Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008135.1 Hibiscus syriacus cultivar Beakdansim tig00110690_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: 79128
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2983 original size:20 final size:20
Alignment explanation
Indices: 2950--2989 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2940 ATTGTTCATG
*
2950 TTTGAACTTTAATCAAGTTA
1 TTTGAACTTCAATCAAGTTA
* *
2970 TTTGAGCTTCAATCGAGTTA
1 TTTGAACTTCAATCAAGTTA
2990 AATTTGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (20 bp):
TTTGAACTTCAATCAAGTTA
Found at i:5517 original size:23 final size:23
Alignment explanation
Indices: 5471--5518 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5461 GAACATGTGC
*
5471 ATGAACACGTTCGCGAACATTAA
1 ATGAACACGTTCGCGAACAATAA
* * *
5494 ATGAACATGTTCGTGAATAATAA
1 ATGAACACGTTCGCGAACAATAA
5517 AT
1 AT
5519 AACGAACACG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (23 bp):
ATGAACACGTTCGCGAACAATAA
Found at i:14283 original size:84 final size:84
Alignment explanation
Indices: 13796--14365 Score: 404
Period size: 84 Copynumber: 6.8 Consensus size: 84
13786 TACTTTGGCC
* * * * *
13796 TCTTCAACAG-C-T-TTCTTAGTTTCTTCT-GCAATCCTCTTTTGCTCCTCTGCCTTAGCCAT-T
1 TCTTCAACAGCCTTCTTCTTAGTTTCTT-TAGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCT
* **
13856 GC-AAGCTCAGCTTGTTTT-CT
65 -CTAA-ATCAGCACGTTTTCCT
* * ** * * * *
13876 TACTTCAACAGCCTTCTTCAT-GTTTTCTTCAGCAATCTTAGTTTGCTCCGCTGCTTCAGCCATC
1 T-CTTCAACAGCCTTCTTCTTAG-TTTCTTTAGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATC
* *
13940 TCTAAATCAGCATGTTTTCTT
64 TCTAAATCAGCACGTTTTCCT
* * *
13961 TCTTCAACGGCCTTCTTCTTAGTTTCTTTAGC-ACCCTCCTCTGCTTCTCTGCTTTAGCCATCTC
1 TCTTCAACAGCCTTCTTCTTAGTTTCTTTAGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCTC
* * *
14025 TGAATCGGCAC-ATTTCCTT
66 TAAATCAGCACGTTTTCC-T
* * * * *
14044 TCATCAACAGCCTTTTTCTTAGTTTCTTCT-GCAATCTTCCTTTGCTCCTCTGCCTTAGCCATCT
1 TCTTCAACAGCCTTCTTCTTAGTTTCTT-TAGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCT
**
14108 C-AAACTCAGCTTGTTTT-CT
65 CTAAA-TCAGCACGTTTTCCT
* * * * * * *
14127 TACTTCAAAAGCATTTTTCAT-GTTTTCTTCAGCAATCTTCCTTTG-TTCTGCTGCTTCAGCCAT
1 T-CTTCAACAGCCTTCTTCTTAG-TTTCTTTAGCAATCTTCCTCTGCTTCT-CTGCTTTAGCCAT
14190 CTCTAAATCAGCACGTTTTCCT
63 CTCTAAATCAGCACGTTTTCCT
* * * *
14212 TCTTCAGCAGCCTTCTTCTTAGTTTCTTTAGCAACCTTCCTCTGTTTCTCCGCTTTAGCCATCTC
1 TCTTCAACAGCCTTCTTCTTAGTTTCTTTAGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCTC
** * *
14277 CGAATCAACACATTTT-CT
66 TAAATCAGCACGTTTTCCT
* * ** *
14295 ATCGTCAACAGCCTGT-TTCTTAGTTT-TTTCTGCAATCTTCCTCAAC-TCCCTTGCTTTAGCCA
1 -TCTTCAACAGCCT-TCTTCTTAGTTTCTTT-AGCAATCTTCCTCTGCTTCTC-TGCTTTAGCCA
*
14357 TTTCTAAAT
62 TCTCTAAAT
14366 TGACAAGTTT
Statistics
Matches: 387, Mismatches: 76, Indels: 50
0.75 0.15 0.10
Matches are distributed among these distances:
80 1 0.00
81 9 0.02
82 5 0.01
83 78 0.20
84 273 0.71
85 21 0.05
ACGTcount: A:0.17, C:0.30, G:0.11, T:0.42
Consensus pattern (84 bp):
TCTTCAACAGCCTTCTTCTTAGTTTCTTTAGCAATCTTCCTCTGCTTCTCTGCTTTAGCCATCTC
TAAATCAGCACGTTTTCCT
Found at i:16121 original size:38 final size:39
Alignment explanation
Indices: 16070--16146 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 39
