Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000129.1 Hibiscus syriacus cultivar Beakdansim tig00000233_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: 121663
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:61 original size:29 final size:29
Alignment explanation
Indices: 1--63 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 29
*
1 ATAGTTTTTAAAACATTTTGAAAACTTAT
1 ATAGTTTTTAAAACATTTCGAAAACTTAT
30 ATAGTTTTTTAAAACATTTCGAAAAACTTAT
1 ATAG-TTTTTAAAACATTTCG-AAAACTTAT
61 ATA
1 ATA
64 TATAATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.13
30 15 0.48
31 12 0.39
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (29 bp):
ATAGTTTTTAAAACATTTCGAAAACTTAT
Found at i:77 original size:36 final size:36
Alignment explanation
Indices: 27--210 Score: 134
Period size: 35 Copynumber: 5.1 Consensus size: 36
17 TTTGAAAACT
*
27 TATATAGTTTTTTAAAACATTTCGAAAAACT-TAT-A
1 TATATAATTTTTTAAAACATTTCGAAAAA-TATATAA
*
62 TATATAATTCTTTTAAAACATTTTGAAAAATATATAA
1 TATATAATT-TTTTAAAACATTTCGAAAAATATATAA
* *
99 TATATAA-TTTTAAAAACATTTTTGGAAAAATTATATAA
1 TATATAATTTTTTAAAACA--TTTCGAAAAA-TATATAA
* * * *
137 TATAT-AGTTTTAAAAACATATTTTTTGAAAACT-TAT-A
1 TATATAATTTTTTAAAAC--A--TTTCGAAAAATATATAA
* *
174 TA-AT-A-TTTTTAAAACATTTTGAAAACTATATAA
1 TATATAATTTTTTAAAACATTTCGAAAAATATATAA
207 TATA
1 TATA
211 GTTTTGAAAT
Statistics
Matches: 130, Mismatches: 7, Indels: 25
0.80 0.04 0.15
Matches are distributed among these distances:
31 11 0.08
32 3 0.02
33 4 0.03
34 1 0.01
35 27 0.21
36 26 0.20
37 21 0.16
38 25 0.19
39 1 0.01
40 11 0.08
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (36 bp):
TATATAATTTTTTAAAACATTTCGAAAAATATATAA
Found at i:223 original size:30 final size:31
Alignment explanation
Indices: 5--209 Score: 171
Period size: 36 Copynumber: 6.0 Consensus size: 31
1 ATAG
*
5 TTTTTAAAACATTTTGAAAACTTATATAGT-
1 TTTTTAAAACATTTTGAAAACTTATATAATA
*
35 TTTTTAAAACATTTCGAAAAACTTATATATATAA
1 TTTTTAAAACATTTTG-AAAACTTATATA-AT-A
*
69 TTCTTTTAAAACATTTTGAAAAATATATAATATATAA
1 -T-TTTTAAAACATTTTGAAAACT-TAT-ATA-AT-A
* *
106 TTTTAAAAACATTTTTGGAAAAATTATATAATATA
1 TTTTTAAAACA-TTTT-GAAAACTTATAT-A-ATA
141 TAGTTTTAAAAACATATTTTTTGAAAACTTATATAATA
1 T--TTTT-AAAAC--A--TTTTGAAAACTTATATAATA
179 TTTTTAAAACATTTTGAAAAC-TATATAATA
1 TTTTTAAAACATTTTGAAAACTTATATAATA
209 T
1 T
210 AGTTTTGAAA
Statistics
Matches: 151, Mismatches: 7, Indels: 34
0.79 0.04 0.18
Matches are distributed among these distances:
30 25 0.17
31 22 0.15
32 1 0.01
33 1 0.01
35 24 0.16
36 33 0.22
37 18 0.12
38 9 0.06
39 1 0.01
40 12 0.08
41 5 0.03
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (31 bp):
TTTTTAAAACATTTTGAAAACTTATATAATA
Found at i:270 original size:35 final size:36
Alignment explanation
Indices: 82--273 Score: 156
Period size: 32 Copynumber: 5.5 Consensus size: 36
72 TTTTAAAACA
* * *
82 TTTTGAAAAATATATAATATATAATTTTAAAAACAT
1 TTTTGAAAACTATATAATATATAGTTTTAAAAATAT
*
118 TTTTGGAAAAATTATATAATATATAGTTTTAAAAACATATT
1 TTTT-G-AAAACTATATAATATATAGTTTT-AAAA-ATA-T
* *
159 TTTTGAAAACT-TAT-ATA-ATA-TTTTTAAAACA-
1 TTTTGAAAACTATATAATATATAGTTTTAAAAATAT
*
190 TTTTGAAAACTATAT-A-ATATAGTTTT-GAAAT-T
1 TTTTGAAAACTATATAATATATAGTTTTAAAAATAT
***
222 TTTTTTTAA--ATATAATATATAGTTTTAAAAATAT
1 TTTTGAAAACTATATAATATATAGTTTTAAAAATAT
*
256 TTTTGAAGA-TATATAATA
1 TTTTGAAAACTATATAATA
274 ATTTATATTA
Statistics
Matches: 126, Mismatches: 16, Indels: 29
