Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007185.1 Hibiscus syriacus cultivar Beakdansim tig00018903_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: 75734
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Found at i:1819 original size:29 final size:31
Alignment explanation
Indices: 1745--1820 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 31
1735 AATTACACGC
1745 TTACTCACTGAA-TTTTATTCTTTCTCATAT
1 TTACTCACTGAACTTTTATTCTTTCTCATAT
*
1775 TTCACTCA-TTATACTTTTAATT-TTT-TCA-AT
1 TT-ACTCACTGA-ACTTTT-ATTCTTTCTCATAT
1805 TTACTCACTGAACTTT
1 TTACTCACTGAACTTT
1821 ATACATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
29 10 0.26
30 10 0.26
31 9 0.23
32 7 0.18
33 3 0.08
ACGTcount: A:0.25, C:0.20, G:0.03, T:0.53
Consensus pattern (31 bp):
TTACTCACTGAACTTTTATTCTTTCTCATAT
Found at i:2998 original size:18 final size:18
Alignment explanation
Indices: 2975--3021 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
2965 TATGTAAATA
*
2975 GTATCGGTACCTCTTTGG
1 GTATCGGTACCCCTTTGG
2993 GTATCGGTACCCCTTTGG
1 GTATCGGTACCCCTTTGG
3011 GTATCGGTACC
1 GTATCGGTACC
3022 ATTTTTGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.13, C:0.26, G:0.28, T:0.34
Consensus pattern (18 bp):
GTATCGGTACCCCTTTGG
Found at i:6786 original size:4 final size:4
Alignment explanation
Indices: 6777--6801 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6767 TTGCTTGAAC
6777 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
6802 AATTAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:11302 original size:21 final size:22
Alignment explanation
Indices: 11265--11305 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
11255 CACTTCAACG
11265 TCTCTGTCCTCCTTTTCTCCTT
1 TCTCTGTCCTCCTTTTCTCCTT
11287 TCTCT-TCCTTCC-TTTCTCC
1 TCTCTGTCC-TCCTTTTCTCC
11306 AAATCCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.00, C:0.44, G:0.02, T:0.54
Consensus pattern (22 bp):
TCTCTGTCCTCCTTTTCTCCTT
Found at i:12324 original size:89 final size:89
Alignment explanation
Indices: 12173--12349 Score: 345
Period size: 89 Copynumber: 2.0 Consensus size: 89
12163 TCATTGTAGC
*
12173 CATAACTTGGTTGGTATACATAAATGATTATAGGTTTTCTACGCTCCATTTTTTAGGCATATATG
1 CATAACTTGGTTGGTATACATAAATGATTATAGGTTTTCTACGCTCCATTTTTGAGGCATATATG
12238 GACATGGTTGGGTGCTTCACCAGT
66 GACATGGTTGGGTGCTTCACCAGT
12262 CATAACTTGGTTGGTATACATAAATGATTATAGGTTTTCTACGCTCCATTTTTGAGGCATATATG
1 CATAACTTGGTTGGTATACATAAATGATTATAGGTTTTCTACGCTCCATTTTTGAGGCATATATG
12327 GACATGGTTGGGTGCTTCACCAG
66 GACATGGTTGGGTGCTTCACCAG
12350 CCACAAGGAA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (89 bp):
CATAACTTGGTTGGTATACATAAATGATTATAGGTTTTCTACGCTCCATTTTTGAGGCATATATG
GACATGGTTGGGTGCTTCACCAGT
Found at i:12822 original size:31 final size:31
Alignment explanation
Indices: 12784--12846 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
12774 TTTCTACCAC
*
12784 TTAATTCCTCATTTACTTTAGCTTATTGTTA
1 TTAATTCCTCATTTACTTCAGCTTATTGTTA
12815 TTAATTCCTCATTTACTTCAGCTTATTGTTA
