Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000889.1 Hibiscus syriacus cultivar Beakdansim tig00001739_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: 35355
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1566 original size:30 final size:31
Alignment explanation
Indices: 1526--1594 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
1516 ACAAGCCTTA
* * *
1526 GAAAATTTTGGGGACC-ATTCTATAATTTTT
1 GAAAAGTTTGGGGACCAAATCGATAATTTTT
* *
1556 GAAAAGTTTGGGTACCAAATCGGTAATTTTT
1 GAAAAGTTTGGGGACCAAATCGATAATTTTT
1587 GAAAAGTT
1 GAAAAGTT
1595 GAAAATTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (31 bp):
GAAAAGTTTGGGGACCAAATCGATAATTTTT
Found at i:5528 original size:21 final size:22
Alignment explanation
Indices: 5494--5535 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5484 AAAGAGAATT
5494 TTTATTTTACATTTT-GATCAA
1 TTTATTTTACATTTTGGATCAA
**
5515 TTTATTTTGGATTTTGGATCA
1 TTTATTTTACATTTTGGATCA
5536 TTCAGTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.24, C:0.07, G:0.12, T:0.57
Consensus pattern (22 bp):
TTTATTTTACATTTTGGATCAA
Found at i:6902 original size:26 final size:27
Alignment explanation
Indices: 6855--6912 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 27
6845 ACGAAAATTG
*
6855 ATTTCAATGTATATACAAAAAGATATGA
1 ATTTCAAGGTATATAC-AAAAGATATGA
6883 ATTTCAAGGTATATAC-AAAGATATGA
1 ATTTCAAGGTATATACAAAAGATATGA
6909 ATTT
1 ATTT
6913 ATGATAGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 14 0.48
28 15 0.52
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (27 bp):
ATTTCAAGGTATATACAAAAGATATGA
Found at i:11276 original size:17 final size:17
Alignment explanation
Indices: 11254--11292 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
11244 AGGCTGTCTT
11254 CTTGTGATGTTGTAAGC
1 CTTGTGATGTTGTAAGC
11271 CTTGTGATGTTGTAAGC
1 CTTGTGATGTTGTAAGC
*
11288 GTTGT
1 CTTGT
11293 TACAACAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.31, T:0.44
Consensus pattern (17 bp):
CTTGTGATGTTGTAAGC
Found at i:16389 original size:60 final size:60
Alignment explanation
Indices: 16325--16505 Score: 170
Period size: 60 Copynumber: 3.2 Consensus size: 60
16315 CATGCAACTA
* *
16325 CCATCTTTTGTAAACTTGGACATGTTGCAATCTTTTGTAAGTAAACTTTACATGTTACTG
1 CCATCTTCTGTAAACTTGGACATGTTGCAATCTTTTGTAAGTAAACTTGACATGTTACTG
* * ** * ** *
16385 CCATCTTCTGT-AA---GTA-A-GTT-TAA-C-TTTGT-A--AATTTGGACATGCAACTA
1 CCATCTTCTGTAAACTTGGACATGTTGCAATCTTTTGTAAGTAAACTTGACATGTTACTG
* *
16433 CCTTCTTTTGTAAACTTGGACATGTTGCAATCTTTTGTAAGTAAACTTGACATGTTACTG
1 CCATCTTCTGTAAACTTGGACATGTTGCAATCTTTTGTAAGTAAACTTGACATGTTACTG
16493 CCATCTTCTGTAA
1 CCATCTTCTGTAA
16506 GTAAGTTTAA
Statistics
Matches: 87, Mismatches: 22, Indels: 24
0.65 0.17 0.18
Matches are distributed among these distances:
48 20 0.23
49 2 0.02
50 1 0.01
51 5 0.06
52 3 0.03
53 3 0.03
54 6 0.07
55 3 0.03
56 3 0.03
57 5 0.06
58 1 0.01
59 2 0.02
60 33 0.38
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (60 bp):
