiscus syriacus cultivar Beakdansim tig00111300_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: 90714
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:750 original size:15 final size:15
Alignment explanation
Indices: 730--764 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
720 CCGTAGGACC
730 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
745 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
760 ACTAC
1 ACTAC
765 AGAACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:4275 original size:37 final size:36
Alignment explanation
Indices: 4234--4478 Score: 177
Period size: 36 Copynumber: 6.9 Consensus size: 36
4224 GGTCGTCTTG
* * *
4234 CTTGAGACTAATTT-ACTTAAAACAAAGTTTTGTCTCT
1 CTTGAGAC-AGTTTCACTTGAAATAAA-TTTTGTCTCT
* *
4271 CTTGAGACAGTTTCTCTTGAAATAAATTTTATCTCT
1 CTTGAGACAGTTTCACTTGAAATAAATTTTGTCTCT
*
4307 CTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCT
1 CTTGAGACAGTTTCACTTGAAATAAATTTTGTCTCT
* * *
4343 CTTGAGACAGTTTCCCTTGAAACAAA------ATCT
1 CTTGAGACAGTTTCACTTGAAATAAATTTTGTCTCT
* * * ** *
4373 -TTGA-ATATGTTTTACATT-AAACAAATTCCGTCTCC
1 CTTGAGACA-GTTTCAC-TTGAAATAAATTTTGTCTCT
** * * *
4408 CTTGAGACAGTTTCTTTTGGAACTAAGTTCTGTCTCT
1 CTTGAGACAGTTTCACTT-GAAATAAATTTTGTCTCT
* *
4445 CTTGAGACAGTTTCTCTTGAAACAAATTTTGTCT
1 CTTGAGACAGTTTCACTTGAAATAAATTTTGTCT
4479 TTGTCTCTCT
Statistics
Matches: 167, Mismatches: 28, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
28 2 0.01
29 16 0.10
30 5 0.03
35 4 0.02
36 92 0.55
37 48 0.29
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (36 bp):
CTTGAGACAGTTTCACTTGAAATAAATTTTGTCTCT
Found at i:4309 original size:36 final size:36
Alignment explanation
Indices: 4261--4508 Score: 190
Period size: 36 Copynumber: 6.9 Consensus size: 36
4251 TAAAACAAAG
*
4261 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
*
4297 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
*
4333 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
* * * * *
4369 ------ATCT-TTGA-ATATGTTTTACATT-AAACAAA
1 TTTTGTCTCTCTTGAGACA-G-TTTCCCTTGAAATAAA
** * ** * *
4398 TTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTT-GAAATAAA
* * *
4435 TTCTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
4471 TTTTGTCTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
1 -----T-TTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
4509 CAAAATCTCT
Statistics
Matches: 169, Mismatches: 25, Indels: 30
0.75 0.11 0.13
Matches are distributed among these distances:
28 2 0.01
29 12 0.07
30 9 0.05
35 7 0.04
36 78 0.46
37 31 0.18
41 1 0.01
42 29 0.17
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
Found at i:4525 original size:144 final size:142
Alignment explanation
Indices: 4265--4655 Score: 485
Period size: 144 Copynumber: 2.8 Consensus size: 142
4255 ACAAAGTTTT
* * * * * *
4265 GTCTCTCTTGAGACAGTTTCTCTT-GAAATAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAA
1 GTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
* *
4329 TAAA----TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGTTTTACAT
66 CAAATTTTTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTCTGAATATGTTTT-CAT
4390 T-AAACAAATTCC
130 TGAAACAAATTCC
*
4402 GTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTCTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1 GTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
4467 CAAATTTTGTCTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTCTGAATATGTTTTCA
66 CAAATTTT-T-TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTCTGAATATGTTTTCA
* *
4532 TTGAAACATATTTC
129 TTGAAACAAATTCC
* * * * *
4546 GTCTCCCTTGAGACAGTTTTCTTTCGGAACTAAGTTTTGTCTCTTTTGTGACATTTTCTTTTGAA
1 GTCTCCCTTGAGACAG-TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
* * * *
4611 ACAAA---ATTTTCTCTCCCTTGAGACAGTTTCTCTTGATACACAAAA
65 ACAAATTTTTTTTGTCTCTCTTGAGACAGTTTCCCTTGA-A-ACAAAA
4656 AAAACCTTTG
Statistics
Matches: 222, Mismatches: 21, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
137 22 0.10
138 38 0.17
140 26 0.12
141 2 0.01
142 6 0.03
143 5 0.02
144 76 0.34
145 47 0.21
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (142 bp):
GTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
CAAATTTTTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTCTGAATATGTTTTCATT
GAAACAAATTCC
Found at i:4641 original size:37 final size:37
Alignment explanation
Indices: 4542--4655 Score: 102
Period size: 37 Copynumber: 3.0 Consensus size: 37
4532 TTGAAACATA
* * * *
4542 TTTCGTCTCCCTTGAGACAGTTTTCTTTCGGAACTAAGT
1 TTTC-TCTCCCTTGAGACAG-TTTCTTTTGAAACAAAAT
* ** * *
4581 TTTGTCTCTTTTGTGACATTTTCTTTTGAAACAAAAT
1 TTTCTCTCCCTTGAGACAGTTTCTTTTGAAACAAAAT
*
4618 TTTCTCTCCCTTGAGACAGTTTCTCTTGATACACAAAA
1 TTTCTCTCCCTTGAGACAGTTTCTTTTGA-A-ACAAAA
4656 AAAACCTTTG
Statistics
Matches: 58, Mismatches: 15, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
37 37 0.64
38 12 0.21
39 9 0.16
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (37 bp):
TTTCTCTCCCTTGAGACAGTTTCTTTTGAAACAAAAT
Found at i:4837 original size:84 final size:84
Alignment explanation
Indices: 4696--4856 Score: 250
Period size: 84 Copynumber: 1.9 Consensus size: 84
4686 CCAAACCTTT
* *
4696 GAGTTCGATTACACTCAGCTCCAAGGCACCTCATTTGCAACATAACTCAAGGCAAGAAGGGCAAT
1 GAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGCAAT
*
4761 TTGCCAACCAAATACATTC
66 CTGCCAACCAAATACATTC
* * * * *
4780 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTAT
1 GAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGCAAT
4845 CTGCCAACCAAA
66 CTGCCAACCAAA
4857 GACCCGACGA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 69 1.00
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (84 bp):
GAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGCAAT
CTGCCAACCAAATACATTC
Found at i:5207 original size:11 final size:11
Alignment explanation
Indices: 5168--5207 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
5158 ATAATAATAA
*
5168 TTATTATTATT
1 TTATTTTTATT
* *
5179 ATATTTATATT
1 TTATTTTTATT
5190 TTATTTTTATT
1 TTATTTTTATT
5201 TTATTTT
1 TTATTTT
5208 GTAGGCGCCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:7511 original size:31 final size:31
Alignment explanation
Indices: 7417--7512 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 31
7407 AGAGTCGAGG
7417 GTTTACCTATG-TCTTTCGGGACATATGGACA
1 GTTTACCTATGTTC-TTCGGGACATATGGACA
* * ** * **
7448 ATATACCTATGTTCTAAGGAACATATAAACA
1 GTTTACCTATGTTCTTCGGGACATATGGACA
* *
7479 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGACA
7510 GTT
1 GTT
7513 GCCGAGGTTC
Statistics
Matches: 48, Mismatches: 16, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
31 46 0.96
32 2 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACA
Found at i:8220 original size:21 final size:21
Alignment explanation
Indices: 8194--8258 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
8184 TTACGAAAGT
8194 CATTGTAGCAAGGCATCGATG
1 CATTGTAGCAAGGCATCGATG
*
8215 CATTGTAGCAGGGCATCGATG
1 CATTGTAGCAAGGCATCGATG
8236 CATTGTAGC-AGTGCATCGATG
1 CATTGTAGCAAG-GCATCGATG
8257 CA
1 CA
8259 CAATTTTGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
20 1 0.02
21 40 0.98
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (21 bp):
CATTGTAGCAAGGCATCGATG
Found at i:8999 original size:20 final size:20
Alignment explanation
Indices: 8976--9024 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
8966 GACGTGTTTT
*
8976 CCTTTAAATATTGTGCTTTC
1 CCTTTAAATATTGTACTTTC
*
8996 CCTTTAAATATTGTATTTTC
1 CCTTTAAATATTGTACTTTC
9016 CCTTTAAAT
1 CCTTTAAAT
9025 CTGTTTGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.51
Consensus pattern (20 bp):
CCTTTAAATATTGTACTTTC
Found at i:10670 original size:21 final size:21
Alignment explanation
Indices: 10641--10693 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
10631 ATTCTGACTA
10641 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* **
10662 TCGCGTTGCGATTTTCGTAAT
1 TCGCATTGCGATTTTCCAAAT
*
10683 TCGCAATGCGA
1 TCGCATTGCGA
10694 ATATGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:10706 original size:20 final size:20
Alignment explanation
Indices: 10677--10775 Score: 144
Period size: 20 Copynumber: 5.0 Consensus size: 20
10667 TTGCGATTTT
*
10677 CGTAATTCGCAATGCGAATA
1 CGTAAATCGCAATGCGAATA
* *
10697 TGTAAATCGCAATGTGAATA
1 CGTAAATCGCAATGCGAATA
