Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006095.1 Hibiscus syriacus cultivar Beakdansim tig00014448_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: 61096
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2511 original size:22 final size:20
Alignment explanation
Indices: 2492--2537 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
2482 ACCAGTATAG
2492 ATACCCGAGCACCAGAGTATCA
1 ATACCC-AGC-CCAGAGTATCA
*
2514 ATACCCAGCCTAGAGTATCA
1 ATACCCAGCCCAGAGTATCA
2534 ATAC
1 ATAC
2538 TACTTTACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.61
21 3 0.13
22 6 0.26
ACGTcount: A:0.37, C:0.30, G:0.15, T:0.17
Consensus pattern (20 bp):
ATACCCAGCCCAGAGTATCA
Found at i:2597 original size:20 final size:21
Alignment explanation
Indices: 2572--2618 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
2562 ATTCAGTGGT
*
2572 TCGATACCAA-TAGGTGGGTA
1 TCGATACCAACCAGGTGGGTA
2592 TCGATA-CAACCAGGTGGGTA
1 TCGATACCAACCAGGTGGGTA
2612 TCGATAC
1 TCGATAC
2619 TAAAGGGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (21 bp):
TCGATACCAACCAGGTGGGTA
Found at i:4030 original size:31 final size:31
Alignment explanation
Indices: 3994--4053 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3984 AACTTAAAAG
* * *
3994 AGTTTTGCAATATTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
4025 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
4054 CAAACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:4272 original size:15 final size:14
Alignment explanation
Indices: 4247--4285 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
4237 ATATATTCAT
4247 AATATTTTTTATAA
1 AATATTTTTTATAA
* *
4261 TATATATTTTTAGAA
1 AATAT-TTTTTATAA
4276 AATATTTTTT
1 AATATTTTTT
4286 TATTTTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
AATATTTTTTATAA
Found at i:4291 original size:21 final size:20
Alignment explanation
Indices: 4265--4313 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
4255 TTATAATATA
*
4265 TATTTTTAGAAAATATTTTTT
1 TATTTTTA-AAAATATTTTAT
*
4286 TATTTTATAAAATTATTTTAT
1 TATTTT-TAAAAATATTTTAT
*
4307 GATTTTT
1 TATTTTT
4314 TTATTTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 21 0.88
22 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (20 bp):
TATTTTTAAAAATATTTTAT
Found at i:4556 original size:16 final size:17
Alignment explanation
Indices: 4537--4582 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 17
4527 ATTTTAATAA
*
4537 TATATAAAATAATTAT-
1 TATATAAAATAAATATC
4553 TATATAAAATTAAATATC
1 TATATAAAA-TAAATATC
4571 TATAATAAAATA
1 TAT-ATAAAATA
4583 TTAAAACTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 9 0.35
17 6 0.23
18 5 0.19
19 6 0.23
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
TATATAAAATAAATATC
Found at i:4557 original size:18 final size:19
Alignment explanation
Indices: 4505--4586 Score: 59
Period size: 18 Copynumber: 4.6 Consensus size: 19
4495 AACTTAAATC
* *
4505 AAAATAATTAAATAAATAT
1 AAAATAATTAATTATATAT
* *
4524 AAAAT-TTTAATAATATAT
1 AAAATAATTAATTATATAT
4542 AAAATAATT-ATTATATA-
1 AAAATAATTAATTATATAT
* *
4559 AAATTAAAT-ATCTATA-AT
1 AAAATAATTAAT-TATATAT
4577 AAAAT-ATTAA
1 AAAATAATTAA
4587 AACTAATATT
