Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006939.1 Hibiscus syriacus cultivar Beakdansim tig00017821_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: 76511
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3208 original size:110 final size:110
Alignment explanation
Indices: 2969--3291 Score: 480
Period size: 110 Copynumber: 3.0 Consensus size: 110
2959 GATGGTAGTT
*
2969 GCTCAAATTCACAGCGAA-GGG-G-C-GACTGTCAACAAACAAC-TTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * *
3029 AATTTTAACTTCATAGCAAAGG--ATTAGACTCGTGACAATACAA
66 AATTTTAACTTCATAGCGAAGGATATTAGACTCGAGACAACACAA
* * *
3072 GATCAACTTCACAGCGAAGAGGCGACTGACTGTCAACAAACAACTTTTTAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
3137 AATTTTAACTTCATAGCGAAGGATATTAGACTCGAGATAACACAA
66 AATTTTAACTTCATAGCGAAGGATATTAGACTCGAGACAACACAA
3182 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * * * *
3247 AATTTCAACTTCATAGTGAATGATATTAGACTCGAAACGACACAA
66 AATTTTAACTTCATAGCGAAGGATATTAGACTCGAGACAACACAA
3292 TTTGCTTGAG
Statistics
Matches: 196, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
103 16 0.08
104 2 0.01
105 1 0.01
106 1 0.01
107 17 0.09
108 40 0.20
110 119 0.61
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
AATTTTAACTTCATAGCGAAGGATATTAGACTCGAGACAACACAA
Found at i:3956 original size:122 final size:120
Alignment explanation
Indices: 3793--4028 Score: 366
Period size: 122 Copynumber: 1.9 Consensus size: 120
3783 ACTTACATTG
3793 GATTTCAACTTCACAAGAAGGATATAATTCAAGGCTCAACTTCACAACGAATGGGTCATCCACGG
1 GATTTCAACTTCACAAGAAGGATATAATTCAAGGCTCAACTTCACAACGAATGGGTCATCCACGG
* * *
3858 TTTCAACTTCACGA-AAGGGAATTATGCTCACCAGCAACATTCATCTTTAGATTT
66 TTTCAACTTCACGACAAGGGAATCATACCCACCAGCAACATTCATCTTTAGATTT
* *
3912 GATTTTAACTTCACGAAGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGTCATCCG
1 GATTTCAACTTCAC-AAGAAGGATAT--AATTCAAGGCTCAACTTCACAACGAATGGGTCATCCA
* *
3977 CGGTTTCAACTTCATGACGAAGGGAATCGTACCCACCAGCAACATTCATCTT
63 CGGTTTCAACTTCACGAC-AAGGGAATCATACCCACCAGCAACATTCATCTT
4029 CAAGAACAAG
Statistics
Matches: 105, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
119 13 0.12
120 11 0.10
122 52 0.50
124 29 0.28
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (120 bp):
GATTTCAACTTCACAAGAAGGATATAATTCAAGGCTCAACTTCACAACGAATGGGTCATCCACGG
TTTCAACTTCACGACAAGGGAATCATACCCACCAGCAACATTCATCTTTAGATTT
Found at i:4127 original size:37 final size:34
Alignment explanation
Indices: 4086--4214 Score: 132
Period size: 36 Copynumber: 3.6 Consensus size: 34
4076 ACAAGGGGTC
* *
4086 GTCTCGCTTGAGACTAATTTACTCAAAACAAAGTTTT
1 GTCTCTCTTGAGAC-AATTT-CTCGAAACAAA-TTTT
*
4123 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCTC--GAAACAAATTTT
* * *
4159 GTCTATCTTGAGACATTTTCCCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAATTT--CTCGAAACAAATTTT
*
4195 GTCTCTCTTGAGACAGTTTC
1 GTCTCTCTTGAGACAATTTC
4215 CCTTGAAGCA
Statistics
Matches: 80, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
34 1 0.01
35 3 0.04
36 54 0.68
37 20 0.25
38 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (34 bp):
GTCTCTCTTGAGACAATTTCTCGAAACAAATTTT
Found at i:4168 original size:36 final size:36
Alignment explanation
Indices: 4111--4226 Score: 187
Period size: 36 Copynumber: 3.2 Consensus size: 36
4101 AATTTACTCA
*
4111 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
4148 AAACAAATTTTGTCTATCTTGAGACATTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
4184 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
4220 AAGCAAA
1 AAACAAA
4227 ATCTTTGAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
36 66 0.90
37 7 0.10
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:4169 original size:21 final size:20
Alignment explanation
Indices: 4143--4205 Score: 55
Period size: 21 Copynumber: 3.3 Consensus size: 20
4133 AGACAGTTTC
4143 TCTTGAAACAAATTTTGTCT
1 TCTTGAAACAAATTTTGTCT
*
4163 ATCTTGAGAC--A-TTT-TC-
1 -TCTTGAAACAAATTTTGTCT
*
4179 CCTTGAAACAAATTTTGTCT
1 TCTTGAAACAAATTTTGTCT
4199 CTCTTGA
1 -TCTTGA
4206 GACAGTTTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
15 7 0.22
17 3 0.09
18 6 0.19
19 3 0.09
21 13 0.41
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.43
Consensus pattern (20 bp):
TCTTGAAACAAATTTTGTCT
Found at i:4340 original size:36 final size:36
Alignment explanation
Indices: 4245--4437 Score: 278
Period size: 36 Copynumber: 5.3 Consensus size: 36
4235 ATACGTATTC
** * *
4245 CTTGAAACAAATTCCGTCTCCCTTGAGATAGTTTCT
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
* * *
4281 TTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCT
1 CTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCT
*
4318 CTTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
* *
4354 CTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
4390 CTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCT
1 CTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCT
4427 CTTGAAACAAA