10717 CGTAAATCGCAATGCGAATA
1 CGTAAATCGCAATGCGAATA
* *
10737 CGTAAATCGTAATGTGAATA
1 CGTAAATCGCAATGCGAATA
*
10757 CGTAAATCGCAACGCGAAT
1 CGTAAATCGCAATGCGAAT
10776 CTGACTATCG
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.24
Consensus pattern (20 bp):
CGTAAATCGCAATGCGAATA
Found at i:10727 original size:40 final size:40
Alignment explanation
Indices: 10677--10775 Score: 162
Period size: 40 Copynumber: 2.5 Consensus size: 40
10667 TTGCGATTTT
* *
10677 CGTAATTCGCAATGCGAATATGTAAATCGCAATGTGAATA
1 CGTAAATCGCAATGCGAATACGTAAATCGCAATGTGAATA
*
10717 CGTAAATCGCAATGCGAATACGTAAATCGTAATGTGAATA
1 CGTAAATCGCAATGCGAATACGTAAATCGCAATGTGAATA
*
10757 CGTAAATCGCAACGCGAAT
1 CGTAAATCGCAATGCGAAT
10776 CTGACTATCG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.24
Consensus pattern (40 bp):
CGTAAATCGCAATGCGAATACGTAAATCGCAATGTGAATA
Found at i:10995 original size:22 final size:22
Alignment explanation
Indices: 10970--11035 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
10960 GGCGATATCT
10970 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
10992 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
11014 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
11036 TTCACGGTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:11416 original size:20 final size:20
Alignment explanation
Indices: 11343--11433 Score: 103
Period size: 20 Copynumber: 4.6 Consensus size: 20
11333 GCGATTCTGT
11343 CGTTGCGATTTTCATTTT-G
1 CGTTGCGATTTTCATTTTCG
** **
11362 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
**
11382 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
11402 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
11422 TGTTGCGATTTT
1 CGTTGCGATTTT
11434 AAGTTTCAGA
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
19 14 0.23
20 48 0.77
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:11440 original size:20 final size:20
Alignment explanation
Indices: 11397--11440 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
11387 CGATAGTCAT
* *
11397 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
11417 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
11437 TTTC
1 TTTC
11441 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:13331 original size:20 final size:20
Alignment explanation
Indices: 13306--13462 Score: 108
Period size: 20 Copynumber: 8.5 Consensus size: 20
13296 AGAATAGTTT
13306 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
13326 ACTATCGCAACGTGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
13346 ATTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
13362 A--ATCGCAATGC-AAAATG
1 ACTATCGCAATGCGAAAATG
** *
13379 AAAATCGTAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
13395 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
13413 ACTATCGTAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
13433 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
13453 ACTATCGCAA
1 ACTATCGCAA
13463 CGAGAGAATC
Statistics
Matches: 110, Mismatches: 13, Indels: 28
0.73 0.09 0.19
Matches are distributed among these distances:
14 13 0.12
16 9 0.08
17 9 0.08
18 4 0.04
19 6 0.05
20 69 0.63
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:13431 original size:34 final size:34
Alignment explanation
Indices: 13329--13431 Score: 84
Period size: 34 Copynumber: 3.1 Consensus size: 34
13319 GAAAATGACT
* * * * * *
13329 ATCGCAACGTGAAAATGATTATCGCAACGAGAGA
1 ATCGCAACGCGAAAATGAATATCGTAAAGCGAAA
* * *
13363 ATCGCAATGC-AAAATGAAAATCGTAACAAC-AAA
1 ATCGCAACGCGAAAATGAATATCGTAA-AGCGAAA
* *
13396 ATCGCAACGCGAAAATGACTATCGTAATGCGAAA
1 ATCGCAACGCGAAAATGAATATCGTAAAGCGAAA
13430 AT
1 AT
13432 GACTATCGCA
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
33 25 0.48
34 27 0.52
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.17
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGAATATCGTAAAGCGAAA
Found at i:13532 original size:20 final size:20
Alignment explanation
Indices: 13507--13575 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
13497 GCGATTCTCT
**
13507 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
13527 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
