Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004591.1 Hibiscus syriacus cultivar Beakdansim tig00010252_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: 80882
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:212 original size:68 final size:69
Alignment explanation
Indices: 106--262 Score: 207
Period size: 68 Copynumber: 2.3 Consensus size: 69
96 TTTTTGAGTG
* * *
106 AGTTCTTCTCATTATGAACTCTTCTAGAAATGTTGGTTCACC-TCCTTCTATAGTGAATTTGAAA
1 AGTTCTTCTCATTATGAACTTTTATAGAAATGCTGGTTCACCAT-CTTCTATAGTGAATTTGAAA
170 GGAACA
65 GGAA-A
* * *
176 AGTTCTTCTCA-TATG-ACTTTTATGGAAATGCTGGTTCACCATCTTCTGTGGTGAATTTGAAAG
1 AGTTCTTCTCATTATGAACTTTTATAGAAATGCTGGTTCACCATCTTCTATAGTGAATTTGAAAG
239 GAAA
66 GAAA
243 AG-T-TTCTCATTATGAACTTT
1 AGTTCTTCTCATTATGAACTTT
263 CTCTTTTAGG
Statistics
Matches: 78, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
65 6 0.08
66 5 0.06
67 8 0.10
68 43 0.55
69 5 0.06
70 11 0.14
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (69 bp):
AGTTCTTCTCATTATGAACTTTTATAGAAATGCTGGTTCACCATCTTCTATAGTGAATTTGAAAG
GAAA
Found at i:3319 original size:7 final size:6
Alignment explanation
Indices: 3298--3378 Score: 69
Period size: 7 Copynumber: 12.8 Consensus size: 6
3288 TGATTCAATT
*
3298 TTTTTCC TTTTT- TTTCTC TTTTTTC TTTTTCC TTTTTTC TTTTT- TTTTTC
1 TTTTT-C TTTTTC TTTTTC -TTTTTC TTTTT-C -TTTTTC TTTTTC TTTTTC
3348 TTTTTTC TTTTT- TTCTTTC TTTTCTC TTTTT
1 -TTTTTC TTTTTC TT-TTTC TTTT-TC TTTTT
3379 TTCTCTGATG
Statistics
Matches: 63, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
5 11 0.17
6 21 0.33
7 26 0.41
8 5 0.08
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:3326 original size:26 final size:25
Alignment explanation
Indices: 3297--3379 Score: 105
Period size: 26 Copynumber: 3.2 Consensus size: 25
3287 TTGATTCAAT
3297 TTTTTTCCTTTTTTTTCTCTTTTTTC
1 TTTTTTCCTTTTTTTT-TCTTTTTTC
*
3323 -TTTTTCCTTTTTTCTTTTTTTTTTC
1 TTTTTTCCTTTTTT-TTTCTTTTTTC
* *
3348 TTTTTTCTTTTTTTCTTTCTTTTCTC
1 TTTTTTCCTTTTTT-TTTCTTTTTTC
3374 TTTTTT
1 TTTTTT
3380 TCTCTGATGG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
25 21 0.41
26 30 0.59
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (25 bp):
TTTTTTCCTTTTTTTTTCTTTTTTC
Found at i:3327 original size:25 final size:24
Alignment explanation
Indices: 3298--3378 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 24
3288 TGATTCAATT
3298 TTTTTCCTTTTTTTTCTCTTTTTTC
1 TTTTTCCTTTTTTTT-TCTTTTTTC
*
3323 TTTTTCCTTTTTTCTTTTTTTTTTC
1 TTTTTCCTTTTTT-TTTCTTTTTTC
* *
3348 TTTTTTCTTTTTTTCTTTCTTTTCTC
1 -TTTTTCCTTTTTT-TTTCTTTTTTC
3374 TTTTT
1 TTTTT
3379 TTCTCTGATG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
25 26 0.52
26 24 0.48
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTTCCTTTTTTTTTCTTTTTTC
Found at i:3334 original size:32 final size:32
Alignment explanation
Indices: 3298--3359 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
3288 TGATTCAATT
3298 TTTTTCCTTTTTTTTCTCTTTTTTCTTTTTCC
1 TTTTTCCTTTTTTTTCTCTTTTTTCTTTTTCC
* *
3330 TTTTTTCTTTTTTTTTTCTTTTTTCTTTTT
1 TTTTTCCTTTTTTTTCTCTTTTTTCTTTTT
3360 TTCTTTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (32 bp):