1 CTTGAAACAAA
4438 AAAAACCTTT
Statistics
Matches: 139, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
36 77 0.55
37 62 0.45
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
Found at i:4407 original size:73 final size:72
Alignment explanation
Indices: 4244--4437 Score: 280
Period size: 73 Copynumber: 2.7 Consensus size: 72
4234 AATACGTATT
** * * * * * *
4244 CCTTGAAACAAATTCCGTCTCCCTTGAGATAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAG
1 CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTTATCTCTCTTGAG
4309 ACAGTTTC
65 ACAGTTTC
* *
4317 TCTTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCTCTCTTGAGA
1 CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCTCTCTTGAGA
4382 CAGTTTC
66 CAGTTTC
4389 CCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 CCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
4438 AAAAACCTTT
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
72 35 0.32
73 73 0.68
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (72 bp):
CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCTCTCTTGAGA
CAGTTTC
Found at i:4621 original size:84 final size:84
Alignment explanation
Indices: 4476--4639 Score: 240
Period size: 84 Copynumber: 2.0 Consensus size: 84
4466 ACACCAAACA
* * * * *
4476 TTCGAGTTCGACTACGCTCAGCTGCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGT
1 TTCGAGTTCGACTACACTCAGCTGCAAGGCACATCATTTGCAGCATAGCTCAAAGCGAGAAGAGC
4541 TATCTGCCACCAAAAGCCC
66 TATCTGCCACCAAAAGCCC
* * *
4560 TTCGAGTTCGATTACACTCAGCT-CAAAGGCACATCATTTGCAGCATAGCTTAAATCGAGAAGAG
1 TTCGAGTTCGACTACACTCAGCTGC-AAGGCACATCATTTGCAGCATAGCTCAAAGCGAGAAGAG
4624 CTATCTGCCACCAAAA
65 CTATCTGCCACCAAAA
4640 AACTGAAGAG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
83 1 0.01
84 70 0.99
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (84 bp):
TTCGAGTTCGACTACACTCAGCTGCAAGGCACATCATTTGCAGCATAGCTCAAAGCGAGAAGAGC
TATCTGCCACCAAAAGCCC
Found at i:4651 original size:84 final size:83
Alignment explanation
Indices: 4479--4667 Score: 209
Period size: 84 Copynumber: 2.3 Consensus size: 83
4469 CCAAACATTC
* * * * * *
4479 GAGTTCGACTACGCTCAGCTGCAAGGCACATCATTTGCAGCATAGCTCAAGGCTAGAAGGGTTAT
1 GAGTTCGATTACACTCAGCT-CAAGGCACATCATTTGCAGCATAGCTCAAAGCGAGAAGAGCTAT
** **
4544 CTGCCACCAAAAGCCCTTC
65 CTGCCACCAAAAGAACTAA
* *
4563 GAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAATCGAGAAGAGCTAT
1 GAGTTCGATTACACTCAGCTC-AAGGCACATCATTTGCAGCATAGCTCAAAGCGAGAAGAGCTAT
4628 CTGCCACCAAAA-AACTGAA
65 CTGCCACCAAAAGAACT-AA
* * *
4647 GAGTTTGATTTCATTCAGCTC
1 GAGTTCGATTACACTCAGCTC
4668 GATGACAGCG
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
83 3 0.03
84 85 0.97
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (83 bp):
GAGTTCGATTACACTCAGCTCAAGGCACATCATTTGCAGCATAGCTCAAAGCGAGAAGAGCTATC
TGCCACCAAAAGAACTAA
Found at i:4910 original size:3 final size:3
Alignment explanation
Indices: 4888--4944 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
4878 AAAAAACATT
*
4888 TTA TTA -TA TTA -TA TTA -TA TTA TTTA TTA TTA TTA TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* *
4931 TTT TTA TTT TTA TT
1 TTA TTA TTA TTA TT
4945 TTTTATAGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 6 0.14
3 35 0.80
4 3 0.07
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:4916 original size:12 final size:12
Alignment explanation
Indices: 4887--4951 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
4877 TAAAAAACAT
4887 TTTATTATATTA
1 TTTATTATATTA
4899 --TATTATATTA
1 TTTATTATATTA
4909 TTTATTATTATTA
1 TTTATTA-TATTA
4922 -TTATT-T-TTA
1 TTTATTATATTA
*
4931 TTT-TTATTTTTA
1 TTTATTA-TATTA
*
4943 TTTTTTATA
1 TTTATTATA
4952 GGTCCCATGT
Statistics
Matches: 44, Mismatches: 1, Indels: 16
0.72 0.02 0.26
Matches are distributed among these distances:
9 5 0.11
10 13 0.30
11 1 0.02
12 17 0.39
13 8 0.18
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTATTATATTA
Found at i:7517 original size:23 final size:22
Alignment explanation
Indices: 7491--7565 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
7481 AAGTGCCACA
*
7491 TAGACTTGTCCTGAAGGACCGCG
1 TAGAATTGTCC-GAAGGACCGCG
* * * *
7514 TAGAATTTATCCCGAATGACCACA
1 TAGAA-TTGT-CCGAAGGACCGCG
7538 TAGAATTGTTCCGAAGGACCGCG
1 TAGAATTG-TCCGAAGGACCGCG
7561 TAGAA
1 TAGAA
7566 CCCTCGACTC
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
23 21 0.52
24 17 0.43
25 2 0.05
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.23
Consensus pattern (22 bp):
TAGAATTGTCCGAAGGACCGCG
Found at i:7534 original size:24 final size:23
Alignment explanation
Indices: 7503--7565 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
7493 GACTTGTCCT
7503 GAAGGACCGCGTAGAATT-TATCCC
1 GAAGGACCGCGTAGAATTGT-T-CC
* * *
7527 GAATGACCACATAGAATTGTTCC
1 GAAGGACCGCGTAGAATTGTTCC
7550 GAAGGACCGCGTAGAA
1 GAAGGACCGCGTAGAA
7566 CCCTCGACTC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 15 0.47
24 16 0.50
