Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009156.1 Hibiscus syriacus cultivar Beakdansim tig00112682_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: 51629
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1011 original size:31 final size:29
Alignment explanation
Indices: 949--1013 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 29
939 TACAATACAA
* *
949 TCCCCCAATATTTAGTGTTTTCAATATGG
1 TCCCCCAACATTTAGTGTTTACAATATGG
*
978 TCCCCCAACATTTAGTTCGTTTACAGTATGG
1 TCCCCCAACATTTAG-T-GTTTACAATATGG
1009 TCCCC
1 TCCCC
1014 GACGAAACTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 14 0.45
30 1 0.03
31 16 0.52
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.37
Consensus pattern (29 bp):
TCCCCCAACATTTAGTGTTTACAATATGG
Found at i:6082 original size:21 final size:21
Alignment explanation
Indices: 6044--6084 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6034 CCGAAGTACC
* *
6044 ACATATATGTTCCAAAGGATT
1 ACATATATATCCCAAAGGATT
*
6065 ACATATATATCCCGAAGGAT
1 ACATATATATCCCAAAGGAT
6085 CACGTAGAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (21 bp):
ACATATATATCCCAAAGGATT
Found at i:6877 original size:22 final size:23
Alignment explanation
Indices: 6827--6882 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
6817 CGATGATCCC
*
6827 TGGTATTGATAC-CCTCCACATA
1 TGGTATTGATACTCATCCACATA
*
6849 -GGTATTGATACTCATCC-CTTA
1 TGGTATTGATACTCATCCACATA
6870 TGGTATTGATACT
1 TGGTATTGATACT
6883 GTTCATACAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (23 bp):
TGGTATTGATACTCATCCACATA
Found at i:8415 original size:17 final size:17
Alignment explanation
Indices: 8393--8436 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
8383 TTCATATATC
8393 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
8410 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
8427 -AAATATCCAA
1 CAAA-ATCCAA
8437 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:10448 original size:20 final size:21
Alignment explanation
Indices: 10400--10462 Score: 74
Period size: 20 Copynumber: 2.9 Consensus size: 21
10390 TTCCCCTGTG
10400 GGGGGGAATCGGTTCCCCTTCAAA
1 GGGGGGAATCGGTT-CCC-TC-AA
10424 GGGGGGAATCGGTTCCCTC-A
1 GGGGGGAATCGGTTCCCTCAA
* *
10444 GGGGGGGATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
10463 TGCACCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.49
22 2 0.05
23 3 0.08
24 14 0.38
ACGTcount: A:0.16, C:0.25, G:0.38, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:14436 original size:19 final size:21
Alignment explanation
Indices: 14402--14441 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
14392 TAAATTCTTC
*
14402 TTCAAAATTTCATTTT-GTTT
1 TTCAAAATTCCATTTTAGTTT
14422 TTCAAAA-TCCATTTTAGTTT
1 TTCAAAATTCCATTTTAGTTT
14442 CTAGAAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55
Consensus pattern (21 bp):
TTCAAAATTCCATTTTAGTTT
Found at i:15578 original size:22 final size:22
Alignment explanation
Indices: 15550--15594 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
15540 ATTACAAATG
15550 AGCACAATAAGTGTTCTTTGAA
1 AGCACAATAAGTGTTCTTTGAA
15572 AGCACAATAAGTGTTCTTTGAA
1 AGCACAATAAGTGTTCTTTGAA
15594 A
1 A
15595 TCAAAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (22 bp):
AGCACAATAAGTGTTCTTTGAA
Found at i:16345 original size:2 final size:2
Alignment explanation
Indices: 16340--16390 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
16330 TTTTTTATTT
16340 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16382 TA TA TA TA T
1 TA TA TA TA T
16391 GTAATATAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16552 original size:23 final size:23
Alignment explanation
Indices: 16525--16572 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
16515 TAAAATTAAT
16525 AATTTGAAAATAAAAAATAAAAA
1 AATTTGAAAATAAAAAATAAAAA
*
16548 AATTTGAAAATAACAAATAAAAA
1 AATTTGAAAATAAAAAATAAAAA
16571 AA
1 AA
