Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007975.1 Hibiscus syriacus cultivar Beakdansim tig00110412_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: 47248
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:723 original size:18 final size:18
Alignment explanation
Indices: 700--739 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
690 ACCTTATCGT
700 ATTATTTTGGTGTTTTCA
1 ATTATTTTGGTGTTTTCA
*
718 ATTATTTTGGTGTTTTTA
1 ATTATTTTGGTGTTTTCA
736 ATTA
1 ATTA
740 ATGAATGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.03, G:0.15, T:0.62
Consensus pattern (18 bp):
ATTATTTTGGTGTTTTCA
Found at i:5370 original size:18 final size:18
Alignment explanation
Indices: 5347--5395 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
5337 AACATAGAAC
*
5347 ATAATATTTATCTAAAAT
1 ATAATATTTATATAAAAT
***
5365 ATAATAAAAATATAAAAT
1 ATAATATTTATATAAAAT
*
5383 AAAATATTTATAT
1 ATAATATTTATAT
5396 CATGCTATAA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATATTTATATAAAAT
Found at i:6483 original size:2 final size:2
Alignment explanation
Indices: 6476--6504 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6466 AAATTTATTA
6476 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6505 ATAATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6605 original size:30 final size:30
Alignment explanation
Indices: 6571--6647 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 30
6561 ACTAAACTCG
* * *
6571 TCCCCGTCCCTATTTAACATAAACGGTTTT
1 TCCCCATCCCCATTTAACATAAACGATTTT
* *
6601 TCCCCATCCCCGTTTAGCATAAACGATTTT
1 TCCCCATCCCCATTTAACATAAACGATTTT
6631 TCCCCATCCCCATTTAA
1 TCCCCATCCCCATTTAA
6648 TTCGGTTTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.23, C:0.35, G:0.08, T:0.34
Consensus pattern (30 bp):
TCCCCATCCCCATTTAACATAAACGATTTT
Found at i:7823 original size:30 final size:32
Alignment explanation
Indices: 7764--7828 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
7754 GAAAATAATA
*
7764 TAAATTAAACACTTCAAAATTTTTGAAAATTT
1 TAAATTAAACACTTCAAAATTTTTGAAAATGT
*
7796 TAAATT-AA-ACTTCCAAATATTTT-AAAATGT
1 TAAATTAAACACTTCAAAAT-TTTTGAAAATGT
7826 TAA
1 TAA
7829 GTTGGTCCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 18 0.60
31 6 0.20
32 6 0.20
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (32 bp):
TAAATTAAACACTTCAAAATTTTTGAAAATGT
Found at i:11151 original size:31 final size:31
Alignment explanation
Indices: 11116--11206 Score: 155
Period size: 31 Copynumber: 2.9 Consensus size: 31
11106 TGCAATATAA
*
11116 TCCCTCAACATTTAGTCCATTTGTAATATGG
1 TCCCTCAACATTTAGTCCGTTTGTAATATGG
*
11147 TCCCTTAACATTTAGTCCGTTTGTAATATGG
1 TCCCTCAACATTTAGTCCGTTTGTAATATGG
*
11178 TCCCTCAACATTTAGTCCGTTTGCAATAT
1 TCCCTCAACATTTAGTCCGTTTGTAATAT
11207 AGTTCCCGAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (31 bp):
TCCCTCAACATTTAGTCCGTTTGTAATATGG
Found at i:11152 original size:60 final size:61
Alignment explanation
Indices: 11085--11206 Score: 147
Period size: 62 Copynumber: 2.0 Consensus size: 61
11075 ACTTTCATTA
* *
11085 GGTCCCTTAACTTTTAAAAC-TTGCAATATAATCCCTCAACATTTAGTCCATTTGTAATAT
1 GGTCCCTTAACATTTAAAACGTTGCAATATAATCCCTCAACATTTAGTCCATTTGCAATAT
*** * ** *
11145 GGTCCCTTAACATTTAGTCCGTTTGTAATATGGTCCCTCAACATTTAGTCCGTTTGCAATAT
1 GGTCCCTTAACATTTAAAACG-TTGCAATATAATCCCTCAACATTTAGTCCATTTGCAATAT
11207 AGTTCCCGAT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 16 0.31
62 35 0.69
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (61 bp):
GGTCCCTTAACATTTAAAACGTTGCAATATAATCCCTCAACATTTAGTCCATTTGCAATAT
