Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006371.1 Hibiscus syriacus cultivar Beakdansim tig00015321_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: 74667
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:628 original size:20 final size:20
Alignment explanation
Indices: 603--672 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
593 GGGAAAATCA
*
603 CAATGCGATACTGACTATTG
1 CAATGCGATACTGACTATCG
623 CAATGCGATACTGACTATCG
1 CAATGCGATACTGACTATCG
*
643 CAATGCGATACTTACTATCG
1 CAATGCGATACTGACTATCG
663 CAATGCGATA
1 CAATGCGATA
673 ATACAAAATC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (20 bp):
CAATGCGATACTGACTATCG
Found at i:715 original size:19 final size:20
Alignment explanation
Indices: 691--729 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
681 TCGCACGAGA
691 CTGAC-TTCGCAACGCGATT
1 CTGACTTTCGCAACGCGATT
710 CTGACTTTCGCAACGCGATT
1 CTGACTTTCGCAACGCGATT
730 TACATAGCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.28
Consensus pattern (20 bp):
CTGACTTTCGCAACGCGATT
Found at i:1316 original size:18 final size:19
Alignment explanation
Indices: 1278--1321 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1268 GCTACGAGAG
*
1278 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
* *
1297 AA-CGCAATGCGAAACCAA
1 AATCGCAACGCGAAACAAA
1315 AATCGCA
1 AATCGCA
1322 TTACGATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:1374 original size:52 final size:52
Alignment explanation
Indices: 1317--1439 Score: 192
Period size: 52 Copynumber: 2.4 Consensus size: 52
1307 GAAACCAAAA
* **
1317 TCGCATTACGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATAGTCATT
*
1369 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATAGTCATT
* *
1421 TCGCGTTGCGATTCTCATT
1 TCGCATTGCGATTTTCATT
1440 ATCTTGTGCG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATAGTCATT
Found at i:1411 original size:33 final size:33
Alignment explanation
Indices: 1374--1436 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
1364 TCATTTCGCA
**
1374 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1407 TTGCGATAGTCATTTCGCGTTGCGATTCTC
1 TTGCGATAGTCATTTCGCGTTGCGATTCTC
1437 ATTATCTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:1438 original size:19 final size:19
Alignment explanation
Indices: 1325--1439 Score: 97
Period size: 19 Copynumber: 6.6 Consensus size: 19
1315 AATCGCATTA
*
1325 CGATTTTCATTTCGCGTTG
1 CGATTCTCATTTCGCGTTG
*
1344 CGATTCTC---T--CATTG
1 CGATTCTCATTTCGCGTTG
* *
1358 CGATTTTCATTTCGCATTG
1 CGATTCTCATTTCGCGTTG
*
1377 CGATTTTCATTTCGCGTTG
1 CGATTCTCATTTCGCGTTG
1396 CGATTCTC---T--CGTTG
1 CGATTCTCATTTCGCGTTG
**
1410 CGATAGTCATTTCGCGTTG
1 CGATTCTCATTTCGCGTTG
1429 CGATTCTCATT
1 CGATTCTCATT
1440 ATCTTGTGCG
Statistics
Matches: 77, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
14 22 0.29
16 2 0.03
17 2 0.03
19 51 0.66
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.44
Consensus pattern (19 bp):
CGATTCTCATTTCGCGTTG
Found at i:3347 original size:93 final size:88
Alignment explanation
Indices: 3182--3361 Score: 288
Period size: 93 Copynumber: 2.0 Consensus size: 88
3172 ATTGCTTAGT
3182 AATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTTGTCT
1 AATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTTGTCT
*
3247 TTTTTTTGTCTTTTGGTTGAAGTA
66 TTGTTTTGTC-TTTGGTTGAAGTA
* *
3271 AATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTT
1 AATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGTATTT
3336 GTCTTTGTTTTGTCTTTGGTTGAAGT
62 GTCTTTGTTTTGTCTTTGGTTGAAGT
3362 TTTGAAATAT
Statistics
Matches: 84, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
89 31 0.37
91 3 0.04
92 14 0.17
93 36 0.43
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (88 bp):
AATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTTGTCT
TTGTTTTGTCTTTGGTTGAAGTA
Found at i:3674 original size:42 final size:42
Alignment explanation
Indices: 3574--3747 Score: 190
Period size: 42 Copynumber: 4.2 Consensus size: 42
3564 CCCGACTCGC
* * * *
3574 CTGTCATCCCTC-AGAGTCCACTCCTATCGTTGAAGA-GCCC
1 CTGTCATCCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCA
* * *
3614 CTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCA
* * * * * *
3656 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCC
1 CTGTCATCCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCA
* * *
3698 CTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCA
3740 CTGTCATC
1 CTGTCATC
3748 GTTGAAGAGG
Statistics
Matches: 105, Mismatches: 27, Indels: 2
0.78 0.20 0.01
Matches are distributed among these distances:
40 10 0.10
41 20 0.19
42 75 0.71
ACGTcount: A:0.21, C:0.39, G:0.17, T:0.24
Consensus pattern (42 bp):
CTGTCATCCCTCGAGAGTCCACTCCCACCGTTCAAGAGGCCA
Found at i:3750 original size:21 final size:21
Alignment explanation
Indices: 3642--3757 Score: 56
Period size: 21 Copynumber: 5.5 Consensus size: 21
3632 CCCCTCCCAC
3642 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
** * *
3663 CCCTCAAGAGTCCACT-CCTAT
1 CGTTCAAGAGGCCACTGTC-AT
* * * *
3684 CATTGAAGAGGCCCCTATCATT
1 CGTTCAAGAGGCCACTGTCA-T
* * * * ** *
3706 C-CTCGAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCACTGTCAT
3726 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
*
3747 CGTTGAAGAGG
1 CGTTCAAGAGG
3758 TACCTCCCAC
Statistics
Matches: 66, Mismatches: 25, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
20 2 0.03
21 61 0.92
22 3 0.05
ACGTcount: A:0.23, C:0.34, G:0.21, T:0.22
Consensus pattern (21 bp):
CGTTCAAGAGGCCACTGTCAT
Found at i:3756 original size:84 final size:83
Alignment explanation
Indices: 3574--3747 Score: 323
Period size: 84 Copynumber: 2.1 Consensus size: 83
3564 CCCGACTCGC
*
3574 CTGTCATCCCTC-AGAGTCCACTCCTATCGTTGAAGAGCCCCTATCATTCCTCGAGAGTCCCCTC
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGCCCCTATCATTCCTCGAGAGTCCCCTC
3638 CCACCGTTCAAGAGGCCA
66 CCACCGTTCAAGAGGCCA
3656 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGA-GCCCCTATCATTCCTCGAGAGTCCCCT
3721 CCCACCGTTCAAGAGGCCA
65 CCCACCGTTCAAGAGGCCA
3740 CTGTCATC
1 CTGTCATC
3748 GTTGAAGAGG
Statistics
Matches: 89, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