1 TTAATTCCTCATTTACTTCAGCTTATTGTTA
12846 T
1 T
12847 CATGTATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.54
Consensus pattern (31 bp):
TTAATTCCTCATTTACTTCAGCTTATTGTTA
Found at i:14714 original size:41 final size:44
Alignment explanation
Indices: 14646--14730 Score: 149
Period size: 41 Copynumber: 2.0 Consensus size: 44
14636 TATAACTACA
14646 TTTCTGTTTGGGGAACAAAAACAGAATTTAAATCTTACAATTCG
1 TTTCTGTTTGGGGAACAAAAACAGAATTTAAATCTTACAATTCG
14690 TTTCTGTTT-GGG-A-AAAAACAGAATTTAAATCTTACAATTCG
1 TTTCTGTTTGGGGAACAAAAACAGAATTTAAATCTTACAATTCG
14731 ACATTCCCAG
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
41 28 0.68
42 1 0.02
43 3 0.07
44 9 0.22
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.35
Consensus pattern (44 bp):
TTTCTGTTTGGGGAACAAAAACAGAATTTAAATCTTACAATTCG
Found at i:21558 original size:9 final size:9
Alignment explanation
Indices: 21514--21574 Score: 50
Period size: 10 Copynumber: 6.3 Consensus size: 9
21504 CTGCTGGAAA
21514 ACCGGTTTG
1 ACCGGTTTG
*
21523 ACCAGTTTTG
1 ACC-GGTTTG
*
21533 AACCGGTTCG
1 -ACCGGTTTG
21543 AACCGGTTTG
1 -ACCGGTTTG
*
21553 ACCGGTCTGG
1 ACCGGT-TTG
*
21563 ACCGGTCTG
1 ACCGGTTTG
21572 ACC
1 ACC
21575 CGACCCGTCT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
9 13 0.31
10 26 0.62
11 3 0.07
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.26
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:21584 original size:14 final size:14
Alignment explanation
Indices: 21562--21609 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
21552 GACCGGTCTG
*
21562 GACCGGTCTGACCC
1 GACCCGTCTGACCC
*
21576 GACCCGTCTCACCC
1 GACCCGTCTGACCC
* *
21590 GACCTGACTGACCC
1 GACCCGTCTGACCC
21604 GACCCG
1 GACCCG
21610 ACCCGACTGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.17, C:0.48, G:0.23, T:0.12
Consensus pattern (14 bp):
GACCCGTCTGACCC
Found at i:22592 original size:32 final size:31
Alignment explanation
Indices: 22519--22595 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
22509 CTAATGTGAC
* * *
22519 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
** **
22550 TCTCGGGTAGGCCCTGCGACCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGACCCTAAGAT-CAT
22582 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
22596 CACGGCCCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
Found at i:22602 original size:63 final size:63
Alignment explanation
Indices: 22519--22642 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
22509 CTAATGTGAC
* ** * *
22519 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GACCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGACCCTAAGATGTGT
* * *
22582 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGACCCTAAGATGT
22643 TCCCTTAGGG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 1 0.02
63 49 0.96
64 1 0.02
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGACCCTAAGATGTGT
Found at i:24599 original size:26 final size:26
Alignment explanation
