Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004561.1 Hibiscus syriacus cultivar Beakdansim tig00010137_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: 63077
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:415 original size:13 final size:14
Alignment explanation
Indices: 384--416 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
374 TAAGGGAAGT
384 ATTTTCAAAAATTG
1 ATTTTCAAAAATTG
398 A-TTTCAAAAA-TG
1 ATTTTCAAAAATTG
410 ATTTTCA
1 ATTTTCA
417 TAATAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.17
13 14 0.78
14 1 0.06
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (14 bp):
ATTTTCAAAAATTG
Found at i:4400 original size:2 final size:2
Alignment explanation
Indices: 4393--4421 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4383 TTCTGCAATA
4393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4422 CACATCTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5043 original size:46 final size:46
Alignment explanation
Indices: 4993--5521 Score: 614
Period size: 46 Copynumber: 11.6 Consensus size: 46
4983 TTTATGCCAT
* ** * *
4993 TAATGCACCGTTATACATTTTTGTTTATGGCATCCATTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCCGA
* *
5039 TAATGCACCGTTATAC-TTTTCATTTGTGACATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCCGA
** * * * *
5084 TAATGCACCGTTATGCATTTTTGTTTATCGCATACTTTCATGCTGA
1 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCCGA
* **
5130 TAATGCACCGTTATGCA-TTTCATTTGTGGCATCATTTCATGCTTA
1 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCCGA
* * * * *
5175 TAATGCACCATTATGCATTTTTATTTATGTCATCCTTTCATGTCGA
1 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCCGA
* * ** * *
5221 TAATGCATCGTTTTATACTTTCATTTCTGGCATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCCGA
* ** * * **
5267 TAAGGCACTATTATGCATTTTCGTTTGTGGCATCCTTTTATGTTGA
1 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCCGA
* * *
5313 TAATGCACCTTTATGCATTTTCATTTGTGGCATCCTTCCATGCCAA
1 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCCGA
* * *
5359 TAATGCATCGTTATGCATTTTCATTTATGACATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCCGA
* *
5405 TAATGCACCATTATGCATTTTCGTTTGTGGCATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCCGA
* * * *
5451 TAATGCACCGTTATGCATTTT-ATTTCTGGTATCCTTTCTTGCTGA
1 TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCCGA
*
5496 TAATGAACCGTTATGCATTTTCATTT
1 TAATGCACCGTTATGCATTTTCATTT
5522 ATTCATTCAT
Statistics
Matches: 402, Mismatches: 78, Indels: 6
0.83 0.16 0.01
Matches are distributed among these distances:
45 115 0.29
46 287 0.71
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.43
Consensus pattern (46 bp):
TAATGCACCGTTATGCATTTTCATTTGTGGCATCCTTTCATGCCGA
Found at i:6045 original size:18 final size:19
Alignment explanation
Indices: 6003--6050 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
5993 GGAATCCATG
6003 GTATCGATACCTTCTTATTA
1 GTATCGATACC-TCTTATTA
6023 GTATCGATACC-C-TATTCA
1 GTATCGATACCTCTTATT-A
*
6041 GTATCAATAC
1 GTATCGATAC
6051 TAATTGCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 4 0.15
18 11 0.42
20 11 0.42
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (19 bp):
GTATCGATACCTCTTATTA
Found at i:7916 original size:27 final size:27
Alignment explanation
Indices: 7858--7909 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
7848 TAATGGAAAT
* *
7858 AATTAAAATAAATTAAGGACTTAATTA
1 AATTAAAATAAATAAAGGACTCAATTA
7885 AATTAAAATAAA-AAAGGAC-CAATTA
1 AATTAAAATAAATAAAGGACTCAATTA
7910 TAAATTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.22
26 6 0.26
27 12 0.52
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.27
Consensus pattern (27 bp):
AATTAAAATAAATAAAGGACTCAATTA
Found at i:11274 original size:2 final size:2
Alignment explanation
Indices: 11257--11498 Score: 190
Period size: 2 Copynumber: 125.5 Consensus size: 2
11247 TTTGACTGGT
* * *
11257 TA TA AA TA TA TA -A TA TA T- TA CA CTA TA -A TA TA -A CA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* *
11295 TA -A TA AA TA TA TA -A TA TA AA TA T- TA TA TA CTA TA CTA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA -TA
* * * *
11337 TA T- TA TA TG TA TA TA T- TA -A AA AA CTA TA TA TA T- TT TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * * * *