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
17 12 0.24
18 30 0.61
19 7 0.14
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATAATTAATTATATAT
Found at i:4585 original size:21 final size:21
Alignment explanation
Indices: 4506--4587 Score: 61
Period size: 21 Copynumber: 4.1 Consensus size: 21
4496 ACTTAAATCA
4506 AAATAATTA-AAT-AAATA-T
1 AAATAATTATAATAAAATATT
* * *
4524 -AA-AATTTTAATAATATATA
1 AAATAATTATAATAAAATATT
*
4543 AAATAATTATTATATAAA-ATT
1 AAATAATTATAATA-AAATATT
4564 AAAT-ATCTATAATAAAATATT
1 AAATAAT-TATAATAAAATATT
4585 AAA
1 AAA
4588 ACTAATATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
16 4 0.08
17 5 0.10
18 4 0.08
20 7 0.15
21 26 0.54
22 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATAATTATAATAAAATATT
Found at i:4618 original size:23 final size:23
Alignment explanation
Indices: 4585--4667 Score: 94
Period size: 23 Copynumber: 3.5 Consensus size: 23
4575 ATAAAATATT
*
4585 AAAACTAATATTTAATTTATTTA
1 AAAATTAATATTTAATTTATTTA
* * * *
4608 AAATTTAATATCTATATAATATTAA
1 AAAATTAATATTTA-AT-TTATTTA
4633 AAAATTAATATTTAATTTATTTA
1 AAAATTAATATTTAATTTATTTA
*
4656 AAAAATAATATT
1 AAAATTAATATT
4668 AAAATTAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
23 27 0.56
24 4 0.08
25 17 0.35
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
AAAATTAATATTTAATTTATTTA
Found at i:4654 original size:48 final size:48
Alignment explanation
Indices: 4552--4658 Score: 146
Period size: 48 Copynumber: 2.2 Consensus size: 48
4542 AAAATAATTA
*
4552 TTATATAAAATTAAATATCTATAATAAAATATTAAAACTAATATTTAAT
1 TTATTTAAAATTAAATATCTATAAT-AAATATTAAAACTAATATTTAAT
* *
4601 TTATTTAAAATTTAATATCTAT-AT-AATATTAAAAAATTAATATTTAAT
1 TTATTTAAAATTAAATATCTATAATAAATATT--AAAACTAATATTTAAT
4649 TTATTTAAAA
1 TTATTTAAAA
4659 AATAATATTA
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
46 6 0.11
48 27 0.51
49 20 0.38
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (48 bp):
TTATTTAAAATTAAATATCTATAATAAATATTAAAACTAATATTTAAT
Found at i:5669 original size:43 final size:42
Alignment explanation
Indices: 5616--5737 Score: 192
Period size: 43 Copynumber: 2.9 Consensus size: 42
5606 AATCTTTCAG
* *
5616 GAATTAGAATCCAATTCATATTCTGTTTGGTTGGCAGGAAATT
1 GAATTGGAATCCAATTCATATTCTGTTTGGTTCGCAGG-AATT
*
5659 GAATTGGAATCCAATTC-CATTCTGTTTGGTTCGCAGGAATT
1 GAATTGGAATCCAATTCATATTCTGTTTGGTTCGCAGGAATT
5700 GAATTGGAATCCAATTCCATATTCTGTTTGGTTCGCAG
1 GAATTGGAATCCAATT-CATATTCTGTTTGGTTCGCAG
5738 ACATGTCAGA
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
41 20 0.27
42 19 0.26
43 34 0.47
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (42 bp):
GAATTGGAATCCAATTCATATTCTGTTTGGTTCGCAGGAATT
Found at i:6541 original size:254 final size:252
Alignment explanation
Indices: 6074--6598 Score: 711
Period size: 254 Copynumber: 2.0 Consensus size: 252
6064 CCCGATCCGA
* * * * *
6074 AATATAAAAAATTATTTTTATTCAATAAAACAGTGACTTAATTGGAAAAAATATATAGAGGGGTA
1 AATAAAAAAAACTATTTTTATTCAATAAAACAATGACTTAATTGAAAAAAATATATAGAAGGGTA
*
6139 TTATTGCAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTTGGGTAGGGTCGGGTCAGG
66 TTATTGCAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTCGGGT---GT--GG--AGG
* * *
