Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002803.1 Hibiscus syriacus cultivar Beakdansim tig00005768_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: 61515
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:638 original size:97 final size:103
Alignment explanation
Indices: 493--701 Score: 335
Period size: 98 Copynumber: 2.1 Consensus size: 103
483 GTATTTAGTA
*
493 TATATGATAATATATAAATAATTTCAAAAATATACATATATATTTTTTG-AAAT-ATAATATATG
1 TATATGATAATATATAAATAATTTCAAAAATATACATATATATATTTTGAAAATAAT-ATATATG
556 TT-TATAGTTTTT-AAT-AA-ATATAGTACGTATTATAT
65 TTATATAGTTTTTAAATAAATATATAGTACGTATTATAT
591 TATATGATAATATAT-AATAATTTCAAAAATATACA-ATATATAATTTTGAAAATAATATATATG
1 TATATGATAATATATAAATAATTTCAAAAATATACATATATAT-ATTTTGAAAATAATATATATG
654 TTATATAGTTTTTAAATAAATATATAGTACGTATTATAT
65 TTATATAGTTTTTAAATAAATATATAGTACGTATTATAT
693 TATATGATA
1 TATATGATA
702 TATTATTTAT
Statistics
Matches: 103, Mismatches: 1, Indels: 10
0.90 0.01 0.09
Matches are distributed among these distances:
96 6 0.06
97 25 0.24
98 28 0.27
99 12 0.12
100 3 0.03
101 2 0.02
102 27 0.26
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.44
Consensus pattern (103 bp):
TATATGATAATATATAAATAATTTCAAAAATATACATATATATATTTTGAAAATAATATATATGT
TATATAGTTTTTAAATAAATATATAGTACGTATTATAT
Found at i:703 original size:97 final size:93
Alignment explanation
Indices: 504--704 Score: 262
Period size: 97 Copynumber: 2.0 Consensus size: 93
494 ATATGATAAT
*
504 ATATAAATAATTTCAAAAATATACATATATATTTTTTGAAATATAATATATGTTTATAGTTTTTA
1 ATAT-AATAATTTCAAAAATATACATATATATATTTTGAAATATAATATATGTTTATAGTTTTTA
569 ATAAATATAGTACGTATTATATTATATGATAA
65 ATAAATATAGTACGTATTATATTATATG---A
601 TATATAATAATTTCAAAAATATACA-ATATATAATTTTGAAA-ATAATATATATGTTATATAGTT
1 -ATATAATAATTTCAAAAATATACATATATAT-ATTTTGAAATAT-A-ATATATGTT-TATAGTT
664 TTTAAATAAATATATAGTACGTATTATATTATATGA
61 TTT-AAT-AA-ATATAGTACGTATTATATTATATGA
700 TATAT
1 -ATAT
705 TATTTATAGT
Statistics
Matches: 95, Mismatches: 1, Indels: 13
0.87 0.01 0.12
Matches are distributed among these distances:
96 8 0.08
97 29 0.31
98 13 0.14
99 16 0.17
100 3 0.03
101 2 0.02
102 24 0.25
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (93 bp):
ATATAATAATTTCAAAAATATACATATATATATTTTGAAATATAATATATGTTTATAGTTTTTAA
TAAATATAGTACGTATTATATTATATGA
Found at i:3334 original size:10 final size:10
Alignment explanation
Indices: 3315--3350 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
3305 ATATATTTTT
3315 ATTTATGTTC
1 ATTTATGTTC
* *
3325 GTTTACGTTC
1 ATTTATGTTC
3335 ATTTATGTTC
1 ATTTATGTTC
3345 ATTTAT
1 ATTTAT
3351 TTTTTACGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.58
Consensus pattern (10 bp):
ATTTATGTTC
Found at i:3398 original size:23 final size:24
Alignment explanation
Indices: 3353--3404 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
3343 TCATTTATTT
3353 TTTACGTTCGTTCATTTGTGTTTG
1 TTTACGTTCGTTCATTTGTGTTTG
* *
3377 TTTACGTTTGTTTA-TTGTGTTTG
1 TTTACGTTCGTTCATTTGTGTTTG
3400 TTTAC
1 TTTAC
3405 ATCCGTTCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.62
Consensus pattern (24 bp):
TTTACGTTCGTTCATTTGTGTTTG
Found at i:4133 original size:8 final size:8
Alignment explanation
Indices: 4120--4152 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
4110 GTAATATCTC
4120 TCTCTCTT
1 TCTCTCTT
4128 TCTCTCTT
1 TCTCTCTT
4136 TCTCTCTT
1 TCTCTCTT
4144 TCTCTCTT
1 TCTCTCTT
4152 T
1 T
4153 ATGGGTCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (8 bp):
TCTCTCTT
Found at i:17635 original size:24 final size:24
Alignment explanation