Found at i:13318 original size:2 final size:2
Alignment explanation
Indices: 13299--13347 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
13289 GATATTAAGG
* *
13299 AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13341 AT AT AT A
1 AT AT AT A
13348 ACGCTTTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:13433 original size:15 final size:16
Alignment explanation
Indices: 13413--13445 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13403 TACGAATTGT
13413 TTTTGA-AAATTTGAA
1 TTTTGATAAATTTGAA
*
13428 TTTTGATTAATTTGAA
1 TTTTGATAAATTTGAA
13444 TT
1 TT
13446 GGAGCCGCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (16 bp):
TTTTGATAAATTTGAA
Found at i:17533 original size:27 final size:27
Alignment explanation
Indices: 17495--17556 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
17485 TTAGGGTTAG
*
17495 AGACCCTTTAGTGGTGTACTCGTGGAA
1 AGACCCTTTAGTGGTGTACTCATGGAA
17522 AGACCCTTTAGTGGTGTACTCATGGAA
1 AGACCCTTTAGTGGTGTACTCATGGAA
17549 AGACCCTT
1 AGACCCTT
17557 AACAGAGGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (27 bp):
AGACCCTTTAGTGGTGTACTCATGGAA
Found at i:28714 original size:16 final size:17
Alignment explanation
Indices: 28695--28727 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28685 ATTGAAGACT
28695 AATTGTA-TAATTATCA
1 AATTGTATTAATTATCA
*
28711 AATTTTATTAATTATCA
1 AATTGTATTAATTATCA
28728 CATCACCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (17 bp):
AATTGTATTAATTATCA
Found at i:30104 original size:16 final size:15
Alignment explanation
Indices: 30085--30115 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
30075 GATTTTTAGA
30085 TCGGGTCAATATCATG
1 TCGGGTCAATA-CATG
30101 TCGGGTCAATACATG
1 TCGGGTCAATACATG
30116 ATCAGTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (15 bp):
TCGGGTCAATACATG
Found at i:30833 original size:18 final size:17
Alignment explanation
Indices: 30780--30836 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
30770 CTTAAACTTT
*
30780 TTATTATTTTATTATAAA
1 TTATAATTTTATT-TAAA
*
30798 TCTAATAATTTTA-ATAAA
1 T-T-ATAATTTTATTTAAA
30816 TTATCAATTTTATTTAAA
1 TTAT-AATTTTATTTAAA
30834 TTA
1 TTA
30837 ATTTATTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 2 0.06
17 8 0.25
18 13 0.41
19 1 0.03
20 8 0.25
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATAATTTTATTTAAA
Found at i:30956 original size:16 final size:16
Alignment explanation
Indices: 30935--30989 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
30925 CGGGTTAAAA
30935 TTCGGTTCGAGTTAAT
1 TTCGGTTCGAGTTAAT
**
30951 TTCGGTTCGAGTTGCT
1 TTCGGTTCGAGTTAAT
* **
30967 TTTGGTTCTTGTTAAT
1 TTCGGTTCGAGTTAAT
30983 TTCGGTT
1 TTCGGTT
30990 TTAGTTGATT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.11, C:0.13, G:0.25, T:0.51
Consensus pattern (16 bp):
TTCGGTTCGAGTTAAT
Found at i:31340 original size:19 final size:20
Alignment explanation
Indices: 31305--31373 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
31295 AACAAATTCA
*
31305 CAACGCG-ATCTCAAATTT-G
1 CAACGCGAAT-TCCAATTTCG
31324 CAACGCGAATTCCAATTTCG
1 CAACGCGAATTCCAATTTCG
* *
31344 CAAC-CCAGTTTCCAATTTCG
1 CAACGCGA-ATTCCAATTTCG
31364 CAACGCGAAT
1 CAACGCGAAT
31374 ATGTAAATCG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
19 16 0.39
20 23 0.56
21 2 0.05
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (20 bp):
CAACGCGAATTCCAATTTCG
Found at i:31460 original size:19 final size:20
Alignment explanation
Indices: 31409--31467 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