11375 TA TA TA TA GA -A AA CTA TA TA TC TT TA GA -A TA TA TA TA AA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11416 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
11458 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11499 TTGAAACAAA
Statistics
Matches: 198, Mismatches: 21, Indels: 42
0.76 0.08 0.16
Matches are distributed among these distances:
1 15 0.08
2 174 0.88
3 9 0.05
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (2 bp):
TA
Found at i:11317 original size:11 final size:12
Alignment explanation
Indices: 11264--11323 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 12
11254 GGTTATAAAT
11264 ATATAATATATTAC
1 ATATAATATA--AC
11278 ACTATAATATAAC
1 A-TATAATATAAC
*
11291 ATAATAATA-AAT
1 AT-ATAATATAAC
11303 ATATAATATAA-
1 ATATAATATAAC
*
11314 ATATTATATA
1 ATATAATATA
11324 CTATACTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
11 15 0.37
12 7 0.17
13 9 0.22
14 1 0.02
15 9 0.22
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATAATATAAC
Found at i:11546 original size:14 final size:15
Alignment explanation
Indices: 11527--11596 Score: 60
Period size: 14 Copynumber: 4.8 Consensus size: 15
11517 TTTTCAAAAC
11527 ATAATATATAT-TAT
1 ATAATATATATATAT
11541 ATAATATACTATATAT
1 ATAATATA-TATATAT
11557 ATAA-ATATA-ATA-
1 ATAATATATATATAT
*
11569 AGAATACTATATACTAT
1 ATAATA-TATATA-TAT
*
11586 AAAATA-ATATA
1 ATAATATATATA
11597 CAATTCAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
12 3 0.06
13 4 0.09
14 14 0.30
15 12 0.26
16 9 0.19
17 5 0.11
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (15 bp):
ATAATATATATATAT
Found at i:18738 original size:12 final size:11
Alignment explanation
Indices: 18721--18769 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
18711 AAATTTTGGC
*
18721 TTTTTTGGCTT
1 TTTTTTTGCTT
18732 TTTTTTTG---
1 TTTTTTTGCTT
*
18740 TTCTTTTGCTT
1 TTTTTTTGCTT
*
18751 TTTTTTTGCCT
1 TTTTTTTGCTT
18762 TTTTTTTG
1 TTTTTTTG
18770 AAAAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
8 7 0.23
11 24 0.77
ACGTcount: A:0.00, C:0.10, G:0.12, T:0.78
Consensus pattern (11 bp):
TTTTTTTGCTT
Found at i:18765 original size:19 final size:19
Alignment explanation
Indices: 18722--18765 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
18712 AATTTTGGCT
18722 TTTTTGGCTTTTTTTTTG-
1 TTTTTGGCTTTTTTTTTGC
*
18740 TTCTTTTGCTTTTTTTTTGCC
1 TT-TTTGGCTTTTTTTTTG-C
18761 TTTTT
1 TTTTT
18766 TTTGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 2 0.09
19 15 0.68
20 3 0.14
21 2 0.09
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.77
Consensus pattern (19 bp):
TTTTTGGCTTTTTTTTTGC
Found at i:23488 original size:3 final size:3
Alignment explanation
Indices: 23421--23475 Score: 87
Period size: 3 Copynumber: 18.7 Consensus size: 3
23411 TTCATTTAAA
23421 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
23466 T-T TAT TAT TA
1 TAT TAT TAT TA
23476 ATAAATATTA
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 3 0.06
3 45 0.92
4 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:24875 original size:23 final size:20
Alignment explanation
Indices: 24844--24889 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 20
24834 TAAATAATAA
*
24844 TTTATTTTTTATATATATATTAT
1 TTTAATTTTTAT-T-TAT-TTAT
24867 TTTAATTTTTATTTATTTAT
1 TTTAATTTTTATTTATTTAT
24887 TTT
1 TTT
24890 TCAATATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 3 0.14
22 1 0.05
23 11 0.50
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTAATTTTTATTTATTTAT
Found at i:25076 original size:27 final size:27
Alignment explanation
Indices: 25045--25099 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
25035 ATATTTTTAA
25045 ATAAATAAATATTTTATTTATAAATAT
1 ATAAATAAATATTTTATTTATAAATAT
* * *
25072 ATAAATTAATATTTTTTTTATAATTAT
1 ATAAATAAATATTTTATTTATAAATAT
25099 A
1 A
25100 ATTTCGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATAAATAAATATTTTATTTATAAATAT
Found at i:36202 original size:12 final size:12
Alignment explanation
Indices: 36185--36240 Score: 75
Period size: 11 Copynumber: 4.9 Consensus size: 12
36175 CTTGAAGAAA
36185 AAGAAAAAAAAG
1 AAGAAAAAAAAG
36197 AAG-AAAAAAAG
1 AAGAAAAAAAAG
36208 AAGAAAAAAAAG
1 AAGAAAAAAAAG
36220 --GAAAAGAAAA-
1 AAGAAAA-AAAAG
36230 AAGAAAAAAAA
1 AAGAAAAAAAA
36241 AGGGGGGTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
10 5 0.12
11 19 0.47
12 16 0.40