25 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.19
Consensus pattern (23 bp):
GAAGGACCGCGTAGAATTGTTCC
Found at i:7537 original size:47 final size:47
Alignment explanation
Indices: 7462--7565 Score: 142
Period size: 47 Copynumber: 2.2 Consensus size: 47
7452 GTCGAAACTG
* *
7462 CCGCTTAGAATTTACACCGAAGTGCCACATAGACTTG-TCCTGAAGGA
1 CCGCGTAGAATTTACACCGAAGTGCCACATAGAATTGTTCC-GAAGGA
7509 CCGCGTAGAATTTATC-CCGAA-TGACCACATAGAATTGTTCCGAAGGA
1 CCGCGTAGAATTTA-CACCGAAGTG-CCACATAGAATTGTTCCGAAGGA
7556 CCGCGTAGAA
1 CCGCGTAGAA
7566 CCCTCGACTC
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
46 2 0.04
47 46 0.88
48 4 0.08
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (47 bp):
CCGCGTAGAATTTACACCGAAGTGCCACATAGAATTGTTCCGAAGGA
Found at i:11265 original size:15 final size:15
Alignment explanation
Indices: 11245--11283 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
11235 GATTCAGAGA
11245 CTCTGAATGAGTTGG
1 CTCTGAATGAGTTGG
*
11260 CTCTGAATGATTTGG
1 CTCTGAATGAGTTGG
*
11275 TTCTGAATG
1 CTCTGAATG
11284 TGACATGCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.21, C:0.13, G:0.28, T:0.38
Consensus pattern (15 bp):
CTCTGAATGAGTTGG
Found at i:11353 original size:23 final size:23
Alignment explanation
Indices: 11323--11367 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
11313 CAAAATGTAC
*
11323 TGTTTTGCTGAATCATTCAGCAT
1 TGTTTTGCTGAATCAGTCAGCAT
11346 TGTTTTGCTGAATCAGTCAGCA
1 TGTTTTGCTGAATCAGTCAGCA
11368 CTGAATCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (23 bp):
TGTTTTGCTGAATCAGTCAGCAT
Found at i:14014 original size:2 final size:2
Alignment explanation
Indices: 14007--14046 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
13997 AGAGTACAAA
*
14007 CT CT CT CT CT CG CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
14047 ATATATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
CT
Found at i:14593 original size:26 final size:27
Alignment explanation
Indices: 14564--14617 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
14554 ATTGAGTTCG
* *
14564 ATTTGATTTAAAAAGTTTA-AAATTTA
1 ATTTAATTTAAAAAATTTACAAATTTA
*
14590 ATTTAATTTAAAAAATTTACGAATTTA
1 ATTTAATTTAAAAAATTTACAAATTTA
14617 A
1 A
14618 AATTATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (27 bp):
ATTTAATTTAAAAAATTTACAAATTTA
Found at i:15534 original size:23 final size:23
Alignment explanation
Indices: 15499--15546 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
15489 ATTAAGTATA
*
15499 ATAATATATTAAGTAGCGCTTAT
1 ATAATATAATAAGTAGCGCTTAT
*
15522 ATAATGTAATAAGTAGCGCTTAT
1 ATAATATAATAAGTAGCGCTTAT
15545 AT
1 AT
15547 TGACATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.38
Consensus pattern (23 bp):
ATAATATAATAAGTAGCGCTTAT
Found at i:16283 original size:182 final size:182
Alignment explanation
Indices: 15975--16426 Score: 715
Period size: 182 Copynumber: 2.5 Consensus size: 182
15965 TTTTACTACT
* *
15975 GGTTTTGTTATTTCGAGACCGATTTTGTCACATTTTTACCTGTTATATTGTTATGGATCGATACA
1 GGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA
** * * * * *
16040 TTTTTATAAAACATCGACATTTTATTAGCGCTATAATTTTTTTTCTTTTAAATTTTAAAAGTGTC
66 TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTC
* * * *
16105 GATACTTATAATAAAGTATCGACACTTTCAACATATCTGGTAGCTCTTTACC
131 GATACTTATAATAAAATATCGACACTATCAACATATCCGGTAGCGCTTTACC
*
16157 GGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA
1 GGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA
16222 TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTC
66 TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTC
16287 GATACTTATAATAAAATATCGACACTATCAACATATCCGGTAGCGCTTTACC
131 GATACTTATAATAAAATATCGACACTATCAACATATCCGGTAGCGCTTTACC
* ** * * *
16339 TGTTTTGTCATTTATAAACCGATTTTGTCATTTTTTTACCTGTTATATTGTGATGGATCGATACA
1 GGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA
*
16404 TTTTTATAAAGTATTGACACTTT
66 TTTTTATAAAGTATCGACACTTT
16427 CAATATATCC
Statistics
Matches: 248, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
182 248 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.44
Consensus pattern (182 bp):
GGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA
TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTC
GATACTTATAATAAAATATCGACACTATCAACATATCCGGTAGCGCTTTACC
Found at i:16657 original size:112 final size:112
Alignment explanation
Indices: 16297--16758 Score: 791
Period size: 112 Copynumber: 4.1 Consensus size: 112
16287 GATACTTATA
* * * * *
16297 ATAAAATATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
16362 TTTGTCATTTTTTTACCTGTTATATTGTGATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
16409 ATAAAGTATTGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
16474 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
16520 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACATGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
