Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004479.1 Hibiscus syriacus cultivar Beakdansim tig00009873_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: 59634
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1487 original size:32 final size:31
Alignment explanation
Indices: 1399--1522 Score: 169
Period size: 31 Copynumber: 4.0 Consensus size: 31
1389 CCTGAAGGAC
* *
1399 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
* *
1430 AAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1461 CAGTCCATATGTCCCGAAAGAACATAGATAAA
1 CAGTCCATATGTCCCG-AAGAACATAGGTAAA
*
1493 CAGTCCATATGTCCCGAAGAACATAAGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1523 CCATCGACAC
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
31 52 0.63
32 30 0.37
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1501 original size:63 final size:62
Alignment explanation
Indices: 1399--1522 Score: 169
Period size: 63 Copynumber: 2.0 Consensus size: 62
1389 CCTGAAGGAC
* * * *
1399 CAGTCCATAGATTCCGAAGAACCTAGGTAAAAAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATAGATCCCGAAGAACATAGATAAAAAGTCCATATATCCCGAAGAACATAAGTAAA
* *
1461 CAGTCCATATG-TCCCGAAAGAACATAGATAAACAGTCCATATGTCCCGAAGAACATAAGTAA
1 CAGTCCATA-GATCCCG-AAGAACATAGATAAAAAGTCCATATATCCCGAAGAACATAAGTAA
1523 CCATCGACAC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
62 13 0.24
63 41 0.76
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (62 bp):
CAGTCCATAGATCCCGAAGAACATAGATAAAAAGTCCATATATCCCGAAGAACATAAGTAAA
Found at i:3368 original size:34 final size:32
Alignment explanation
Indices: 3330--3404 Score: 82
Period size: 37 Copynumber: 2.2 Consensus size: 32
3320 ATTATAGATT
3330 AAATTATAAAT-ATTATTTTATAATATTCAATCACA
1 AAATTATAAATAATTA-TTT-T-ATA-TCAATCACA
3365 AATTATTATAAATAATTATTTTATATCAATCAC-
1 AA--ATTATAAATAATTATTTTATATCAATCACA
3398 AAATTAT
1 AAATTAT
3405 TAATTTAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
31 5 0.14
33 2 0.05
34 8 0.22
35 5 0.14
36 1 0.03
37 12 0.32
38 4 0.11
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (32 bp):
AAATTATAAATAATTATTTTATATCAATCACA
Found at i:3405 original size:34 final size:37
Alignment explanation
Indices: 3332--3406 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 37
3322 TATAGATTAA
3332 ATTATAAATATTATTTTATAATATTCAATCACAAATT
1 ATTATAAATATTATTTTATAATATTCAATCACAAATT
3369 ATTATAAATAATTA-TTT-T-ATA-TCAATCACAAATT
1 ATTATAAAT-ATTATTTTATAATATTCAATCACAAATT
3403 ATTA
1 ATTA
3407 ATTTAATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
34 17 0.46
35 3 0.08
36 1 0.03
37 12 0.32
38 4 0.11
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (37 bp):
ATTATAAATATTATTTTATAATATTCAATCACAAATT
Found at i:5439 original size:23 final size:23
Alignment explanation
Indices: 5413--5458 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5403 AGGGTCTAGC
* *
5413 ATATTATAAGAGACGAACATATA
1 ATATTATAAGAGACAAAAATATA
*
5436 ATATTTTAAGAGACAAAAATATA
1 ATATTATAAGAGACAAAAATATA
5459 TTATCAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (23 bp):
ATATTATAAGAGACAAAAATATA
Found at i:10560 original size:87 final size:87
Alignment explanation
Indices: 10466--10640 Score: 350
Period size: 87 Copynumber: 2.0 Consensus size: 87
10456 GTATCGAAAT
10466 CTTTTTAAAATTGGTATATTTTATATATTATATATATAATTTATATGGTAAAAAAAGATTTAGAA
1 CTTTTTAAAATTGGTATATTTTATATATTATATATATAATTTATATGGTAAAAAAAGATTTAGAA
10531 ACATTTAGGGTGTTAATTGACA
66 ACATTTAGGGTGTTAATTGACA
10553 CTTTTTAAAATTGGTATATTTTATATATTATATATATAATTTATATGGTAAAAAAAGATTTAGAA
1 CTTTTTAAAATTGGTATATTTTATATATTATATATATAATTTATATGGTAAAAAAAGATTTAGAA
10618 ACATTTAGGGTGTTAATTGACA
66 ACATTTAGGGTGTTAATTGACA
10640 C
1 C
10641 CCTCAATACA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.43
Consensus pattern (87 bp):