6204 TATTTTTCACCCTAAACCTGAACCGACCTGACCCGAATATCACACTGAAAAAAACTGACCTGACC
124 TATTTTTCACCCTAAACCCGAACCGACCCGACCCGAATATCACACTGAAAAAAACTGACCCGACC
* * *
6269 GACCAAAATAAAGTTTCACCCGACCTGACCCGAATATATGAATTAGAAATCC-A-ACCCGAAAT
189 AACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACACCCGAAAT
6331 AATAAAAAAAACTATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAAAATTATATATAGAA
1 AATAAAAAAAACTATTTTTATTCAAT-AAAACAATGACTTAATTG--AAAAAA--ATATATAGAA
*
6396 GGGTATTATTG-TATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGT-T-G-GGT
61 GGGTATTATTGCAATTATTCCTAAATATATAAGGTAAAATTATATAT-TTTTCGGGTGTGGAGGT
* *
6457 ATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAATTGACCCGACC
125 ATTTTTCACCCTAAACCCGAAC-CGACCCGACCCGAATATCACACTGAAAAAAACTGACCCGA-C
6522 CAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAGCCGACCCGA
188 CAACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGA--C-ACCCGA
6587 AAT
250 AAT
6590 AATAAAAAA
1 AATAAAAAA
6599 TATTTTTTAT
Statistics
Matches: 240, Mismatches: 15, Indels: 24
0.86 0.05 0.09
Matches are distributed among these distances:
252 24 0.10
253 36 0.15
254 51 0.21
255 2 0.01
257 24 0.10
258 18 0.08
259 18 0.08
260 5 0.02
261 34 0.14
262 28 0.12
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.27
Consensus pattern (252 bp):
AATAAAAAAAACTATTTTTATTCAATAAAACAATGACTTAATTGAAAAAAATATATAGAAGGGTA
TTATTGCAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTCGGGTGTGGAGGTATTTTT
CACCCTAAACCCGAACCGACCCGACCCGAATATCACACTGAAAAAAACTGACCCGACCAACCAAA
ATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACACCCGAAAT
Found at i:10196 original size:12 final size:12
Alignment explanation
Indices: 10179--10203 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10169 TATAAATTTC
10179 AAAATCATTTTT
1 AAAATCATTTTT
10191 AAAATCATTTTT
1 AAAATCATTTTT
10203 A
1 A
10204 CCTATAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (12 bp):
AAAATCATTTTT
Found at i:13150 original size:11 final size:11
Alignment explanation
Indices: 13129--13162 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
13119 CAATCATGTT
13129 ACCATATATAA
1 ACCATATATAA
13140 A-CATGATATAA
1 ACCAT-ATATAA
13151 ACCATATATAA
1 ACCATATATAA
13162 A
1 A
13163 ATTTCTTACC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 3 0.14
11 15 0.71
12 3 0.14
ACGTcount: A:0.56, C:0.15, G:0.03, T:0.26
Consensus pattern (11 bp):
ACCATATATAA
Found at i:15050 original size:3 final size:3
Alignment explanation
Indices: 15042--15069 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
15032 AACAAAGAGT
15042 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
15070 GAATAACAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:16228 original size:23 final size:21
Alignment explanation
Indices: 16198--16253 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 21
16188 GTCAAATTTG
*
16198 ATTTTAATGTTTTTATTTTACAA
1 ATTTTAATGTTTTTATCTT--AA
*
16221 ATTTTAATTTTTTTATCTTAA
1 ATTTTAATGTTTTTATCTTAA
*
16242 ATTTAAATGTTT
1 ATTTTAATGTTT
16254 ATGCTTGTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 12 0.41
23 17 0.59
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (21 bp):