0.74 0.09 0.17
Matches are distributed among these distances:
30 4 0.03
31 13 0.10
32 26 0.21
33 10 0.08
34 9 0.07
35 12 0.10
36 7 0.06
37 4 0.03
38 24 0.19
39 9 0.07
40 3 0.02
41 5 0.04
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (36 bp):
TTTTGAAAACTATATAATATATAGTTTTAAAAATAT
Found at i:319 original size:13 final size:13
Alignment explanation
Indices: 289--330 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
279 TATTATATTA
*
289 TTATTATTATTATT
1 TTATTATT-TTCTT
303 TTATTTATTTT-TT
1 TTA-TTATTTTCTT
316 TTATTATTTTCTT
1 TTATTATTTTCTT
329 TT
1 TT
331 CATGTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 7 0.27
13 9 0.35
14 5 0.19
15 5 0.19
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (13 bp):
TTATTATTTTCTT
Found at i:1669 original size:2 final size:2
Alignment explanation
Indices: 1662--1741 Score: 151
Period size: 2 Copynumber: 40.0 Consensus size: 2
1652 TGTATACATA
*
1662 AT AT AT AT AT AT AT AT AT AT AT AT AT AG 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
1704 AT AT AT AT 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
1742 CTTGTTCTTT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9992 original size:28 final size:28
Alignment explanation
Indices: 9935--10001 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
9925 AATTTATTCC
* * *
9935 TTTTTTTATTTGAATTTTCCTTCTTTATT
1 TTTTTTTATTTGAATTTTCATTATTCA-T
9964 TTTTTTTATTT-AATATTT-ATTATTCAT
1 TTTTTTTATTTGAAT-TTTCATTATTCAT
*
9991 TTTATTTATTT
1 TTTTTTTATTT
10002 TACAGTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 11 0.33
28 8 0.24
29 14 0.42
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.73
Consensus pattern (28 bp):
TTTTTTTATTTGAATTTTCATTATTCAT
Found at i:19091 original size:22 final size:22
Alignment explanation
Indices: 19049--19088 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
19039 CTAATGGTTC
19049 AATGATCAAAATATAATAAATT
1 AATGATCAAAATATAATAAATT
*
19071 AATGA-CATAA-ATAATAAA
1 AATGATCAAAATATAATAAA
19089 AATCTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 4 0.24
22 5 0.29
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (22 bp):
AATGATCAAAATATAATAAATT
Found at i:22319 original size:6 final size:6
Alignment explanation
Indices: 22308--22336 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
22298 ATATATTTAA
22308 AATTTT AATTTT AATTTT AATTTT AATTT
1 AATTTT AATTTT AATTTT AATTTT AATTT
22337 CGGTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
AATTTT
Found at i:24355 original size:16 final size:16
Alignment explanation
Indices: 24334--24416 Score: 87
Period size: 16 Copynumber: 5.2 Consensus size: 16
24324 GCTCCAAACT
24334 ACAGCTTCTAACAGCA
1 ACAGCTTCTAACAGCA
*
24350 ACAGCTCCTAACAGCA
1 ACAGCTTCTAACAGCA
* *
24366 GCAACTT-TAAACAGCA
1 ACAGCTTCT-AACAGCA
*
24382 ACAGCTCCTAACAGCA
1 ACAGCTTCTAACAGCA
* * *
24398 GCAACTTCAAACAGCA
1 ACAGCTTCTAACAGCA
24414 ACA
1 ACA
24417 TGATCCCAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
15 1 0.02
16 51 0.96
17 1 0.02
ACGTcount: A:0.41, C:0.33, G:0.12, T:0.14
Consensus pattern (16 bp):
ACAGCTTCTAACAGCA
Found at i:24369 original size:19 final size:19
Alignment explanation
Indices: 24345--24402 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
24335 CAGCTTCTAA
24345 CAGCAACAGCTCCTAACAG
1 CAGCAACAGCTCCTAACAG
*
24364 CAGC-A-A-CT-TTAA-A-
1 CAGCAACAGCTCCTAACAG