CCATCTTCTGTAAACTTGGACATGTTGCAATCTTTTGTAAGTAAACTTGACATGTTACTG
Found at i:16490 original size:108 final size:108
Alignment explanation
Indices: 16301--16518 Score: 418
Period size: 108 Copynumber: 2.0 Consensus size: 108
16291 TTTGCCATTT
16301 TTTGTAAATTTGGACATGCAACTACCATCTTTTGTAAACTTGGACATGTTGCAATCTTTTGTAAG
1 TTTGTAAATTTGGACATGCAACTACCATCTTTTGTAAACTTGGACATGTTGCAATCTTTTGTAAG
*
16366 TAAACTTTACATGTTACTGCCATCTTCTGTAAGTAAGTTTAAC
66 TAAACTTGACATGTTACTGCCATCTTCTGTAAGTAAGTTTAAC
*
16409 TTTGTAAATTTGGACATGCAACTACCTTCTTTTGTAAACTTGGACATGTTGCAATCTTTTGTAAG
1 TTTGTAAATTTGGACATGCAACTACCATCTTTTGTAAACTTGGACATGTTGCAATCTTTTGTAAG
16474 TAAACTTGACATGTTACTGCCATCTTCTGTAAGTAAGTTTAAC
66 TAAACTTGACATGTTACTGCCATCTTCTGTAAGTAAGTTTAAC
16517 TT
1 TT
16519 GTTGCTGTCA
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (108 bp):
TTTGTAAATTTGGACATGCAACTACCATCTTTTGTAAACTTGGACATGTTGCAATCTTTTGTAAG
TAAACTTGACATGTTACTGCCATCTTCTGTAAGTAAGTTTAAC
Found at i:16505 original size:33 final size:32
Alignment explanation
Indices: 16442--16606 Score: 109
Period size: 33 Copynumber: 5.0 Consensus size: 32
16432 ACCTTCTTTT
*
16442 GTAAACTTGGACATGT--TGCAATCTTTTGTAA
1 GTAAACTT-GACATGTACTGCCATCTTTTGTAA
*
16473 GTAAACTTGACATGTTACTGCCATCTTCTGTAA
1 GTAAACTTGACATG-TACTGCCATCTTTTGTAA
** * * * * * *
16506 GTAAGTTTAACTTGTTGCTGTCATTTTTTGAAA
1 GTAAACTTGACATG-TACTGCCATCTTTTGTAA
* * * *
16539 GTAAACTTAACATGCAGTTGCCATATTTTGTAA
1 GTAAACTTGACATGTA-CTGCCATCTTTTGTAA
* **
16572 GTAAACTTGTTCATGATACTGTTATCTTTTGTAA
1 GTAAACTTG-ACATG-TACTGCCATCTTTTGTAA
16606 G
1 G
16607 GAAAATGTTG
Statistics
Matches: 101, Mismatches: 27, Indels: 9
0.74 0.20 0.07
Matches are distributed among these distances:
30 6 0.06
31 9 0.09
33 68 0.67
34 17 0.17
35 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (32 bp):
GTAAACTTGACATGTACTGCCATCTTTTGTAA
Found at i:16618 original size:24 final size:24
Alignment explanation
Indices: 16591--16647 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
16581 TTCATGATAC
16591 TGTTATCTTTTGTAAGGAAAATGT
1 TGTTATCTTTTGTAAGGAAAATGT
16615 TGTTATCTTTTGTAAGGAAAATGT
1 TGTTATCTTTTGTAAGGAAAATGT
*
16639 TGTCATCTT
1 TGTTATCTT
16648 ATATAAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.47
Consensus pattern (24 bp):
TGTTATCTTTTGTAAGGAAAATGT
Found at i:16690 original size:36 final size:36
Alignment explanation
Indices: 16642--16711 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
16632 AAAATGTTGT
** *
16642 CATCTTATATAAATTTGGATATGCTTCCATATTTGC
1 CATCTTATATAAATTTAAATATGCTGCCATATTTGC
*
16678 CATCTT-TAATAAATTTAAATGTGCTGCCATATTT
1 CATCTTAT-ATAAATTTAAATATGCTGCCATATTT
16712 TGTAAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 1 0.03
36 28 0.97
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (36 bp):
CATCTTATATAAATTTAAATATGCTGCCATATTTGC
Found at i:18978 original size:62 final size:61
Alignment explanation
Indices: 18884--19019 Score: 146