16573 CTGGGTACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (23 bp):
AATTTGAAAATAAAAAATAAAAA
Found at i:19653 original size:60 final size:60
Alignment explanation
Indices: 19528--19677 Score: 146
Period size: 60 Copynumber: 2.5 Consensus size: 60
19518 TTTGGGGACC
* * *
19528 AATTTAGAA-AGAGAG-ACATAATTTAGGGATGAAATTATAATGTTAAAAATTTTAATAATT
1 AATTTAGAATA-AGAGTA-ATAGTTTAGGGATGAAATTATAATGTTAAAAATTTTAAAAACT
*
19588 AATTTAGAATAAGAGTAATAGTTTAGGGATGAAATTGA-AATATTTAAAAA-TTTAAAAACT
1 AATTTAGAATAAGAGTAATAGTTTAGGGATGAAATT-ATAAT-GTTAAAAATTTTAAAAACT
* * * * * *
19648 GATTTATAGTGAGAGTTATAGTTTAAGGAT
1 AATTTAGAATAAGAGTAATAGTTTAGGGAT
19678 ATATGATGAA
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
60 66 0.87
61 10 0.13
ACGTcount: A:0.46, C:0.01, G:0.17, T:0.35
Consensus pattern (60 bp):
AATTTAGAATAAGAGTAATAGTTTAGGGATGAAATTATAATGTTAAAAATTTTAAAAACT
Found at i:20709 original size:23 final size:23
Alignment explanation
Indices: 20663--20710 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
20653 AATTATATCG
*
20663 TTGTGACATATTTTTATTTGTCT
1 TTGTGACATATTTTTATCTGTCT
*
20686 TTGTGACATGTTTTTCATCT-TCT
1 TTGTGACATATTTTT-ATCTGTCT
20709 TT
1 TT
20711 ATTAGTCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.15, C:0.12, G:0.12, T:0.60
Consensus pattern (23 bp):
TTGTGACATATTTTTATCTGTCT
Found at i:20983 original size:17 final size:16
Alignment explanation
Indices: 20961--20994 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
20951 TATAATCAAA
*
20961 TTTATTCGTATCTATTT
1 TTTATTCGAATCT-TTT
20978 TTTATTCGAATCTTTT
1 TTTATTCGAATCTTTT
20994 T
1 T
20995 GTTGAGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTATTCGAATCTTTT
Found at i:21330 original size:21 final size:21
Alignment explanation
Indices: 21301--21374 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
21291 GACTTGCATT
21301 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
21322 TCACGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
21342 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
21363 TCGCGTTGCGAT
1 TCGCGTTGCGAT
21375 TTTCCATTTC
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:21344 original size:41 final size:41
Alignment explanation
Indices: 21297--21397 Score: 193
Period size: 41 Copynumber: 2.5 Consensus size: 41
21287 ATTCGACTTG
21297 CATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTC
*
21338 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTC
21379 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
21398 CTACAGTTGT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTC
Found at i:21350 original size:20 final size:20
Alignment explanation
Indices: 21325--21394 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
21315 TTGAAAATCA
21325 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* ** **
21345 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGAT-TTTCCATTTCG
21366 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
21386 CGTTGCGAT
1 CGTTGCGAT
21395 AGTCTACAGT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 24 0.62
21 15 0.38
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:21414 original size:22 final size:22
Alignment explanation
Indices: 21386--21435 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
21376 TTCCATTTCG
21386 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* *
21408 TGTTGCGATAGTCTACATTTGT
1 CGTTGCGATAGTCTACAGTTGT
21430 CGTTGC
1 CGTTGC
21436 AATTTTCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.40
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:22067 original size:6 final size:6
Alignment explanation
Indices: 22053--22101 Score: 89
Period size: 6 Copynumber: 8.2 Consensus size: 6
22043 TCGTCTCGTC
*
22053 TCGTCG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
22101 T
1 T
22102 AATACGTGTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.00, C:0.18, G:0.47, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:22223 original size:19 final size:19