Indices: 24570--24626 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
24560 TATTGTCTTT
24570 TTTTTCTATATCAAATCTCTATTTTA
1 TTTTTCTATATCAAATCTCTATTTTA
*** *
24596 TTTTTCTATATTGTATCTCTATTTTC
1 TTTTTCTATATCAAATCTCTATTTTA
24622 TTTTT
1 TTTTT
24627 TTCATTAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.14, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTTCTATATCAAATCTCTATTTTA
Found at i:33348 original size:36 final size:37
Alignment explanation
Indices: 33265--33352 Score: 124
Period size: 37 Copynumber: 2.4 Consensus size: 37
33255 TTCTCTTTCA
* *
33265 TCCCCTGATGAAGGACCATCAGCATCTCCTTCAGCCT
1 TCCCCTGATGAAGGACCATCAACACCTCCTTCAGCCT
* *
33302 TCACCTGATGAAGGACCATCAACACCTCCTTC-TCCT
1 TCCCCTGATGAAGGACCATCAACACCTCCTTCAGCCT
*
33338 TCCCCAGATGAAGGA
1 TCCCCTGATGAAGGA
33353 GCACCTCCTT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
36 16 0.36
37 29 0.64
ACGTcount: A:0.25, C:0.36, G:0.16, T:0.23
Consensus pattern (37 bp):
TCCCCTGATGAAGGACCATCAACACCTCCTTCAGCCT
Found at i:33358 original size:30 final size:26
Alignment explanation
Indices: 33324--33387 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 26
33314 GGACCATCAA
33324 CACCTCCTTCTCCTTCCCCAGATGAAGGAG
1 CACCTCCTTCT-C--CCCC-GATGAAGGAG
33354 CACCTCC-T-TCCCCCGATGAAGGAG
1 CACCTCCTTCTCCCCCGATGAAGGAG
33378 CACCTCCTTC
1 CACCTCCTTC
33388 CTCCAATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
24 17 0.53
25 5 0.16
27 1 0.03
28 1 0.03
29 1 0.03
30 7 0.22
ACGTcount: A:0.19, C:0.44, G:0.16, T:0.22
Consensus pattern (26 bp):
CACCTCCTTCTCCCCCGATGAAGGAG
Found at i:33365 original size:24 final size:24
Alignment explanation
Indices: 33333--33396 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
33323 ACACCTCCTT
33333 CTCCTTCCCCAGATGAAGGAGCAC
1 CTCCTTCCCCAGATGAAGGAGCAC
*
33357 CTCCTTCCCCCGATGAAGGAGCAC
1 CTCCTTCCCCAGATGAAGGAGCAC
33381 CTCCTTCCTCCA-ATGA
1 CTCCTTCC-CCAGATGA
33397 TTCCTTCTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 35 0.95
25 2 0.05
ACGTcount: A:0.22, C:0.41, G:0.17, T:0.20
Consensus pattern (24 bp):
CTCCTTCCCCAGATGAAGGAGCAC
Found at i:36024 original size:21 final size:23
Alignment explanation
Indices: 35999--36047 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
35989 ATGATCTTAA
*
35999 TTTTAATAAA-TTAAA-ATAAAC
1 TTTTAATAAAGATAAACATAAAC
* *
36020 TTTTATTAAAGATAAACATAAAT
1 TTTTAATAAAGATAAACATAAAC
36043 TTTTA
1 TTTTA
36048 TGTTATGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 9 0.39
22 4 0.17
23 10 0.43
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTTAATAAAGATAAACATAAAC
Found at i:36045 original size:22 final size:20
Alignment explanation
Indices: 35997--36045 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
35987 GTATGATCTT
*
35997 AATTTTAATAAATTAAAATA
1 AATTTTAATAAAATAAAATA
*
36017 AACTTTTATTAAAGATAAACATA
1 AA-TTTTAATAAA-ATAAA-ATA
36040 AATTTT
1 AATTTT
36046 TATGTTATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.08
21 9 0.38
22 8 0.33