24377 CAGCAACAGCTCCTAACAG
1 CAGCAACAGCTCCTAACAG
24396 CAGCAAC
1 CAGCAAC
24403 TTCAAACAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
13 4 0.13
14 2 0.06
15 4 0.13
16 4 0.13
17 4 0.13
18 2 0.06
19 11 0.35
ACGTcount: A:0.40, C:0.34, G:0.14, T:0.12
Consensus pattern (19 bp):
CAGCAACAGCTCCTAACAG
Found at i:24384 original size:32 final size:32
Alignment explanation
Indices: 24338--24416 Score: 140
Period size: 32 Copynumber: 2.5 Consensus size: 32
24328 CAAACTACAG
*
24338 CTTCTAACAGCAACAGCTCCTAACAGCAGCAA
1 CTTCAAACAGCAACAGCTCCTAACAGCAGCAA
*
24370 CTTTAAACAGCAACAGCTCCTAACAGCAGCAA
1 CTTCAAACAGCAACAGCTCCTAACAGCAGCAA
24402 CTTCAAACAGCAACA
1 CTTCAAACAGCAACA
24417 TGATCCCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.41, C:0.33, G:0.11, T:0.15
Consensus pattern (32 bp):
CTTCAAACAGCAACAGCTCCTAACAGCAGCAA
Found at i:33716 original size:18 final size:18
Alignment explanation
Indices: 33693--33727 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
33683 GAGAGTCCCC
33693 AGCCTGCTGAAC-CTGAAT
1 AGCCTGCT-AACGCTGAAT
33711 AGCCTGCTAACGCTGAA
1 AGCCTGCTAACGCTGAA
33728 GAGATCGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (18 bp):
AGCCTGCTAACGCTGAAT
Found at i:39274 original size:23 final size:24
Alignment explanation
Indices: 39234--39279 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
39224 TCATCAATTT
*
39234 CACACAAAACTCAAACATAAAATGA
1 CACAAAAAACTC-AACATAAAATGA
*
39259 CACAAAAAACTC-ACATTAAAT
1 CACAAAAAACTCAACATAAAAT
39280 TGGGCTGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
25 11 0.58
ACGTcount: A:0.59, C:0.24, G:0.02, T:0.15
Consensus pattern (24 bp):
CACAAAAAACTCAACATAAAATGA
Found at i:47332 original size:21 final size:22
Alignment explanation
Indices: 47285--47343 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 22
47275 GTTTAAGGTA
*
47285 TATTTTATTATATTTAATATTTTG
1 TATTTAATT-TATTTAATA-TTTG
47309 TATTTAATTTATTTAATA-TTG
1 TATTTAATTTATTTAATATTTG
*
47330 TATTTAATTAATTT
1 TATTTAATTTATTT
47344 TTTTTGCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 16 0.48
23 9 0.27
24 8 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.64
Consensus pattern (22 bp):
TATTTAATTTATTTAATATTTG
Found at i:49104 original size:33 final size:33
Alignment explanation
Indices: 49067--49134 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
49057 TTACCCGATG
**
49067 CCGCCGCCGCCACCGTCACCTAGTTTTATGACC
1 CCGCCGCCGCCACCGTCACAAAGTTTTATGACC
*
49100 CCGCCGCCGCTACCGTCACAAAGTTTTATGACC
1 CCGCCGCCGCCACCGTCACAAAGTTTTATGACC
49133 CC
1 CC
49135 TCCTGGAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.18, C:0.44, G:0.18, T:0.21
Consensus pattern (33 bp):
CCGCCGCCGCCACCGTCACAAAGTTTTATGACC
Found at i:53049 original size:24 final size:23
Alignment explanation
Indices: 52991--53050 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
52981 GAACGAAAAT
*
52991 ATAACATAATAAATTTTTTACAC
1 ATAACATAATAAATTTTTTACAA
*
53014 ATAAACGT-ATAATATTTTTT-CAA
1 AT-AACATAATAA-ATTTTTTACAA
53037 ATAATCATAATAAA
1 ATAA-CATAATAAA
53051 CAATAAGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
22 2 0.07
23 13 0.43
24 15 0.50
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (23 bp):
ATAACATAATAAATTTTTTACAA
Found at i:54004 original size:24 final size:25
Alignment explanation
Indices: 53964--54010 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
53954 ATTTTAAATT