82 12 0.13
83 23 0.26
84 54 0.61
ACGTcount: A:0.21, C:0.39, G:0.17, T:0.24
Consensus pattern (83 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGCCCCTATCATTCCTCGAGAGTCCCCTC
CCACCGTTCAAGAGGCCA
Found at i:3764 original size:42 final size:41
Alignment explanation
Indices: 3627--3777 Score: 142
Period size: 42 Copynumber: 3.6 Consensus size: 41
3617 TCATTCCTCG
* * *
3627 AGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCATCCCTCA
1 AGAGT-CCCTCCCACCATTCAAGAGGCCACTGTCATCCTTGA
* * * * * *
3669 AGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCG-
1 AGAGTCC-CTCCCACCATTCAAGAGGCCACTGTCA-TCCTTGA
* *
3711 AGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCATCGTTGA
1 AGAGT-CCCTCCCACCATTCAAGAGGCCACTGTCATCCTTGA
*
3753 AGAGGTACCTCCCACCATTCAAGAG
1 AGA-GTCCCTCCCACCATTCAAGAG
3778 CCCGATTCAC
Statistics
Matches: 85, Mismatches: 19, Indels: 10
0.75 0.17 0.09
Matches are distributed among these distances:
41 6 0.07
42 72 0.85
43 7 0.08
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (41 bp):
AGAGTCCCTCCCACCATTCAAGAGGCCACTGTCATCCTTGA
Found at i:3777 original size:84 final size:84
Alignment explanation
Indices: 3574--3777 Score: 270
Period size: 84 Copynumber: 2.5 Consensus size: 84
3564 CCCGACTCGC
* * * * *
3574 CTGTCATCCCTC-AGAGTCCACTCCTATCGTTGAAGA-GCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTACACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
3637 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * *
3656 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTACACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
3721 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** *
3740 CTGTCATCGTTGAAGAGGTAC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTACACTCCCACCATTCAAGAG
3778 CCCGATTCAC
Statistics
Matches: 111, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
82 12 0.11
83 23 0.21
84 73 0.66
85 3 0.03
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTACACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:5126 original size:13 final size:13
Alignment explanation
Indices: 5110--5142 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5100 ATTGTTTAAT
5110 TGATTTGTAAAGG
1 TGATTTGTAAAGG
*
5123 TGA-TTGTAAAGT
1 TGATTTGTAAAGG
5135 TGATTTGT
1 TGATTTGT
5143 TTAATTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (13 bp):
TGATTTGTAAAGG
Found at i:5270 original size:19 final size:19
Alignment explanation
Indices: 5255--5295 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
5245 TATCGCAATT
5255 AGAAATGAAAATCGCAACG
1 AGAAATGAAAATCGCAACG
*
5274 CGAAATGAAAATCGCAACG
1 AGAAATGAAAATCGCAACG
5293 AGA
1 AGA
5296 GAATCGCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.17, G:0.22, T:0.10
Consensus pattern (19 bp):
AGAAATGAAAATCGCAACG
Found at i:5363 original size:33 final size:32
Alignment explanation
Indices: 5321--5446 Score: 166
Period size: 33 Copynumber: 3.9 Consensus size: 32
5311 ATTAAATTCG
*
5321 CGTTGCGATTTTCATTTCGCATTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
5354 CGTTGCGATTTTTATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
5387 CGTTGCGA-TTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
5419 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
5447 AGTAATTTTC
Statistics
Matches: 81, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
30 3 0.04
32 24 0.30
33 51 0.63
35 3 0.04
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:5421 original size:65 final size:66
Alignment explanation
Indices: 5314--5445 Score: 221
Period size: 65 Copynumber: 2.0 Consensus size: 66
5304 ACGCGAAATT
* * *
5314 AAATTCGCGTTGCGATTTTCATTTCGCATTGTGATTCCCTCGTTGCGATTTTTATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
5379 G
66 G
*
5380 AAATTAGCGTTGCGA-TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
5444 G
66 G
5445 A
1 A
5446 TAGTAATTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
65 48 0.77
66 14 0.23
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:7957 original size:19 final size:20
Alignment explanation
Indices: 7933--8019 Score: 142
Period size: 20 Copynumber: 4.5 Consensus size: 20
7923 CATCATCAAA
*
7933 ATCGCAATGCG-AAATGGCT
1 ATCGCAACGCGAAAATGGCT
7952 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
7972 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
7992 ATCGCAACGCG-AAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
8011 ATCGTAACG
1 ATCGCAACG
8020 ACAAATCGCA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
19 26 0.40
20 39 0.60
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:8007 original size:39 final size:39
Alignment explanation
Indices: 7933--8019 Score: 140
Period size: 39 Copynumber: 2.2 Consensus size: 39
7923 CATCATCAAA
*
7933 ATCGCAATGCGAAATGGCTATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAATGGCTATCGCAACGCGAAAATGGCT
7972 ATCGCAACGCGAAAATGGCTATCGCAACGCG-AAATGGCT
1 ATCGCAACGCG-AAATGGCTATCGCAACGCGAAAATGGCT
*
8011 ATCGTAACG
1 ATCGCAACG
8020 ACAAATCGCA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
39 26 0.58
40 19 0.42
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.17
Consensus pattern (39 bp):
ATCGCAACGCGAAATGGCTATCGCAACGCGAAAATGGCT
Found at i:8085 original size:19 final size:19
Alignment explanation
Indices: 8044--8108 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
8034 GAAATGAAAA
8044 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
8060 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
8077 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
8096 TCGCATTGCGATT
1 TCGCATTGCGATT
8109 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.25
16 3 0.07
17 3 0.07
19 27 0.61
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:8139 original size:20 final size:20
Alignment explanation
Indices: 8114--8152 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
8104 CGATTCTCTC
8114 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
8134 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
8153 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:8254 original size:14 final size:14
Alignment explanation