TTTTTCCTTTTTTTTCTCTTTTTTCTTTTTCC
Found at i:3380 original size:19 final size:19
Alignment explanation
Indices: 3296--3382 Score: 104
Period size: 19 Copynumber: 4.5 Consensus size: 19
3286 CTTGATTCAA
*
3296 TTTTTTTCCTTTTTTTTCTC
1 TTTTTTT-CTTTCTTTTCTC
* *
3316 TTTTTTCTTTTTCCTTTTTTC
1 TTTTTT-TCTTT-CTTTTCTC
*
3337 TTTTTTT-TTTCTTTTTTC
1 TTTTTTTCTTTCTTTTCTC
3355 TTTTTTTCTTTCTTTTCTC
1 TTTTTTTCTTTCTTTTCTC
3374 TTTTTTTCT
1 TTTTTTTCT
3383 CTGATGGATG
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
18 15 0.25
19 22 0.37
20 10 0.17
21 13 0.22
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTTTCTTTCTTTTCTC
Found at i:6893 original size:27 final size:28
Alignment explanation
Indices: 6863--6916 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
6853 TGAAAAATGA
* *
6863 CACAAACAAAAGA-AATAAGTTAGTGTC
1 CACAAACAAAAGAGAAGAAATTAGTGTC
6890 CACAAACAAAAGAGAAGAAATTAGTGT
1 CACAAACAAAAGAGAAGAAATTAGTGT
6917 ACATGTAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.54, C:0.13, G:0.17, T:0.17
Consensus pattern (28 bp):
CACAAACAAAAGAGAAGAAATTAGTGTC
Found at i:13188 original size:23 final size:23
Alignment explanation
Indices: 13158--13207 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
13148 AAATTGGATT
13158 ATGGGTGAATGTTGGATCTGTAA
1 ATGGGTGAATGTTGGATCTGTAA
13181 ATGGGTGAATGTTGGATCTGTAA
1 ATGGGTGAATGTTGGATCTGTAA
13204 ATGG
1 ATGG
13208 TCTTTAAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.04, G:0.36, T:0.34
Consensus pattern (23 bp):
ATGGGTGAATGTTGGATCTGTAA
Found at i:22153 original size:24 final size:24
Alignment explanation
Indices: 22082--22154 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
22072 TGCCGCATAT
* * *
22082 ATTTTTCCCGAAGGATCAAGTAGA
1 ATTTATCCCGAAGGACCACGTAGA
* *
22106 ATTTGTCCCGAAGGACCACATAGA
1 ATTTATCCCGAAGGACCACGTAGA
* *
22130 ATTTATCCCGATGGACCGCGTAGA
1 ATTTATCCCGAAGGACCACGTAGA
22154 A
1 A
22155 CCCTTGACTC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (24 bp):
ATTTATCCCGAAGGACCACGTAGA
Found at i:24041 original size:38 final size:39
Alignment explanation
Indices: 23955--24058 Score: 140
Period size: 38 Copynumber: 2.7 Consensus size: 39
23945 AAACTTTTAA
* *
23955 TTTCAAGGGAAACTGTCTCGAGTGAGATGAAATTCGGTG
1 TTTCAAGGGAAACTATCTCAAGTGAGATGAAATTCGGTG
*
23994 TTTCAAGGGAAACTATCTCAAGAT-AGATG-AATTTGGTG
1 TTTCAAGGGAAACTATCTCAAG-TGAGATGAAATTCGGTG
* *
24032 TTTTAAGGGAAACTATCTCAAGGGAGA
1 TTTCAAGGGAAACTATCTCAAGTGAGA
24059 CAAAGTTGAA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
38 32 0.55
39 25 0.43
40 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.29
Consensus pattern (39 bp):
TTTCAAGGGAAACTATCTCAAGTGAGATGAAATTCGGTG
Found at i:29650 original size:35 final size:35
Alignment explanation
Indices: 29609--29684 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
29599 AAAACAGTCC
* *
29609 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
29644 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
29679 TCAATT
1 TCAATT
29685 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:30234 original size:130 final size:130