16585 TTTGTCTTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
16632 ATAAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACTGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
16697 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
16744 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
16759 AAACCGACAA
Statistics
Matches: 331, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
111 106 0.32
112 225 0.68
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:16691 original size:223 final size:224
Alignment explanation
Indices: 16297--16758 Score: 791
Period size: 223 Copynumber: 2.1 Consensus size: 224
16287 GATACTTATA
* *
16297 ATAAAATATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGAT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAAACCGAT
*
16362 TTTGTCATTTTTTTACCTGTTATATTGTGATGGATCGATACATTTTTATAAAGTATTGACACTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTGATGGATCGATACATTTTTATAAAGTATCGACACTTT
16427 CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCA-TTTTTTACCT
131 CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCT
*
16491 GTTATATTGTTATGGATCGATACATTTTT
196 GTTATATTGTTATGGATCAATACATTTTT
* * * * *
16520 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACATGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAAACCGAT
* *
16585 TTTGTCTTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTGATGGATCGATACATTTTTATAAAGTATCGACACTTT
* *
16650 CAATATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACTGGTTTTGTCATTTTTTTACCT
131 CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCT
*
16715 GTTATATTGTTATGGATCAATATATTTTT
196 GTTATATTGTTATGGATCAATACATTTTT
16744 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
16759 AAACCGACAA
Statistics
Matches: 224, Mismatches: 14, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
223 172 0.77
224 52 0.23
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (224 bp):
ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAAACCGAT
TTTGTCATTTTTTTACCTGTTATATTGTGATGGATCGATACATTTTTATAAAGTATCGACACTTT
CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCT
GTTATATTGTTATGGATCAATACATTTTT
Found at i:17700 original size:15 final size:16
Alignment explanation
Indices: 17677--17713 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
17667 AATAATTTAA
*
17677 TATTTTATTAAA-TTT
1 TATTATATTAAATTTT
17692 TATTATATTAAATTTT
1 TATTATATTAAATTTT
17708 TATTAT
1 TATTAT
17714 TTTTGTAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTATATTAAATTTT
Found at i:18453 original size:19 final size:19
Alignment explanation
Indices: 18429--18472 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
18419 GCATACCCTA
18429 GGTGCACTAAGAGTGCATC
1 GGTGCACTAAGAGTGCATC
18448 GGTGCACTAAGAGTGCATC
1 GGTGCACTAAGAGTGCATC
*
18467 GATGCA
1 GGTGCA
18473 TAAAATGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.20
Consensus pattern (19 bp):
GGTGCACTAAGAGTGCATC
Found at i:18620 original size:91 final size:91
Alignment explanation
Indices: 18458--18623 Score: 230
Period size: 91 Copynumber: 1.8 Consensus size: 91
18448 GGTGCACTAA
**
18458 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGCATGGTC
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAAACTGAGTGCATCGATGCATGGTC
*
18523 TTGTGCATCGATGCATCAAATGCACT
66 TGGTGCATCGATGCATCAAATGCACT
* * *
18549 GAGTGCATCGATGCATAAAATGCATTCTATG-TTTGAAAAATTAATTG-GTGTATCGATGCATGG
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAA--AACTGAGTGCATCGATGCATGG
18612 AT-TGGTGCATCG
64 -TCTGGTGCATCG
18624 GTGTATCACT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
90 9 0.14
91 54 0.82
92 3 0.05
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (91 bp):
GAGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAAACTGAGTGCATCGATGCATGGTC
TGGTGCATCGATGCATCAAATGCACT
Found at i:21019 original size:33 final size:33
Alignment explanation
Indices: 20977--21041 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
20967 GTAACTTATG
*
20977 TAACATTCTTGTATGATCTAATAGATCCTTGTA
1 TAACATTCTTGTATGATCTAATAGATCATTGTA
*
21010 TAACATTCTTGTATGATCTCATAGATCATTGT
1 TAACATTCTTGTATGATCTAATAGATCATTGT
21042 CATATAACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.43
Consensus pattern (33 bp):
TAACATTCTTGTATGATCTAATAGATCATTGTA
Found at i:21377 original size:14 final size:14
Alignment explanation
Indices: 21358--21392 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
21348 TGTGCATGTA
21358 ATCATATAGATCAT
1 ATCATATAGATCAT
* *
21372 ATCATATAGCTTAT
1 ATCATATAGATCAT
21386 ATCATAT
1 ATCATAT
21393 TTTCATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (14 bp):
ATCATATAGATCAT
Found at i:22001 original size:17 final size:18
Alignment explanation
Indices: 21967--22004 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
21957 CCCAAAAAAA
*
21967 GTCAACGGCTAGTCAACG
1 GTCAACGGCGAGTCAACG
21985 GTCAACGGCGA-TCAACG
1 GTCAACGGCGAGTCAACG
22002 GTC
1 GTC