Indices: 8235--8271 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
8225 CATCAATTAA
8235 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
8249 ACAAATCATCTTTT
1 ACAAATCAACATTT
8263 ACAAATCAA
1 ACAAATCAA
8272 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:10152 original size:20 final size:20
Alignment explanation
Indices: 10110--10175 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
10100 TAGTTTACTT
* * **
10110 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAAATGACTA
10130 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
10150 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
10170 TCGCAA
1 TCGCAA
10176 TGCGAAATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.41, C:0.26, G:0.18, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:10184 original size:19 final size:20
Alignment explanation
Indices: 10129--10185 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
10119 GAAACTTAAA
* *
10129 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGGAAATGACT
*
10149 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
*
10169 ATCGCAATGC-GAAATGA
1 ATCGCAACGCGGAAATGA
10186 AAATCGCAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 6 0.19
20 26 0.81
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:10204 original size:14 final size:14
Alignment explanation
Indices: 10185--10224 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
10175 ATGCGAAATG
*
10185 AAAATCGCAATGAC
1 AAAATCGCAACGAC
10199 AAAATCGCAACGAC
1 AAAATCGCAACGAC
10213 AAAATCGCAACG
1 AAAATCGCAACG
10225 CGAAACACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.50, C:0.25, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:10277 original size:14 final size:14
Alignment explanation
Indices: 10258--10315 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
10248 TTTCATTTCG
*
10258 CGTTGCAATTTTGT
1 CGTTGCGATTTTGT
*
10272 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
10288 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
10304 CGTTGCGATTTT
1 CGTTGCGATTTT
10316 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:10322 original size:33 final size:33
Alignment explanation
Indices: 10241--10331 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
10231 ACAAATCGCA
* *
10241 TTGCGATTTTCATTTCGCGTTGCAATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
10274 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
10306 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
10332 AGCCATTTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:10367 original size:20 final size:20
Alignment explanation
Indices: 10318--10370 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
10308 GCGATTTTCA
*
10318 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
10338 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
10358 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
10371 AGTAAACTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:10875 original size:18 final size:18
Alignment explanation
Indices: 10849--10893 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
10839 GTCGATCAGA
*
10849 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
10867 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
10885 TGATGGCTC
1 TGATGGCTC
10894 CCAAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:12258 original size:20 final size:20
Alignment explanation
Indices: 12210--12268 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
12200 AATAGTTTCT
** *
12210 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
12230 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
12250 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
12269 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:12556 original size:22 final size:22
Alignment explanation
Indices: 12529--12572 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
12519 GATGGAGATA
12529 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
12551 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
12573 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.45, T:0.18
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:12785 original size:20 final size:20
Alignment explanation
Indices: 12760--12811 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
12750 ATTATGTATT
12760 ATCGCGTTGCGAAAGTCAAA
1 ATCGCGTTGCGAAAGTCAAA
**
12780 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAAA
*
12800 ATCTCGTTGCGA
1 ATCGCGTTGCGA
12812 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAAA
Found at i:12845 original size:20 final size:20
Alignment explanation
Indices: 12739--12850 Score: 75
Period size: 20 Copynumber: 5.5 Consensus size: 20
12729 CGCTTTGAAA
*
12739 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * **
12760 ATCGCGTTGCGAAAGTCAAA
1 ATCGCATTGCGATAGTCAGT
* *
12780 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
12800 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
12821 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
12841 ATCGCATTGC
1 ATCGCATTGC
12851 AATTTTCCCA
Statistics
Matches: 73, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
19 5 0.07
20 43 0.59
21 23 0.32
22 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:12872 original size:41 final size:41
Alignment explanation
Indices: 12780--12874 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
12770 GAAAGTCAAA
* * * * ** *
12780 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCCAAT
*
12821 ATCGCATTGCGATAGTCAGTATCGCATTGCAATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTT-CCAAT
12863 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
12875 TTACTTATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCCAAT
Found at i:13794 original size:14 final size:14
Alignment explanation
Indices: 13775--13805 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13765 CAAAATTATT
13775 TAAATAAATTCAAA
1 TAAATAAATTCAAA
*
13789 TAAATAAATTCTAA
1 TAAATAAATTCAAA
13803 TAA
1 TAA
13806 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATAAATTCAAA
Found at i:13822 original size:19 final size:19