31399 AATTCGCGTT
*
31409 GCGATAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
31429 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
* **
31449 -TGAATTTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
31468 AGGTTTTAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:35019 original size:20 final size:20
Alignment explanation
Indices: 34994--35057 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
34984 ATGTTGCGAT
34994 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
35014 CAACGCGAAA-T--AA---G
1 CAACGCGAAAGTCAAATTCG
*
35028 CAACGCGAAAGTCAAATTCA
1 CAACGCGAAAGTCAAATTCG
35048 CAACGCGAAA
1 CAACGCGAAA
35058 TAAGCGTTGC
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
14 11 0.30
15 1 0.03
17 4 0.11
19 1 0.03
20 20 0.54
ACGTcount: A:0.45, C:0.25, G:0.19, T:0.11
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:35037 original size:34 final size:34
Alignment explanation
Indices: 34994--35092 Score: 153
Period size: 34 Copynumber: 2.9 Consensus size: 34
34984 ATGTTGCGAT
34994 CAACGCGAAAGTCAAATTCGCAACGCGAAATAAG
1 CAACGCGAAAGTCAAATTCGCAACGCGAAATAAG
*
35028 CAACGCGAAAGTCAAATTCACAACGCGAAATAAG
1 CAACGCGAAAGTCAAATTCGCAACGCGAAATAAG
*** *
35062 CGTTGCGATAGTCAAATTCGCAACGCGAAAT
1 CAACGCGAAAGTCAAATTCGCAACGCGAAAT
35093 CGCAAACCGA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.15
Consensus pattern (34 bp):
CAACGCGAAAGTCAAATTCGCAACGCGAAATAAG
Found at i:35170 original size:20 final size:20
Alignment explanation
Indices: 35145--35183 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
35135 CAACGCTTAT
35145 TTCGCGTTGTGAATTTACCA
1 TTCGCGTTGTGAATTTACCA
35165 TTCGCGTTGTGAATTTACC
1 TTCGCGTTGTGAATTTACC
35184 TTCAACAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (20 bp):
TTCGCGTTGTGAATTTACCA
Found at i:35284 original size:25 final size:25
Alignment explanation
Indices: 35246--35295 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
35236 AAATCAATTA
*
35246 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
35271 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
35296 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:35715 original size:39 final size:39
Alignment explanation
Indices: 35672--35758 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
35662 TCTGATGCTC
35672 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
35711 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
35750 ATCAAAATC
1 ATCAAAATC
35759 TACAACTTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:36025 original size:20 final size:20
Alignment explanation
Indices: 35999--36072 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
35989 CGTGAAATAA
35999 GCGTTGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTTTC
* * *
36019 ACGTTGCAAATTTGACTTCC
1 GCGTTGCGAATTTGACTTTC
* *
36039 GCATTGCGAATTTAACTTTC
1 GCGTTGCGAATTTGACTTTC
36059 GCGTTGCGAATTTG
1 GCGTTGCGAATTTG
36073 TACCTTCAAC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTTTC
Found at i:36217 original size:14 final size:14
Alignment explanation
Indices: 36181--36222 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
36171 ATAATTCTTA
36181 TTTACAAATCAAAT
1 TTTACAAATCAAAT
**
36195 TAAACAAATCAAAT
1 TTTACAAATCAAAT
*
36209 TTTATAAAT-AAAT
1 TTTACAAATCAAAT
36222 T
1 T
36223 AATCAAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTACAAATCAAAT
Found at i:37739 original size:42 final size:42
Alignment explanation
Indices: 37643--37741 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 42