Alignment explanation
Indices: 30081--30328 Score: 397
Period size: 130 Copynumber: 1.9 Consensus size: 130
30071 TATTTATATA
* **
30081 ATCAATTTGGTACTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATATGACATGTG
1 ATCAATTTGGTACTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATATGACATGTG
* * *
30146 TTAGCACATGATCATGACACGTGTCATTGGTGACACCTGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
* *
30211 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTACTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATATGACATGTG
* * *
30276 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
30329 GAAGAAAATT
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTACTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATATGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:30359 original size:130 final size:129
Alignment explanation
Indices: 30095--30359 Score: 291
Period size: 130 Copynumber: 2.0 Consensus size: 129
30085 ATTTGGTACT
* ** *
30095 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATATGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATATGACATGTGTTAACACATGATCA
* * *** * * **** *
30160 TGACACGTGTCATTGGTGACACCTGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
*
30225 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATATGACATGTGTTAACACATGATCA
* * * *
30290 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
30354 -A
128 CA
30355 AAATT
1 AAATT
30360 TGGGTCTTAG
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
130 98 0.88
132 8 0.07
133 5 0.05
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATATGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:30815 original size:16 final size:18
Alignment explanation
Indices: 30794--30827 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
30784 ATTTCTTATT
30794 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
30810 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
30828 TAAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:31473 original size:29 final size:29
Alignment explanation
Indices: 31418--31474 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
31408 GTGCAATAAT
* * * *
31418 TAAAGGATTGAAATTAAAATATTGAAAAA
1 TAAAGGATAGAAATAAAAAGATAGAAAAA
*
31447 TAAAGGATAGAAATAAAAAGGTAGAAAA
1 TAAAGGATAGAAATAAAAAGATAGAAAA
31475 TCAAAGTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (29 bp):
TAAAGGATAGAAATAAAAAGATAGAAAAA
Found at i:33303 original size:3 final size:3
Alignment explanation
Indices: 33297--33361 Score: 50
Period size: 3 Copynumber: 23.0 Consensus size: 3
33287 TAATAATGGT
*
33297 ATA ATA ATA ATA AT- ATA ATA ACA ATA A-A A-A ATA ATTA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
* * *
33339 GTA ATG AT- ATT ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
33362 CTAACATTAC
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 9 0.18
3 39 0.76
4 3 0.06
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:33305 original size:14 final size:14
Alignment explanation
Indices: 33286--33361 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
33276 TTTTTAAAGT