22005 CAGGCGGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (18 bp):
GTCAACGGCGAGTCAACG
Found at i:28692 original size:25 final size:25
Alignment explanation
Indices: 28658--28709 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
28648 ATAGAGTGAG
28658 CTTTAGAAAGCTCAGTAATACAGAA
1 CTTTAGAAAGCTCAGTAATACAGAA
*
28683 CTTTGGAAAGCTCAGTAATACAGAA
1 CTTTAGAAAGCTCAGTAATACAGAA
28708 CT
1 CT
28710 ATCAGATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (25 bp):
CTTTAGAAAGCTCAGTAATACAGAA
Found at i:29153 original size:24 final size:24
Alignment explanation
Indices: 29119--29190 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
29109 ATACGGAGAT
* *
29119 ATCAGAAATCAAAATAAAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
29143 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
29167 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
29191 GTAATCTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.53, C:0.17, G:0.12, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:29205 original size:48 final size:48
Alignment explanation
Indices: 29119--29210 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
29109 ATACGGAGAT
* *
29119 ATCAGAAATCAAAATAAAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAAAATTCAGATAAGATATCAGAACAGAATCCAG
* * ** *
29167 ATCAGAAATCAAAACAGAATTCAGGTAATCTATTAGAACAGAAT
1 ATCAGAAATCAAAACAAAATTCAGATAAGATATCAGAACAGAAT
29211 TCAAGTCGGA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAAAACAAAATTCAGATAAGATATCAGAACAGAATCCAG
Found at i:32572 original size:2 final size:2
Alignment explanation
Indices: 32565--32605 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
32555 ATAAATTTAT
32565 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32606 GAAATTGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33077 original size:23 final size:23
Alignment explanation
Indices: 33034--33077 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
33024 CCAAATAACC
* *
33034 AAAAACATGACATAGAGGCAGAG
1 AAAAACATGACATAAAAGCAGAG
*
33057 AAAAACATGTCATAAAAGCAG
1 AAAAACATGACATAAAAGCAG
33078 GATACGTGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.14, G:0.20, T:0.11
Consensus pattern (23 bp):
AAAAACATGACATAAAAGCAGAG
Found at i:35060 original size:2 final size:2
Alignment explanation
Indices: 35055--35141 Score: 158
Period size: 2 Copynumber: 44.0 Consensus size: 2
35045 TCACACACAC
35055 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
*
35097 CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35138 AT AT
1 AT AT
35142 GGCTATGATC
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 81 0.99
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35236 original size:2 final size:2
Alignment explanation
Indices: 35229--35272 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
35219 GTGTAATAGG
35229 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
35271 AT
1 AT
35273 GAAAAAAGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36284 original size:15 final size:15
Alignment explanation
Indices: 36243--36285 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
36233 TAAGATTATC
36243 ACTGAGAATGTAAGATT
1 ACTGAGAA--TAAGATT
*
36260 ACCAGAGAATAAGATT
1 A-CTGAGAATAAGATT
36276 ACTGAGAATA
1 ACTGAGAATA
36286 TTGTATTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 8 0.35
16 8 0.35
17 1 0.04
18 6 0.26
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.23
Consensus pattern (15 bp):
ACTGAGAATAAGATT
Found at i:37763 original size:2 final size:2
Alignment explanation
Indices: 37756--37840 Score: 163
Period size: 2 Copynumber: 43.0 Consensus size: 2
37746 ATTTTAACTC
37756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
37797 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
37839 AT
1 AT
37841 TTGAAATAAT
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 81 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:48363 original size:2 final size:2
Alignment explanation
Indices: 48356--48384 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
48346 TATTGACCCA
48356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48385 ATTTTCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48979 original size:20 final size:20
Alignment explanation
Indices: 48954--49001 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
48944 AATTTCAGAA
*
48954 TGCTACAGGGGTATCGATAC
1 TGCTACAGGGGTACCGATAC
48974 TGCTACAGGGGTACCGATAC
1 TGCTACAGGGGTACCGATAC
48994 TGCTACAG
1 TGCTACAG
49002 TAATTTCGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (20 bp):
TGCTACAGGGGTACCGATAC
Found at i:52248 original size:34 final size:34
Alignment explanation
Indices: 52169--52238 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
52159 ATAATATAAT
*
52169 TTCACATCTCTTGAAATTTTATAATTCTAGACCA
1 TTCACATTTCTTGAAATTTTATAATTCTAGACCA
52203 TTCACATTTCTTGAAATTTTATAATTCTAGACCA
1 TTCACATTTCTTGAAATTTTATAATTCTAGACCA
52237 TT