13547 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
13567 CGTTGCGAT
1 CGTTGCGAT
13576 TTTCGCGTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:13533 original size:34 final size:34
Alignment explanation
Indices: 13490--13589 Score: 101
Period size: 40 Copynumber: 2.8 Consensus size: 34
13480 GAAATGAAAA
* *
13490 TCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
1 TCGCGTTGCGATTCTCGCGTTGCGATAGTCAAAT
**
13524 TCGCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGAT--TC----TCGCGTTGCGATAGTCAAAT
*
13564 TCGCGTTGCGATTTTCGCGTTGCGAT
1 TCGCGTTGCGATTCTCGCGTTGCGAT
13590 TTTAAGTTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
34 23 0.42
36 2 0.04
38 1 0.02
40 29 0.53
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (34 bp):
TCGCGTTGCGATTCTCGCGTTGCGATAGTCAAAT
Found at i:13579 original size:14 final size:14
Alignment explanation
Indices: 13560--13592 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
13550 TGCGATAGTC
13560 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
13574 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
13588 ATTTT
1 ATTTT
13593 AAGTTTCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.09, C:0.18, G:0.24, T:0.48
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:14117 original size:18 final size:20
Alignment explanation
Indices: 14080--14119 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
14070 CCTGTCATCG
14080 TTCAAGAGGCCTCCCCTATCA
1 TTCAAGAGGCCT-CCCTATCA
14101 TTCAAGAGG-CT-CCTATCA
1 TTCAAGAGGCCTCCCTATCA
14119 T
1 T
14120 CCCTCAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
20 2 0.11
21 9 0.47
ACGTcount: A:0.25, C:0.33, G:0.15, T:0.28
Consensus pattern (20 bp):
TTCAAGAGGCCTCCCTATCA
Found at i:15551 original size:14 final size:14
Alignment explanation
Indices: 15532--15567 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
15522 ATTGTTTAAT
15532 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
15546 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
15560 TGATTTGT
1 TGATTTGT
15568 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:15761 original size:34 final size:34
Alignment explanation
Indices: 15673--15768 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
15663 AAAACAGACT
* * **
15673 ATCGCAACGCGAAAATTACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
*
15707 ATCGCAATGCG-AAATGAAAATCGTAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
15740 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
15769 CGAAACTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.53
34 26 0.47
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.15
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:15808 original size:20 final size:19
Alignment explanation
Indices: 15779--15845 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
15769 CGAAACTAAA
*
15779 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
15799 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
15815 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
15832 TTCGCATTGCGATT
1 TTCGCATTGCGATT
15846 CTCTCGTCGC
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
14 6 0.15
16 7 0.18
17 4 0.10
18 3 0.08
19 8 0.21
20 11 0.28
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:15840 original size:33 final size:33
Alignment explanation
Indices: 15783--15878 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
15773 ACTAAATTCG
15783 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
15817 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* ** *
15850 CGTCGCGATAGTCATTTCGGCGTTGCGAT
1 CGTTGCGATTTTCATTTC-GCATTGCGAT
15879 AGTCAATTCC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 34 0.60
34 23 0.40
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:15879 original size:20 final size:20
Alignment explanation
Indices: 15854--15943 Score: 119
Period size: 20 Copynumber: 4.5 Consensus size: 20
15844 TTCTCTCGTC
*
15854 GCGATAGTCATTTCGGCGTT
1 GCGATAGTCATTTCCGCGTT
*
15874 GCGATAGTCAATTCCGCGTT
1 GCGATAGTCATTTCCGCGTT
*
15894 GCGATAGTCATTTCCGTGTT
1 GCGATAGTCATTTCCGCGTT
**
15914 GTAATAGTCATATT-CGCGTT