Indices: 17607--17653 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
17597 GAGAACCAAG
*
17607 ATAAA-CTTAAATATACCATTAAAA
1 ATAAAGCTTAAACAT-CCATTAAAA
*
17631 ATAAAGTTTAAACATCCATTAAA
1 ATAAAGCTTAAACATCCATTAAA
17654 CCAACCACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.30
Consensus pattern (24 bp):
ATAAAGCTTAAACATCCATTAAAA
Found at i:23006 original size:23 final size:23
Alignment explanation
Indices: 22976--23050 Score: 84
Period size: 23 Copynumber: 3.4 Consensus size: 23
22966 GCACAGGTAG
22976 TGCATCGATGCACCGATAGGGAA
1 TGCATCGATGCACCGATAGGGAA
* * * *
22999 TGCATCGATACACTG-T--GCAG
1 TGCATCGATGCACCGATAGGGAA
*
23019 CGCATCGATGCACCGATAGGGAA
1 TGCATCGATGCACCGATAGGGAA
23042 TGCATCGAT
1 TGCATCGAT
23051 ACACTGTGCA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
20 14 0.36
21 1 0.03
22 1 0.03
23 23 0.59
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCATCGATGCACCGATAGGGAA
Found at i:23025 original size:20 final size:20
Alignment explanation
Indices: 23000--23070 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
22990 GATAGGGAAT
23000 GCATCGATACACTGTGCAGC
1 GCATCGATACACTGTGCAGC
* * * **
23020 GCATCGATGCACCGATAGGGAAT
1 GCATCGATACACTG-T--GCAGC
23043 GCATCGATACACTGTGCAGC
1 GCATCGATACACTGTGCAGC
23063 GCATCGAT
1 GCATCGAT
23071 GCATACCTTC
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
20 22 0.58
21 1 0.03
22 1 0.03
23 14 0.37
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (20 bp):
GCATCGATACACTGTGCAGC
Found at i:23025 original size:43 final size:43
Alignment explanation
Indices: 22977--23073 Score: 194
Period size: 43 Copynumber: 2.3 Consensus size: 43
22967 CACAGGTAGT
22977 GCATCGATGCACCGATAGGGAATGCATCGATACACTGTGCAGC
1 GCATCGATGCACCGATAGGGAATGCATCGATACACTGTGCAGC
23020 GCATCGATGCACCGATAGGGAATGCATCGATACACTGTGCAGC
1 GCATCGATGCACCGATAGGGAATGCATCGATACACTGTGCAGC
23063 GCATCGATGCA
1 GCATCGATGCA
23074 TACCTTCATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.19
Consensus pattern (43 bp):
GCATCGATGCACCGATAGGGAATGCATCGATACACTGTGCAGC
Found at i:23989 original size:103 final size:103
Alignment explanation
Indices: 23805--24022 Score: 366
Period size: 103 Copynumber: 2.1 Consensus size: 103
23795 GTCGAGGGTC
*
23805 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATATGTGAAGTATGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAAGTATGGTGAGACACATAC
*
23870 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
* * *
23908 TATGTGGTCCTTCGGGACGTATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAAGTATGGTGAGACACATAC
*
23973 TTGAT-CTCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCT-TAGCATATGTATATGATTCTTAAGGAATGA
24011 TATGTGGTCCTT
1 TATGTGGTCCTT
24023 ATGGACATTA
Statistics
Matches: 108, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
102 2 0.02
103 106 0.98
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAAGTATGGTGAGACACATAC
TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:24088 original size:23 final size:23
Alignment explanation
Indices: 24062--24106 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
24052 AATTCTTCGC
24062 GGCACTCCGGTGCAATTATATGT
1 GGCACTCCGGTGCAATTATATGT
24085 GGCACTCCGGTGCAATTATATG
1 GGCACTCCGGTGCAATTATATG
24107 AGCTATGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTATATGT
Found at i:35037 original size:15 final size:15
Alignment explanation
Indices: 35017--35046 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35007 AAATAAATCG
35017 GGGTCGGATTGGGTC
1 GGGTCGGATTGGGTC
*
35032 GGGTCGGGTTGGGTC
1 GGGTCGGATTGGGTC
35047 AAGTCAGGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.13, G:0.57, T:0.27