*
53964 TATATATTTTTTAATAAAATTTATA
1 TATACATTTTTTAATAAAATTTATA
53989 TATACATTTTTT-ATAAAATTTA
1 TATACATTTTTTAATAAAATTTA
54011 AAAGATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TATACATTTTTTAATAAAATTTATA
Found at i:59337 original size:14 final size:14
Alignment explanation
Indices: 59318--59349 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
59308 TTAAATGATA
59318 AACGAACACAAATG
1 AACGAACACAAATG
*
59332 AACGAACATAAATG
1 AACGAACACAAATG
59346 AACG
1 AACG
59350 GATGTAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.19, G:0.16, T:0.09
Consensus pattern (14 bp):
AACGAACACAAATG
Found at i:59395 original size:24 final size:24
Alignment explanation
Indices: 59368--59438 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
59358 CAAACATAAG
* *
59368 CGAACGTAAATGAACACAAATGAA
1 CGAACATAAACGAACACAAATGAA
* *
59392 CGAACTTAAACGAACAC-AATAAA
1 CGAACATAAACGAACACAAATGAA
* *
59415 TGAACATAAACGAACATAAATGAA
1 CGAACATAAACGAACACAAATGAA
59439 AACAATTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 19 0.49
24 20 0.51
ACGTcount: A:0.56, C:0.17, G:0.13, T:0.14
Consensus pattern (24 bp):
CGAACATAAACGAACACAAATGAA
Found at i:59435 original size:20 final size:22
Alignment explanation
Indices: 59332--59438 Score: 78
Period size: 20 Copynumber: 4.7 Consensus size: 22
59322 AACACAAATG
59332 AACGAACATAAATGAACGGATGTA
1 AACGAACATAAATGAAC-GAT-TA
* **
59356 AACAAACATAAGCGAACG--TA
1 AACGAACATAAATGAACGATTA
* *
59376 AATGAACACAAATGAACGAACTTA
1 AACGAACATAAATGAACG-A-TTA
59400 AACGAACACAATAAATGAAC-A-TA
1 AACG-A-AC-ATAAATGAACGATTA
59423 AACGAACATAAATGAA
1 AACGAACATAAATGAA
59439 AACAATTTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
20 24 0.36
21 2 0.03
22 1 0.02
23 7 0.11
24 19 0.29
25 2 0.03
26 2 0.03
27 9 0.14
ACGTcount: A:0.56, C:0.16, G:0.14, T:0.14
Consensus pattern (22 bp):
AACGAACATAAATGAACGATTA
Found at i:59799 original size:26 final size:24
Alignment explanation
Indices: 59763--59825 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 24
59753 CAAAGGACTC
59763 GTTCGTTCATTTACATTCGATTATAT
1 GTTCGTTCATTTACATTC-ATT-TAT
**
59789 GTTCGTTCATTTATGTTCATTTAT
1 GTTCGTTCATTTACATTCATTTAT
*
59813 ATTCGTTCATTTA
1 GTTCGTTCATTTA
59826 TGTTAGAACA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 15 0.44
25 3 0.09
26 16 0.47
ACGTcount: A:0.21, C:0.14, G:0.11, T:0.54
Consensus pattern (24 bp):
GTTCGTTCATTTACATTCATTTAT
Found at i:59805 original size:14 final size:14
Alignment explanation
Indices: 59786--59829 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
59776 CATTCGATTA
59786 TATGTTCGTTCATT
1 TATGTTCGTTCATT
59800 TA---T-GTTCATT
1 TATGTTCGTTCATT
*
59810 TATATTCGTTCATT
1 TATGTTCGTTCATT
59824 TATGTT
1 TATGTT
59830 AGAACAGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
10 9 0.36
11 1 0.04
13 1 0.04
14 14 0.56
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.59
Consensus pattern (14 bp):
TATGTTCGTTCATT
Found at i:60336 original size:14 final size:14
Alignment explanation
Indices: 60301--60347 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
60291 TTACAGGCCT
* *
60301 ACATAAACGAACAA
1 ACATAAATGAACGA
60315 ACATAAATGAACGA
1 ACATAAATGAACGA
* *
60329 ACATAAATAAACGG
1 ACATAAATGAACGA
60343 ACATA
1 ACATA
60348 TCACCGAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.60, C:0.17, G:0.11, T:0.13
Consensus pattern (14 bp):
ACATAAATGAACGA