1 GCGATAGTCAT-TTCCGCGTT
15934 GCGATAGTCA
1 GCGATAGTCA
15944 AATGAATGTC
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
20 58 0.97
21 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
GCGATAGTCATTTCCGCGTT
Found at i:18388 original size:24 final size:24
Alignment explanation
Indices: 18361--18407 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
18351 CAAAATCCGA
18361 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
18385 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
18408 AAAACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:18416 original size:24 final size:24
Alignment explanation
Indices: 18365--18416 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
18355 ATCCGAGTAT
*** *
18365 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAAAAC
*
18389 TGACCAAGATCAAATTTCGAAAAC
1 TGACCAAGATCAAAGTTCGAAAAC
18413 TGAC
1 TGAC
18417 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAAAAC
Found at i:19273 original size:20 final size:20
Alignment explanation
Indices: 19245--19331 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
19235 AAATTCAGTA
19245 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
* *
19265 TTGCAATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
19285 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
19305 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
19325 TTGCGAT
1 TTGCGAT
19332 TTACGTATTC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:19341 original size:20 final size:20
Alignment explanation
Indices: 19318--19370 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
19308 CGATAGTCAG
*
19318 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
19338 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
19358 ATTCGCATTGCGA
1 ATTCGCATTGCGA
19371 ATTAGGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:19391 original size:21 final size:21
Alignment explanation
Indices: 19367--19412 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
19357 TATTCGCATT
19367 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
19388 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
19409 GCGA
1 GCGA
19413 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:19433 original size:41 final size:40
Alignment explanation
Indices: 19388--19475 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
19378 AAATCGCAAC
*
19388 GCGAATTTGGAAAATCGCA-ATGCGATAGTCAGA-ATCGCGTT
1 GCGAATTTGGAAAAT-G-ATATGCGATA-CCAGAGATCGCGTT
* * *
19429 GCGAATCTGGAAACTGATTTGCGATACCAGAGATCGCGTT
1 GCGAATTTGGAAAATGATATGCGATACCAGAGATCGCGTT
19469 GCGAATT
1 GCGAATT
19476 ATCGATCGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
39 5 0.12
40 22 0.55
41 13 0.32
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (40 bp):
GCGAATTTGGAAAATGATATGCGATACCAGAGATCGCGTT
Found at i:25013 original size:34 final size:34
Alignment explanation
Indices: 24975--25049 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
24965 TTAAAGCGTG
*
24975 GTGTGGCTGGAATTGAAGATTCCTTATGTCTGTT
1 GTGTGGCTGGAATTGAAGATTCCTTATGTCCGTT
25009 GTGTGGCTGGAATTGAAGATTCCTTATGTCCGTT
1 GTGTGGCTGGAATTGAAGATTCCTTATGTCCGTT
25043 GTGTGGC
1 GTGTGGC
25050 AGATTTGGGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.16, C:0.13, G:0.32, T:0.39
Consensus pattern (34 bp):
GTGTGGCTGGAATTGAAGATTCCTTATGTCCGTT
Found at i:27626 original size:18 final size:18
Alignment explanation
Indices: 27586--27628 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
27576 AAAAAACTAT
* *
27586 GAGAGAGAAAGAGAGTGT
1 GAGAGAGAAAGAGAGAGA
* *
27604 TAGAGAGAAAGTGAGAGA
1 GAGAGAGAAAGAGAGAGA
27622 GAGAGAG
1 GAGAGAG
27629 TGTGCCATAG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.44, T:0.09
Consensus pattern (18 bp):
GAGAGAGAAAGAGAGAGA
Found at i:48101 original size:20 final size:20
Alignment explanation
Indices: 48063--48113 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
48053 ATAAAAAATA
48063 TTAAT-TTTTAATTTTATAACTT
1 TTAATATTTTAA--TTATAA-TT
48085 TT-ATATTTTAATTATAATT
1 TTAATATTTTAATTATAATT
48104 TTAATATTTT
1 TTAATATTTT
48114 TTTGTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 4 0.15
20 13 0.48