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAG
Found at i:36211 original size:23 final size:25
Alignment explanation
Indices: 36185--36241 Score: 84
Period size: 23 Copynumber: 2.4 Consensus size: 25
36175 CTTGAAGAAA
*
36185 AAGAAAAAAAA-GAAGA-AAAAAAG
1 AAGAAAAAAAAGGAAAAGAAAAAAG
36208 AAGAAAAAAAAGGAAAAGAAAAAAG
1 AAGAAAAAAAAGGAAAAGAAAAAAG
36233 AA-AAAAAAA
1 AAGAAAAAAA
36242 GGGGGGTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
23 11 0.35
24 11 0.35
25 9 0.29
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (25 bp):
AAGAAAAAAAAGGAAAAGAAAAAAG
Found at i:36240 original size:11 final size:11
Alignment explanation
Indices: 36182--36241 Score: 77
Period size: 12 Copynumber: 5.4 Consensus size: 11
36172 ATGCTTGAAG
36182 AAAAAGAAAAA
1 AAAAAGAAAAA
36193 AAAGAAGAAAAA
1 AAA-AAGAAAAA
*
36205 AAGAAG-AAAA
1 AAAAAGAAAAA
*
36215 AAAAGGAAAAGA
1 AAAAAGAAAA-A
36227 AAAAAGAAAAA
1 AAAAAGAAAAA
36238 AAAA
1 AAAA
36242 GGGGGGTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
10 8 0.19
11 14 0.33
12 20 0.48
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:37910 original size:93 final size:93
Alignment explanation
Indices: 37060--37908 Score: 1369
Period size: 93 Copynumber: 9.1 Consensus size: 93
37050 AACAAGTGCC
* *
37060 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATACGAACCCCA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
* * * * *
37125 AAAACCAATCATTGGATCTGAAATATGA
66 AAACCCCATCATTGGATTTGAAAGATAA
37153 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
37218 AAACCCCATCATTGGATTTGAAAGATAA
66 AAACCCCATCATTGGATTTGAAAGATAA
*
37246 ATGTTCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
37311 AAACCCCATCATTGGATTTGAAAGATAA
66 AAACCCCATCATTGGATTTGAAAGATAA
* *
37339 ATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTTGGTATGAACCCCA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
*
37404 AAACCCCATCATTGGATTTGACAGATAA
66 AAACCCCATCATTGGATTTGAAAGATAA
* * *
37432 ATGTGCTCATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATATGGTTTGGTGTGAACCCCA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
37497 AAACCCCATCATTGGATTTGAAAGATAA
66 AAACCCCATCATTGGATTTGAAAGATAA
37525 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
* *
37590 AAACCCTATCATTGGATTTAAAAGATAA
66 AAACCCCATCATTGGATTTGAAAGATAA
37618 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
* *
37683 AAACCCCATCATTGGACTTGAAAGATGA
66 AAACCCCATCATTGGATTTGAAAGATAA
* * * *
37711 GTGTGCTCATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTTGGTATCAAACCAC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-GAACCCC
* * * *
37776 AGAA-CCAATCATTGGATTTGAAATATGA
65 AAAACCCCATCATTGGATTTGAAAGATAA
* *
37804 ATGTGCTCATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCAC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATG-AACCCC
* * * *
37869 ATAA-CCAATCATTGAATTTGAAAGATGA
65 AAAACCCCATCATTGGATTTGAAAGATAA
*
37897 ATGTGATCATAG
1 ATGTGCTCATAG
37909 TAGAAATAAG
Statistics
Matches: 712, Mismatches: 42, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
93 704 0.99
94 8 0.01
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (93 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
AAACCCCATCATTGGATTTGAAAGATAA
Found at i:38882 original size:113 final size:113
Alignment explanation
Indices: 38684--39132 Score: 677
Period size: 113 Copynumber: 4.0 Consensus size: 113
38674 TAGCAAAGAT
*
38684 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
* *
38749 AGAAGGAAGAATAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
38797 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
* *
38862 AGAAGGAAGAATAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *
38910 TCAAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTAATATGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
* * *
38975 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGT
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * **** * *
39023 TCAAATTCATCACTTGATGGATCA-ATATTTCCAGAGAAAGTTCATAATAAGAAGAACTTATCTG
1 TCAAATCCATCACTTGATGGATCAGCT-TTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTG
* * *
39087 AAG-AGGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTT
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTT
39133 ACATAATTCT
Statistics
Matches: 314, Mismatches: 21, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