Found at i:75163 original size:15 final size:15
Alignment explanation
Indices: 75145--75174 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
75135 CCACGGTGCT
75145 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
75160 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
75175 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:78195 original size:17 final size:17
Alignment explanation
Indices: 78175--78210 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
78165 AAAAAGCTTG
*
78175 ATTGATGTAATTTTTTA
1 ATTGATGTAATTTCTTA
*
78192 ATTGATTTAATTTCTTA
1 ATTGATGTAATTTCTTA
78209 AT
1 AT
78211 ACAAAGACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (17 bp):
ATTGATGTAATTTCTTA
Found at i:78981 original size:17 final size:17
Alignment explanation
Indices: 78961--79003 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
78951 ATATTATAAT
78961 ATTATA-AATTTCAAATA
1 ATTATATAATTTCAAA-A
*
78978 ATTATATAATTTTAAAA
1 ATTATATAATTTCAAAA
*
78995 ATTAAATAA
1 ATTATATAA
79004 ATTAGTCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTATATAATTTCAAAA
Found at i:78985 original size:19 final size:18
Alignment explanation
Indices: 78963--79006 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
78953 ATTATAATAT
78963 TATAAATTTCAAATAATTA
1 TATAAATTTCAAA-AATTA
*
78982 TAT-AATTTTAAAAATTA
1 TATAAATTTCAAAAATTA
*
78999 AATAAATT
1 TATAAATT
79007 AGTCTTGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 7 0.32
18 12 0.55
19 3 0.14
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
TATAAATTTCAAAAATTA
Found at i:78996 original size:27 final size:28
Alignment explanation
Indices: 78939--79005 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
78929 TTAGCTGTTT
* *
78939 AATTTTAAATAAATATTATAATATTATA
1 AATTTCAAATAAATATTATAATATTAAA
* *
78967 AATTTCAAATAATTA-TATAATTTTAAA
1 AATTTCAAATAAATATTATAATATTAAA
78994 AA-TT-AAATAAAT
1 AATTTCAAATAAAT
79006 TAGTCTTGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 7 0.21
26 2 0.06
27 12 0.35
28 13 0.38
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (28 bp):
AATTTCAAATAAATATTATAATATTAAA
Found at i:79001 original size:25 final size:27
Alignment explanation
Indices: 78943--79005 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
78933 CTGTTTAATT
*
78943 TTAAATAAATATTATAATATTATAAAT
1 TTAAATAAATATTATAATATTATAAAA
* *
78970 TTCAAATAATTA-TATAATTTTA-AAAA
1 TT-AAATAAATATTATAATATTATAAAA
78996 TTAAATAAAT
1 TTAAATAAAT
79006 TAGTCTTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 7 0.23
26 5 0.16
27 11 0.35
28 8 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
TTAAATAAATATTATAATATTATAAAA
Found at i:80037 original size:26 final size:25
Alignment explanation
Indices: 80008--80069 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
79998 ACAGATAAAA
* * *
80008 TATAATTATATTATAATTTTTTATGT
1 TATAATTATAATATAA-ATTATATGT
*
80034 TATAATTAGTAATATAAATTATATTT
1 TATAATTA-TAATATAAATTATATGT
80060 TATAATTATA
1 TATAATTATA
80070 CAAATTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 2 0.06
26 22 0.71
27 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (25 bp):
TATAATTATAATATAAATTATATGT
Found at i:80557 original size:17 final size:17
Alignment explanation
Indices: 80535--80573 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
80525 ATATTTTAAA
80535 AAAATATA-AAAATATTT
1 AAAATATATAAAA-ATTT
80552 AAAATATATAAAAATTT