37633 GCAGAAAAGA
* * * * *
37643 CCTCTTGAACGATGAAAGGGGACTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGAAAGAGGACTCTTGAACGATAGGAGGCG
* * * *
37685 CTTATTCG-ATGATGAGAGAGGCCTCTTGAACGATAGGAGGCG
1 CCTCTT-GAATGATGAAAGAGGACTCTTGAACGATAGGAGGCG
37727 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
37742 TAGGTGCATC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
41 1 0.02
42 42 0.95
43 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.23
Consensus pattern (42 bp):
CCTCTTGAATGATGAAAGAGGACTCTTGAACGATAGGAGGCG
Found at i:39998 original size:13 final size:13
Alignment explanation
Indices: 39976--40020 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
39966 GGGTTTCTTC
*
39976 AACAAAAAGATAA
1 AACAAAAAGACAA
*
39989 AACGAAAAGACAA
1 AACAAAAAGACAA
40002 AACAAAAAGACAA
1 AACAAAAAGACAA
40015 AACAAA
1 AACAAA
40021 GACAAATACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.76, C:0.13, G:0.09, T:0.02
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:40016 original size:26 final size:24
Alignment explanation
Indices: 39976--40026 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 24
39966 GGGTTTCTTC
*
39976 AACAAAAAGATAAAACGAAAAGACAA
1 AACAAAAAGACAAAAC--AAAGACAA
40002 AACAAAAAGACAAAACAAAGACAA
1 AACAAAAAGACAAAACAAAGACAA
40026 A
1 A
40027 TACTAACTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 9 0.38
26 15 0.62
ACGTcount: A:0.75, C:0.14, G:0.10, T:0.02
Consensus pattern (24 bp):
AACAAAAAGACAAAACAAAGACAA
Found at i:40023 original size:11 final size:12
Alignment explanation
Indices: 39980--40026 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
39970 TTCTTCAACA
*
39980 AAAAGATAAAAC
1 AAAAGACAAAAC
39992 GAAAAGACAAAAC
1 -AAAAGACAAAAC
40005 AAAAAGACAAAAC
1 -AAAAGACAAAAC
40018 -AAAGACAAA
1 AAAAGACAAA
40027 TACTAACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 9 0.28
13 23 0.72
ACGTcount: A:0.74, C:0.13, G:0.11, T:0.02
Consensus pattern (12 bp):
AAAAGACAAAAC
Found at i:40274 original size:22 final size:22
Alignment explanation
Indices: 40233--40282 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
40223 ATGGAGATAA
40233 ACGGATTTCGTCGAAAATGGAG-
1 ACGGATTTCGTCGAAAATGG-GT
* *
40255 ACGGATTTCGTCGGAGATGGGT
1 ACGGATTTCGTCGAAAATGGGT
40277 ACGGAT
1 ACGGAT
40283 GTCGCCGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.26, C:0.14, G:0.36, T:0.24
Consensus pattern (22 bp):
ACGGATTTCGTCGAAAATGGGT
Found at i:40435 original size:20 final size:20
Alignment explanation
Indices: 40410--40493 Score: 109
Period size: 20 Copynumber: 4.2 Consensus size: 20
40400 GCGTAAAAAC
*
40410 ATTTGACTTTTGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
40430 ATTTGACTATCGCGTTACGA
1 ATTTGACTTTCGCGTTGCGA
*
40450 ATTTGAC-TTC-TGTGTGCGA
1 ATTTGACTTTCGCGT-TGCGA
40469 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
40489 ATTTG
1 ATTTG
40494 GAAAATCGCA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
18 2 0.04
19 13 0.24
20 37 0.69
21 2 0.04
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.42
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:40472 original size:39 final size:40
Alignment explanation
Indices: 40410--40493 Score: 125
Period size: 39 Copynumber: 2.1 Consensus size: 40
40400 GCGTAAAAAC
*
40410 ATTTGACTTTTGCGTTGCGAATTTGACTATCGCGTTACGA
1 ATTTGACTTCTGCGTTGCGAATTTGACTATCGCGTTACGA
* * *
40450 ATTTGACTTCTGTG-TGCGAATTTGACTTTCGCGTTGCGA
1 ATTTGACTTCTGCGTTGCGAATTTGACTATCGCGTTACGA
40489 ATTTG
1 ATTTG