CTTTTTAAAATTGGTATATTTTATATATTATATATATAATTTATATGGTAAAAAAAGATTTAGAA
ACATTTAGGGTGTTAATTGACA
Found at i:10691 original size:3 final size:3
Alignment explanation
Indices: 10683--10759 Score: 147
Period size: 3 Copynumber: 26.0 Consensus size: 3
10673 GACCGTTTGA
10683 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT-
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
10730 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
10760 GGAATGAAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 71 0.97
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
CTC
Found at i:11020 original size:167 final size:166
Alignment explanation
Indices: 10745--11074 Score: 597
Period size: 167 Copynumber: 2.0 Consensus size: 166
10735 CCTCCTCCTC
* *
10745 CTCCTCCTCCTCCTCGGAATGAAAAATGAATTTAGGACCATTTCATTTGGGGCATTCACCCTACT
1 CTCCTCCTCCTCCTCGGAATGAAAAATGAACTTAGGACCATTTCATTCGGGGCATTCACCCTACT
*
10810 ATAGAGTTAATGAAGATGTATTTTCATATGACGCAGCTCTACATTCATCATTGGTGACAACTTAC
66 ATAGAGTTAATGAAGATGTATTTTCATATGACGCAGCTCTACATGCATCATTGGTGACAACTTAC
*
10875 CTCTTGGAAAATATACCCAAACATACTCCATCATAT
131 CTCTTGGAAAAGATACCCAAACATACTCCATCATAT
*
10911 CTCCTCCTCCTCCTTGGAATGAAAAATGAAACTTAGGACCATTTCATTCGGGGCATTCACCCTAC
1 CTCCTCCTCCTCCTCGGAATGAAAAATG-AACTTAGGACCATTTCATTCGGGGCATTCACCCTAC
10976 TATAGAGTTAATGAAGATGTATTTTCATATGACGCAGCTCTACATGCATCATTGGTGACAACTTA
65 TATAGAGTTAATGAAGATGTATTTTCATATGACGCAGCTCTACATGCATCATTGGTGACAACTTA
*
11041 CCTCTTGGAAAAGGTACCCAAACATACTCCATCA
130 CCTCTTGGAAAAGATACCCAAACATACTCCATCA
11075 CTAGAAGGAA
Statistics
Matches: 157, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
166 27 0.17
167 130 0.83
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (166 bp):
CTCCTCCTCCTCCTCGGAATGAAAAATGAACTTAGGACCATTTCATTCGGGGCATTCACCCTACT
ATAGAGTTAATGAAGATGTATTTTCATATGACGCAGCTCTACATGCATCATTGGTGACAACTTAC
CTCTTGGAAAAGATACCCAAACATACTCCATCATAT
Found at i:11903 original size:11 final size:12
Alignment explanation
Indices: 11887--11915 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
11877 TAAAATAAAA
11887 TTTTAATTT-AT
1 TTTTAATTTGAT
11898 TTTTAATTTGAT
1 TTTTAATTTGAT
11910 TTTTAA
1 TTTTAA
11916 GGAGAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (12 bp):
TTTTAATTTGAT
Found at i:15236 original size:20 final size:20
Alignment explanation
Indices: 15208--15252 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
15198 TCCAGTTTCA
*
15208 CAACGCGAATTTGTAAATCG
1 CAACACGAATTTGTAAATCG
15228 CAACACGAATTTGTAAATCG
1 CAACACGAATTTGTAAATCG
15248 CAACA
1 CAACA
15253 TAGAAGTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (20 bp):
CAACACGAATTTGTAAATCG
Found at i:15399 original size:19 final size:19
Alignment explanation
Indices: 15375--15445 Score: 124
Period size: 19 Copynumber: 3.7 Consensus size: 19
15365 TCGCAACGCG
15375 GAATTTCAAATTCGTAACT
1 GAATTTCAAATTCGTAACT
* *
15394 GAATTTCAAATTTGCAACT
1 GAATTTCAAATTCGTAACT
15413 GAATTTCAAATTCGTAACT
1 GAATTTCAAATTCGTAACT
15432 GAATTTCAAATTCG
1 GAATTTCAAATTCG
15446 CAACACGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
GAATTTCAAATTCGTAACT
Found at i:15411 original size:60 final size:60
Alignment explanation
Indices: 15277--15392 Score: 198
Period size: 60 Copynumber: 1.9 Consensus size: 60
15267 GCAACGCAAT
*
15277 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAATTTGTAAATCGTAACACAAA
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAATTTGCAAATCGTAACACAAA
15337 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGGAATTT-CAAATTCGTAAC
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGC-GAATTTGCAAA-TCGTAAC
15393 TGAATTTCAA
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
60 40 0.75
61 13 0.25
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.21
Consensus pattern (60 bp):
AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAATTTGCAAATCGTAACACAAA
Found at i:15424 original size:38 final size:38
Alignment explanation
Indices: 15359--15449 Score: 146
Period size: 38 Copynumber: 2.3 Consensus size: 38
15349 AACACAAAAG
*
15359 TCAAATTCGCAACGCGGAATTTCAAATTCGTAACTGAATT
1 TCAAATTCGCAA--CTGAATTTCAAATTCGTAACTGAATT
*
15399 TCAAATTTGCAACTGAATTTCAAATTCGTAACTGAATT
1 TCAAATTCGCAACTGAATTTCAAATTCGTAACTGAATT
15437 TCAAATTCGCAAC
1 TCAAATTCGCAAC
15450 ACGAATTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
38 37 0.77
40 11 0.23
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (38 bp):
TCAAATTCGCAACTGAATTTCAAATTCGTAACTGAATT
Found at i:15457 original size:20 final size:20
Alignment explanation
Indices: 15225--15469 Score: 164
Period size: 20 Copynumber: 12.4 Consensus size: 20
15215 AATTTGTAAA
*
15225 TCGCAACACGAATTTGTAAA-
1 TCGCAACACGAATTT-CAAAT
* *
15245 TCGCAACATAGAA-GTCAAAT
1 TCGCAACA-CGAATTTCAAAT
* *
15265 TCGCAACGC-AATAGTCAAAT
1 TCGCAACACGAAT-TTCAAAT
* **
15285 TCGCAACACAAAAGTCAAAT
1 TCGCAACACGAATTTCAAAT
* *
15305 TCGCAACGCGAATTTGTAAA-
1 TCGCAACACGAATTT-CAAAT
* * **
15325 TCGTAACACAAAAGTCAAAT
1 TCGCAACACGAATTTCAAAT
* **
15345 TCGCAACACAAAAGTCAAAT
1 TCGCAACACGAATTTCAAAT
*
15365 TCGCAACGCGGAATTTCAAAT
1 TCGCAACAC-GAATTTCAAAT
* *
15386 TCGTAAC-TGAATTTCAAAT
1 TCGCAACACGAATTTCAAAT
* *
15405 TTGCAAC-TGAATTTCAAAT
1 TCGCAACACGAATTTCAAAT
* *
15424 TCGTAAC-TGAATTTCAAAT
1 TCGCAACACGAATTTCAAAT
*
15443 TCGCAACACGAATTT-AATT
1 TCGCAACACGAATTTCAAAT
15462 TCGCAACA
1 TCGCAACA
15470 GGTTTTAGTT
Statistics
Matches: 184, Mismatches: 32, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
18 2 0.01
19 68 0.37
20 92 0.50
21 22 0.12
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (20 bp):
TCGCAACACGAATTTCAAAT
Found at i:15464 original size:19 final size:19
Alignment explanation
Indices: 15432--15488 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 19
15422 ATTCGTAACT
*
15432 GAATTTCAAATTCGCAACAC
1 GAATTT-AATTTCGCAACAC
15452 GAATTTAATTTCGCAACA-
1 GAATTTAATTTCGCAACAC
** *
15470 GGTTTTAGTTTCGCAACAC
1 GAATTTAATTTCGCAACAC
15489 AAACGTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 15 0.47
19 11 0.34
20 6 0.19
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (19 bp):
GAATTTAATTTCGCAACAC
Found at i:16258 original size:12 final size:12
Alignment explanation
Indices: 16237--16270 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
16227 ACCACATTTC
*
16237 CAATACCAAACA
1 CAATATCAAACA
16249 CAATATCAAACA
1 CAATATCAAACA
*
16261 CAATCTCAAA
1 CAATATCAAA
16271 ACCCACAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:17031 original size:23 final size:22
Alignment explanation
Indices: 17005--17068 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
16995 CAGCTCATAT
17005 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
17028 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
17051 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
17069 TATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:17763 original size:21 final size:21
Alignment explanation
Indices: 17739--17781 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17729 TTCATATTCG
*
17739 TTGAGGGGGTATCAATTCCCC
1 TTGAAGGGGTATCAATTCCCC
* *
17760 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCAATTCCCC
17781 T
1 T
17782 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCAATTCCCC
Found at i:23862 original size:23 final size:23
Alignment explanation
Indices: 23836--23899 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
23826 CAGCTCATAT
23836 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCTAAGTGCCACGTAG
*
23859 AATTGCACC-AGAGTGCCGCGTAG
1 AATTGCACCTA-AGTGCCACGTAG
23882 AATTGCACCGT-AGTGCCA
1 AATTGCACC-TAAGTGCCA