1 AAAATATATAAAAATTT
80569 AAAAT
1 AAAAT
80574 TTAGGGTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATATATAAAAATTT
Found at i:80738 original size:21 final size:21
Alignment explanation
Indices: 80714--80754 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
80704 AATTTTTTAC
*
80714 ATATAATT-TTAATTGATTATA
1 ATAT-ATTATTAATTAATTATA
80735 ATATATTATTAATTAATTAT
1 ATATATTATTAATTAATTAT
80755 TTAAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
ATATATTATTAATTAATTATA
Found at i:82966 original size:2 final size:2
Alignment explanation
Indices: 82961--82986 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
82951 TCTCTCTCTC
82961 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
82987 ATAATCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:98273 original size:22 final size:22
Alignment explanation
Indices: 98245--98297 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
98235 TTCCATTTCG
98245 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
98267 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
98289 CGTTGCGAT
1 CGTTGCGAT
98298 TTTCCAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:98555 original size:6 final size:6
Alignment explanation
Indices: 98534--98567 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
98524 TCTCGTCTCG
98534 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
98568 AGTAATACGT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.36
6 18 0.64
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:98706 original size:22 final size:22
Alignment explanation
Indices: 98634--98708 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
98624 TATTTTTTTA
* *
98634 ACTATCACAACAACAACTGTAG
1 ACTATCGCAACGACAACTGTAG
* *
98656 ACTATCGCAACG--AA-TTTGG
1 ACTATCGCAACGACAACTGTAG
**
98675 AAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGACAACTGTAG
98697 ACTATCGCAACG
1 ACTATCGCAACG
98709 CGAAATGAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
19 13 0.32
20 2 0.05
21 2 0.05
22 23 0.57
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (22 bp):
ACTATCGCAACGACAACTGTAG
Found at i:98719 original size:41 final size:42
Alignment explanation
Indices: 98641--98724 Score: 111
Period size: 41 Copynumber: 2.0 Consensus size: 42
98631 TTAACTATCA
*
98641 CAACAACAACTGTAGACTATCGCAACGAATTTGG-AAAATCG
1 CAACAACAACTGTAGACTATCGCAACGAATATGGAAAAATCG
*
98682 CAACGACAACTGTAGACTATCGCAACGCGAA-AT-GAAAAATCG
1 CAACAACAACTGTAGACTATCGCAA--CGAATATGGAAAAATCG
98724 C
1 C
98725 GTTGCGATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
41 25 0.66
42 9 0.24
43 4 0.11
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.17
Consensus pattern (42 bp):
CAACAACAACTGTAGACTATCGCAACGAATATGGAAAAATCG
Found at i:98742 original size:41 final size:41
Alignment explanation
Indices: 98697--98806 Score: 193
Period size: 41 Copynumber: 2.7 Consensus size: 41
98687 ACAACTGTAG
*
98697 ACTATCGCAACGCGAAATGAAAAATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCGTTACGATTTTCA
*
98738 ACTATCGCAACGCGAAATGAAAAATCGCTTTACGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCGTTACGATTTTCA
*
98779 ACTATCGCAACGCGCAATGAAAAATCGC
1 ACTATCGCAACGCGAAATGAAAAATCGC
98807 AACGCGAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGAAAAATCGCGTTACGATTTTCA
Found at i:98806 original size:61 final size:61
Alignment explanation