Consensus pattern (15 bp):
GGGTCGGATTGGGTC
Found at i:36020 original size:29 final size:30
Alignment explanation
Indices: 35961--36024 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
35951 AAATAGTCTT
35961 CAAAC-TTTTGAGTATTTCAATTTCATCCC
1 CAAACTTTTTGAGTATTTCAATTTCATCCC
*
35990 CAAACTTTTTGA-TCATTTCAGTTTCAT-CC
1 CAAACTTTTTGAGT-ATTTCAATTTCATCCC
36019 CAAACT
1 CAAACT
36025 ATACATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.41
Consensus pattern (30 bp):
CAAACTTTTTGAGTATTTCAATTTCATCCC
Found at i:52016 original size:179 final size:180
Alignment explanation
Indices: 51799--52971 Score: 1492
Period size: 180 Copynumber: 6.6 Consensus size: 180
51789 GATACAAATG
* * *
51799 AAAAATATATCGATCTATAACAATATAACATGTAAAAATATGAC-AATCGGTCTCAAAATGACAA
1 AAAAATGTATCGATCTATAACAATATAACAGGTAAAAATATGACAAACCGGTCTCAAAATGACAA
* * *
51863 AACCGGTAAAACGCTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTC
66 AACAGGTAAAA-ACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT-
*
51928 T-GAATTTAAAAGAGAAGAAGTTATA-CGCCTAAAAAATGTCGACACTTTAT
129 TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
* * ** *
51978 GAAAATGTATCGATCCATAACAATATAACAACTAAAAATATAACAAAACCGGTCTCAAAATGACA
1 AAAAATGTATCGATCTATAACAATATAACAGGTAAAAATATGAC-AAACCGGTCTCAAAATGACA
*
52043 AAACAGGTAAATAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAATTATCGACACTTT
65 AAACAGGTAAA-AACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
* * *
52108 TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAA
129 TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
* *
52160 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAAAAAACC-G--T-AAAAT----
1 AAAAATGTATCGATCTATAACAATATAACAGGTAAAAATATG-ACAAACCGGTCTCAAAATGACA
* * *
52217 ------GT------TACCGGATATGTTGAAAGTGTCGATAATTTAATACAAGTATCGATACTTTT
65 AAACAGGTAAAAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTT
* *
52270 TGAATTT-AAA-AG-AGAAGTTATAACGCCTAAAAAGTGTCGACACTTTAT
130 GGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
* * **
52318 GAAAATGTATCGATCCATAACAATATAACAACTAAAAATATGACAAAACCGGTCTCAAAATGACA
1 AAAAATGTATCGATCTATAACAATATAACAGGTAAAAATATGAC-AAACCGGTCTCAAAATGACA
*
52383 AAACAGGTAAATAACTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
65 AAACAGGTAAA-AACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
* *
52448 TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTA-
129 TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
* **
52499 AAAAATGTATTGATCTATAACAATATAACAGGT-AAAATATGACAAAAGAGGTCT-ACAAATGAC
1 AAAAATGTATCGATCTATAACAATATAACAGGTAAAAATATGAC-AAACCGGTCTCA-AAATGAC
* * * * * * *
52562 AAAACCGATAAAAAGATACCAGATATCTTGAAAGTGTCGATAATTTAATATAAGTATTGACACTT
64 AAAACAGGTAAAAA-CTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
*
52627 TTGGAATTTAAAAGAG-AGAAGTTATA-CGCCTAAAAATTGTCGACACTTTAT
128 TTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
* * *
52678 GAAAATGTATCGATCTATAACAATATAACAGCTAAAAATATGACAAAACCGGTTTC-AAATGACA
1 AAAAATGTATCGATCTATAACAATATAACAGGTAAAAATATGAC-AAACCGGTCTCAAAATGACA
* *
52742 AAACAGGTAAAAACTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATAGACACTTTT
65 AAACAGGTAAAAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTT
* * * *
52807 GAAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAA
130 GGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
*
52858 AAAAATGTATCGATCTATAACAATATAACAGGTAAAAATATGACAAAACCAGTCTCAAAATGACA
1 AAAAATGTATCGATCTATAACAATATAACAGGTAAAAATATGAC-AAACCGGTCTCAAAATGACA
* ** * * *