Alignment explanation
Indices: 22181--22224 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
22171 CAACGCGAAT
*
22181 TTGCGAATTATAGATCGCA
1 TTGCGAATTATAGATCACA
*
22200 ATGCGAATTATAGATCACA
1 TTGCGAATTATAGATCACA
22219 TTGCGA
1 TTGCGA
22225 TTTTGTTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (19 bp):
TTGCGAATTATAGATCACA
Found at i:29074 original size:12 final size:13
Alignment explanation
Indices: 29044--29082 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
29034 CAATTGTGCA
29044 AAAAATATATTAT
1 AAAAATATATTAT
*
29057 AAAAAATGTATTAT
1 -AAAAATATATTAT
29071 AAAAATAT-TTAT
1 AAAAATATATTAT
29083 TAAATGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 4 0.17
13 7 0.30
14 12 0.52
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
AAAAATATATTAT
Found at i:29084 original size:15 final size:14
Alignment explanation
Indices: 29043--29075 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
29033 ACAATTGTGC
*
29043 AAAAAATATATTAT
1 AAAAAATGTATTAT
29057 AAAAAATGTATTAT
1 AAAAAATGTATTAT
29071 AAAAA
1 AAAAA
29076 TATTTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (14 bp):
AAAAAATGTATTAT
Found at i:37943 original size:18 final size:18
Alignment explanation
Indices: 37922--37957 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
37912 GAAATTTGAA
*
37922 TTAAAAAACCGTTAAAAT
1 TTAAAAAACCATTAAAAT
*
37940 TTAAAAACCCATTAAAAT
1 TTAAAAAACCATTAAAAT
37958 AATTAGCTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.14, G:0.03, T:0.28
Consensus pattern (18 bp):
TTAAAAAACCATTAAAAT
Found at i:38579 original size:29 final size:29
Alignment explanation
Indices: 38536--38630 Score: 111
Period size: 29 Copynumber: 3.3 Consensus size: 29
38526 TATTTTATTG
* * *
38536 AGTCCATCAACTATTAAAAATTATAAAAT
1 AGTCCCTCAATTATTAAAAGTTATAAAAT
* * *
38565 AGTCTCTTAATTATTAAAAGTTACAAAAT
1 AGTCCCTCAATTATTAAAAGTTATAAAAT
*
38594 AGTCCCTCGATTATTAAAAGTTATAAAAT
1 AGTCCCTCAATTATTAAAAGTTATAAAAT
38623 CA-TCCCTC
1 -AGTCCCTC
38631 GACTATAGGG
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 54 0.98
30 1 0.02
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (29 bp):
AGTCCCTCAATTATTAAAAGTTATAAAAT
Found at i:43923 original size:31 final size:33
Alignment explanation
Indices: 43885--43956 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 33
43875 ATTATTCTTG
43885 TTATATATGCATAT-TACTTTCTATTAAT-TTA
1 TTATATATGCATATATACTTTCTATTAATGTTA
* ** * *
43916 TTATATATGTATATATGTTTTTTATTAGTGTTA
1 TTATATATGCATATATACTTTCTATTAATGTTA
43949 TTATATAT
1 TTATATAT
43957 ATATATTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 13 0.38
32 10 0.29
33 11 0.32
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (33 bp):
TTATATATGCATATATACTTTCTATTAATGTTA
Found at i:44063 original size:20 final size:20
Alignment explanation
Indices: 44040--44077 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44030 TTTATTATTA
44040 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
44060 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
44078 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:44109 original size:16 final size:18
Alignment explanation
Indices: 44088--44122 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
44078 TTTACTCATT
44088 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
44104 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
44122 T
1 T
44123 GTTTTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:47285 original size:25 final size:24
Alignment explanation
Indices: 47257--47337 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 24
47247 CAATCAAGAA
47257 CAAAAAAGAAAAGAAGCAAAAAAAG
1 CAAAAAAGAAAA-AAGCAAAAAAAG
47282 CAAAAAA-AAAAAA-CAAAGAAAAG
1 CAAAAAAGAAAAAAGCAAA-AAAAG
*
47305 -AGAAACAAGAACAAAAGAAAAAAAGAG
1 CA-AAA-AAGAA-AAAAGCAAAAAA-AG
47332 CAAAAA
1 CAAAAA
47338 TCAAAAAGAA
Statistics
Matches: 47, Mismatches: 1, Indels: 15