Period size: 62 Copynumber: 2.2 Consensus size: 61
18874 TAGATTGTAG
* * **
18884 CCTTAGTTTTTAAATTTTTTAATTCAGTCACTTAGATTAAACTTTAGACTATTTGTTAGAA
1 CCTTAGATTTTAAATTTTTTAATTCAGCCACTTAGATTAAACTTTAGACTATTAATTAGAA
* * * * * * * * *
18945 CTTTAGATTTTAGATTCTTTTACTTTAGCCACTTAGGTTAGATTTTAGATTATTAATTAGAG
1 CCTTAGATTTTAAATT-TTTTAATTCAGCCACTTAGATTAAACTTTAGACTATTAATTAGAA
19007 CCTTAGATTTTAA
1 CCTTAGATTTTAA
19020 GTCCTTTAAT
Statistics
Matches: 59, Mismatches: 15, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
61 13 0.22
62 46 0.78
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48
Consensus pattern (61 bp):
CCTTAGATTTTAAATTTTTTAATTCAGCCACTTAGATTAAACTTTAGACTATTAATTAGAA
Found at i:22160 original size:22 final size:21
Alignment explanation
Indices: 22142--22206 Score: 84
Period size: 22 Copynumber: 3.2 Consensus size: 21
22132 AACGGTCAAC
22142 GGTC-CGGTCGGGTCGGGTCG
1 GGTCACGGTCGGGTCGGGTCG
22162 GGTCAACGGTCGGGTCGGGTCG
1 GGTC-ACGGTCGGGTCGGGTCG
*
22184 GGTC-GGGTC-GGTC-GGTCG
1 GGTCACGGTCGGGTCGGGTCG
22202 GGTCA
1 GGTCA
22207 GACCTTTCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
18 9 0.22
19 4 0.10
20 8 0.20
22 20 0.49
ACGTcount: A:0.05, C:0.23, G:0.52, T:0.20
Consensus pattern (21 bp):
GGTCACGGTCGGGTCGGGTCG
Found at i:22165 original size:27 final size:27
Alignment explanation
Indices: 22135--22192 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
22125 GAAAGTCAAC
22135 GGTCAACGGTCCGGTCGGGTCGGGTCG
1 GGTCAACGGTCCGGTCGGGTCGGGTCG
*
22162 GGTCAACGGTCGGGTCGGGTCGGGTCG
1 GGTCAACGGTCCGGTCGGGTCGGGTCG
22189 GGTC
1 GGTC
22193 GGTCGGTCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.07, C:0.24, G:0.50, T:0.19
Consensus pattern (27 bp):
GGTCAACGGTCCGGTCGGGTCGGGTCG
Found at i:22198 original size:4 final size:5
Alignment explanation
Indices: 22142--22205 Score: 78
Period size: 5 Copynumber: 12.8 Consensus size: 5
22132 AACGGTCAAC
* *
22142 GGTCC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCG GGTC-
1 GGTCG GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG
22193 GGTC- GGTCG GGTC
1 GGTCG GGTCG GGTC
22206 AGACCTTTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
4 8 0.15
5 41 0.77
7 4 0.08
ACGTcount: A:0.03, C:0.23, G:0.53, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:29428 original size:7 final size:7
Alignment explanation
Indices: 29416--29453 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
29406 GTCAAAGAAA
29416 GTCAACG
1 GTCAACG
29423 GTCAACG
1 GTCAACG
29430 GTCAACG
1 GTCAACG
*
29437 GTCAATG
1 GTCAACG
29444 GTCAACG
1 GTCAACG
29451 GTC
1 GTC
29454 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:29460 original size:5 final size:5
Alignment explanation
Indices: 29450--29498 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
29440 AATGGTCAAC
*
29450 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC- GGTC- GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