Alignment explanation
Indices: 13800--13858 Score: 50
Period size: 19 Copynumber: 3.0 Consensus size: 19
13790 AAATAAATTC
13800 TAATAATTTAAATAATATA
1 TAATAATTTAAATAATATA
*
13819 TAATCAATTT-CATAATATTCA
1 TAAT-AATTTAAATAATA-T-A
*
13840 TAA-AATTCAAAATAATATA
1 TAATAATT-TAAATAATATA
13859 GTTTTGTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
19 15 0.47
20 7 0.22
21 10 0.31
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATAATTTAAATAATATA
Found at i:15015 original size:29 final size:29
Alignment explanation
Indices: 14981--15039 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
14971 CCTAAATTAA
*
14981 TTTGATGTCATTGCTTACATTAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
*
15010 TTTGATGTCATTTCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
15039 T
1 T
15040 AGGTGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:19700 original size:29 final size:29
Alignment explanation
Indices: 19666--19724 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
19656 CCTAAATTAA
19666 TTTGATGTCATTGATTACATCAATTTAGT
1 TTTGATGTCATTGATTACATCAATTTAGT
**
19695 TTTGATGTCATTTCTTACATCAATTTAGT
1 TTTGATGTCATTGATTACATCAATTTAGT
19724 T
1 T
19725 AGGTGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGATTACATCAATTTAGT
Found at i:21175 original size:30 final size:30
Alignment explanation
Indices: 21136--21193 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
21126 AATAATCTAC
21136 ATAACATAGATTAAAACA-ATTAAAACAGCA
1 ATAACATAGA-TAAAACAGATTAAAACAGCA
* * *
21166 ATAATATAGATAATATAGATTAAAACAG
1 ATAACATAGATAAAACAGATTAAAACAG
21194 GACTACTGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.24
Consensus pattern (30 bp):
ATAACATAGATAAAACAGATTAAAACAGCA
Found at i:22670 original size:13 final size:14
Alignment explanation
Indices: 22648--22682 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
22638 CCTATTACCA
22648 TGCACTATATATTT
1 TGCACTATATATTT
22662 TGCAC-ATATATTT
1 TGCACTATATATTT
*
22675 TGAACTAT
1 TGCACTAT
22683 TTGTGCATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (14 bp):
TGCACTATATATTT
Found at i:23971 original size:18 final size:19
Alignment explanation
Indices: 23948--23984 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
23938 TGAAGAGAGA
23948 ATGATATAT-AAATATATG
1 ATGATATATAAAATATATG
23966 ATGATATATGAAAATATAT
1 ATGATATAT-AAAATATAT
23985 ATTATAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
ATGATATATAAAATATATG
Found at i:24710 original size:17 final size:15
Alignment explanation
Indices: 24680--24710 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
24670 CAAAATAATC
24680 ATTCCTTTTATATAT
1 ATTCCTTTTATATAT
*
24695 ATTCCTTTTGTATAT
1 ATTCCTTTTATATAT
24710 A
1 A
24711 ATTACACGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.13, G:0.03, T:0.58
Consensus pattern (15 bp):
ATTCCTTTTATATAT
Found at i:25097 original size:49 final size:51
Alignment explanation
Indices: 25019--25140 Score: 164
Period size: 49 Copynumber: 2.5 Consensus size: 51
25009 TAAAAAAGTG
*
25019 TAACAATT-AACACATACTTATATCGGTGTAAGTATATACATCT-CTCAGCC
1 TAACAATTAAACACATACTTACATCGGTGTAAGTATATACATCTCCT-AGCC
*
25069 TAA-AATTAAACACATACTTACAT-GGTGTAAGTATGTACATCTCCTAGCC
1 TAACAATTAAACACATACTTACATCGGTGTAAGTATATACATCTCCTAGCC
* *
25118 TAACAA-TAAATATATACTTACAT
1 TAACAATTAAACACATACTTACAT
25141 ACGTGCATCT
Statistics
Matches: 65, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
49 44 0.68
50 21 0.32
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (51 bp):
TAACAATTAAACACATACTTACATCGGTGTAAGTATATACATCTCCTAGCC
Found at i:30080 original size:15 final size:15
Alignment explanation
Indices: 30060--30090 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30050 CAAAATAATC
30060 ATTCCTTTTGTATAT
1 ATTCCTTTTGTATAT
*
30075 ATTCCTTTTGTTTAT
1 ATTCCTTTTGTATAT
30090 A
1 A
30091 ATTACACGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.61
Consensus pattern (15 bp):
ATTCCTTTTGTATAT
Found at i:30479 original size:49 final size:50
Alignment explanation
Indices: 30398--30498 Score: 150
Period size: 49 Copynumber: 2.0 Consensus size: 50
30388 TGTAACAATT
* * *
30398 AACACATACTTATATCGGTGTAAGTATATACATCTCTTAGCCTAAAAATA
1 AACACATACTTACATCGGTGTAAGTATATACATCTCCTAACCTAAAAATA
* *
30448 AACACATACTTACAT-GGTGTAAGTATGTACATCTCCTAACCTAACAATA
1 AACACATACTTACATCGGTGTAAGTATATACATCTCCTAACCTAAAAATA
30497 AA
1 AA
30499 TATATATACT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 32 0.70
50 14 0.30
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.30
Consensus pattern (50 bp):
AACACATACTTACATCGGTGTAAGTATATACATCTCCTAACCTAAAAATA
Found at i:30585 original size:17 final size:17
Alignment explanation
Indices: 30565--30598 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
30555 AAATTTTATT
30565 AAAA-AATAATAAAATTA
1 AAAATAATAA-AAAATTA
30582 AAAATAATAAAAAATTA
1 AAAATAATAAAAAATTA
30599 TATTTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATAATAAAAAATTA
Found at i:33941 original size:18 final size:19
Alignment explanation
Indices: 33918--33954 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
33908 TGAAGAGAAA
33918 ATGATATAT-AAATATATG
1 ATGATATATAAAATATATG
33936 ATGATATATGAAAATATAT
1 ATGATATAT-AAAATATAT
33955 ATTATAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
ATGATATATAAAATATATG
Found at i:34269 original size:3 final size:3
Alignment explanation
Indices: 34263--34347 Score: 113
Period size: 3 Copynumber: 29.0 Consensus size: 3
34253 TTTTTTATCT
34263 TTA TTA TTA TTA TT- TTA TTA TT- TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
34308 TTA TTA TTA TTTA TTT TTA TTA TTA ATA TTA TTA TCA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
34348 CAAACAAGCC
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
2 6 0.08
3 63 0.88
4 3 0.04
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:34286 original size:28 final size:28
Alignment explanation
Indices: 34255--34342 Score: 115
Period size: 28 Copynumber: 3.0 Consensus size: 28
34245 CATTTTGTTT
*
34255 TTTTATCT-TTATTATTATTATTTTATTA
1 TTTTAT-TATTATTATTATTATATTATTA
34283 TTTTATTATTATTATTATTATATTATTA
1 TTTTATTATTATTATTATTATATTATTA
*