**
33286 ATAATAATGGTATA
1 ATAATAATAATATA
33300 ATAATAATAATATA
1 ATAATAATAATATA
* *
33314 ATAACAATAA-AAA
1 ATAATAATAATATA
*
33327 ATAATTAATAATGTA
1 ATAA-TAATAATATA
*
33342 ATGAT-AT--TATA
1 ATAATAATAATATA
33353 ATAATAATA
1 ATAATAATA
33362 CTAACATTAC
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
11 7 0.15
12 2 0.04
13 8 0.17
14 27 0.56
15 4 0.08
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.34
Consensus pattern (14 bp):
ATAATAATAATATA
Found at i:35033 original size:13 final size:13
Alignment explanation
Indices: 35017--35061 Score: 63
Period size: 14 Copynumber: 3.3 Consensus size: 13
35007 CCCCCTTTTC
35017 TTTTCCTCTTTCTT
1 TTTTCCT-TTTCTT
*
35031 TTTTCATTTTCTT
1 TTTTCCTTTTCTT
35044 TTTTCCATTTTCTT
1 TTTTCC-TTTTCTT
35058 TTTT
1 TTTT
35062 TCATTTTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 11 0.39
14 17 0.61
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCCTTTTCTT
Found at i:35046 original size:14 final size:14
Alignment explanation
Indices: 35025--35068 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
35015 TCTTTTCCTC
35025 TTTC-TTTTTTCAT
1 TTTCTTTTTTTCAT
*
35038 TTTCTTTTTTCCAT
1 TTTCTTTTTTTCAT
35052 TTTCTTTTTTTCAT
1 TTTCTTTTTTTCAT
35066 TTT
1 TTT
35069 ATCTTCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
13 4 0.14
14 24 0.86
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCTTTTTTTCAT
Found at i:39276 original size:10 final size:11
Alignment explanation
Indices: 39261--39307 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
39251 TTTCAATTCC
39261 TTTATCTT-TT
1 TTTATCTTGTT
39271 TTTATCTTGTT
1 TTTATCTTGTT
*
39282 TTAATCTTGTT
1 TTTATCTTGTT
*
39293 TCTTACCTT-TT
1 T-TTATCTTGTT
39304 TTTA
1 TTTA
39308 GCACCTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 11 0.34
11 16 0.50
12 5 0.16
ACGTcount: A:0.13, C:0.13, G:0.04, T:0.70
Consensus pattern (11 bp):
TTTATCTTGTT
Found at i:39686 original size:18 final size:18
Alignment explanation
Indices: 39635--39697 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
39625 TTTTTCAAAA
*
39635 AAAAAAAGAAGAAAAAGGCC
1 AAAAAAATAA-AAAAA-GCC
*
39655 AAAAAAATAGAAAAAGCC
1 AAAAAAATAAAAAAAGCC
** *
39673 AAAAAGCTAAAAAAAGTC
1 AAAAAAATAAAAAAAGCC
39691 AAAAAAA
1 AAAAAAA
39698 ATTTGAAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
18 22 0.63
19 5 0.14
20 8 0.23
ACGTcount: A:0.73, C:0.10, G:0.13, T:0.05
Consensus pattern (18 bp):
AAAAAAATAAAAAAAGCC
Found at i:43312 original size:7 final size:7
Alignment explanation
Indices: 43302--43340 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
43292 CCTTAAATCC
*
43302 TAAACTA
1 TAAACCA
*
43309 TAAACCT
1 TAAACCA
43316 TAAACCA
1 TAAACCA
43323 TAAACCA
1 TAAACCA
*
43330 TAAACCT
1 TAAACCA
43337 TAAA
1 TAAA
43341 TTATACTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCA
Found at i:43314 original size:21 final size:22
Alignment explanation
Indices: 43290--43341 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
43280 CCTTGCAATG
*
43290 AACCTTAAATCC-TAAACTATA
1 AACCTTAAATCCATAAACCATA
43311 AACCTTAAA-CCATAAACCATA
1 AACCTTAAATCCATAAACCATA
43332 AACCTTAAAT