52923 AAACCGGTAAAGCGCTACTGAATATGTTGAAAGTGTTGATACTTTAATA
65 AAACAGGTAAA-AACTACCGGATATGTTGAAAGTGTCGATACTTTAATA
52972 AGTACGCGTA
Statistics
Matches: 869, Mismatches: 85, Indels: 77
0.84 0.08 0.07
Matches are distributed among these distances:
157 1 0.00
158 76 0.09
159 3 0.00
160 3 0.00
161 54 0.06
162 5 0.01
168 2 0.00
172 2 0.00
178 87 0.10
179 164 0.19
180 193 0.22
181 150 0.17
182 128 0.15
183 1 0.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.27
Consensus pattern (180 bp):
AAAAATGTATCGATCTATAACAATATAACAGGTAAAAATATGACAAACCGGTCTCAAAATGACAA
AACAGGTAAAAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTTG
GAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAT
Found at i:52499 original size:340 final size:341
Alignment explanation
Indices: 51856--52907 Score: 1646
Period size: 340 Copynumber: 3.0 Consensus size: 341
51846 CGGTCTCAAA
* *
51856 ATGACAAAACCGGTAAAACGCTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGA
1 ATGACAAAACC-GTAAAAAGATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGA
*
51921 CACTTTCTGAATTTAAAAGAGAAGAAGTTATACGCCTAAAAAATGTCGACACTTTATGAAAATGT
65 CACTTTTTGAATTTAAAAGAG-AGAAGTTATACGCCTAAAAAATGTCGACACTTTATGAAAATGT
*
51986 ATCGATCCATAACAATATAACAACTAAAAATATAACAAAACCGGTCTCAAAATGACAAAACAGGT
129 ATCGATCCATAACAATATAACAACTAAAAATATGACAAAACCGGTCTCAAAATGACAAAACAGGT
* *
52051 AAATAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAATTATCGACACTTTTGGAATTT
194 AAATAACTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTTGGAATTT
*
52116 AAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATGTATCGATCCATAAC
259 AAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATGTATCGATCTATAAC
52181 AATATAACAGGTAAAAAT
324 AATATAACAGGTAAAAAT
* * * * *
52199 ATGAAAAAACCGTAAAATGTTACCGGATATGTTGAAAGTGTCGATAATTTAATACAAGTATCGAT
1 ATGACAAAACCGTAAAAAGATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGAC
*
52264 ACTTTTTGAATTT-AAA-AGAGAAGTTATAACGCCTAAAAAGTGTCGACACTTTATGAAAATGTA
66 ACTTTTTGAATTTAAAAGAGAGAAGTTAT-ACGCCTAAAAAATGTCGACACTTTATGAAAATGTA
52327 TCGATCCATAACAATATAACAACTAAAAATATGACAAAACCGGTCTCAAAATGACAAAACAGGTA
130 TCGATCCATAACAATATAACAACTAAAAATATGACAAAACCGGTCTCAAAATGACAAAACAGGTA
52392 AATAACTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTTGGAATTTA
195 AATAACTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTTGGAATTTA
*
52457 AAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTT-AAAAAATGTATTGATCTATAACA
260 AAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATGTATCGATCTATAACA
52521 ATATAACAGGTAAAATATGACAAAAGAGGTCT
325 ATATAACAGG-------T---AAAA-A----T
* *
52553 ACAAATGACAAAACCGATAAAAAGATACCAGATATCTTGAAAGTGTCGATAATTTAATATAAGTA
1 ----ATGACAAAACCG-TAAAAAGATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTA
* * *
52618 TTGACACTTTTGGAATTTAAAAGAGAGAAGTTATACGCCTAAAAATTGTCGACACTTTATGAAAA
61 TCGACACTTTTTGAATTTAAAAGAGAGAAGTTATACGCCTAAAAAATGTCGACACTTTATGAAAA
* * *
52683 TGTATCGATCTATAACAATATAACAGCTAAAAATATGACAAAACCGGTTTC-AAATGACAAAACA
126 TGTATCGATCCATAACAATATAACAACTAAAAATATGACAAAACCGGTCTCAAAATGACAAAACA
* *
52747 GGTAAA-AACTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATAGACACTTTTGAAA
191 GGTAAATAACTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTTGGAA
52811 TTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATGTATCGATCTAT
256 TTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATGTATCGATCTAT
52876 AACAATATAACAGGTAAAAAT
321 AACAATATAACAGGTAAAAAT
52897 ATGACAAAACC
1 ATGACAAAACC
52908 AGTCTCAAAA
Statistics
Matches: 657, Mismatches: 28, Indels: 51
0.89 0.04 0.07