23900 TATAATAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (23 bp):
AATTGCACCTAAGTGCCACGTAG
Found at i:24594 original size:21 final size:21
Alignment explanation
Indices: 24570--24612 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
24560 TTCATATTCG
* *
24570 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
24591 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
24612 T
1 T
24613 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:27991 original size:20 final size:20
Alignment explanation
Indices: 27942--27991 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
27932 ATGTTGCGAT
*
27942 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTAAAATTCG
* *
27962 CAATGTGAAAGTAAAATTCG
1 CAACGCGAAAGTAAAATTCG
*
27982 CGACGCGAAA
1 CAACGCGAAA
27992 TAAGCGTTGC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAGTAAAATTCG
Found at i:28598 original size:18 final size:18
Alignment explanation
Indices: 28577--28613 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28567 GTAATTGGAG
28577 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
28595 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
28613 T
1 T
28614 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:28620 original size:24 final size:24
Alignment explanation
Indices: 28569--28621 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
28559 TTTCAGATGT
* * *
28569 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
28593 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
28617 AATTT
1 AATTT
28622 CGGTTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:29580 original size:20 final size:20
Alignment explanation
Indices: 29531--29568 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
29521 ATGTTGCGAT
29531 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
29551 CAACGCGAAAGTCAAATT
1 CAACGCGAAAGTCAAATT
29569 TTCATCGCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:29686 original size:20 final size:20
Alignment explanation
Indices: 29661--29702 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
29651 GCAACGCTTA
29661 TTTCGCGTTGCGAATTTACC
1 TTTCGCGTTGCGAATTTACC
29681 TTTCGCGTTGCGAATTTACC
1 TTTCGCGTTGCGAATTTACC
29701 TT
1 TT
29703 CAACATGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTACC
Found at i:29821 original size:66 final size:65
Alignment explanation
Indices: 29750--29925 Score: 257
Period size: 66 Copynumber: 2.6 Consensus size: 65
29740 AATTTAAAAC
29750 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATC-AATT
29815 A
65 A
* *
29816 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
29880 AACAAATCAACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAGCAAAAAAA
29926 GTGAACCTCA
Statistics
Matches: 101, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
64 16 0.16
65 25 0.25
66 34 0.34
68 4 0.04
69 16 0.16
70 6 0.06
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTA
Found at i:30051 original size:24 final size:24
Alignment explanation
Indices: 30011--30093 Score: 141
Period size: 24 Copynumber: 3.5 Consensus size: 24
30001 CAAACATTTG
30011 CTAAAACC-ACACTTTCTACACAT
1 CTAAAACCAACACTTTCTACACAT
30034 CTAAAACCAACACTTTCTACACAT
1 CTAAAACCAACACTTTCTACACAT
* *
30058 CTAAAACCAATACTTTCTGCACAT
1 CTAAAACCAACACTTTCTACACAT
30082 CTAAAACCAACA
1 CTAAAACCAACA
30094 AACATCAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
23 8 0.14
24 48 0.86
ACGTcount: A:0.42, C:0.33, G:0.01, T:0.24
Consensus pattern (24 bp):
CTAAAACCAACACTTTCTACACAT
Found at i:30297 original size:20 final size:20
Alignment explanation
Indices: 30208--30285 Score: 122
Period size: 20 Copynumber: 3.9 Consensus size: 20
30198 ACTTTCAGCA
30208 CGCGTTGCGAATTTGACT-T
1 CGCGTTGCGAATTTGACTAT
*
30227 CTGTGTTGCGAATTTGACTAT