ATTTTAATGTTTTTATCTTAA
Found at i:16871 original size:20 final size:20
Alignment explanation
Indices: 16846--16887 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
16836 AGAAGTACTG
16846 TATTATTCTTACAGTATCGA
1 TATTATTCTTACAGTATCGA
**
16866 TATTATTCTTGTAGTATCGA
1 TATTATTCTTACAGTATCGA
16886 TA
1 TA
16888 CCCAAGGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (20 bp):
TATTATTCTTACAGTATCGA
Found at i:19587 original size:26 final size:26
Alignment explanation
Indices: 19558--19609 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
19548 GAAGGAAAAA
19558 AAATTCAAATTACATATATAATTCCT
1 AAATTCAAATTACATATATAATTCCT
19584 AAATTCAAATTACATATATAATTCCT
1 AAATTCAAATTACATATATAATTCCT
19610 GGGAGTTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (26 bp):
AAATTCAAATTACATATATAATTCCT
Found at i:24818 original size:28 final size:28
Alignment explanation
Indices: 24763--24818 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
24753 TTGCAAACTC
* *
24763 ACCCAAATCAAAGCCTCATTTTTTCTAA
1 ACCCAAATCAAAGCCTCATTTCTCCTAA
* * *
24791 ACCCAAATCCAAGCTTCCTTTCTCCTAA
1 ACCCAAATCAAAGCCTCATTTCTCCTAA
24819 TAACTAGTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.32, C:0.34, G:0.04, T:0.30
Consensus pattern (28 bp):
ACCCAAATCAAAGCCTCATTTCTCCTAA
Found at i:25573 original size:3 final size:3
Alignment explanation
Indices: 25567--25601 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
25557 TATTTATTTG
*
25567 TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
25602 TTATAAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:29163 original size:2 final size:2
Alignment explanation
Indices: 29156--29183 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29146 TTATTGCAAG
29156 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29184 ATGAATCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34249 original size:21 final size:22
Alignment explanation
Indices: 34223--34263 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
34213 TAAAATACTT
*
34223 AAAATATAA-AAAAATAAATAC
1 AAAATATAATAAAAACAAATAC
34244 AAAATATAATAAAAACAAAT
1 AAAATATAATAAAAACAAAT
34264 CATTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.20
Consensus pattern (22 bp):
AAAATATAATAAAAACAAATAC
Found at i:34284 original size:21 final size:20
Alignment explanation
Indices: 34260--34301 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
34250 TAATAAAAAC
*
34260 AAATCATTTAAAAATAATATT
1 AAAT-ATTTAAAAAAAATATT
*
34281 AAATTTTTAAAAAAAATATT
1 AAATATTTAAAAAAAATATT
34301 A
1 A
34302 GAAGCTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATTTAAAAAAAATATT
Found at i:35065 original size:30 final size:31
Alignment explanation
Indices: 35031--35096 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 31
35021 AATAAATAAG
*
35031 CCTTTAAACTTTC-TATAAA-AATTAGTTAAA-
1 CCTTTAAA-TTTCATA-AAACAATCAGTTAAAT
35061 CCTTT-AATTTCATAAAACAATCAGTTAAAT
1 CCTTTAAATTTCATAAAACAATCAGTTAAAT
35091 CCTTTA
1 CCTTTA
35097 TCGCGTCTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
28 7 0.23
29 14 0.45
30 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (31 bp):
CCTTTAAATTTCATAAAACAATCAGTTAAAT