Matches are distributed among these distances:
339 40 0.06
340 215 0.33
341 3 0.00
342 62 0.09
343 10 0.02
344 1 0.00
346 1 0.00
348 1 0.00
349 8 0.01
350 1 0.00
352 1 0.00
354 1 0.00
358 112 0.17
359 109 0.17
360 81 0.12
361 11 0.02
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.27
Consensus pattern (341 bp):
ATGACAAAACCGTAAAAAGATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGAC
ACTTTTTGAATTTAAAAGAGAGAAGTTATACGCCTAAAAAATGTCGACACTTTATGAAAATGTAT
CGATCCATAACAATATAACAACTAAAAATATGACAAAACCGGTCTCAAAATGACAAAACAGGTAA
ATAACTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTTGGAATTTAA
AAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATGTATCGATCTATAACAA
TATAACAGGTAAAAAT
Found at i:53398 original size:17 final size:18
Alignment explanation
Indices: 53363--53428 Score: 80
Period size: 19 Copynumber: 3.6 Consensus size: 18
53353 CTTTTATTTA
*
53363 ATATTATATGTAAAAAATG
1 ATATTATAGGT-AAAAATG
53382 ATATTATAGGT-AAAATG
1 ATATTATAGGTAAAAATG
*
53399 ATATTATAGATAGAAAATG
1 ATATTATAGGTA-AAAATG
*
53418 ATATTTTAGGT
1 ATATTATAGGT
53429 TGTATAAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
17 16 0.39
19 25 0.61
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (18 bp):
ATATTATAGGTAAAAATG
Found at i:54732 original size:24 final size:24
Alignment explanation
Indices: 54677--54736 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
54667 GTTGAAGAAT
54677 GTTTTTTTA--ATATAAAATGATA
1 GTTTTTTTATTATATAAAATGATA
* **
54699 GTATAGTTATTATATAAAATGATA
1 GTTTTTTTATTATATAAAATGATA
*
54723 TTTTTTTTATTATA
1 GTTTTTTTATTATA
54737 AATGCAAGTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
22 6 0.21
24 23 0.79
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.53
Consensus pattern (24 bp):
GTTTTTTTATTATATAAAATGATA
Found at i:54981 original size:9 final size:9
Alignment explanation
Indices: 54967--55017 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
54957 GTTATTGTCA
*
54967 AGGAGGTAG
1 AGGAGGCAG
*
54976 AGGAGGCAT
1 AGGAGGCAG
*
54985 AGGAGGTAG
1 AGGAGGCAG
*
54994 AGGAGGCAA
1 AGGAGGCAG
*
55003 AGGAAGCAG
1 AGGAGGCAG
55012 AGGAGG
1 AGGAGG
55018 TAGTGGAGAA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.37, C:0.06, G:0.51, T:0.06
Consensus pattern (9 bp):
AGGAGGCAG
Found at i:54990 original size:18 final size:18
Alignment explanation
Indices: 54966--55017 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
54956 GGTTATTGTC
54966 AAGGAGGTAGAGGAGGCA
1 AAGGAGGTAGAGGAGGCA
*
54984 TAGGAGGTAGAGGAGGCA
1 AAGGAGGTAGAGGAGGCA
* *
55002 AAGGAAGCAGAGGAGG
1 AAGGAGGTAGAGGAGG
55018 TAGTGGAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.38, C:0.06, G:0.50, T:0.06
Consensus pattern (18 bp):
AAGGAGGTAGAGGAGGCA
Found at i:55006 original size:27 final size:27
Alignment explanation
Indices: 54967--55025 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
54957 GTTATTGTCA
* * * *
54967 AGGAGGTAGAGGAGGCATAGGAGGTAG
1 AGGAGGCAAAGGAAGCAGAGGAGGTAG
54994 AGGAGGCAAAGGAAGCAGAGGAGGTAG
1 AGGAGGCAAAGGAAGCAGAGGAGGTAG
*
55021 TGGAG
1 AGGAG
55026 AAGGAAGAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.36, C:0.05, G:0.51, T:0.08
Consensus pattern (27 bp):
AGGAGGCAAAGGAAGCAGAGGAGGTAG
Found at i:60502 original size:12 final size:13
Alignment explanation
Indices: 60473--60504 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
60463 ATGCAAATAG
60473 AAGATGAATCCAC
1 AAGATGAATCCAC
60486 AAGATGAATCC-C
1 AAGATGAATCCAC
60498 AAGATGA
1 AAGATGA
60505 TGATGAGGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.16
Consensus pattern (13 bp):
AAGATGAATCCAC
Done.