21 2 0.07
22 8 0.30
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTAATATTTTAATTATAATT
Found at i:48387 original size:38 final size:38
Alignment explanation
Indices: 48336--48411 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
48326 AAGCTGCTCC
48336 CTCTGCTCAGTTTCCTCCTCTTCAGGTCCCTTTGCTTT
1 CTCTGCTCAGTTTCCTCCTCTTCAGGTCCCTTTGCTTT
48374 CTCTGCTCAGTTTCCTCCTCTTCAGGTCCCTTTGCTTT
1 CTCTGCTCAGTTTCCTCCTCTTCAGGTCCCTTTGCTTT
48412 ATTTTTCTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.05, C:0.37, G:0.13, T:0.45
Consensus pattern (38 bp):
CTCTGCTCAGTTTCCTCCTCTTCAGGTCCCTTTGCTTT
Found at i:50240 original size:7 final size:7
Alignment explanation
Indices: 50230--50255 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
50220 AATGATATTT
50230 GATTTCA
1 GATTTCA
50237 GATTTCA
1 GATTTCA
50244 GATTTCA
1 GATTTCA
50251 GATTT
1 GATTT
50256 TTACTGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (7 bp):
GATTTCA
Found at i:53822 original size:22 final size:23
Alignment explanation
Indices: 53791--53837 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
53781 TAATCGCGAG
53791 TTTAGAAGATACGA-TTCTGGGC
1 TTTAGAAGATACGATTTCTGGGC
* *
53813 TTTAGCAGATACGATTTTTGGGC
1 TTTAGAAGATACGATTTCTGGGC
53836 TT
1 TT
53838 ATTTAGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (23 bp):
TTTAGAAGATACGATTTCTGGGC
Found at i:58273 original size:21 final size:21
Alignment explanation
Indices: 58249--58296 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
58239 AATTTCCCCT
* *
58249 TAATGAACTTTTATAATGTAA
1 TAATAAACTTTTATAATATAA
58270 TAATAAACTTTTATAATATAA
1 TAATAAACTTTTATAATATAA
58291 TAATAA
1 TAATAA
58297 TTCATCCAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (21 bp):
TAATAAACTTTTATAATATAA
Found at i:58551 original size:26 final size:26
Alignment explanation
Indices: 58495--58551 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
58485 ACCAGAACTC
*
58495 AGTAATTCAAATATCTAAGAAAAGAA
1 AGTACTTCAAATATCTAAGAAAAGAA
58521 AGTACTTCAAATATCTAAGAAAAGAA
1 AGTACTTCAAATATCTAAGAAAAGAA
58547 AGTAC
1 AGTAC
58552 ATTAACAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.54, C:0.11, G:0.12, T:0.23
Consensus pattern (26 bp):
AGTACTTCAAATATCTAAGAAAAGAA
Found at i:61055 original size:15 final size:16
Alignment explanation
Indices: 61026--61058 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
61016 TTTGATTTTA
61026 ATTTTATATTTAAATT
1 ATTTTATATTTAAATT
61042 ATTTTATA-TTAAATT
1 ATTTTATATTTAAATT
61057 AT
1 AT
61059 AATAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTATATTTAAATT
Found at i:71307 original size:42 final size:42
Alignment explanation
Indices: 71243--71339 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
71233 TTATCAAAGT
* * *
71243 AAGTCCTTCGGGCCATCGGTAAGTCTTTCGAGCATGATGATG
1 AAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATAATG
* *
71285 AAGTCCTTCGGGTCATCAGTAAGTCTTTTGAGCATGATAATT
1 AAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATAATG
*
71327 AAATCCTTCGGGT
1 AAGTCCTTCGGGT
71340 AATTTTTAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.32
Consensus pattern (42 bp):
AAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATAATG
Found at i:71392 original size:80 final size:80
Alignment explanation
Indices: 71298--71788 Score: 793
Period size: 80 Copynumber: 6.1 Consensus size: 80
71288 TCCTTCGGGT
* * *
71298 CATCAGTAAGTCTTTTGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGA
*
71363 GTAGTGAAGCAAACC
66 GTAGTGAAGCAAATC
* * *
71378 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTAGGGTAATTTGTAAGCCTTCACCGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGA
71443 GTAGTGAAGCAAATC
66 GTAGTGAAGCAAATC
71458 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGA
*
71523 GTAGTAAAGCAAATC
66 GTAGTGAAGCAAATC
* * * *
71538 CATCAATAAGTCTTTTGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGA
*
71603 GTAGTGAAGCAAACC
66 GTAGTGAAGCAAATC
* * * * *
71618 CATCAGTAAGTTTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGACTTCACCAAAGA
1 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGA
71683 GTAGTGAAGCAAATC
66 GTAGTGAAGCAAATC
* *