1 TT
52239 GAGTTTTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (34 bp):
TTCACATTTCTTGAAATTTTATAATTCTAGACCA
Found at i:52465 original size:2 final size:2
Alignment explanation
Indices: 52458--52484 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52448 ATTGTCACCT
52458 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
52485 GATTATGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53559 original size:2 final size:2
Alignment explanation
Indices: 53552--53586 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
53542 TATGTTCTTT
53552 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53587 TGTATATGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53559 original size:16 final size:16
Alignment explanation
Indices: 53520--53593 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
53510 CATAAATAAC
53520 TATATATATGTTATAT
1 TATATATATGTTATAT
* * * *
53536 AATTTATATGTTCTTT
1 TATATATATGTTATAT
*
53552 TATATATATATATATAT
1 TATATATATGT-TATAT
*
53569 ATATATATATATATATAT
1 -TATATATATGT-TATAT
*
53587 TGTATAT
1 TATATAT
53594 GACATTTACA
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
16 20 0.43
17 9 0.20
18 17 0.37
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (16 bp):
TATATATATGTTATAT
Found at i:55030 original size:17 final size:17
Alignment explanation
Indices: 55004--55037 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
54994 TTTCTTTGTT
55004 TTTATATATA-TTTTTA
1 TTTATATATACTTTTTA
55020 TTTATTATATACTTTTTA
1 TTTA-TATATACTTTTTA
55038 CCCTTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 6 0.38
18 6 0.38
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATATATACTTTTTA
Found at i:55076 original size:18 final size:17
Alignment explanation
Indices: 55045--55087 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
55035 TTACCCTTTT
*
55045 TATATTTTCTTT-CTT-
1 TATATTTTATTTCCTTC
55060 TAT-TTTTATTTCCTTC
1 TATATTTTATTTCCTTC
55076 TATATTTTATTT
1 TATATTTTATTT
55088 TGTTATTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 7 0.29
15 6 0.25
16 3 0.12
17 8 0.33
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (17 bp):
TATATTTTATTTCCTTC
Found at i:55145 original size:3 final size:3
Alignment explanation
Indices: 55137--55167 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
55127 GTCATGTATA
55137 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
55168 TTCTTCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:55211 original size:45 final size:45
Alignment explanation
Indices: 55162--55248 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
55152 TATTATTATT
* **
55162 ATTATTTTCTTCATTTTATTTATTTTTAT-CTTTGCTTTATTTCTC
1 ATTATTTTCTTCATTTCATGCATTTTTATACTTT-CTTTATTTCTC
* *
55207 ATTATTTTCTTTATTTCATGCATTTTTTTACTTTCTTTATTT
1 ATTATTTTCTTCATTTCATGCATTTTTATACTTTCTTTATTT
55249 TTAATTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 32 0.89
46 4 0.11
ACGTcount: A:0.16, C:0.13, G:0.02, T:0.69
Consensus pattern (45 bp):
ATTATTTTCTTCATTTCATGCATTTTTATACTTTCTTTATTTCTC
Found at i:55222 original size:9 final size:9
Alignment explanation
Indices: 55163--55249 Score: 54
Period size: 9 Copynumber: 9.8 Consensus size: 9
55153 ATTATTATTA
55163 TTATTTTCT
1 TTATTTTCT
* *
55172 TCATTTTAT
1 TTATTTTCT
55181 TTATTTT-T
1 TTATTTTCT
* * *
55189 ATCTTTGCT
1 TTATTTTCT
*
55198 TTATTTCTCA
1 TTATTT-TCT
55208 TTATTTTCT
1 TTATTTTCT
55217 TTA-TTTCAT
1 TTATTTTC-T
**
55226 GCATTTT-T
1 TTATTTTCT
*
55234 TTACTTTCT
1 TTATTTTCT
55243 TTATTTT
1 TTATTTT
55250 TAATTTTTTA
Statistics
Matches: 56, Mismatches: 17, Indels: 10
0.67 0.20 0.12
Matches are distributed among these distances:
8 14 0.25
9 32 0.57
10 10 0.18
ACGTcount: A:0.15, C:0.13, G:0.02, T:0.70
Consensus pattern (9 bp):
TTATTTTCT
Found at i:55230 original size:21 final size:20
Alignment explanation
Indices: 55196--55240 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
55186 TTTATCTTTG
55196 CTTTATTTCTCATTATTTT-
1 CTTTATTTCTCATTATTTTA
*
55215 CTTTATTTCATGCATTTTTTTA
1 CTTTATTTC-T-CATTATTTTA
55237 CTTT
1 CTTT
55241 CTTTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 1 0.05
21 8 0.36
22 4 0.18
ACGTcount: A:0.16, C:0.16, G:0.02, T:0.67
Consensus pattern (20 bp):
CTTTATTTCTCATTATTTTA
Found at i:57097 original size:13 final size:13
Alignment explanation
Indices: 57081--57139 Score: 54
Period size: 13 Copynumber: 4.7 Consensus size: 13
57071 TTTTTTGTGT
*
57081 GTTTGTGTTGTTC
1 GTTTATGTTGTTC
57094 GTTTAT-TGTGTTC
1 GTTTATGT-TGTTC
57107 GTTTATGTTCGTTC
1 GTTTATGTT-GTTC
*
57121 G-TT-CGTT-TTC
1 GTTTATGTTGTTC
57131 GTTTATGTT
1 GTTTATGTT
57140 CGTTTATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
10 4 0.11
11 2 0.05
12 7 0.18
13 19 0.50
14 6 0.16
ACGTcount: A:0.05, C:0.10, G:0.24, T:0.61
Consensus pattern (13 bp):
GTTTATGTTGTTC
Found at i:59821 original size:94 final size:94
Alignment explanation
Indices: 59703--59953 Score: 291