1 C-GCGTTGCGAATTTGACTAT
*
30248 CGCGTTGCAAATTTGACTAT
1 CGCGTTGCGAATTTGACTAT
30268 CGCGTTGCGAATTTGACT
1 CGCGTTGCGAATTTGACT
30286 TATATGTTGC
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
19 1 0.02
20 50 0.94
21 2 0.04
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGAATTTGACTAT
Found at i:30314 original size:20 final size:20
Alignment explanation
Indices: 30291--30337 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
30281 TGACTTATAT
30291 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
30311 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
30331 GTTGCGA
1 GTTGCGA
30338 AATTGGAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:30331 original size:60 final size:60
Alignment explanation
Indices: 30208--30338 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 60
30198 ACTTTCAGCA
* * * *
30208 CGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTATCGCGTTGCAAATTTGACTAT
1 CGCGTTGCGAATTTGACTTATATGTTGCGAATTTGACAATCGCGTTGCAAATTTGACGAT
*
30268 CGCGTTGCGAATTTGACTTATATGTTGCG-ATTT-ACAAATTCGCGTTGC-GATTT-ACAGATT
1 CGCGTTGCGAATTTGACTTATATGTTGCGAATTTGAC-AA-TCGCGTTGCAAATTTGAC-GA-T
30328 CGCGTTGCGAA
1 CGCGTTGCGAA
30339 ATTGGAAAGT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
58 4 0.06
59 10 0.16
60 48 0.77
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (60 bp):
CGCGTTGCGAATTTGACTTATATGTTGCGAATTTGACAATCGCGTTGCAAATTTGACGAT
Found at i:30375 original size:20 final size:20
Alignment explanation
Indices: 30306--30378 Score: 55
Period size: 20 Copynumber: 3.6 Consensus size: 20
30296 GATTTACAAA
* *
30306 TTCGCGTTGCG-ATTTACAG
1 TTCGCGTTGCGAAATTAAAG
30325 ATTCGCGTTGCGAAATTGGAAAG
1 -TTCGCGTTGCGAAATT--AAAG
*
30348 -T-G-GATTGCGAAATTATAG
1 TTCGCG-TTGCGAAATTAAAG
30366 TTCGCGTTGCGAA
1 TTCGCGTTGCGAA
30379 TTTGTTGGTC
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
18 3 0.07
19 2 0.05
20 30 0.70
21 5 0.12
23 3 0.07
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.32
Consensus pattern (20 bp):
TTCGCGTTGCGAAATTAAAG
Found at i:42142 original size:2 final size:2
Alignment explanation
Indices: 42135--42180 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
42125 AAGGTCACTA
42135 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42177 AT AT
1 AT AT
42181 TTCTCTTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42744 original size:3 final size:3
Alignment explanation
Indices: 42736--42806 Score: 83
Period size: 3 Copynumber: 23.3 Consensus size: 3
42726 TTAACTCTCC
* *
42736 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-G TCT CTCGT T-A
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TC-T TCT
42781 TCT CTCT TCT TCT TCT TCT TCT TCT T
1 TCT -TCT TCT TCT TCT TCT TCT TCT T
42807 TAGTAATGTC
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.03
3 50 0.85
4 6 0.10
5 1 0.02
ACGTcount: A:0.01, C:0.32, G:0.03, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:52064 original size:94 final size:94
Alignment explanation
Indices: 51900--52084 Score: 300
Period size: 94 Copynumber: 2.0 Consensus size: 94
51890 CAGAGGTTTG
*
51900 AATCTTGATGTTTGCGAATGGAGCAAATTGGATCTGAATGATCGCCCTCGCCTCTATAGTACATG
1 AATCTTGATGTTTGCGAATGGAGCAAATTGGATCGGAATGATCGCCCTCGCCTCTATAGTACATG
*
51965 GTCTGAATTAGTAGGTCAATAAATCAAAT
66 ATCTGAATTAGTAGGTCAATAAATCAAAT
*
51994 AATCTTGATGTTTGCGAATGGAGCAAATTAGG-TCGGAATGGTCGCCCTCGCCTCTATAGTACAT
1 AATCTTGATGTTTGCGAATGGAGCAAATT-GGATCGGAATGATCGCCCTCGCCTCTATAGTACAT
* * *
52058 TATCTGAATTAGTCGGTCAATAGATCA
65 GATCTGAATTAGTAGGTCAATAAATCA
52085 TATACCAGTG
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
94 82 0.98
95 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (94 bp):
AATCTTGATGTTTGCGAATGGAGCAAATTGGATCGGAATGATCGCCCTCGCCTCTATAGTACATG
ATCTGAATTAGTAGGTCAATAAATCAAAT
Done.