71698 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGA
71763 GTAGTGAAGCAAATC
66 GTAGTGAAGCAAATC
*
71778 CGTCAGTAAGT
1 CATCAGTAAGT
71789 GCCATCAGTA
Statistics
Matches: 376, Mismatches: 35, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 376 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (80 bp):
CATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGA
GTAGTGAAGCAAATC
Found at i:71727 original size:240 final size:240
Alignment explanation
Indices: 71298--71788 Score: 901
Period size: 240 Copynumber: 2.0 Consensus size: 240
71288 TCCTTCGGGT
71298 CATCAGTAAGTCTTTTGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTTGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
71363 GTAGTGAAGCAAACCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTAGGGTAATTTGTA
66 GTAGTGAAGCAAACCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTAGGGTAATTTGTA
* *
71428 AGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGTCTTTCGAGCATGATAATTAAATCC
131 AGACTTCACCAAAGAGTAGTGAAGCAAATCCATCAGTAAGTCTTTCGAGCATGATAATTAAATCC
71493 TTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTAAAGCAAATC
196 TTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTAAAGCAAATC
*
71538 CATCAATAAGTCTTTTGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTTGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
* *
71603 GTAGTGAAGCAAACCCATCAGTAAGTTTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTA
66 GTAGTGAAGCAAACCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTAGGGTAATTTGTA
71668 AGACTTCACCAAAGAGTAGTGAAGCAAATCCATCAGTAAGTCTTTCGAGCATGATAATTAAATCC
131 AGACTTCACCAAAGAGTAGTGAAGCAAATCCATCAGTAAGTCTTTCGAGCATGATAATTAAATCC
* * *
71733 TTCGGGTAATTTTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
196 TTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTAAAGCAAATC
*
71778 CGTCAGTAAGT
1 CATCAGTAAGT
71789 GCCATCAGTA
Statistics
Matches: 241, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
240 241 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (240 bp):
CATCAGTAAGTCTTTTGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGA
GTAGTGAAGCAAACCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTAGGGTAATTTGTA
AGACTTCACCAAAGAGTAGTGAAGCAAATCCATCAGTAAGTCTTTCGAGCATGATAATTAAATCC
TTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTAAAGCAAATC
Found at i:72441 original size:106 final size:106
Alignment explanation
Indices: 72268--72461 Score: 336
Period size: 106 Copynumber: 1.8 Consensus size: 106
72258 AAGATTGTTC
* *
72268 GAGTTCTACTCCCTGAAGTAAGGAGTAGCGAACCCGTAGGCAGAAGATTGTTCGAGTTCTACTCC
1 GAGTTCTACTCCCTGAAGCAAGGAGTAGCGAACCCGTAAGCAGAAGATTGTTCGAGTTCTACTCC
*
72333 TTGAAGCAAGAGGGAGCGAACCCTTAGGAAGAAGATATTTT
66 TTGAAGCAAGAGGGAGCAAACCCTTAGGAAGAAGATATTTT
*
72374 GAGTTCTACTCCTTGAAGCAAGAGAG-AGCGAACCCGTAAGCAGAAGATTGTTCGAGTTCTACTC
1 GAGTTCTACTCCCTGAAGCAAG-GAGTAGCGAACCCGTAAGCAGAAGATTGTTCGAGTTCTACTC
72438 CTTGAAGCAAGAGGGAGCAAACCC
65 CTTGAAGCAAGAGGGAGCAAACCC
72462 ACTGGTTGAA
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
106 80 0.96
107 3 0.04
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.22
Consensus pattern (106 bp):
GAGTTCTACTCCCTGAAGCAAGGAGTAGCGAACCCGTAAGCAGAAGATTGTTCGAGTTCTACTCC
TTGAAGCAAGAGGGAGCAAACCCTTAGGAAGAAGATATTTT
Found at i:72479 original size:53 final size:53
Alignment explanation
Indices: 72255--72461 Score: 301
Period size: 53 Copynumber: 3.9 Consensus size: 53
72245 AGAATCACAC
* * *
72255 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGTAAG-GAGTAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAG-GGAGCGAACCCGTAGG
*
72308 CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCTTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * *
72361 AAGAAGATAT-TTTGAGTTCTACTCCTTGAAGCAAGAGAGAGCGAACCCGTAAG
1 CAGAAGAT-TGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGG
*
72414 CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCAAACCC
1 CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCC
72462 ACTGGTTGAA
Statistics
Matches: 138, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
52 1 0.01
53 135 0.98
54 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAGG
Done.