23 5 0.21
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (20 bp):
AATTTTAATAAAATAAAATA
Found at i:42872 original size:121 final size:122
Alignment explanation
Indices: 42585--42888 Score: 348
Period size: 122 Copynumber: 2.5 Consensus size: 122
42575 AAATCACGTA
* ** * * *
42585 TTTAATATCTAAATTATCAGTTTTGGTTTGTTTTAGA-ATTTAAGCTTTTAATTTTTTTAAGATC
1 TTTAATACCTAAATTATCAGTTTTGGTTTGTTTTA-ATACATAAACTTTCAATTTTTTTAAAATC
* * *
42649 ATATCTAAAGTTTAATTCTTGTTTTATTTTATTACCCCGCCGTTAAACACTTAACGCT
65 ATATCTAAAGTTTAATTCTTGTTTCATTTTAGTACCCCGCCGTTAAAAACTTAACGCT
* * * ** * *
42707 TTTAGTACTTAAGTTATCAGTTTTATTTTGTTTTAGTACCTAAACTTTCAATTTTTTTAAAATCA
1 TTTAATACCTAAATTATCAGTTTTGGTTTGTTTTAATACATAAACTTTCAATTTTTTTAAAATCA
* *
42772 TA-CATAAAGTTTAGTT-TCTGTTTCATTTTAGTA-CCCGTCGTTAAAAACTTAACGCT
66 TATC-TAAAGTTTAATTCT-TGTTTCATTTTAGTACCCCGCCGTTAAAAACTTAACGCT
* ** *
42828 TTTAATACCTAAACTATCAGTTTTGGTCCGTTTTAATACATAAAC-TTCAATTTTTTCAAAA
1 TTTAATACCTAAATTATCAGTTTTGGTTTGTTTTAATACATAAACTTTCAATTTTTTTAAAA
42889 CTTAACGTTA
Statistics
Matches: 151, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
120 15 0.10
121 58 0.38
122 78 0.52
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (122 bp):
TTTAATACCTAAATTATCAGTTTTGGTTTGTTTTAATACATAAACTTTCAATTTTTTTAAAATCA
TATCTAAAGTTTAATTCTTGTTTCATTTTAGTACCCCGCCGTTAAAAACTTAACGCT
Found at i:43260 original size:25 final size:24
Alignment explanation
Indices: 43227--43275 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
43217 AATTTATTGC
43227 TTAACTCGTTGCTCACTAAGCTCA
1 TTAACTCGTTGCTCACTAAGCTCA
**
43251 TTAACCTCGTTGCTCGTTAAGCTCA
1 TTAA-CTCGTTGCTCACTAAGCTCA
43276 CCAAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.22, C:0.29, G:0.14, T:0.35
Consensus pattern (24 bp):
TTAACTCGTTGCTCACTAAGCTCA
Found at i:50434 original size:23 final size:23
Alignment explanation
Indices: 50403--50480 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
50393 TGATATGTTC
*
50403 TCTGTCTTTATGGCACATTTATT
1 TCTGCCTTTATGGCACATTTATT
*
50426 TCTGCCTTTATGGTACATTTATT
1 TCTGCCTTTATGGCACATTTATT
* * *
50449 TCTGCCTTTGTGACACGTTT-TT
1 TCTGCCTTTATGGCACATTTATT
50471 CTCTGCCTTT
1 -TCTGCCTTT
50481 TTGGTACCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
22 2 0.04
23 46 0.96
ACGTcount: A:0.13, C:0.22, G:0.14, T:0.51
Consensus pattern (23 bp):
TCTGCCTTTATGGCACATTTATT
Found at i:50525 original size:11 final size:12
Alignment explanation
Indices: 50498--50525 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
50488 CTTACTATTT
50498 TTTTTGCCATTG
1 TTTTTGCCATTG
50510 TTTTTGCCATTG
1 TTTTTGCCATTG
50522 TTTT
1 TTTT
50526 CGTTTGTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.14, G:0.14, T:0.64
Consensus pattern (12 bp):
TTTTTGCCATTG
Found at i:52510 original size:50 final size:51
Alignment explanation
Indices: 52403--52524 Score: 167
Period size: 50 Copynumber: 2.4 Consensus size: 51
52393 ATTTGTTCCC
* * *
52403 ACTCGATTTGGTTAAAACTCGAAGTTCGCGAGTAATTTCTGAGTGTGTTGA