29499 AGACCGGTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 8 0.21
5 27 0.69
7 4 0.10
ACGTcount: A:0.04, C:0.22, G:0.53, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:29471 original size:22 final size:22
Alignment explanation
Indices: 29443--29487 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
29433 AACGGTCAAT
29443 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
29465 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
29487 G
1 G
29488 TCGGTCGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.09, C:0.22, G:0.51, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:29507 original size:9 final size:9
Alignment explanation
Indices: 29495--29561 Score: 62
Period size: 10 Copynumber: 7.0 Consensus size: 9
29485 CGGTCGGTCG
*
29495 GGTCAGACC
1 GGTCAAACC
29504 GGTCAAACC
1 GGTCAAACC
29513 GGTTCAAACC
1 GG-TCAAACC
*
29523 GGTTCGAACC
1 GG-TCAAACC
*
29533 GGTTGAAACC
1 GG-TCAAACC
*
29543 GATCAAACC
1 GGTCAAACC
29552 GGTCAGAACC
1 GGTCA-AACC
29562 TTTGACTCGT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
9 20 0.41
10 29 0.59
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:29521 original size:10 final size:10
Alignment explanation
Indices: 29501--29554 Score: 67
Period size: 10 Copynumber: 5.6 Consensus size: 10
29491 GTCGGGTCAG
29501 ACCGG-TCAA
1 ACCGGTTCAA
29510 ACCGGTTCAA
1 ACCGGTTCAA
*
29520 ACCGGTTCGA
1 ACCGGTTCAA
*
29530 ACCGGTTGAA
1 ACCGGTTCAA
*
29540 ACC-GATCAA
1 ACCGGTTCAA
29549 ACCGGT
1 ACCGGT
29555 CAGAACCTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
9 12 0.32
10 25 0.68
ACGTcount: A:0.30, C:0.30, G:0.24, T:0.17
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:29560 original size:29 final size:29
Alignment explanation
Indices: 29495--29561 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
29485 CGGTCGGTCG
*
29495 GGTCAG-ACCGGTCAAACCGGTTCAAACC
1 GGTCAGAACCGGTCAAACCGGATCAAACC
*
29523 GGTTC-GAACCGGTTGAAACC-GATCAAACC
1 GG-TCAGAACCGG-TCAAACCGGATCAAACC
29552 GGTCAGAACC
1 GGTCAGAACC
29562 TTTGACTCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
28 5 0.15
29 22 0.67
30 6 0.18
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.15
Consensus pattern (29 bp):
GGTCAGAACCGGTCAAACCGGATCAAACC
Found at i:33104 original size:135 final size:136
Alignment explanation
Indices: 32815--33212 Score: 469
Period size: 136 Copynumber: 2.9 Consensus size: 136
32805 AGCTAGGAAT
* ** * ***
32815 ATTAAAAGACTAAAATAAGAA-TAAACCTAAGGTTTAGACTCTAATATTAAACCCTAGCCAATTT
1 ATTAAAAGACTAAAATAA-AATTAAACCTAA-ATGAAGGCTCTAATATTAAACCCTAATGAATTT
* * * * * *
32879 TAAGAGATTTTATTCAAGTGAATAATCAAAATAGAACCTCGACCATAAGTGA-GGACCATTTTAA
64 TAA-A-A-TTTATTAAATTGAATAATTAAATTGGAACCTCGAGCATAAGTGATGG-CCA-TTTAA
*
32943 AAAATTCTCCTAA
124 AAAATTCACCTAA
*
32956 ATTAAAAGACTAAAATAAAATTAAACCTAAATGAAGGCTCTACTATTAAACCCTAATGAATTTTA
1 ATTAAAAGACTAAAATAAAATTAAACCTAAATGAAGGCTCTAATATTAAACCCTAATGAATTTTA
* *