Period size: 93 Copynumber: 2.7 Consensus size: 94
59693 GCTTATAATT
* *
59703 TTATATATACAATAAAGCTTGAGTTGTCCCTATAAAGCATTTGGTT-AACGCCCCAGCTTTATGG
1 TTATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCAGCTTTA-GG
59767 ATAAGAGTT-AGCTAGA-CTGATAAAGGTG-A
65 ATAAGA-TTCAGCTA-ACCTGATAAAGGTGAA
* * * *
59796 TTATACTATACAATAAAGCTTGAGTTATCCCTCTAAAGCAATTGGTTAAACGTCTCGGCTTTA-G
1 TTATA-TATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCAGCTTTAGG
* *
59860 AGAATATTCAGCTAACCTGATAAAGGTGATA
65 ATAAGATTCAGCTAACCTGATAAAGGTGA-A
* * * *
59891 TTATATATACAATAATA--TTAAGTTGTCCCTCTAGAGAAATTGGTTAAACGCTCCAGCTTTAGG
1 TTATATATACAATAA-AGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCAGCTTTAGG
59954 GATTCAGCTA
Statistics
Matches: 134, Mismatches: 16, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
92 3 0.02
93 63 0.47
94 49 0.37
95 19 0.14
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (94 bp):
TTATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCAGCTTTAGGA
TAAGATTCAGCTAACCTGATAAAGGTGAA
Found at i:61133 original size:21 final size:21
Alignment explanation
Indices: 61099--61178 Score: 82
Period size: 21 Copynumber: 4.0 Consensus size: 21
61089 TAATTTACTC
*
61099 AAACAAAGTTTTGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTG
61121 AAACAAATTTTGTCTCTCTTG
1 AAACAAATTTTGTCTCTCTTG
* *
61142 AGAC--A-GTT-TC-C-CTTG
1 AAACAAATTTTGTCTCTCTTG
61157 AAACAAATTTTGTCTCTCTTG
1 AAACAAATTTTGTCTCTCTTG
61178 A
1 A
61179 GACAGTTTCC
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
15 7 0.15
16 1 0.02
17 3 0.06
18 4 0.09
19 3 0.06
20 1 0.02
21 21 0.45
22 7 0.15
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (21 bp):
AAACAAATTTTGTCTCTCTTG
Found at i:61151 original size:36 final size:36
Alignment explanation
Indices: 61111--61415 Score: 315
Period size: 36 Copynumber: 8.5 Consensus size: 36
61101 ACAAAGTTTT
61111 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
61147 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
61183 GTTTCCCTTGAAACAAA------ATCT-TTGA-ATA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
61211 TGTTT-TACATT-AAACAAATTTCGTCTCCCTTGAAACA
1 -GTTTCT-C-TTGAAACAAATTTTGTCTCTCTTGAGACA
* * * * * *
61248 GTTTCTTTTGGAACTAAGTTTTATCTCTCTTCAGATA
1 GTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
61285 GTTTCTCTTGAAACAAATTTTGTCTTTGTCTATCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTC----TC--TCTTGAGACA
61327 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
61363 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
61399 GTTTCCCTTGAAACAAA
1 GTTTCTCTTGAAACAAA
61416 ATCTTCGAAT
Statistics
Matches: 226, Mismatches: 23, Indels: 40
0.78 0.08 0.14
Matches are distributed among these distances:
28 2 0.01
29 16 0.07
30 5 0.02
35 4 0.02
36 133 0.59
37 30 0.13
38 2 0.01
40 2 0.01
42 32 0.14
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.41
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:61355 original size:21 final size:21
Alignment explanation
Indices: 61330--61394 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
61320 TGAGACAGTT
61330 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
61351 TCTCTTGAGAC--A-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
61368 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
61387 TCTCTTGA
1 TCTCTTGA
61395 GACAGTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 7 0.21
16 1 0.03
17 3 0.09
18 4 0.12
19 3 0.09
20 1 0.03
21 15 0.44
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.42
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:61367 original size:78 final size:72
Alignment explanation
Indices: 61222--61479 Score: 244
Period size: 78 Copynumber: 3.6 Consensus size: 72
61212 GTTTTACATT
* * * * * * *
61222 AAACAAATTTCGTCTCCCTTGAAACAGTTTCTTTTGGAACTAAGTTTTATCTCTCTTCAGATAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTTATCTCTCTTCAGACAGT
*
61287 TTCTCTTG
65 TTCCCTTG
* *
61295 AAACAAATTTTGTCTTTGTCTATCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAG
1 AAACAAATTTTGTC----TC--TCTTGAGACAGTTTCTCTTGAAACAAATTTTATCTCTCTTCAG
61360 ACAGTTTCCCTTG
60 ACAGTTTCCCTTG
* * *
61373 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA----ATCT-TC--GA-ATATGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCTCTCTTCAGACA-GT
61430 TTCCCTTG
65 TTCCCTTG
* *
61438 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
61480 CCCACCGTTG
Statistics
Matches: 163, Mismatches: 14, Indels: 23
0.81 0.07 0.12
Matches are distributed among these distances:
64 2 0.01
65 16 0.10
66 36 0.22
67 2 0.01
68 3 0.02
72 26 0.16
73 13 0.08
74 2 0.01
77 2 0.01
78 41 0.25
79 20 0.12
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (72 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCTCTCTTCAGACAGTT
TCCCTTG
Found at i:61468 original size:66 final size:65
Alignment explanation
Indices: 61355--61547 Score: 230