1 ACTCGATTTGGTTAAAACTCGAAGTTCGCAAGTAATTTCTGAATGTGTCGA
*
52454 ACTCGATTTGGTTAAAACTCG-AGTTCGCAAGTAGTTTCTGAATAG-GTCGA
1 ACTCGATTTGGTTAAAACTCGAAGTTCGCAAGTAATTTCTGAAT-GTGTCGA
* *
52504 ATTCGATTTGATTAAAACTCG
1 ACTCGATTTGGTTAAAACTCG
52525 GTTAATGTCC
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
50 42 0.66
51 22 0.34
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (51 bp):
ACTCGATTTGGTTAAAACTCGAAGTTCGCAAGTAATTTCTGAATGTGTCGA
Found at i:53180 original size:3 final size:3
Alignment explanation
Indices: 53169--53216 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
53159 TATTATTATT
* * * *
53169 ATG ACG ATG ATG ATG GT- ATT ATG GTG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
53216 A
1 A
53217 CATGTTGCTG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
2 1 0.03
3 36 0.97
ACGTcount: A:0.31, C:0.02, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:53190 original size:20 final size:20
Alignment explanation
Indices: 53165--53203 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53155 TTATTATTAT
53165 TATTATGACGATGATGATGG
1 TATTATGACGATGATGATGG
**
53185 TATTATGGTGATGATGATG
1 TATTATGACGATGATGATG
53204 ATGATGATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.31, T:0.38
Consensus pattern (20 bp):
TATTATGACGATGATGATGG
Found at i:60578 original size:18 final size:17
Alignment explanation
Indices: 60535--60586 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 17
60525 GATATAAATG
*
60535 TAAATA-AAAATATAAA
1 TAAATATAAATTATAAA
*
60551 TAAATTTAAATTATAAA
1 TAAATATAAATTATAAA
*
60568 TAGAATATAAATTTTAAA
1 TA-AATATAAATTATAAA
60586 T
1 T
60587 TTTTAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 5 0.17
17 11 0.37
18 14 0.47
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
TAAATATAAATTATAAA
Found at i:61239 original size:37 final size:37
Alignment explanation
Indices: 61166--61239 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
61156 TTCTATTTTA
*
61166 AATTTTGTAAAAAAAATTATATAAATATTATGAATTT
1 AATTTTGTAAAAAAAATTATATAAATATTATCAATTT
* * *
61203 AATTTTTTAAAGAAAA-TATATAAATATTTTACAATTT
1 AATTTTGTAAAAAAAATTATATAAATATTAT-CAATTT
61240 GTAATATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 13 0.41
37 19 0.59
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (37 bp):
AATTTTGTAAAAAAAATTATATAAATATTATCAATTT
Found at i:61420 original size:20 final size:20
Alignment explanation
Indices: 61384--61421 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
61374 ATCCTATTCT
**
61384 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
61404 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
61422 GTGAATCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:66270 original size:16 final size:16
Alignment explanation
Indices: 66249--66281 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
66239 TCCACTCAAC
66249 TATGGTAAAAAATTAT
1 TATGGTAAAAAATTAT
*
66265 TATGGTCAAAAATTAT
1 TATGGTAAAAAATTAT
66281 T
1 T