16060 GATATGGCAA
16070 TGACATAAAATTAGTAAGCTG-TTTTTTATATAACCATC
1 TGACATAAAATTAGTAAGCTGTTTTTTTATATAACCATC
* *
16108 TGACATTAAATTAGTAAGTTGTTTTTTTTATATAACCAT
1 TGACATAAAATTAGTAAGCTG-TTTTTTTATATAACCAT
16147 GAAGTCAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 19 0.54
40 16 0.46
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.44
Consensus pattern (39 bp):
TGACATAAAATTAGTAAGCTGTTTTTTTATATAACCATC
Found at i:20630 original size:19 final size:20
Alignment explanation
Indices: 20608--20651 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
20598 TTTTTTTAGT
*
20608 AAATTTAAATATAA-TTTAA
1 AAATATAAATATAATTTTAA
**
20627 AAATATATTTATAATTTTAA
1 AAATATAAATATAATTTTAA
20647 AAATA
1 AAATA
20652 AATTTATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATATAAATATAATTTTAA
Found at i:20647 original size:20 final size:19
Alignment explanation
Indices: 20617--20658 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
20607 TAAATTTAAA
*
20617 TATAATTTAAAAATATATT
1 TATAATTTAAAAATAAATT
20636 TATAATTTTAAAAATAAATT
1 TATAA-TTTAAAAATAAATT
20656 TAT
1 TAT
20659 GAAATTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATAATTTAAAAATAAATT
Found at i:22464 original size:18 final size:18
Alignment explanation
Indices: 22431--22465 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22421 TGAAGAAGAA
**
22431 CAAGATGTGATTCCTCCG
1 CAAGATGTGAACCCTCCG
22449 CAAGATGTGAACCCTCC
1 CAAGATGTGAACCCTCC
22466 ATAGGATATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
CAAGATGTGAACCCTCCG
Found at i:31558 original size:30 final size:30
Alignment explanation
Indices: 31494--31562 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
31484 TATTTTTTAT
* *
31494 AAAAAATTAAACAAGCCCTCAAACTTTCTA
1 AAAAAATCAAACAAGCCCTCAAACTTACTA
* *
31524 AAAAAATCAAACAAGCCCTCAAACTTAGTC
1 AAAAAATCAAACAAGCCCTCAAACTTACTA
31554 AAAAAATCA
1 AAAAAATCA
31563 GTTAAACCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.54, C:0.23, G:0.04, T:0.19
Consensus pattern (30 bp):
AAAAAATCAAACAAGCCCTCAAACTTACTA
Found at i:33206 original size:9 final size:9
Alignment explanation
Indices: 33192--33245 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
33182 GGCTGCTGGA
33192 AACCGGTTT
1 AACCGGTTT
*
33201 AACCGGTTCG
1 AACCGGTT-T
33211 AACCGGTTT
1 AACCGGTTT
* *
33220 GACCGGTCTG
1 AACCGGT-TT
33230 AACCGGTTT
1 AACCGGTTT
*
33239 GACCGGT
1 AACCGGT
33246 CTGACCCGAC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
9 21 0.58
10 15 0.42
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (9 bp):
AACCGGTTT
Found at i:33216 original size:19 final size:20
Alignment explanation
Indices: 33192--33249 Score: 86
Period size: 19 Copynumber: 3.0 Consensus size: 20
33182 GGCTGCTGGA
*
33192 AACCGGTTTAACCGGTTC-G
1 AACCGGTTTGACCGGTTCTG
33211 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTCTG
33230 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTCTG
33249 A
1 A
33250 CCCGACCCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
18 2 0.05
19 35 0.95
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.26
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTCTG
Found at i:33250 original size:9 final size:9
Alignment explanation