34311 TTATTATTTATTTTTATTATTAATATTATTA
1 TT-TTA-TTATTATTATTATT-ATATTATTA
34342 T
1 T
34343 CATTACAAAC
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
27 1 0.02
28 27 0.50
29 3 0.06
30 13 0.24
31 10 0.19
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (28 bp):
TTTTATTATTATTATTATTATATTATTA
Found at i:34326 original size:39 final size:43
Alignment explanation
Indices: 34257--34347 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 43
34247 TTTTGTTTTT
* *
34257 TTATCTTTATTATTATTATTTTATTATTTTATTATTATTATTA
1 TTATCATTATTATTATTATTTTATTATTTTATTATTAATATTA
34300 TTAT-ATTATTATTATTA-TTTA-T-TTTTATTATTAATATTA
1 TTATCATTATTATTATTATTTTATTATTTTATTATTAATATTA
34339 TTATCATTA
1 TTATCATTA
34348 CAAACAAGCC
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
39 20 0.44
40 5 0.11
41 4 0.09
42 12 0.27
43 4 0.09
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (43 bp):
TTATCATTATTATTATTATTTTATTATTTTATTATTAATATTA
Found at i:36244 original size:2 final size:2
Alignment explanation
Indices: 36237--36264 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36227 AAAACCCTAA
36237 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
36265 TTAATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37126 original size:15 final size:15
Alignment explanation
Indices: 37106--37136 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
37096 CAAAATAATC
37106 ATTCCTTTTGTATAT
1 ATTCCTTTTGTATAT
*
37121 ATTCCTTTTGTTTAT
1 ATTCCTTTTGTATAT
37136 A
1 A
37137 ATTACACGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.61
Consensus pattern (15 bp):
ATTCCTTTTGTATAT
Found at i:37524 original size:49 final size:50
Alignment explanation
Indices: 37443--37556 Score: 158
Period size: 49 Copynumber: 2.3 Consensus size: 50
37433 TGTAACAATT
* * *
37443 AACACATACTTATATCGGTGTAAGTATATACATCTCTCAGCCTAAAAATA
1 AACACATACTTACATCGGTGTAAGTATATACATCTCCCAACCTAAAAATA
* *
37493 AACACATACTTACAT-GGTGTAAGTATGTACATCTCCCAACCTAACAATA
1 AACACATACTTACATCGGTGTAAGTATATACATCTCCCAACCTAAAAATA
* *
37542 AATATATACTTACAT
1 AACACATACTTACAT
37557 ACGTGCATCT
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
49 43 0.75
50 14 0.25
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (50 bp):
AACACATACTTACATCGGTGTAAGTATATACATCTCCCAACCTAAAAATA
Found at i:37629 original size:17 final size:17
Alignment explanation
Indices: 37609--37642 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
37599 AAATTTTATT
37609 AAAA-AATAATAAAATTA
1 AAAATAATAA-AAAATTA
37626 AAAATAATAAAAAATTA
1 AAAATAATAAAAAATTA
37643 TATTTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATAATAAAAAATTA
Found at i:40982 original size:18 final size:19
Alignment explanation
Indices: 40959--40995 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
40949 TGAAGAGAGA
40959 ATGATATAT-AAATATATG
1 ATGATATATAAAATATATG
40977 ATGATATATGAAAATATAT
1 ATGATATAT-AAAATATAT
40996 ATTATAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
ATGATATATAAAATATATG
Found at i:41311 original size:3 final size:3
Alignment explanation
Indices: 41303--41396 Score: 131
Period size: 3 Copynumber: 32.0 Consensus size: 3
41293 TTTTTTATCT
41303 TTA TTA TTA TTA TT- TTA TTA TT- TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
41348 TTA TTA TTA TTA TTA TTA TTTA TTT TTA TTA TTA ATA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
41394 TTA
1 TTA
41397 CAAACAGGCC
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
2 6 0.07
3 72 0.89
4 3 0.04
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:44167 original size:15 final size:15
Alignment explanation
Indices: 44147--44177 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
44137 CAAAATAATC
44147 ATTCCTTTTGTATAT
1 ATTCCTTTTGTATAT
*
44162 ATTCCTTTTGTTTAT
1 ATTCCTTTTGTATAT
44177 A
1 A
44178 ATTACACGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.61
Consensus pattern (15 bp):
ATTCCTTTTGTATAT
Found at i:44565 original size:49 final size:50
Alignment explanation
Indices: 44484--44597 Score: 149
Period size: 49 Copynumber: 2.3 Consensus size: 50
44474 TGTAACAATT
* ** *
44484 AACACATACTTATATCGGTGTAAGTATATACATCTCTTAGCCTAAAAATA
1 AACACATACTTACATCGGTGTAAGTATATACATCTCCCAACCTAAAAATA
* *
44534 AACACATACTTACAT-GGTGTAAGTATGTACATCTCCCAACCTAACAATA
1 AACACATACTTACATCGGTGTAAGTATATACATCTCCCAACCTAAAAATA
* *
44583 AATATATACTTACAT
1 AACACATACTTACAT
44598 ACGTGCATCT
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 42 0.75
50 14 0.25
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (50 bp):
AACACATACTTACATCGGTGTAAGTATATACATCTCCCAACCTAAAAATA
Found at i:44669 original size:17 final size:17
Alignment explanation
Indices: 44649--44682 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
44639 AAATTTTATT
44649 AAAA-AATAATAAAATTA
1 AAAATAATAA-AAAATTA
44666 AAAATAATAAAAAATTA
1 AAAATAATAAAAAATTA
44683 TATTTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATAATAAAAAATTA
Found at i:48023 original size:18 final size:19
Alignment explanation
Indices: 48000--48036 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
47990 TGAAGAGAGA
48000 ATGATATAT-AAATATATG
1 ATGATATATAAAATATATG
48018 ATGATATATGAAAATATAT
1 ATGATATAT-AAAATATAT
48037 ATTATAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
ATGATATATAAAATATATG
Found at i:48354 original size:3 final size:3
Alignment explanation
Indices: 48348--48435 Score: 119
Period size: 3 Copynumber: 30.0 Consensus size: 3
48338 TTTTTTATCT
48348 TTA TTA TTA TTA TT- TTA TTA TT- TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
48393 TTA TTA TTA TTA TTTA TTT TTA TTA TTA ATA TTA TTA TCA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
48436 CAAACAGGCC
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
2 6 0.08
3 66 0.88
4 3 0.04
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:48372 original size:22 final size:23
Alignment explanation
Indices: 48348--48428 Score: 121
Period size: 22 Copynumber: 3.6 Consensus size: 23
48338 TTTTTTATCT
48348 TTATTATTATTATTTTATTATT-
1 TTATTATTATTATTTTATTATTA
*
48370 TTATTATTATTATTATATTATTA
1 TTATTATTATTATTTTATTATTA
*
48393 TTATTATTATTA-TTTATTTTTA
1 TTATTATTATTATTTTATTATTA