66282 TTGAACATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.39
Consensus pattern (16 bp):
TATGGTAAAAAATTAT
Found at i:66820 original size:30 final size:30
Alignment explanation
Indices: 66779--66835 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
66769 TTTGTTTTTT
66779 TTAACTCATTAAATATAGTTTATTTTTGTC
1 TTAACTCATTAAATATAGTTTATTTTTGTC
* * *
66809 TTAACTTATTAAATATATTTTGTTTTT
1 TTAACTCATTAAATATAGTTTATTTTT
66836 ATTTTAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (30 bp):
TTAACTCATTAAATATAGTTTATTTTTGTC
Found at i:66910 original size:74 final size:74
Alignment explanation
Indices: 66817--66973 Score: 210
Period size: 74 Copynumber: 2.1 Consensus size: 74
66807 TCTTAACTTA
* * * *
66817 TTAAATAT-ATTTTGTTTTTATTTTAATGTAAAAATATATTTTATTATTATC-TATTAATAATAT
1 TTAAATTTCATTTTATTTTTATTTTAATGTAAAAATATATTTT-GTATTAACTTATTAATAATAT
*
66880 TTTATATGTC
65 TTTATATATC
* * *
66890 TTAAATTTCATTTTATTTTTATTTTAATGTAAAACTATATTTTGTCTTAACTTATTAGTAATATT
1 TTAAATTTCATTTTATTTTTATTTTAATGTAAAAATATATTTTGTATTAACTTATTAATAATATT
66955 TTATATATC
66 TTATATATC
*
66964 TTAAAATTCA
1 TTAAATTTCA
66974 AAAATATATT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
73 12 0.16
74 61 0.84
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.56
Consensus pattern (74 bp):
TTAAATTTCATTTTATTTTTATTTTAATGTAAAAATATATTTTGTATTAACTTATTAATAATATT
TTATATATC
Found at i:67339 original size:21 final size:20
Alignment explanation
Indices: 67302--67341 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
67292 TAATTGGAAT
* *
67302 AAAATAATTTTATTAAATTA
1 AAAATAAATTAATTAAATTA
67322 AAAATAAATTAATGTAAATT
1 AAAATAAATTAAT-TAAATT
67342 GAGTCCATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
AAAATAAATTAATTAAATTA
Found at i:68511 original size:428 final size:425
Alignment explanation
Indices: 67716--68569 Score: 1555
Period size: 428 Copynumber: 2.0 Consensus size: 425
67706 ATAAGCCCGT
* *
67716 GGAATGAACTTTTGGTGAAACAAACTTCTTAACGTTGTATTGAGTAAGCTCATGGAATAAACTTT
1 GGAATGAACTTTTGGTGAAACAAACTTCTTAACGTTGTATTGAGTAAACCCATGGAATAAACTTT
* *
67781 TTTTAAGTTATTTTAAAAAAATTCGGAAATACAAAATTTTATATTATTTGAAGTGTGAAATTAGA
66 TTTTAAGTTATTTTAAAAAAATTCGGAAATACAAAATTATATATTATTTGAAGTATGAAATTAGA
67846 TTATTAATAAAAAATATCTAAATTATATAAAATAAAATTTTCATAAGGTGACATCTCCCCTAATA
131 TTATTAATAAAAAATATCTAAATTATATAAAATAAAATTTTCATAAGGTGACATCTCCCCTAATA
* *
67911 TCCCCTTGAGTAACTCTGAGTTAGCCTGTGCGCATCGTTTTATGTCACAAGTAGCATTGGGTAAA
196 TCCCCTTGAGTAACTCTGAGTTAACCTGTGCGCATCATTTTATGTCACAAGTAGCATTGGGTAAA
67976 GTTAAAGAGCCCGTTTGGATCAAGTATTTTAGGATTCCTGGCAGACATATTTTTTTCCTGACTAA
261 GTTAAAGAGCCCGTTTGGATCAAGTATTTTAGGATTCCTGGCAGACATATTTTTTTCCTGACTAA
* *
68041 GGATATCCATGTTTGATTGGGTATTTTTTCCTAAAGGAGGGCAATATTTCTTTCCCAAGTGTATT
326 GGATATCCATGTTTGATTGGGTATTCTTTCCTAAAGGAGGGCAATATTTCTTTCCCAAATGTATT
68106 TATTCCTGGAAATGTTATTCCCACACATCTATTAG
391 TATTCCTGGAAATGTTATTCCCACACATCTATTAG
*
68141 GGAATGAACTTTTGGTGAAACAAACTTCTTAGCGTTGTATTGAGTAAACCCATGGAATAAACTTT