Indices: 98741--98874 Score: 207
Period size: 61 Copynumber: 2.2 Consensus size: 61
98731 ATTTTCAACT
* *
98741 ATCGCAACGCGAAAT-GAAAAATCGCTTTACGATTTTCAACTATCGCAACGCGCAATGAAAA
1 ATCGCAACGCGAAATAG-AAAATCGCGTTACGATTTTCAACTATCGCAACGCGAAATGAAAA
* *
98802 ATCGCAACGCGAAATAGAAAATCGCGTTGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATAGAAAATCGCGTTACGATTTTCAACTATCGCAACGCGAAATGAAAA
*
98863 ATCGTAACGCGA
1 ATCGCAACGCGA
98875 TTTTCAACTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
61 66 0.99
62 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.20
Consensus pattern (61 bp):
ATCGCAACGCGAAATAGAAAATCGCGTTACGATTTTCAACTATCGCAACGCGAAATGAAAA
Found at i:98807 original size:20 final size:20
Alignment explanation
Indices: 98782--98826 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
98772 ATTTTCAACT
*
98782 ATCGCAACGCGCAAT-GAAAA
1 ATCGCAACGCGAAATAG-AAA
98802 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATAGAAA
98822 ATCGC
1 ATCGC
98827 GTTGCGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.11
Consensus pattern (20 bp):
ATCGCAACGCGAAATAGAAA
Found at i:98847 original size:41 final size:41
Alignment explanation
Indices: 98802--98898 Score: 131
Period size: 41 Copynumber: 2.4 Consensus size: 41
98792 GCAATGAAAA
***
98802 ATCGCAACGCGAAATAGAAAATCGCGTTGCGATTTTCAACT
1 ATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACT
* *
98843 ATCGCAACGCGAAATGGAAAATCGTAACGCGATTTTCAACT
1 ATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACT
* *
98884 ATCACAATGCGAAAT
1 ATCGCAACGCGAAAT
98899 GCAACGCGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (41 bp):
ATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACT
Found at i:98854 original size:21 final size:21
Alignment explanation
Indices: 98830--98895 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
98820 AAATCGCGTT
98830 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
** ** * *
98851 GCGAAATGGAA-AATCGTAAC
1 GCGATTTTCAACTATCGCAAC
* *
98871 GCGATTTTCAACTATCACAAT
1 GCGATTTTCAACTATCGCAAC
98892 GCGA
1 GCGA
98896 AATGCAACGC
Statistics
Matches: 30, Mismatches: 14, Indels: 2
0.65 0.30 0.04
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (21 bp):
GCGATTTTCAACTATCGCAAC
Found at i:98876 original size:102 final size:101
Alignment explanation
Indices: 98700--98886 Score: 306
Period size: 102 Copynumber: 1.8 Consensus size: 101
98690 ACTGTAGACT
98700 ATCGCAACGCGAAATGAAAAATCGCGTTGCGATTTTCAACTATCGCAACGCGAAATGAAAAATCG
1 ATCGCAACGCGAAATGAAAAATCGCGTTGCGATTTTCAACTATCGCAACGCGAAATGAAAAATCG
*
98765 CTTTACGATTTTCAACTATCGCAACGCGCAATGAAAA
66 C-TAACGATTTTCAACTATCGCAACGCGCAATGAAAA
*
98802 ATCGCAACGCGAAAT-AGAAAATCGCGTTGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
1 ATCGCAACGCGAAATGA-AAAATCGCGTTGCGATTTTCAACTATCGCAACGCGAAATGAAAAATC
98866 G-TAACGCGATTTTCAACTATC
65 GCTAA--CGATTTTCAACTATC
98887 ACAATGCGAA
Statistics
Matches: 80, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
100 2 0.03
101 1 0.01
102 77 0.96
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.23
Consensus pattern (101 bp):
ATCGCAACGCGAAATGAAAAATCGCGTTGCGATTTTCAACTATCGCAACGCGAAATGAAAAATCG
CTAACGATTTTCAACTATCGCAACGCGCAATGAAAA
Found at i:101159 original size:19 final size:20
Alignment explanation
Indices: 101105--101152 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
101095 AAAAAATAAT
101105 AAAATATTATAATATTTAGA