0.75 0.02 0.24
Matches are distributed among these distances:
22 5 0.11
23 10 0.21
24 6 0.13
25 9 0.19
26 8 0.17
27 8 0.17
28 1 0.02
ACGTcount: A:0.78, C:0.09, G:0.14, T:0.00
Consensus pattern (24 bp):
CAAAAAAGAAAAAAGCAAAAAAAG
Found at i:47336 original size:8 final size:8
Alignment explanation
Indices: 47258--47330 Score: 60
Period size: 9 Copynumber: 9.0 Consensus size: 8
47248 AATCAAGAAC
47258 AAAAAAGA
1 AAAAAAGA
*
47266 AAAGAAGCA
1 AAAAAAG-A
47275 AAAAAAGCA
1 AAAAAAG-A
47284 AAAAAA-A
1 AAAAAAGA
*
47291 AAAACA-A
1 AAAAAAGA
*
47298 AGAAAAGA
1 AAAAAAGA
*
47306 GAAACAAGA
1 -AAAAAAGA
*
47315 ACAAAAGA
1 AAAAAAGA
47323 AAAAAAGA
1 AAAAAAGA
47331 GCAAAAATCA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
7 11 0.21
8 20 0.38
9 21 0.40
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:47999 original size:22 final size:22
Alignment explanation
Indices: 47974--48022 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
47964 CCATCAATCT
* *
47974 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
47996 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
48018 TTTGA
1 TTTGA
48023 CCAACACAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:48488 original size:28 final size:28
Alignment explanation
Indices: 48455--48511 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
48445 TTTTATATGA
48455 GGCATCTTTGGGGATTCAACATCCTAAT
1 GGCATCTTTGGGGATTCAACATCCTAAT
48483 GGCATCTTTGGGGATTCAACATCCTAAT
1 GGCATCTTTGGGGATTCAACATCCTAAT
48511 G
1 G
48512 CGAATTATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (28 bp):
GGCATCTTTGGGGATTCAACATCCTAAT
Found at i:49014 original size:36 final size:36
Alignment explanation
Indices: 48967--49243 Score: 267
Period size: 36 Copynumber: 8.0 Consensus size: 36
48957 AGTAGAAGAG
48967 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
49003 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
49039 TTTCGTCTATCTTGAGACAGTTT-CCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
49074 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
49110 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
** * ** * *
49139 TTCCGTCTCCCTTGAGACAG-TTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
49175 TTTTGTCTCTCTTGAGACAG-TT--CTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
49207 TTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
49244 ACCTTTGAAT
Statistics
Matches: 195, Mismatches: 30, Indels: 31
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.01
29 19 0.10
30 2 0.01
32 5 0.03
33 15 0.08
34 8 0.04
35 41 0.21
36 99 0.51
37 4 0.02
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:49081 original size:71 final size:72
Alignment explanation
Indices: 48971--49243 Score: 259
Period size: 71 Copynumber: 3.9 Consensus size: 72
48961 GAAGAGTTTT
* * *
48971 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAAC
1 GTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
49036 AAATTTC
66 AAATTTC
*
49043 GTCTATCTTGAGACAGTTT-CCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
49107 AAA----
66 AAATTTC
* * * * ** * ** *
49110 --ATAT-TTGA-ATATGTTTTCTTTGAAACAAATTCCGTCTCCCTTGAGACAG-TTCTTTTGGAA
1 GTCTATCTTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
* *
49170 CTAAGTTTT
65 C-AAATTTC
* *
49179 GTCTCTCTTGAGACAG-TT--CTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAA
1 GTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAA
49240 CAAA
65 CAAA
49244 ACCTTTGAAT
Statistics
Matches: 161, Mismatches: 27, Indels: 29
0.74 0.12 0.13
Matches are distributed among these distances:
63 2 0.01
64 17 0.11
65 32 0.20
68 4 0.02
69 23 0.14
70 9 0.06
71 49 0.30
72 23 0.14
73 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (72 bp):
GTCTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
AAATTTC
Found at i:49251 original size:134 final size:135
Alignment explanation
Indices: 48987--49306 Score: 403