*
48415 TTATTAATATTATT
1 TTATTATTATTATT
48429 ATCATTACAA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
22 40 0.75
23 13 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TTATTATTATTATTTTATTATTA
Found at i:51201 original size:15 final size:15
Alignment explanation
Indices: 51181--51212 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
51171 TCAAAATAAT
51181 TATTCCTTTTGTATA
1 TATTCCTTTTGTATA
*
51196 TATTCCTTTTGTTTA
1 TATTCCTTTTGTATA
51211 TA
1 TA
51213 ATTACACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.06, T:0.62
Consensus pattern (15 bp):
TATTCCTTTTGTATA
Found at i:51600 original size:49 final size:50
Alignment explanation
Indices: 51519--51632 Score: 149
Period size: 49 Copynumber: 2.3 Consensus size: 50
51509 TGTAACAATT
* ** *
51519 AACACATACTTATATCGGTGTAAGTATATACATCTCTTAGCCTAAAAATA
1 AACACATACTTACATCGGTGTAAGTATATACATCTCCCAACCTAAAAATA
* *
51569 AACACATACTTACAT-GGTGTAAGTATGTACATCTCCCAACCTAACAATA
1 AACACATACTTACATCGGTGTAAGTATATACATCTCCCAACCTAAAAATA
* *
51618 AATATATACTTACAT
1 AACACATACTTACAT
51633 ACGTGCATCT
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 42 0.75
50 14 0.25
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (50 bp):
AACACATACTTACATCGGTGTAAGTATATACATCTCCCAACCTAAAAATA
Found at i:51704 original size:17 final size:17
Alignment explanation
Indices: 51684--51717 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
51674 AAATTTTATT
51684 AAAA-AATAATAAAATTA
1 AAAATAATAA-AAAATTA
51701 AAAATAATAAAAAATTA
1 AAAATAATAAAAAATTA
51718 TATTTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATAATAAAAAATTA
Found at i:55057 original size:18 final size:19
Alignment explanation
Indices: 55034--55070 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
55024 TGAAGAGAGA
55034 ATGATATAT-AAATATATG
1 ATGATATATAAAATATATG
55052 ATGATATATGAAAATATAT
1 ATGATATAT-AAAATATAT
55071 ATTATAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
ATGATATATAAAATATATG
Found at i:55385 original size:3 final size:3
Alignment explanation
Indices: 55379--55483 Score: 146
Period size: 3 Copynumber: 36.0 Consensus size: 3
55369 TTTTTTATCT
55379 TTA TTA TTA TTA TT- TTA TTA TT- TTA TTA TT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
55424 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTTA TTT TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* *
55469 ATA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA
55484 CAAACAGGCC
Statistics
Matches: 91, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
2 8 0.09
3 80 0.88
4 3 0.03
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:55385 original size:9 final size:8
Alignment explanation
Indices: 55379--55467 Score: 101
Period size: 8 Copynumber: 10.6 Consensus size: 8
55369 TTTTTTATCT
55379 TTATTATTA
1 TTATT-TTA
55388 TTATTTTA
1 TTATTTTA
55396 TTATTTTA
1 TTATTTTA
55404 TTATTTTA
1 TTATTTTA
55412 TTA--TTA
1 TTATTTTA
55418 TTATTATTA
1 TTATT-TTA
55427 TTATTATTA
1 TTATT-TTA
*
55436 TTATATTA
1 TTATTTTA
55444 TTATTATTA
1 TTATT-TTA
55453 TTTATTTTTA
1 -TTA-TTTTA
55463 TTATT
1 TTATT
55468 AATATTATTA
Statistics
Matches: 72, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
6 6 0.08
8 31 0.43
9 27 0.38
10 6 0.08
11 2 0.03
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TTATTTTA
Found at i:56841 original size:18 final size:18
Alignment explanation
Indices: 56807--56848 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
56797 TTTAATAATT
*
56807 TTTTATATTTTGCATTTA
1 TTTTATATTTTGAATTTA
*
56825 TTTTATAATTTT-AATTTC
1 TTTTAT-ATTTTGAATTTA
56843 TTTTAT
1 TTTTAT
56849 TTTGATCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTATATTTTGAATTTA
Found at i:57112 original size:17 final size:15
Alignment explanation
Indices: 57072--57114 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
57062 TTTAATTTAA
*
57072 TTTTTATTTTATTAT
1 TTTTTATTTTAATAT
57087 TTTTGTATTGTTAATAT
1 TTTT-TATT-TTAATAT
57104 TTATTTATTTT
1 TT-TTTATTTT
57115 TTTAATACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 4 0.17
16 6 0.25
17 12 0.50
18 2 0.08
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (15 bp):
TTTTTATTTTAATAT
Found at i:57366 original size:2 final size:2
Alignment explanation
Indices: 57359--57398 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
57349 AAAACCCTAA
57359 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
57399 TTTAATATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58257 original size:15 final size:15
Alignment explanation
Indices: 58237--58267 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
58227 CAAAATAATC
58237 ATTCCTTTTGTATAT
1 ATTCCTTTTGTATAT
*
58252 ATTCCTTTTGTTTAT
1 ATTCCTTTTGTATAT
58267 A
1 A
58268 CACGTGTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.61
Consensus pattern (15 bp):
ATTCCTTTTGTATAT
Found at i:58636 original size:49 final size:49
Alignment explanation
Indices: 58562--58676 Score: 151
Period size: 49 Copynumber: 2.3 Consensus size: 49
58552 GTGTAACAAT
* * *
58562 TAAAACATACTTATATCGGTGTAAGTATATACATCTCTCAGCCTAAAAA
1 TAAAACATACTTACATCGGTGTAAGTATATACATCTCCCAACCTAAAAA
* *
58611 TAAACACATACTTACAT-GGTGTAAGTATGTACATCTCCCAACCTAACAA
1 TAAA-ACATACTTACATCGGTGTAAGTATATACATCTCCCAACCTAAAAA
*
58660 TAAATATATACTTACAT
1 TAAA-ACATACTTACAT
58677 ACGTGCATCT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
49 47 0.81
50 11 0.19
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (49 bp):
TAAAACATACTTACATCGGTGTAAGTATATACATCTCCCAACCTAAAAA
Found at i:58746 original size:16 final size:16
Alignment explanation
Indices: 58725--58760 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
58715 TATAAATTTT
58725 ATTAAAAA-ATAATAAA
1 ATTAAAAATATAA-AAA
58741 ATTAAAAATATAAAAA
1 ATTAAAAATATAAAAA
58757 ATTA
1 ATTA
58761 TATTTTCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
ATTAAAAATATAAAAA
Found at i:62186 original size:16 final size:16
Alignment explanation
Indices: 62167--62211 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
62157 AGTTTACAAT
*
62167 TAAATAATAAAA-AAAC
1 TAAA-AATAAAATAAAA
62183 T-AAAATAAAATAAAA
1 TAAAAATAAAATAAAA
62198 TAAAAATAAAATAA