33021 CAATCTATTAAATTGAATAATTAAATTGGAACCTCGAGCATAAGTGATGGCCATTT-AAAAATTC
66 AAATTTATTAAATTGAATAATTAAATTGGAACCTCGAGCATAAGTGATGGCCATTTAAAAAATTC
33085 ACCTAA
131 ACCTAA
* * * * *
33091 GTTAAAAGACTAAAATGAAATTAAACCCAAAATGAAGGCTCTAGTATTAAACTCTAATGAATTTT
1 ATTAAAAGACTAAAATAAAATTAAA-CCTAAATGAAGGCTCTAATATTAAACCCTAATGAATTTT
* * * *
33156 AAAATTTATTAAATTGAATAATTAAATTGGAATCTTGAGCATAAGTGGTGACCATTT
65 AAAATTTATTAAATTGAATAATTAAATTGGAACCTCGAGCATAAGTGATGGCCATTT
33213 TAAATATTTT
Statistics
Matches: 226, Mismatches: 28, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
135 36 0.16
136 90 0.40
137 40 0.18
138 3 0.01
139 1 0.00
140 29 0.13
141 27 0.12
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (136 bp):
ATTAAAAGACTAAAATAAAATTAAACCTAAATGAAGGCTCTAATATTAAACCCTAATGAATTTTA
AAATTTATTAAATTGAATAATTAAATTGGAACCTCGAGCATAAGTGATGGCCATTTAAAAAATTC
ACCTAA
Found at i:33257 original size:136 final size:135
Alignment explanation
Indices: 32897--33278 Score: 462
Period size: 136 Copynumber: 2.8 Consensus size: 135
32887 TTTATTCAAG
* * * *
32897 TGAATAATCAAAATAGAACCTCGACCATAAGTGAG-GACCATTTTAAAAAATTCTCCTAAATTAA
1 TGAATAATTAAATTGGAACCTCGAGCATAAGTG-GTGACCATTTT-AAAAATTCTCCTAAATTAA
* * * *
32961 AAGACTAAAATAAAATTAAACCTAAATGAAGGCTCTACTATTAAACCCTAATGAATTTTACAATC
64 AAGACTAAAATGAAATAAAACC-AAATGAAGGCTCTAGTATTAAACCCTAATGAATTTTAAAATC
33026 TATTAAAT
128 TATTAAAT
* * * *
33034 TGAATAATTAAATTGGAACCTCGAGCATAAGTGATGGCCA-TTTAAAAATTCACCTAAGTTAAAA
1 TGAATAATTAAATTGGAACCTCGAGCATAAGTGGTGACCATTTTAAAAATTCTCCTAAATTAAAA
* * *
33098 GACTAAAATGAAATTAAACCCAAAATGAAGGCTCTAGTATTAAACTCTAATGAATTTTAAAATTT
66 GACTAAAATGAAA-TAAAACC-AAATGAAGGCTCTAGTATTAAACCCTAATGAATTTTAAAATCT
33163 ATTAAAT
129 ATTAAAT
* * * * * * *
33170 TGAATAATTAAATTGGAATCTTGAGCATAAGTGGTGACCATTTTAAATATTTTCTTAAATTTAAG
1 TGAATAATTAAATTGGAACCTCGAGCATAAGTGGTGACCATTTTAAAAATTCTCCTAAATTAAAA
* * *
33235 GATTAAAGTGAAATAAAACCAAATGTTAAAGCTCTAGTATTAAA
66 GACTAAAATGAAATAAAACCAAATG--AAGGCTCTAGTATTAAA
33279 ACCCAACGAA
Statistics
Matches: 209, Mismatches: 31, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
135 36 0.17
136 96 0.46
137 77 0.37
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.31
Consensus pattern (135 bp):
TGAATAATTAAATTGGAACCTCGAGCATAAGTGGTGACCATTTTAAAAATTCTCCTAAATTAAAA
GACTAAAATGAAATAAAACCAAATGAAGGCTCTAGTATTAAACCCTAATGAATTTTAAAATCTAT
TAAAT
Found at i:33502 original size:21 final size:21
Alignment explanation
Indices: 33473--33525 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
33463 ATTCTGACTA
33473 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
33494 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
33515 TCGCAATGCGA
1 TCGCATTGCGA
33526 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:33540 original size:20 final size:20
Alignment explanation
Indices: 33515--33620 Score: 185
Period size: 20 Copynumber: 5.3 Consensus size: 20
33505 TTTTCCTAAT
*
33515 TCGCAATGCGAATACGTAAA
1 TCGCAATGCAAATACGTAAA