Period size: 134 Copynumber: 2.4 Consensus size: 135
48977 CTTGAGACAG
* *
48987 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG-TTCTCTTGAAACAAATTTCGTCTATCTT
* *
49052 GAGACAGTTTCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTG
65 GAGACAGTTTCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTTG
*
49117 AATATG
130 AATATA
* * ** * * * * *
49123 TTTTCTTTGAAACAAATTCCGTCTCCCTTGAGACAGTTCTTTTGGAACTAAGTTTTGTCTCTCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTCTCTTGAAAC-AAATTTCGTCTATCTT
* *
49188 GAGACAG-TT-CTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACCTTT
65 GAGACAGTTTCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
*
49250 GAATTTA
129 GAATATA
* * *
49257 TTTCCCCTAAAACAAATTTTATCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT-CTCTTGAAACA
49307 CAAAATCTTC
Statistics
Matches: 155, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
133 6 0.04
134 79 0.51
135 20 0.13
136 50 0.32
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (135 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTCTCTTGAAACAAATTTCGTCTATCTTG
AGACAGTTTCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTTGA
ATATA
Found at i:49342 original size:67 final size:68
Alignment explanation
Indices: 49218--49374 Score: 187
Period size: 68 Copynumber: 2.4 Consensus size: 68
49208 TTTCGTCTAT
* **
49218 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAACAAA-TTTTATC
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACAAATTTTTATC
49280 TCC
66 TCC
* * * *
49283 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTT-CCCTTAAACATAATTTTTGT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACA-AATTTTTAT
*
49347 TTCC
65 CTCC
* *
49351 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
49375 ACAGATATCT
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
65 17 0.22
66 11 0.14
67 20 0.26
68 29 0.38
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACAAATTTTTATC
TCC
Found at i:50552 original size:208 final size:209
Alignment explanation
Indices: 50003--50924 Score: 1246
Period size: 208 Copynumber: 4.5 Consensus size: 209
49993 GCACTCGAGG
* * * *
50003 CAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAA-ACATTTCTCAATTTTC
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAACAACA-ACTTCTCAA-TTTC
*
50066 AGAGCCAATTTCAACTTCACAACGAAGGATA-TGGACTCCAGACAACGCAAGTTCAACTTCACGA
63 AGAGCCAATTTCAACTT-ACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGA
* * *
50130 CGAAGGGATCGCTGCCTGTC-ACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGA
127 CGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGA
*
50194 AGGATATTGGACTTCAGA
192 AGGATATTGGACTCCAGA
*
50212 C-ACGCAAGTTC-ACTTCACGACGAAGGGACCGCTGCCTGTCAAC-ACAAC-T-TCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
50272 GCCAATTTCAACTTTACAATGAAGGATATTGGACTTCAGACAACGCAAGTTCAAACTTCACGACG
66 GCCAATTTCAAC-TTACAACGAAGGATATTGGACTTCAGACAACGCAAGTTC-AACTTCACGACG
*
50337 AAGGGACCGCTGCTTGTCAACAGCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
129 AAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
50402 GATATTGGACTCCAGA
194 GATATTGGACTCCAGA
50418 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTGCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCT-CAATTTCAG
50483 AGCCAATTTCAACTT-C-ACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGA
65 AGCCAATTTCAACTTACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGA
* * *
50546 AGGGACCGCTGCTTGTCAATAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGG
130 AGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
50611 ATATTGGACTCCAGA
195 ATATTGGACTCCAGA
* * * * *
50626 CAATGCAAGGTCAACTTCACGACGAA-GGACCGCTGCTTGTCAACAACAATTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
50690 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
66 GCCAATTTCAACTT-ACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGA
** *
50755 A-GGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCAATTTC-ACTTCATAACGAAGG
130 AGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
*
50813 ATATTGGACTCGAGA
195 ATATTGGACTCCAGA
* * * * * *** *
50828 CAA--CATAGTTC-ACTTCACAACGAAGAGACGGCTG-GT-TCAACAAACAATTTC-CCGGTCCA
1 CAACGCA-AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCA
* *
50887 GAGCCAATTTCAACTTCACGACGGAGGATATTGGACTT
64 GAGCCAATTTCAACTT-ACAACGAAGGATATTGGACTT
50925 GGAACAATGC
Statistics
Matches: 651, Mismatches: 44, Indels: 46
0.88 0.06 0.06
Matches are distributed among these distances:
199 43 0.07
200 24 0.04
201 11 0.02
202 31 0.05
203 43 0.07
204 29 0.04
205 30 0.05
206 87 0.13
207 65 0.10
208 175 0.27
209 86 0.13
210 2 0.00
211 3 0.00
212 22 0.03
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (209 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
TATTGGACTCCAGA
Found at i:50674 original size:104 final size:105
Alignment explanation
Indices: 50003--50923 Score: 1264
Period size: 103 Copynumber: 9.0 Consensus size: 105
49993 GCACTCGAGG
* * * *
50003 CAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAA-ACATTTCTCAATTTTC
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAACAACA-ACTTCTCAA-TTTC
50066 AGAGCCAATTTCAACTTCACAACGAAGGATA-TGGACTCCAGA
63 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
50108 CAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGCCTGTC-ACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
50172 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
50212 C-ACGCAAGTTC-ACTTCACGACGAAGGGACCGCTGCCTGTCAAC-ACAAC-T-TCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * *
50272 GCCAATTTCAACTTTACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
50312 CAACGCAAGTTCAAACTTCACGACGAAGGGACCGCTGCTTGTCAACAGCAACTTCTCAATTTCAG
1 CAACGCAAGTTC-AACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAG
50377 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
50418 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTGCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCT-CAATTTCAG
*
50483 AGCCAATTTCAACTT--C-ACGAAGGATATTGGACTTCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
50521 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAATAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
50586 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * *
50626 CAATGCAAGGTCAACTTCACGACGAA-GGACCGCTGCTTGTCAACAACAATTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
50690 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
50730 CAACGCAAGTTCAACTTCACGACGAA-GGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** * *
50789 TTCAATTTC-ACTTCATAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * *** *
50828 CAA--CATAGTTC-ACTTCACAACGAAGAGACGGCTG-GT-TCAACAAACAATTTC-CCGGTCCA
1 CAACGCA-AGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCA
* *
50887 GAGCCAATTTCAACTTCACGACGGAGGATATTGGACT
64 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
50924 TGGAACAATG
Statistics
Matches: 750, Mismatches: 43, Indels: 50
0.89 0.05 0.06
Matches are distributed among these distances:
95 5 0.01
96 17 0.02
97 14 0.02
98 34 0.05
99 12 0.02
100 64 0.09
101 34 0.05
102 58 0.08
103 153 0.20
104 149 0.20
105 124 0.17
106 86 0.11
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:51541 original size:36 final size:36
Alignment explanation
Indices: 51457--51555 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 36
51447 TTTCGTCATA
* *
51457 CTAGGATTCAAACTCCTAAAAATATGATAGAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
51493 -T-GGATTCAAACTCCT-AAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
51526 GCTAGGATTCAAACTCCTAAAAATAGGATA
1 -CTAGGATTCAAACTCCTAAAAATAGGATA
51556 TAGTTCTACT
Statistics
Matches: 57, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
33 16 0.28
34 14 0.25
35 2 0.04
36 14 0.25
37 11 0.19
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
Done.