40494 GAAAATCGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 28 0.70
40 12 0.30
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.42
Consensus pattern (40 bp):
ATTTGACTTCTGCGTTGCGAATTTGACTATCGCGTTACGA
Found at i:40566 original size:20 final size:20
Alignment explanation
Indices: 40517--40570 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
40507 CGATTTACAT
*
40517 ATTCGTGTTGCGAAATTGGA
1 ATTCGAGTTGCGAAATTGGA
*
40537 A-ACTGAGTTGCGAAATTGGA
1 ATTC-GAGTTGCGAAATTGGA
*
40557 ATTCGCGTTGCGAA
1 ATTCGAGTTGCGAA
40571 TTTGAGATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.30
Consensus pattern (20 bp):
ATTCGAGTTGCGAAATTGGA
Found at i:42937 original size:42 final size:43
Alignment explanation
Indices: 42834--43100 Score: 222
Period size: 42 Copynumber: 6.3 Consensus size: 43
42824 TGAGAACAAA
* * * * *
42834 AAACGCCGTAATAGGTCAAGATATATCGCGGCGTTTTTGGAAT
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAT
* *
42877 AAACGCCGCAAAAGGTCGATATCTATAGTGGCGTTTTTGGAA-
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAT
* * * *
42919 CAACGCGGCAAAATGTCGAGATCTATAGCGGCGTTTTTGGAAA
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAT
* * * * * ***
42962 AAACTCCGTAAAAGGTC-AGTTCTATAGCAGTGTTTTCATAAT
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAT
* * * *
43004 AAACGTCGCAAAAGGTC-AGATCTATAGCGGTGTTTTGGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAT
* * * * *
43046 AAACGTCGC-AAAGATC-ATATCTATAGCGTCGTTTTTTG-AT
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAT
43086 ACAATCGCCGCAAAA
1 A-AA-CGCCGCAAAA
43101 AGGCTCATAA
Statistics
Matches: 179, Mismatches: 41, Indels: 8
0.79 0.18 0.04
Matches are distributed among these distances:
40 2 0.01
41 25 0.14
42 102 0.57
43 50 0.28
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAT
Found at i:43098 original size:84 final size:84
Alignment explanation
Indices: 42835--43100 Score: 238
Period size: 85 Copynumber: 3.1 Consensus size: 84
42825 GAGAACAAAA
* * * * * *
42835 AACGCCGTAATAGGTCAAGATATATCGCGGCGTTTTTGGAATAAACGCCGCAAAAGGTCGATATC
1 AACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAAAAAACGTCGC-AAAGGTC-ATATC
* * *
42900 TATAGTGGCGTTTTTGGA-AC
64 TATAGCGTCGTTTTTTGATAC
* * * *
42920 AACGCGGCAAAATGTCGAGATCTATAGCGGCGTTTTTGGAAAAAAC-TCCGTAAAAGGTCAGT-T
1 AACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAAAAAACGT-CG-CAAAGGTCA-TAT
* *
42983 CTATAGCAGT-GTTTTCATAATA-
63 CTATAGC-GTCGTTTT-TTGATAC
* * * * *
43005 AACGTCGCAAAAGGTC-AGATCTATAGCGGTGTTTTGGGAACAAACGTCGCAAAGATCATATCTA
1 AACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAAAAAACGTCGCAAAGGTCATATCTA
43069 TAGCGTCGTTTTTTGATAC
66 TAGCGTCGTTTTTTGATAC
43088 AATCGCCGCAAAA
1 AA-CGCCGCAAAA
43101 AGGCTCATAA
Statistics
Matches: 144, Mismatches: 26, Indels: 23
0.75 0.13 0.12
Matches are distributed among these distances:
82 7 0.05
83 22 0.15
84 50 0.35
85 64 0.44
86 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (84 bp):
AACGCCGCAAAAGGTCAAGATCTATAGCGGCGTTTTTGGAAAAAACGTCGCAAAGGTCATATCTA
TAGCGTCGTTTTTTGATAC
Found at i:45865 original size:40 final size:39
Alignment explanation
Indices: 45803--45900 Score: 133
Period size: 40 Copynumber: 2.5 Consensus size: 39
45793 ACACGTTAGG
* *
45803 CTATAGTGGCGTTTGTACAAAACGCCACTAAAGTACAAGT
1 CTATAGCGGCG-TTGTAAAAAACGCCACTAAAGTACAAGT
45843 CTATAGCGGCGTTGTATAAAAACGCCACTAAAGTACAAGT
1 CTATAGCGGCGTTGTA-AAAAACGCCACTAAAGTACAAGT
* * *
45883 CTTTAACGACGTTGTAAA
1 CTATAGCGGCGTTGTAAA
45901 CACAAAGGGA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