1 TAAAAATAAAATAA
62212 TTAATTACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 7 0.27
15 6 0.23
16 13 0.50
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (16 bp):
TAAAAATAAAATAAAA
Found at i:62203 original size:6 final size:5
Alignment explanation
Indices: 62172--62211 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
62162 ACAATTAAAT
*
62172 AATAA AA-AA ACTAA AATAA AATAA AATAAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AAT-AA AATAA AATAA
62212 TTAATTACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 3 0.10
5 23 0.74
6 5 0.16
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:62203 original size:11 final size:11
Alignment explanation
Indices: 62168--62211 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
62158 GTTTACAATT
62168 AAATAATAA-AA
1 AAATAA-AATAA
62179 AAACTAAAAT-A
1 AAA-TAAAATAA
62190 AAATAAAATAA
1 AAATAAAATAA
62201 AAATAAAATAA
1 AAATAAAATAA
62212 TTAATTACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.20
11 21 0.70
12 3 0.10
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:66901 original size:20 final size:20
Alignment explanation
Indices: 66876--67005 Score: 136
Period size: 20 Copynumber: 6.5 Consensus size: 20
66866 GGGAAAATCA
*
66876 CAATGCGATACTGACTATTG
1 CAATGCGATACTGACTATCG
66896 CAATGCGATACTGACTATCG
1 CAATGCGATACTGACTATCG
*
66916 CAATGCGATACTTACTATCG
1 CAATGCGATACTGACTATCG
* *
66936 CAATGCGATAAT-ACAAAATCG
1 CAATGCGATACTGAC--TATCG
* * *
66957 CAACGAGATACTGACTTTCG
1 CAATGCGATACTGACTATCG
* * *
66977 CAACGCGATTCTGACTTTCG
1 CAATGCGATACTGACTATCG
*
66997 CAACGCGAT
1 CAATGCGAT
67006 TTACATAGCG
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.02
20 79 0.82
21 13 0.14
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
CAATGCGATACTGACTATCG
Found at i:66978 original size:41 final size:40
Alignment explanation
Indices: 66882--66985 Score: 104
Period size: 41 Copynumber: 2.6 Consensus size: 40
66872 ATCACAATGC
* * * *
66882 GATACTGACTATT-GCAATGCGATACTGACTATCGCAATGC
1 GATACTGACT-TTCGCAATGCGATAATGACAATCGCAACGA
* *
66922 GATACTTACTATCGCAATGCGATAAT-ACAAAATCGCAACGA
1 GATACTGACTTTCGCAATGCGATAATGAC--AATCGCAACGA
*
66963 GATACTGACTTTCGCAACGCGAT
1 GATACTGACTTTCGCAATGCGAT
66986 TCTGACTTTC
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
39 3 0.06
40 21 0.40
41 28 0.54
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (40 bp):
GATACTGACTTTCGCAATGCGATAATGACAATCGCAACGA
Found at i:67592 original size:18 final size:19
Alignment explanation
Indices: 67554--67597 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
67544 GCTACGAGAG
*
67554 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
* *
67573 AA-CGCAATGCGAAACCAA
1 AATCGCAACGCGAAACAAA
67591 AATCGCA
1 AATCGCA
67598 TTACGATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:67615 original size:19 final size:18
Alignment explanation
Indices: 67593--67735 Score: 95
Period size: 19 Copynumber: 8.1 Consensus size: 18
67583 GAAACCAAAA
*
67593 TCGCATTACGATTTTCATT
1 TCGCATTGCGA-TTTCATT
*
67612 TCGCGTTGCGA-TTC---
1 TCGCATTGCGATTTCATT
*
67626 TCTCATTGCGATTTCATT
1 TCGCATTGCGATTTCATT
67644 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
67663 TCGCGTTGCGA-TTC-TC
1 TCGCATTGCGATTTCATT
*
67679 TCG--TTGCGATAGTCATT
1 TCGCATTGCGAT-TTCATT
*
67696 TCGCGTTGCGATTCTCATT
1 TCGCATTGCGATT-TCATT
***
67715 ATCTTGTTGCGATTTCATT
1 -TCGCATTGCGATTTCATT
67734 TC
1 TC
67736 AACCAAAAGA
Statistics
Matches: 100, Mismatches: 12, Indels: 25
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.15
15 3 0.03
16 6 0.06
17 10 0.10
18 12 0.12
19 43 0.43
20 11 0.11
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:67648 original size:51 final size:52
Alignment explanation
Indices: 67593--67728 Score: 193
Period size: 51 Copynumber: 2.6 Consensus size: 52
67583 GAAACCAAAA
* *
67593 TCGCATTACGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGAT-TTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATAGTCATT
*
67644 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATAGTCATT
* * **
67696 TCGCGTTGCGATTCTCATTATCTTGTTGCGATT
1 TCGCATTGCGATTTTCATT-TCGCGTTGCGATT
67729 TCATTTCAAC
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
51 43 0.57
52 22 0.29
53 11 0.14
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATAGTCATT
Found at i:67695 original size:33 final size:33
Alignment explanation
Indices: 67649--67711 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
67639 TCATTTCGCA
**
67649 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
67682 TTGCGATAGTCATTTCGCGTTGCGATTCTC
1 TTGCGATAGTCATTTCGCGTTGCGATTCTC
67712 ATTATCTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:69276 original size:63 final size:62
Alignment explanation
Indices: 69178--69301 Score: 230
Period size: 63 Copynumber: 2.0 Consensus size: 62
69168 GTTACGTGAT
69178 GAGGTCAATGCCTGCATGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTA
1 GAGGTCAATGCCTGCATGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTA
*
69240 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGT
1 GAGGTCAATGCC-TGCATGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGT
69302 GGAGTCTACT
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 12 0.20
63 48 0.80
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (62 bp):
GAGGTCAATGCCTGCATGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTA
Found at i:69943 original size:42 final size:42
Alignment explanation
Indices: 69891--70028 Score: 179
Period size: 42 Copynumber: 3.3 Consensus size: 42
69881 CCACTCCTAT
*
69891 CGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
* * * * * * *
69933 CGTTCAAGAGGCCACTGTCATCCCTCAAGAGTCCACTCCTAT
1 CGTTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
* *
69975 CATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT-CCAC
1 CGTTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
70016 CGTTCAAGAGGCC
1 CGTTCAAGAGGCC
70029 ACTGTCATCG
Statistics
Matches: 77, Mismatches: 19, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
41 13 0.17
42 64 0.83
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
Found at i:70004 original size:84 final size:81