1 AACCTTAAAT
43342 TATACTTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (22 bp):
AACCTTAAATCCATAAACCATA
Found at i:43412 original size:14 final size:14
Alignment explanation
Indices: 43393--43445 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
43383 GTCTTTGTAA
43393 TAAACCTTAAACCC
1 TAAACCTTAAACCC
* **
43407 TAAACCATAAACTA
1 TAAACCTTAAACCC
* *
43421 TAAACATCAAACCC
1 TAAACCTTAAACCC
*
43435 TAAACCCTAAA
1 TAAACCTTAAA
43446 TCTAATTATG
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:45575 original size:23 final size:23
Alignment explanation
Indices: 45537--45622 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
45527 AAGATTCAAA
* *
45537 CGAGCTTCAATCGAGCTTAAAGT
1 CGAGCTTGAATCGAGCTCAAAGT
* *
45560 CGATCTTGAATCGAGCTCAAATT
1 CGAGCTTGAATCGAGCTCAAAGT
*
45583 CGAGCTTGAATTGAGCTCAAAGT
1 CGAGCTTGAATCGAGCTCAAAGT
* *
45606 CAAGCTTGAATCAAGCT
1 CGAGCTTGAATCGAGCT
45623 TGAATTGAGC
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (23 bp):
CGAGCTTGAATCGAGCTCAAAGT
Found at i:45633 original size:11 final size:11
Alignment explanation
Indices: 45537--45633 Score: 68
Period size: 11 Copynumber: 8.5 Consensus size: 11
45527 AAGATTCAAA
*
45537 CGAGCTTCAAT
1 CGAGCTTGAAT
*
45548 CGAGCTTAAAGT
1 CGAGCTTGAA-T
*
45560 CGATCTTGAAT
1 CGAGCTTGAAT
**
45571 CGAGCTCAAATT
1 CGAGCTTGAA-T
45583 CGAGCTTGAAT
1 CGAGCTTGAAT
* **
45594 TGAGCTCAAAGT
1 CGAGCTTGAA-T
*
45606 CAAGCTTGAAT
1 CGAGCTTGAAT
*
45617 CAAGCTTGAAT
1 CGAGCTTGAAT
*
45628 TGAGCT
1 CGAGCT
45634 CAAAATTGAG
Statistics
Matches: 66, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
11 41 0.62
12 25 0.38
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (11 bp):
CGAGCTTGAAT
Found at i:52902 original size:22 final size:24
Alignment explanation
Indices: 52852--52902 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 24
52842 ACCCAAAATG
*
52852 GTTTTTATTTTAATAAAAATTAAT
1 GTTTTTATTTTAATAAAAATCAAT
*
52876 G--TTTATTTT-ATTAAAA-CAAT
1 GTTTTTATTTTAATAAAAATCAAT
52896 GTTTTTA
1 GTTTTTA
52903 AGTCGACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
20 4 0.17
21 6 0.26
22 12 0.52
24 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (24 bp):
GTTTTTATTTTAATAAAAATCAAT
Found at i:53876 original size:19 final size:19
Alignment explanation
Indices: 53852--53922 Score: 133
Period size: 19 Copynumber: 3.7 Consensus size: 19
53842 AATACACTTG
53852 ATGCATCGATGCACCAGCC
1 ATGCATCGATGCACCAGCC
53871 ATGCATCGATGCACCAGCC
1 ATGCATCGATGCACCAGCC
53890 ATGCATCGATGCACCAGCC
1 ATGCATCGATGCACCAGCC
*
53909 ATGCTTCGATGCAC
1 ATGCATCGATGCAC
53923 TCAGGCTTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.25, C:0.35, G:0.21, T:0.18
Consensus pattern (19 bp):
ATGCATCGATGCACCAGCC
Found at i:61404 original size:45 final size:46
Alignment explanation
Indices: 61292--61413 Score: 183
Period size: 46 Copynumber: 2.7 Consensus size: 46
61282 CAATAAATTG
* * * *
61292 AACATCGAATGCATTTCATGCATCGATGCACTTAGGGTTTTATGAA
1 AACATCGAATGCATTTAATGCATCGATGCACTCAGGCTTTTATCAA
61338 AACATCGAATGCATTTAATGCATCGATGCACTCAGGCTTTT-TCAA
1 AACATCGAATGCATTTAATGCATCGATGCACTCAGGCTTTTATCAA
* *