Indices: 33212--33251 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
33202 ACCGGTTCGA
*
33212 ACCGGTTTG
1 ACCGGTCTG
33221 ACCGGTCTG
1 ACCGGTCTG
*
33230 AACCGGTTTG
1 -ACCGGTCTG
33240 ACCGGTCTG
1 ACCGGTCTG
33249 ACC
1 ACC
33252 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:33258 original size:5 final size:5
Alignment explanation
Indices: 33248--33305 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
33238 TGACCGGTCT
* *
33248 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
33297 GACCC GACC
1 GACCC GACC
33306 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:33274 original size:22 final size:22
Alignment explanation
Indices: 33248--33312 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
33238 TGACCGGTCT
33248 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
33270 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
33292 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
33313 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:33314 original size:7 final size:7
Alignment explanation
Indices: 33302--33332 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
33292 GACCCGACCC
33302 GACCGTT
1 GACCGTT
33309 GACCGTT
1 GACCGTT
33316 GACCGTT
1 GACCGTT
33323 GACCGTT
1 GACCGTT
33330 GAC
1 GAC
33333 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:36241 original size:65 final size:65
Alignment explanation
Indices: 36081--36241 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 65
36071 TTGTTTAAGG
* * * **
36081 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAAGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAAGATTT
36144 A
65 A
* *
36145 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAAGATTTA
*
36209 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
36242 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAAGATTTA
Found at i:37815 original size:149 final size:149
Alignment explanation
Indices: 37642--37944 Score: 579
Period size: 149 Copynumber: 2.0 Consensus size: 149
37632 GAGTCGAGGG
37642 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
37707 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
37772 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
37791 TCTACGCGGTCCTTTGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
37856 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCTTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
37921 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
37940 TCTAC
1 TCTAC
37945 ACGGCACTTC
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:39209 original size:23 final size:23
Alignment explanation
Indices: 39175--39235 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
39165 CTCGTATAAA
*
39175 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
39198 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
39221 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
39236 TACAAGATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:39756 original size:26 final size:26
Alignment explanation
Indices: 39710--39773 Score: 60
Period size: 26 Copynumber: 2.4 Consensus size: 26
39700 TTTTGTTCTA
*
39710 ATAAGTTCATATTTATCATTTAATA-C
1 ATAA-TTCTTATTTATCATTTAATATC
*
39736 ATAGATTCTTATTTCAT-ATTTTATATC