Alignment explanation
Indices: 69865--70037 Score: 310
Period size: 84 Copynumber: 2.1 Consensus size: 81
69855 CCCGACTCGC
*
69865 CTGTCATCCCTCAAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCC
1 CTGTCATCCCTCAAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT-C
69930 CACCGTTCAAGAGGCCA
65 CACCGTTCAAGAGGCCA
69947 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTC-A-AGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
70012 CCACCGTTCAAGAGGCCA
64 CCACCGTTCAAGAGGCCA
70030 CTGTCATC
1 CTGTCATC
70038 GTTGAAGAGG
Statistics
Matches: 88, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
82 12 0.14
83 27 0.31
84 49 0.56
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (81 bp):
CTGTCATCCCTCAAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCC
ACCGTTCAAGAGGCCA
Found at i:70040 original size:21 final size:20
Alignment explanation
Indices: 69933--70047 Score: 52
Period size: 21 Copynumber: 5.5 Consensus size: 20
69923 CCCCTCCCAC
69933 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACT-TCAT
** * *
69954 CCCTCAAGAGTCCACTCCTAT
1 CGTTCAAGAGGCCACTTC-AT
* * *
69975 CATTGAAGAGGCCCCTATCATT
1 CGTTCAAGAGGCCACT-TCA-T
* * * * * *
69997 C-CTCGAGAGTCCCCTCCAC
1 CGTTCAAGAGGCCACTTCAT
70016 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACT-TCAT
*
70037 CGTTGAAGAGG
1 CGTTCAAGAGG
70048 TACTCCCACA
Statistics
Matches: 66, Mismatches: 23, Indels: 10
0.67 0.23 0.10
Matches are distributed among these distances:
19 1 0.02
20 13 0.20
21 49 0.74
22 3 0.05
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (20 bp):
CGTTCAAGAGGCCACTTCAT
Found at i:71424 original size:13 final size:13
Alignment explanation
Indices: 71408--71437 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
71398 TTTAATTGAT
71408 TTGTAAAAGGTGA
1 TTGTAAAAGGTGA
*
71421 TTGTAAAAGTTGA
1 TTGTAAAAGGTGA
71434 TTGT
1 TTGT
71438 TTAATTGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.40
Consensus pattern (13 bp):
TTGTAAAAGGTGA
Found at i:71579 original size:18 final size:18
Alignment explanation
Indices: 71556--71608 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
71546 CGCAATTAGA
71556 AATGAAAATCGCAACGCG
1 AATGAAAATCGCAACGCG
71574 AATGAAAATCGCAA--CG
1 AATGAAAATCGCAACGCG
*
71590 -A-GAGAATCGCAACGCG
1 AATGAAAATCGCAACGCG
71606 AAT
1 AAT
71609 TAAATTCGCG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 10 0.33
15 1 0.03
16 4 0.13
17 1 0.03
18 14 0.47
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (18 bp):
AATGAAAATCGCAACGCG
Found at i:71654 original size:33 final size:32
Alignment explanation
Indices: 71617--71742 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
71607 ATTAAATTCG
*
71617 CGTTGCGATTTTCATTTCGCATTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
71650 CGTTGCGATTTT-ATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
71682 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
71715 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
71743 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
31 3 0.04
32 24 0.29
33 53 0.64
34 3 0.04
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:71690 original size:65 final size:66
Alignment explanation
Indices: 71610--71741 Score: 230
Period size: 65 Copynumber: 2.0 Consensus size: 66
71600 AACGCGAATT
* *
71610 AAATTCGCGTTGCGATTTTCATTTCGCATTGTGATTCCCTCGTTGCGATTTT-ATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
71674 G
66 G
*
71675 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
71740 G
66 G
71741 A
1 A
71742 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
65 49 0.78
66 14 0.22
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:74250 original size:19 final size:19
Alignment explanation
Indices: 74196--74280 Score: 136
Period size: 19 Copynumber: 4.5 Consensus size: 19
74186 CATCATCAAA
*
74196 ATCGCAATGCG-AATGGCT
1 ATCGCAACGCGAAATGGCT
74214 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCG-AAATGGCT
74234 ATCGCAACGCGAAATGGCT
1 ATCGCAACGCGAAATGGCT
74253 ATCGCAACGCGAAATGGCT
1 ATCGCAACGCGAAATGGCT
*
74272 ATCGTAACG
1 ATCGCAACG
74281 ACAAAATCGC
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
18 10 0.16
19 35 0.56
20 18 0.29
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.18
Consensus pattern (19 bp):
ATCGCAACGCGAAATGGCT
Found at i:74329 original size:14 final size:16
Alignment explanation
Indices: 74309--74381 Score: 64
Period size: 14 Copynumber: 4.5 Consensus size: 16
74299 ATGAAATCGC
74309 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
74324 -TTGCGATTTTCATTCG
1 ATTGCGATTTTC-TTCG
74340 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
*
74359 CATTGCGATTCTC-TCG
1 -ATTGCGATTTTCTTCG
74375 -TTGCGAT
1 ATTGCGAT
74382 AGTCAGTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 18 0.35
16 6 0.12
18 11 0.22
19 16 0.31
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:74360 original size:19 final size:18
Alignment explanation
Indices: 74305--74368 Score: 91
Period size: 19 Copynumber: 3.7 Consensus size: 18
74295 CGAAATGAAA
74305 TCGCATTGCGATTTTC--
1 TCGCATTGCGATTTTCAT
74321 TCG--TTGCGATTTTCAT
1 TCGCATTGCGATTTTCAT
74337 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCA-T
74356 TCGCATTGCGATT
1 TCGCATTGCGATT
74369 CTCTCGTTGC
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.26
16 6 0.14
18 12 0.28
19 14 0.33
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTTCAT
Found at i:74399 original size:20 final size:20
Alignment explanation
Indices: 74374--74412 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
74364 CGATTCTCTC
74374 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
74394 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
74413 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:74514 original size:14 final size:14
Alignment explanation
Indices: 74495--74531 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
74485 CATCAATTAA
74495 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
74509 ACAAATCATCTTTT
1 ACAAATCAACATTT
74523 ACAAATCAA
1 ACAAATCAA
74532 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Done.