61383 AACATCTAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTAATGCATCGATGCAC
61414 ACTTAGTGCA
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
45 32 0.46
46 38 0.54
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (46 bp):
AACATCGAATGCATTTAATGCATCGATGCACTCAGGCTTTTATCAA
Found at i:67922 original size:35 final size:35
Alignment explanation
Indices: 67871--68010 Score: 121
Period size: 35 Copynumber: 4.0 Consensus size: 35
67861 TGGGAAACTG
*
67871 TCTCAAGTGAGATGAAATTTTGTTTCAAGAGAAAA
1 TCTCGAGTGAGATGAAATTTTGTTTCAAGAGAAAA
67906 TCTCGAGTGAGATGAAATTTGTTTGTTTCAAGAGAAACAA
1 TCTCGAGTGAGATGAAA--T-TTTGTTTCAAGAG-AA-AA
* * *
67946 TTTC-A---AG-TGAAATTTTATTTCAAGGGAAATTA
1 TCTCGAGTGAGATGAAATTTTGTTTCAAGAGAAA--A
* *
67978 TCTCGAGCGAGAT-AAATTTTGTTTAAAGAGAAA
1 TCTCGAGTGAGATGAAATTTTGTTTCAAGAGAAA
68011 CGATCTTGAG
Statistics
Matches: 85, Mismatches: 8, Indels: 23
0.73 0.07 0.20
Matches are distributed among these distances:
30 1 0.01
31 2 0.02
32 15 0.18
33 2 0.02
35 21 0.25
36 21 0.25
37 2 0.02
38 13 0.15
39 3 0.04
40 5 0.06
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.34
Consensus pattern (35 bp):
TCTCGAGTGAGATGAAATTTTGTTTCAAGAGAAAA
Found at i:68588 original size:16 final size:15
Alignment explanation
Indices: 68573--68601 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
68563 ATGTTGTATG
68573 TGATG-AAAGATGTA
1 TGATGCAAAGATGTA
68587 TGATGCAAAGATGTA
1 TGATGCAAAGATGTA
68602 AATTTATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.41, C:0.03, G:0.28, T:0.28
Consensus pattern (15 bp):
TGATGCAAAGATGTA
Found at i:72633 original size:23 final size:24
Alignment explanation
Indices: 72570--72635 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
72560 CACCACTGCT
* * *
72570 CATATAATTTGCATCGAAGTGCCA
1 CATAGAATATGCACCGAAGTGCCA
*
72594 CGTAGAATATGCACCGAAGTGCCA
1 CATAGAATATGCACCGAAGTGCCA
*
72618 TATAG-ATATGTC-CCGAAG
1 CATAGAATATG-CACCGAAG
72636 GACCGCGTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
23 11 0.31
24 24 0.69
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (24 bp):
CATAGAATATGCACCGAAGTGCCA
Found at i:72646 original size:23 final size:23
Alignment explanation
Indices: 72620--72687 Score: 82
Period size: 24 Copynumber: 2.9 Consensus size: 23
72610 AAGTGCCATA
*
72620 TAGATATGTCCCGAAGGACCGCG
1 TAGATTTGTCCCGAAGGACCGCG
*
72643 TAGAATTTATCCCGAAGGACCGCG
1 TAG-ATTTGTCCCGAAGGACCGCG
* *
72667 TGAAATTTGTCCCGAATGACC
1 T-AGATTTGTCCCGAAGGACC
72688 ACTTAGAACC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
23 3 0.08
24 34 0.89
25 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
TAGATTTGTCCCGAAGGACCGCG
Found at i:72658 original size:24 final size:24
Alignment explanation
Indices: 72628--72687 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
72618 TATAGATATG
72628 TCCCGAAGGACCGCGT-AGAATTTA
1 TCCCGAAGGACCGCGTGA-AATTTA
*
72652 TCCCGAAGGACCGCGTGAAATTTG
1 TCCCGAAGGACCGCGTGAAATTTA
*
72676 TCCCGAATGACC
1 TCCCGAAGGACC
72688 ACTTAGAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 32 0.97
25 1 0.03
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.20