1 ATA-ATTCTTATTT-ATCATTTAATATC
*
39763 ATATTTCTTAT
1 ATAATTCTTAT
39774 ACCACTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 25 0.78
27 7 0.22
ACGTcount: A:0.33, C:0.11, G:0.03, T:0.53
Consensus pattern (26 bp):
ATAATTCTTATTTATCATTTAATATC
Found at i:54621 original size:23 final size:23
Alignment explanation
Indices: 54592--54654 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
54582 ACCCCCATGA
*
54592 GGGAACCGATTCCCCTTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
54615 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
54638 GGGAACCGATTCCCCCT
1 GGGAACCGATTCCCCCT
54655 AGGGGAATCG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.32, G:0.25, T:0.22
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:54674 original size:20 final size:19
Alignment explanation
Indices: 54613--54678 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
54603 CCCCTTTTGA
*
54613 AGGGGAACCGATTCCCCCTTT
1 AGGGGAACCGA-TCCCCC-CT
*
54634 GAAGGGGAACCGATTCCCCCT
1 --AGGGGAACCGATCCCCCCT
*
54655 AGGGGAATCGATACCCCCCT
1 AGGGGAACCGAT-CCCCCCT
54675 -GGGG
1 AGGGG
54679 TTCTGGTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 15 0.39
20 6 0.16
21 1 0.03
22 5 0.13
23 11 0.29
ACGTcount: A:0.21, C:0.32, G:0.30, T:0.17
Consensus pattern (19 bp):
AGGGGAACCGATCCCCCCT
Found at i:67715 original size:6 final size:6
Alignment explanation
Indices: 67704--67752 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
67694 GCCAAAACTC
*
67704 GTGGCT GTGGCT GT-GCT GTGGTT GTGG-T G-GGCT GTGGGCT GTGGCT
1 GTGGCT GTGGCT GTGGCT GTGGCT GTGGCT GTGGCT GT-GGCT GTGGCT
67750 GTG
1 GTG
67753 CTTTCTGCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
4 2 0.05
5 9 0.24
6 21 0.55
7 6 0.16
ACGTcount: A:0.00, C:0.12, G:0.53, T:0.35
Consensus pattern (6 bp):
GTGGCT
Found at i:67723 original size:11 final size:11
Alignment explanation
Indices: 67707--67754 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
67697 AAAACTCGTG
67707 GCTGTGGCTGT
1 GCTGTGGCTGT
*
67718 GCTGTGGTTGT
1 GCTGTGGCTGT
*
67729 GGTG-GGCTGT
1 GCTGTGGCTGT
67739 GGGCTGTGGCTGT
1 --GCTGTGGCTGT
67752 GCT
1 GCT
67755 TTCTGCTTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
10 5 0.17
11 16 0.53
12 3 0.10
13 6 0.20
ACGTcount: A:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (11 bp):
GCTGTGGCTGT
Found at i:78345 original size:29 final size:29
Alignment explanation
Indices: 78248--78438 Score: 196
Period size: 28 Copynumber: 6.7 Consensus size: 29
78238 AAGCCCAAGG
*
78248 AACCAGAGAAGCCGAAAGAGGCTGAGAAGA
1 AACCAGAGAAGCCGAAAGA-GCCGAGAAGA
* * *
78278 AACC--CG-AGCCTAAAGAGGCTGAGAAGA
1 AACCAGAGAAGCCGAAAGA-GCCGAGAAGA
* *
78305 AACC-GAGCAGCCTAAAGAGCCGAGAAGA
1 AACCAGAGAAGCCGAAAGAGCCGAGAAGA
* * *
78333 AATCTGAGAAGCCGAAAGAGGCGAGAAG-
1 AACCAGAGAAGCCGAAAGAGCCGAGAAGA
*
78361 AAGCAGAGAAGCCGAAAGAGGCCGAGAAGA
1 AACCAGAGAAGCCGAAAGA-GCCGAGAAGA
*
78391 AGCCAGAGAAGCCGAAAGAGCCGAG-AGA
1 AACCAGAGAAGCCGAAAGAGCCGAGAAGA
* *
78419 AACCGGAGAAGCCTAAAGAG
1 AACCAGAGAAGCCGAAAGAG
78439 TCTGGGGAGA
Statistics
Matches: 140, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
27 24 0.17
28 51 0.36
29 44 0.31
30 21 0.15
ACGTcount: A:0.44, C:0.19, G:0.33, T:0.04
Consensus pattern (29 bp):
AACCAGAGAAGCCGAAAGAGCCGAGAAGA