1 AAAATATTATAATATTTAGA
101125 AAAATATTATAATATTTAGA
1 AAAATATTATAATATTTAGA
101145 AAAATATT
1 AAAATATT
101153 GAATATTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (20 bp):
AAAATATTATAATATTTAGA
Found at i:112262 original size:12 final size:12
Alignment explanation
Indices: 112245--112278 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
112235 AAGTCTTAAT
112245 TAGGTTTGAGAA
1 TAGGTTTGAGAA
112257 TAGGTTTGAGAA
1 TAGGTTTGAGAA
*
112269 TAAGTTTGAG
1 TAGGTTTGAG
112279 TTATGTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (12 bp):
TAGGTTTGAGAA
Found at i:112980 original size:34 final size:33
Alignment explanation
Indices: 112926--112994 Score: 77
Period size: 34 Copynumber: 2.0 Consensus size: 33
112916 CGACCCGATA
* * *
112926 AATATTAAAAATAATTATTTATATATATATATAT
1 AATATTAAAAAT-ATTATTTAAATAAAAATATAT
112960 AATATTAATAAAT-TTAATTTAAATAAAAATATAT
1 AATATTAA-AAATATT-ATTTAAATAAAAATATAT
112994 A
1 A
112995 TTTAATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
33 2 0.07
34 24 0.80
35 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
AATATTAAAAATATTATTTAAATAAAAATATAT
Found at i:113001 original size:23 final size:23
Alignment explanation
Indices: 112971--113017 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
112961 ATATTAATAA
112971 ATTTAATTTAAATAAAAATATAT
1 ATTTAATTTAAATAAAAATATAT
* *
112994 ATTTAATTTAAATATATATATAT
1 ATTTAATTTAAATAAAAATATAT
113017 A
1 A
113018 CCCGGCCCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTAATTTAAATAAAAATATAT
Found at i:113062 original size:12 final size:12
Alignment explanation
Indices: 113035--113080 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
113025 CGATTCTCGG
113035 CCCAATA-CCGA
1 CCCAATACCCGA
*
113046 CCCAATACCCAA
1 CCCAATACCCGA
*
113058 CCCAATACCCGG
1 CCCAATACCCGA
113070 CCCAATACCCG
1 CCCAATACCCG
113081 TTTAAATAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
11 7 0.23
12 24 0.77
ACGTcount: A:0.33, C:0.50, G:0.09, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:116070 original size:22 final size:21
Alignment explanation
Indices: 116028--116067 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
116018 AAGACTATTT
116028 TCATTTTTTAATTTTGAAATA
1 TCATTTTTTAATTTTGAAATA
116049 TCATTTTTGT-ATTTTGAAA
1 TCATTTTT-TAATTTTGAAA
116068 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (21 bp):
TCATTTTTTAATTTTGAAATA
Found at i:118722 original size:15 final size:14
Alignment explanation
Indices: 118688--118725 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
118678 AACATATAAG
118688 CATCCAAATTCAAA
1 CATCCAAATTCAAA
118702 CAATCCACAATTCAAA
1 C-ATCCA-AATTCAAA
118718 CATCCAAA
1 CATCCAAA
118726 ATGTTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.14
15 10 0.45
16 9 0.41
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (14 bp):
CATCCAAATTCAAA
Found at i:120648 original size:21 final size:22
Alignment explanation
Indices: 120601--120665 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
120591 TGATTCCTGT
* * *
120601 GGGGGAATCAATTCCCCTTCAAA
1 GGGGGAATCGATTCCTCTGC-AA
*
120624 GGGGGAATCGGTTCC-CTGCAA
1 GGGGGAATCGATTCCTCTGCAA
*
120645 GGGGGTATCGATTCCTCTGCA
1 GGGGGAATCGATTCCTCTGCA
120666 CCAAAATACT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 15 0.42
22 8 0.22
23 13 0.36
ACGTcount: A:0.22, C:0.25, G:0.31, T:0.23
Consensus pattern (22 bp):
GGGGGAATCGATTCCTCTGCAA
Done.