1 GGAATGAACTTTTGGTGAAACAAACTTCTTAACGTTGTATTGAGTAAACCCATGGAATAAAC-TT
* *
68206 TTTTTAAGTTGTTTTTAAAAAATTCGGAAATACAAAATTATATATTATTTGAAGTATGAAATTAG
65 TTTTTAAGTTATTTTAAAAAAATTCGGAAATACAAAATTATATATTATTTGAAGTATGAAATTAG
68271 ATTATTAATAAAAAATATCTAAATTATATAAAATAAAATTTTCATAAGGTGACATCTCCCCTAAT
130 ATTATTAATAAAAAATATCTAAATTATATAAAATAAAATTTTCATAAGGTGACATCTCCCCTAAT
*
68336 ATCCCCTTGAGTTCAACTCTGAGTTAACCTGTGCGCATCATTTTATGTCACAAGTAGTATTGGGT
195 ATCCCCTTGAG-T-AACTCTGAGTTAACCTGTGCGCATCATTTTATGTCACAAGTAGCATTGGGT
*
68401 AAAGTTAAAGAGCCCGTTTGGATCAAGTATTTTAGGATTCCTGGCAGGCATATTTTTTTCCTGAC
258 AAAGTTAAAGAGCCCGTTTGGATCAAGTATTTTAGGATTCCTGGCAGACATATTTTTTTCCTGAC
*
68466 TAAGGATATCCATGTTTGATTGGGTATTCTTTCCTAAATGAGGGCAATATTTCTTTCCCAAATGT
323 TAAGGATATCCATGTTTGATTGGGTATTCTTTCCTAAAGGAGGGCAATATTTCTTTCCCAAATGT
68531 ATTTATTCCTGGAAATGTTATTCCCACACATCTATTAG
388 ATTTATTCCTGGAAATGTTATTCCCACACATCTATTAG
68569 G
1 G
68570 TATTCTTTTA
Statistics
Matches: 412, Mismatches: 14, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
425 59 0.14
426 139 0.34
427 1 0.00
428 213 0.52
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (425 bp):
GGAATGAACTTTTGGTGAAACAAACTTCTTAACGTTGTATTGAGTAAACCCATGGAATAAACTTT
TTTTAAGTTATTTTAAAAAAATTCGGAAATACAAAATTATATATTATTTGAAGTATGAAATTAGA
TTATTAATAAAAAATATCTAAATTATATAAAATAAAATTTTCATAAGGTGACATCTCCCCTAATA
TCCCCTTGAGTAACTCTGAGTTAACCTGTGCGCATCATTTTATGTCACAAGTAGCATTGGGTAAA
GTTAAAGAGCCCGTTTGGATCAAGTATTTTAGGATTCCTGGCAGACATATTTTTTTCCTGACTAA
GGATATCCATGTTTGATTGGGTATTCTTTCCTAAAGGAGGGCAATATTTCTTTCCCAAATGTATT
TATTCCTGGAAATGTTATTCCCACACATCTATTAG
Found at i:68716 original size:16 final size:16
Alignment explanation
Indices: 68695--68732 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
68685 CCTAGTAATA
68695 TTTCTTATCCTCTCCC
1 TTTCTTATCCTCTCCC
*
68711 TTTCTTCTCCTCTCCC
1 TTTCTTATCCTCTCCC
68727 TTTCTT
1 TTTCTT
68733 TACAATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.03, C:0.42, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTCTTATCCTCTCCC
Found at i:71911 original size:31 final size:31
Alignment explanation
Indices: 71852--71911 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
71842 TTAAATGTTG
* * *
71852 ATGTAAAATTTTAATATATTTTACATTAATT
1 ATGTAAAATTTTAATATAATTAAAATTAATT
71883 ATGT-AAATTTTAATATTAATTAAAATTAA
1 ATGTAAAATTTTAATA-TAATTAAAATTAA
71912 AATAATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (31 bp):
ATGTAAAATTTTAATATAATTAAAATTAATT
Found at i:74192 original size:30 final size:27
Alignment explanation
Indices: 74158--74223 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 27
74148 GTATCTTTTC
74158 AATAAATTGAATGATAATTTATAGTAATTT
1 AATAAATT-AATGATAATTT-TA-TAATTT
*
74188 AATAAAATTAATGATCATTTTATAATTT
1 AAT-AAATTAATGATAATTTTATAATTT
*
74216 TATAAATT
1 AATAAATT
74224 TTAATGACCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
27 5 0.15
28 8 0.24
29 2 0.06
30 13 0.39
31 5 0.15
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (27 bp):
AATAAATTAATGATAATTTTATAATTT
Done.