Consensus pattern (24 bp):
TCCCGAAGGACCGCGTGAAATTTA
Found at i:72845 original size:15 final size:15
Alignment explanation
Indices: 72827--72912 Score: 93
Period size: 15 Copynumber: 5.7 Consensus size: 15
72817 CACATAGGGT
72827 ATTTTCACATAGAAC
1 ATTTTCACATAGAAC
* *
72842 ATTTTCACTTAGCAC
1 ATTTTCACATAGAAC
*
72857 ATTCTCACATAGAAC
1 ATTTTCACATAGAAC
*
72872 ATTTTCATATTA-AAC
1 ATTTTCACA-TAGAAC
* * *
72887 ATATTCACATATAAA
1 ATTTTCACATAGAAC
72902 ATTTTCACATA
1 ATTTTCACATA
72913 CCAATAAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
14 2 0.03
15 54 0.93
16 2 0.03
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (15 bp):
ATTTTCACATAGAAC
Found at i:79596 original size:24 final size:23
Alignment explanation
Indices: 79554--79600 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
79544 ATATAATTTA
* *
79554 CACCGAAGTGCCACGTAGAATATG
1 CACCAAAGTGCCACATAG-ATATG
*
79578 CACCAAAGTGCCATATAGATATG
1 CACCAAAGTGCCACATAGATATG
79601 TCCCGAAGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.19
Consensus pattern (23 bp):
CACCAAAGTGCCACATAGATATG
Found at i:79668 original size:25 final size:25
Alignment explanation
Indices: 79600--79669 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
79590 ATATAGATAT
* * *
79600 GTCCCGAAGGAACGCTTAG-AATTT
1 GTCCCGAAGGACCGCATAGAAATTC
* *
79624 GTCTCGAAGGACCACATAGAAATTC
1 GTCCCGAAGGACCGCATAGAAATTC
*
79649 GTCCCGAAGGACCGCGTAGAA
1 GTCCCGAAGGACCGCATAGAA
79670 CCCTCAACTC
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
24 15 0.41
25 22 0.59
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (25 bp):
GTCCCGAAGGACCGCATAGAAATTC
Found at i:79806 original size:15 final size:15
Alignment explanation
Indices: 79788--79851 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
79778 ATAGAGCACA
*
79788 TTCACATATGATATT
1 TTCACATATGACATT
*
79803 TTCACGTA-GAACATT
1 TTCACATATG-ACATT
* **
79818 TTCACTTACCACATT
1 TTCACATATGACATT
79833 TTCACATA-GAACATT
1 TTCACATATG-ACATT
79848 TTCA
1 TTCA
79852 TATTAAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
14 1 0.03
15 39 0.98
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (15 bp):
TTCACATATGACATT
Found at i:79822 original size:30 final size:30
Alignment explanation
Indices: 79800--79886 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
79790 CACATATGAT
* *
79800 ATTTTCACGTAGAACATTTTCACTTACCAC
1 ATTTTCACATAGAACATTTTCACATACCAC
* * *
79830 ATTTTCACATAGAACATTTTCATATTA-AAT
1 ATTTTCACATAGAACATTTTCACA-TACCAC
* * *
79860 ATATTCACATATAATATTTTCACATAC
1 ATTTTCACATAGAACATTTTCACATAC
79887 TAATAAAATG
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 2 0.04
30 42 0.91
31 2 0.04
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (30 bp):
ATTTTCACATAGAACATTTTCACATACCAC
Found at i:79875 original size:15 final size:16
Alignment explanation
Indices: 79857--79891 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
79847 TTTCATATTA
79857 AATATATTCACATA-T
1 AATATATTCACATACT
*
79872 AATATTTTCACATACT
1 AATATATTCACATACT
79888 AATA
1 AATA
79892 AAATGAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATATTCACATACT
Done.