33535 TCGCAATGCAAATACGTAAA
1 TCGCAATGCAAATACGTAAA
* *
33555 TCGCAATGCGAATATGTAAA
1 TCGCAATGCAAATACGTAAA
33575 TCGCAATGCAAATACGTAAA
1 TCGCAATGCAAATACGTAAA
33595 TCGCAATGCAAATACGTAAA
1 TCGCAATGCAAATACGTAAA
33615 TCGCAA
1 TCGCAA
33621 CGCGAATCTG
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (20 bp):
TCGCAATGCAAATACGTAAA
Found at i:33637 original size:20 final size:20
Alignment explanation
Indices: 33614--33720 Score: 187
Period size: 20 Copynumber: 5.3 Consensus size: 20
33604 AAATACGTAA
* *
33614 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
33634 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
33654 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
33674 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
33694 ATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
33714 ATCGCAA
1 ATCGCAA
33721 TACTGAATTT
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 84 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:33640 original size:60 final size:60
Alignment explanation
Indices: 33515--33627 Score: 208
Period size: 60 Copynumber: 1.9 Consensus size: 60
33505 TTTTCCTAAT
* *
33515 TCGCAATGCGAATACGTAAATCGCAATGCAAATACGTAAATCGCAATGCGAATATGTAAA
1 TCGCAATGCAAATACGTAAATCGCAATGCAAATACGTAAATCGCAACGCGAATATGTAAA
33575 TCGCAATGCAAATACGTAAATCGCAATGCAAATACGTAAATCGCAACGCGAAT
1 TCGCAATGCAAATACGTAAATCGCAATGCAAATACGTAAATCGCAACGCGAAT
33628 CTGACTATCG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (60 bp):
TCGCAATGCAAATACGTAAATCGCAATGCAAATACGTAAATCGCAACGCGAATATGTAAA
Found at i:33658 original size:60 final size:60
Alignment explanation
Indices: 33534--33721 Score: 170
Period size: 60 Copynumber: 3.1 Consensus size: 60
33524 GAATACGTAA
* * * * * * *
33534 ATCGCAATGCAAATACGTAAATCGCAATGCGAATATGTA-AATCGCAATGCAAATAC-GTA-A
1 ATCGCAATGCAAATACGTAAATCGCAACGCGAATCTG-ACTATCGCAACG-AGATTCTG-ACT
33594 ATCGCAATGCAAATACGTAAATCGCAACGCGAATCTGACTATCGCAACGAGATTCTGACT
1 ATCGCAATGCAAATACGTAAATCGCAACGCGAATCTGACTATCGCAACGAGATTCTGACT
* * * * * * *
33654 ATCGCAACG-AGATTC-TGACTATCGCAACGAGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAATGCAAATACGT-A-AATCGCAACGCGAATCTGACTATCGCAACGAGATTCTGACT
33714 ATCGCAAT
1 ATCGCAAT
33722 ACTGAATTTC
Statistics
Matches: 108, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
58 1 0.01
59 11 0.10
60 96 0.89
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (60 bp):
ATCGCAATGCAAATACGTAAATCGCAACGCGAATCTGACTATCGCAACGAGATTCTGACT
Found at i:34573 original size:23 final size:24
Alignment explanation
Indices: 34546--34598 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 24
34536 GTATTCGAAA
34546 TTTGATCTTGGTCAATAC-CGGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
34569 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
34593 TTTGAT
1 TTTGAT
34599 GATTTTTAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.42
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Done.