Found at i:40344 original size:253 final size:253
Alignment explanation
Indices: 39896--40396 Score: 957
Period size: 253 Copynumber: 2.0 Consensus size: 253
39886 AGAACAGATA
* *
39896 ATGGAAGAGAATACACAAGCGAAGAATTTGATGACTTTTTCAGAAAAGAAGGCATCAAAAGACAG
1 ATGGAAGAGAATACACAAGCGAAAAATTTGATGACTTTTGCAGAAAAGAAGGCATCAAAAGACAG
39961 TTCACAGTGGCAAACACTCCTCAACAAAATGGAGTGGCAGAGTGGATGAACAGAACCTTGTTAGA
66 TTCACAGTGGCAAACACTCCTCAACAAAATGGAGTGGCAGAGTGGATGAACAGAACCTTGTTAGA
*
40026 AAGAACAAGAGCAATGTTGATGGATGCAGGCCTAGAAAAATCATTCTGGGCAGAAGCAGTCAATA
131 AAGAACAAGAGCAATGTTGAGGGATGCAGGCCTAGAAAAATCATTCTGGGCAGAAGCAGTCAATA
40091 CCGCCTCTTATTTGGTGAATCGAGCTCCATCAACTGCAATAGAGCTGAAGACAATTTG
196 CCGCCTCTTATTTGGTGAATCGAGCTCCATCAACTGCAATAGAGCTGAAGACAATTTG
* *
40149 ATGGAAGAGAATACACAAGCGAAAAATTTGATGACTTTTGCAGGAAAGAAGGCATCAAAAGATAG
1 ATGGAAGAGAATACACAAGCGAAAAATTTGATGACTTTTGCAGAAAAGAAGGCATCAAAAGACAG
40214 TTCACAGTGGCAAACACTCCTCAACAAAATGGAGTGGCAGAGTGGATGAACAGAACCTTGTTAGA
66 TTCACAGTGGCAAACACTCCTCAACAAAATGGAGTGGCAGAGTGGATGAACAGAACCTTGTTAGA
40279 AAGAACAAGAGCAATGTTGAGGGATGCAGGCCTAGAAAAATCATTCTGGGCAGAAGCAGTCAATA
131 AAGAACAAGAGCAATGTTGAGGGATGCAGGCCTAGAAAAATCATTCTGGGCAGAAGCAGTCAATA
40344 CCGCCTCTTATTTGGTGAATCGAGCTCCATCAACTGCAATAGAGCTGAAGACA
196 CCGCCTCTTATTTGGTGAATCGAGCTCCATCAACTGCAATAGAGCTGAAGACA
40397 CCAATGGAGA
Statistics
Matches: 243, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
253 243 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (253 bp):
ATGGAAGAGAATACACAAGCGAAAAATTTGATGACTTTTGCAGAAAAGAAGGCATCAAAAGACAG
TTCACAGTGGCAAACACTCCTCAACAAAATGGAGTGGCAGAGTGGATGAACAGAACCTTGTTAGA
AAGAACAAGAGCAATGTTGAGGGATGCAGGCCTAGAAAAATCATTCTGGGCAGAAGCAGTCAATA
CCGCCTCTTATTTGGTGAATCGAGCTCCATCAACTGCAATAGAGCTGAAGACAATTTG
Found at i:46914 original size:24 final size:24
Alignment explanation
Indices: 46868--46914 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
46858 TTATCCAGAA
**
46868 GATGTATAAAACATATATGTACAT
1 GATGTATAAAACATATACATACAT
*
46892 GATGTATAAAACATCTACATACA
1 GATGTATAAAACATATACATACA
46915 ATGTCATGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.30
Consensus pattern (24 bp):
GATGTATAAAACATATACATACAT
Found at i:51031 original size:16 final size:16
Alignment explanation
Indices: 51012--51043 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
51002 TGAAATACTT
51012 AGTTCATCAAATCCTC
1 AGTTCATCAAATCCTC
51028 AGTTCATCAAATCCTC
1 AGTTCATCAAATCCTC
51044 GATCTAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.31
Consensus pattern (16 bp):
AGTTCATCAAATCCTC
Found at i:53774 original size:24 final size:25
Alignment explanation
Indices: 53741--53790 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
53731 AGTCTTCCAG
* *
53741 ATGATGTATA-AAACATCTATGTAC
1 ATGATCTATAGAAACATCTATATAC
53765 ATGATCTATAGAAACATCTATATAC
1 ATGATCTATAGAAACATCTATATAC
53790 A
1 A
53791 ATGTCATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (25 bp):
ATGATCTATAGAAACATCTATATAC
Found at i:54396 original size:30 final size:30
Alignment explanation
Indices: 54327--54394 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
54317 CAACCATTCT
*
54327 CAAATTTTCCAAAATTATCAAATTGGTCCCC
1 CAAATTTTCAAAAATTATCAAATTGGT-CCC