39 7 0.13
40 45 0.87
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (39 bp):
CTATAGCGGCGTTGTAAAAAACGCCACTAAAGTACAAGT
Found at i:46090 original size:20 final size:20
Alignment explanation
Indices: 46067--46115 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
46057 ATTCTGGAGA
46067 AGTGTGGAACCTTATGGAAG
1 AGTGTGGAACCTTATGGAAG
46087 AGTGTGGAACCTTATGGAAG
1 AGTGTGGAACCTTATGGAAG
*
46107 AGTATGGAA
1 AGTGTGGAA
46116 GAATATGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.08, G:0.35, T:0.24
Consensus pattern (20 bp):
AGTGTGGAACCTTATGGAAG
Found at i:46112 original size:10 final size:10
Alignment explanation
Indices: 46079--46139 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
46069 TGTGGAACCT
46079 TATGGAAGAG
1 TATGGAAGAG
* ***
46089 TGTGGAACCT
1 TATGGAAGAG
46099 TATGGAAGAG
1 TATGGAAGAG
*
46109 TATGGAAGAA
1 TATGGAAGAG
46119 TATGGAAG-G
1 TATGGAAGAG
*
46128 GAGTGGAAGAG
1 TA-TGGAAGAG
46139 T
1 T
46140 GTAGAGCTTC
Statistics
Matches: 37, Mismatches: 12, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
9 1 0.03
10 35 0.95
11 1 0.03
ACGTcount: A:0.36, C:0.03, G:0.39, T:0.21
Consensus pattern (10 bp):
TATGGAAGAG
Found at i:46122 original size:20 final size:20
Alignment explanation
Indices: 46079--46126 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
46069 TGTGGAACCT
* **
46079 TATGGAAGAGTGTGGAACCT
1 TATGGAAGAGTATGGAACAA
*
46099 TATGGAAGAGTATGGAAGAA
1 TATGGAAGAGTATGGAACAA
46119 TATGGAAG
1 TATGGAAG
46127 GGAGTGGAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.35, T:0.23
Consensus pattern (20 bp):
TATGGAAGAGTATGGAACAA
Found at i:47133 original size:6 final size:7
Alignment explanation
Indices: 47111--47159 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
47101 TTTTTTATGA
*
47111 AGTGAAT
1 AGTGAAC
47118 AGTGAAC
1 AGTGAAC
47125 AGT-AAC
1 AGTGAAC
47131 AGTGAAC
1 AGTGAAC
*
47138 GGT-AAC
1 AGTGAAC
47144 -GTGAAC
1 AGTGAAC
47150 AGTGAAC
1 AGTGAAC
47157 AGT
1 AGT
47160 ACACGTGAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
5 2 0.05
6 12 0.32
7 23 0.62
ACGTcount: A:0.41, C:0.12, G:0.29, T:0.18
Consensus pattern (7 bp):
AGTGAAC
Found at i:47136 original size:13 final size:13
Alignment explanation
Indices: 47118--47159 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
47108 TGAAGTGAAT
47118 AGTGAACAGTAAC
1 AGTGAACAGTAAC
*
47131 AGTGAACGGTAAC
1 AGTGAACAGTAAC
47144 -GTGAACAGTGAAC
1 AGTGAACAGT-AAC
47157 AGT
1 AGT
47160 ACACGTGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.32
13 15 0.60
14 2 0.08
ACGTcount: A:0.40, C:0.14, G:0.29, T:0.17
Consensus pattern (13 bp):
AGTGAACAGTAAC
Found at i:47152 original size:19 final size:20
Alignment explanation
Indices: 47128--47170 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
47118 AGTGAACAGT
*
47128 AACAGTGAACGGTA-ACGTG
1 AACAGTGAACAGTACACGTG
47147 AACAGTGAACAGTACACGTG
1 AACAGTGAACAGTACACGTG
47167 AACA
1 AACA
47171 ATATACAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.42, C:0.19, G:0.26, T:0.14
Consensus pattern (20 bp):
AACAGTGAACAGTACACGTG
Found at i:47178 original size:20 final size:20
Alignment explanation
Indices: 47128--47181 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
47118 AGTGAACAGT
* *
47128 AACAGTGAACGGTA-ACGTG
1 AACAATGAACAGTACACGTG
*
47147 AACAGTGAACAGTACACGTG
1 AACAATGAACAGTACACGTG
47167 AACAAT-ATACAGTAC
1 AACAATGA-ACAGTAC
47182 CGATACACTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.17
Consensus pattern (20 bp):
AACAATGAACAGTACACGTG
Done.