112 41 0.13
113 273 0.87
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:39235 original size:105 final size:103
Alignment explanation
Indices: 39110--39316 Score: 258
Period size: 105 Copynumber: 2.0 Consensus size: 103
39100 AGTTCACAAT
* * * *
39110 GAGAAGAGCTTGTTCAACCTTTT-ACAT-AATTCTATCACAGAAGCAAATAGATTAGCATCAACC
1 GAGAAAAGCTTATTCAACCTTTTGA-ATGAATT-TATCACAGAAGCAAATAGATCAACATCAACC
39173 TTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTAAAGAG
64 ---CCAGTAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAG
* * * *
39215 GAGAAAAGCTTATTCAACCTTTTGAATGACTTTATCACAGAAGGAAATAGGTCAACATCATCCCC
1 GAGAAAAGCTTATTCAACCTTTTGAATGAATTTATCACAGAAGCAAATAGATCAACATCAACCCC
* *
39280 AGTGGAAAGTTTATAATGAGAAGAACTCATCTAAAGA
66 AGTAGAAAGTTCATAATGAGAAGAACTCATCTAAAGA
39317 AAGAGAAGAA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
102 4 0.04
103 32 0.36
105 49 0.55
106 4 0.04
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (103 bp):
GAGAAAAGCTTATTCAACCTTTTGAATGAATTTATCACAGAAGCAAATAGATCAACATCAACCCC
AGTAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAG
Found at i:39531 original size:3 final size:3
Alignment explanation
Indices: 39461--39518 Score: 93
Period size: 3 Copynumber: 19.7 Consensus size: 3
39451 TTCATTTAAA
39461 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39506 TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TA
39519 ATAAATATTA
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 3 0.06
3 48 0.92
4 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41145 original size:26 final size:27
Alignment explanation
Indices: 41092--41145 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
41082 ATATTTTTAA
41092 ATAAATAAATATTTTATTTATAAATAT
1 ATAAATAAATATTTTATTTATAAATAT
* *
41119 ATAAATTAATATTTT-TTTATAATTAT
1 ATAAATAAATATTTTATTTATAAATAT
41145 A
1 A
41146 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
ATAAATAAATATTTTATTTATAAATAT
Found at i:53900 original size:24 final size:24
Alignment explanation
Indices: 53867--53921 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
53857 TGACGGTTGG
*
53867 ATATAGAAGCTTGTGCTTTTTCAGC
1 ATAT-GAAGCTTGTGCTTTTGCAGC
53892 ATATGAAGCTTGTGCTTTTGCAGC
1 ATATGAAGCTTGTGCTTTTGCAGC
*
53916 AGATGA
1 ATATGA
53922 GTCCCCTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (24 bp):
ATATGAAGCTTGTGCTTTTGCAGC
Found at i:54458 original size:81 final size:78
Alignment explanation
Indices: 54333--54485 Score: 184
Period size: 81 Copynumber: 1.9 Consensus size: 78
54323 AAATAAAATA
* * *
54333 TTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTGAATTATAATC-TTTAATGT
1 TTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTACAATCTTTTAATGA
54397 TTATTTAAAAAAC
66 TTATTTAAAAAAC
* * * *
54410 TTATTTAATT-ATTCCGAATTATATATACCAATTAAAAGAGTTGTAATCTAAATTACATTCTTTT
1 TTATTTAATTAATT-C-AATTAAATATA-C-ATT-AAAGACTTATAATCTAAATTACAATCTTTT
54474 AATGATTATTTA
61 AATGATTATTTA
54486 CTATATTCGG
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
76 3 0.05
77 11 0.17
78 10 0.16
79 1 0.02
80 3 0.05
81 21 0.33
82 14 0.22
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.45
Consensus pattern (78 bp):
TTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTACAATCTTTTAATGA
TTATTTAAAAAAC
Found at i:59552 original size:21 final size:20
Alignment explanation
Indices: 59528--59581 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
59518 ATTGTATACC
59528 ATATATTATATTTTTCAAAA
1 ATATATTATATTTTTCAAAA
*
59548 A-ATATGATATGTTTTCAAAA
1 ATATATTATAT-TTTTCAAAA
*
59568 TTATATTATTATTT
1 ATATATTA-TATTT
59582 ATGTTTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 8 0.29
20 10 0.36
21 7 0.25
22 3 0.11
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (20 bp):
ATATATTATATTTTTCAAAA
Found at i:59657 original size:16 final size:18
Alignment explanation
Indices: 59612--59671 Score: 79
Period size: 16 Copynumber: 3.4 Consensus size: 18
59602 CAAAGCCATA
*
59612 TATATATGTTTTCAAAAC
1 TATATATATTTTCAAAAC
59630 TATATAATATTTTCAAAA-
1 TATAT-ATATTTTCAAAAC
59648 T-TATATATTTTCAAAAC
1 TATATATATTTTCAAAAC
*
59665 CATATAT
1 TATATAT
59672 TGTATACATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
16 12 0.32
17 3 0.08
18 11 0.30
19 11 0.30
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
TATATATATTTTCAAAAC
Done.