* *
54358 CAACTTTTCAAAAATTAT-ATAA-TGGTCTC
1 CAAATTTTCAAAAATTATCA-AATTGGTCCC
54387 CAAATTTT
1 CAAATTTT
54395 TCTAAGGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 9 0.28
30 5 0.16
31 18 0.56
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.37
Consensus pattern (30 bp):
CAAATTTTCAAAAATTATCAAATTGGTCCC
Found at i:57649 original size:21 final size:19
Alignment explanation
Indices: 57615--57660 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 19
57605 TTGAAGAATT
57615 ATGATGAATAGTATCGATA
1 ATGATGAATAGTATCGATA
57634 ATGATGCAATTAGTATCGATA
1 ATGATG-AA-TAGTATCGATA
*
57655 CTGATG
1 ATGATG
57661 TAGGTATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 16 0.67
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.33
Consensus pattern (19 bp):
ATGATGAATAGTATCGATA
Found at i:58459 original size:46 final size:46
Alignment explanation
Indices: 58341--58923 Score: 829
Period size: 46 Copynumber: 12.7 Consensus size: 46
58331 AAATGCGTTT
*
58341 GGCATGAAAGGATGCCATAAATGAAAATGCATAATGGTGCATT-TA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* * * *
58386 GTCATGAAAGGATGCCTTAAATGAAAATGCATAACGATGCATTATT
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* *
58432 GGGATGAAAGGATGCCATAAAAT-AAAATTCATAACGGTGCATTATA
1 GGCATGAAAGGATGCCAT-AAATGAAAATGCATAACGGTGCATTATA
*
58478 GGCATGAAAGGTTGCCATAAAATGAAAATGCATAACGGTGCATTATA
1 GGCATGAAAGGATGCCAT-AAATGAAAATGCATAACGGTGCATTATA
**
58525 GGCATGAAAGGATGCCATAAATGAAAATGCATAACAATGCATTATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* * *
58571 GGCATGAAAGGATGCCAT-AA--AAAATGCATAACGATGTATTATT
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
58614 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* * *
58660 GGCGTGAAAGGATGCCATAAATGAAAATGCGTAATGGTGCATTATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
58706 GGCATGAAAGGATGCCATAAA-GAAAAATGCATAACGGTGCATTATA
1 GGCATGAAAGGATGCCATAAATG-AAAATGCATAACGGTGCATTATA
* *
58752 GGAATGAAAGGATGCCATAAATGAAAATGCATAACTGTGCATTATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* *
58798 GGCATGAAAGGATGCCATAAAT-AAAATGCATAACAGTACATTATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* * ** * *
58843 GGCACGAAAGGATGCCATAAATGAAAATGCTTAACAATGCATAATT
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
* *
58889 GGCATGAAAGGATGCCACCAAATGAAAATACATAA
1 GGCATGAAAGGATGCCA-TAAATGAAAATGCATAA
58924 TGGTATTAAC
Statistics
Matches: 484, Mismatches: 44, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
43 38 0.08
44 2 0.00
45 84 0.17
46 302 0.62
47 58 0.12
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.23
Consensus pattern (46 bp):
GGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATA
Found at i:60336 original size:26 final size:26
Alignment explanation
Indices: 60300--60371 Score: 144
Period size: 26 Copynumber: 2.8 Consensus size: 26
60290 TGTTATTACA
60300 CATAAGGTCGTGCCCACCATAATACG
1 CATAAGGTCGTGCCCACCATAATACG
60326 CATAAGGTCGTGCCCACCATAATACG
1 CATAAGGTCGTGCCCACCATAATACG
60352 CATAAGGTCGTGCCCACCAT
1 CATAAGGTCGTGCCCACCAT
60372 GCACTAAGTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.19
Consensus pattern (26 bp):
CATAAGGTCGTGCCCACCATAATACG
Done.