Found at i:78378 original size:28 final size:28
Alignment explanation
Indices: 78251--78438 Score: 184
Period size: 29 Copynumber: 6.6 Consensus size: 28
78241 CCCAAGGAAC
78251 CAGAGAAGCCGAAAGAGGCTGAGAAGAAA
1 CAGAGAAGCCGAAAGAGGC-GAGAAGAAA
** *
78280 C-CCG-AGCCTAAAGAGGCTGAGAAGAAA
1 CAGAGAAGCCGAAAGAGGC-GAGAAGAAA
* * * *
78307 CCGAGCAGCCTAAAGAGCCGAGAAGAAA
1 CAGAGAAGCCGAAAGAGGCGAGAAGAAA
* *
78335 TCTGAGAAGCCGAAAGAGGCGAGAAGAAG
1 -CAGAGAAGCCGAAAGAGGCGAGAAGAAA
*
78364 CAGAGAAGCCGAAAGAGGCCGAGAAGAAGC
1 CAGAGAAGCCGAAAGAGG-CGAGAAGAA-A
*
78394 CAGAGAAGCCGAAAGAGCCGAG-AGAAA
1 CAGAGAAGCCGAAAGAGGCGAGAAGAAA
* *
78421 CCGGAGAAGCCTAAAGAG
1 -CAGAGAAGCCGAAAGAG
78439 TCTGGGGAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
27 23 0.17
28 47 0.35
29 49 0.36
30 17 0.12
ACGTcount: A:0.44, C:0.19, G:0.34, T:0.04
Consensus pattern (28 bp):
CAGAGAAGCCGAAAGAGGCGAGAAGAAA
Found at i:78399 original size:12 final size:11
Alignment explanation
Indices: 78339--78429 Score: 69
Period size: 9 Copynumber: 9.2 Consensus size: 11
78329 AAGAAATCTG
78339 AGAAGCCGA-A
1 AGAAGCCGAGA
*
78349 AG-AGGCGAGA
1 AGAAGCCGAGA
78359 AGAAG-C-AG-
1 AGAAGCCGAGA
78367 AGAAGCCGA-A
1 AGAAGCCGAGA
*
78377 AGAGGCCGAGA
1 AGAAGCCGAGA
78388 AGAAGCC-AG-
1 AGAAGCCGAGA
78397 AGAAGCCGA-A
1 AGAAGCCGAGA
78407 AG-AGCCGAG-
1 AGAAGCCGAGA
*
78416 AGAAACCGGAGA
1 AGAAGCC-GAGA
78428 AG
1 AG
78430 CCTAAAGAGT
Statistics
Matches: 65, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
8 5 0.08
9 23 0.35
10 23 0.35
11 12 0.18
12 2 0.03
ACGTcount: A:0.45, C:0.18, G:0.37, T:0.00
Consensus pattern (11 bp):
AGAAGCCGAGA
Found at i:78412 original size:18 final size:19
Alignment explanation
Indices: 78338--78419 Score: 78
Period size: 20 Copynumber: 4.3 Consensus size: 19
78328 GAAGAAATCT
*
78338 GAGAAGCCGAAAGAGGCGA
1 GAGAAGCCGAAAGAGCCGA
* *
78357 GAAGAAGCAGAGA-AGCCGA
1 G-AGAAGCCGAAAGAGCCGA
* *
78376 AAGAGGCCGAGAAGAAGCC-A
1 GAGAAGCCGA-AAG-AGCCGA
78396 GAGAAGCCGAAAGAGCCGA
1 GAGAAGCCGAAAGAGCCGA
78415 GAGAA
1 GAGAA
78420 ACCGGAGAAG
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
18 11 0.22
19 16 0.33
20 18 0.37
21 4 0.08
ACGTcount: A:0.45, C:0.17, G:0.38, T:0.00
Consensus pattern (19 bp):
GAGAAGCCGAAAGAGCCGA
Found at i:78475 original size:18 final size:18
Alignment explanation
Indices: 78452--78514 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
78442 GGGGAGAAGA
*
78452 AGGCTGATAAACCAAAAG
1 AGGCTGAGAAACCAAAAG
* *
78470 AGGCTGAGAAGCCTAAAG
1 AGGCTGAGAAACCAAAAG
* *
78488 AGGGTGGGGAGAAACCCAAAG
1 AGGCT---GAGAAACCAAAAG
78509 AGGCTG
1 AGGCTG
78515 CTCCGGCGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 20 0.57
21 15 0.43
ACGTcount: A:0.40, C:0.16, G:0.35, T:0.10
Consensus pattern (18 bp):
AGGCTGAGAAACCAAAAG
Found at i:78766 original size:22 final size:22
Alignment explanation
Indices: 78727--78773 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
78717 CAGGTAGGAT
78727 ATGGCGGCGGCCCGCACCGGTGA
1 ATGGCGGCGGCCCGCACC-GTGA
78750 ATGGCGGCGG-CCGCACCGTGA
1 ATGGCGGCGGCCCGCACCGTGA
78771 ATG
1 ATG
78774 TTTTAGCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.29
22 7 0.29
23 10 0.42
ACGTcount: A:0.15, C:0.32, G:0.43, T:0.11
Consensus pattern (22 bp):
ATGGCGGCGGCCCGCACCGTGA
Done.