Period size: 66 Copynumber: 2.9 Consensus size: 65
61345 TTTGTCTCTC
* *
61355 TTGAGA-CAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
1 TTGAGATC-GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAACC
61419 -
65 G
* **
61419 TTCGA-ATATGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACCC
1 TT-GAGAT-CGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA-AA
61483 ACCG
62 ACCG
* ** *
61487 TTGAGATCGTTTCCCTTGAAACAAATTTCGTCTCGTTTGAGACAATTTTCCCTTGAAACAA
1 TTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGAC-AGTTTCCCTTGAAACAA
61548 GAAATTTTAT
Statistics
Matches: 110, Mismatches: 11, Indels: 14
0.81 0.08 0.10
Matches are distributed among these distances:
64 3 0.03
65 16 0.15
66 54 0.49
67 33 0.30
68 4 0.04
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (65 bp):
TTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAACCG
Found at i:62112 original size:43 final size:42
Alignment explanation
Indices: 62007--62125 Score: 145
Period size: 43 Copynumber: 2.9 Consensus size: 42
61997 TGCAGCAAAG
* *
62007 AATCCATGATTTCAACTCCACGAC-GAGGAAATCGTACTCAC
1 AATCCACGATTTCAACTCCACGACGGAGGAAATCGTACCCAC
*
62048 -ATCCACGATTTCAACTCCACGACGGA-GAATATTGTACCCAC
1 AATCCACGATTTCAACTCCACGACGGAGGAA-ATCGTACCCAC
* * *
62089 AAATCCACGATTTCAACTTCACGACGAAGGATATCGT
1 -AATCCACGATTTCAACTCCACGACGGAGGAAATCGT
62126 GCCAAATCTA
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
40 25 0.38
41 11 0.17
43 28 0.42
44 2 0.03
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.23
Consensus pattern (42 bp):
AATCCACGATTTCAACTCCACGACGGAGGAAATCGTACCCAC
Found at i:64231 original size:3 final size:3
Alignment explanation
Indices: 64218--64291 Score: 132
Period size: 3 Copynumber: 25.0 Consensus size: 3
64208 ATTATGTTTC
64218 ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
64265 ATT ATT ATT ATT ATT ATT ATT GTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
64292 TCATATTTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 66 0.97
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:64572 original size:16 final size:15
Alignment explanation
Indices: 64547--64627 Score: 67
Period size: 16 Copynumber: 5.2 Consensus size: 15
64537 TTTCTTTGTT
*
64547 TTTATATATATTTTA
1 TTTATTTATATTTTA
64562 TTTATTATATATTTTA
1 TTTATT-TATATTTTA
* *
64578 CCCTT-TTTATATTTTC
1 --TTTATTTATATTTTA
64594 TTTATTTAT-TTTTA
1 TTTATTTATATTTTA
*
64608 TTTCCTTTTATATTTTA
1 TTT--ATTTATATTTTA
64625 TTT
1 TTT
64628 TGTTATTTGC
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
14 9 0.17
15 10 0.19
16 22 0.42
17 10 0.19
18 2 0.04
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATTTATATTTTA
Found at i:64615 original size:32 final size:31
Alignment explanation
Indices: 64553--64627 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
64543 TGTTTTTATA
64553 TATATTTTATTTATTATATATTTTACCCTTTT
1 TATATTTTATTTATTATATATTTTACCC-TTT
* *
64585 TATATTTTCTTTATT-TAT-TTTTATTTCCTTT
1 TATATTTTATTTATTATATATTTTA--CCCTTT
64616 TATATTTTATTT
1 TATATTTTATTT
64628 TGTTATTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
30 5 0.13
31 17 0.45
32 16 0.42
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (31 bp):
TATATTTTATTTATTATATATTTTACCCTTT
Found at i:64685 original size:3 final size:3
Alignment explanation
Indices: 64677--64729 Score: 97
Period size: 3 Copynumber: 17.3 Consensus size: 3
64667 GCCATGTATA
64677 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
64723 TAT TAT T
1 TAT TAT T
64730 TTCTTCATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:64785 original size:45 final size:43
Alignment explanation
Indices: 64725--64830 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 43
64715 ATTATTATTA
* *
64725 TTATTTTC-TTCATTTTATTTATTTTATTCA-TTTTTACCTTTTCT
1 TTATTTTCATT-ATTTTATTTATTTCATGCATTTTTTA-C-TTTCT
*
64769 TTATTTCTCATTATTTTCTTTATTTCATGCATTTTTTACTTTCT
1 TTATTT-TCATTATTTTATTTATTTCATGCATTTTTTACTTTCT
*
64813 TTATTTTCATTTTTTTAT
1 TTATTTTCATTATTTTAT
64831 CTAACAAATT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
43 10 0.19
44 17 0.31
45 19 0.35
46 8 0.15
ACGTcount: A:0.16, C:0.13, G:0.01, T:0.70
Consensus pattern (43 bp):
TTATTTTCATTATTTTATTTATTTCATGCATTTTTTACTTTCT
Found at i:66410 original size:27 final size:28
Alignment explanation
Indices: 66358--66416 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
66348 TCAAAGTTCT
* *
66358 GGTCAACGATGGTCAATGGTGATCAA-C
1 GGTCAACGACGGTCAACGGTGATCAACC
*
66385 GGTCAACG-CGGTCAACGGTAGGTCAACC
1 GGTCAACGACGGTCAACGGT-GATCAACC
66413 GGTC
1 GGTC
66417 GGGTCAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 9 0.33
27 13 0.48
28 5 0.19
ACGTcount: A:0.25, C:0.24, G:0.32, T:0.19
Consensus pattern (28 bp):
GGTCAACGACGGTCAACGGTGATCAACC
Found at i:68567 original size:12 final size:12
Alignment explanation
Indices: 68547--68593 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
68537 ACGGAGATAT
68547 CAGAAATCAGAA
1 CAGAAATCAGAA
* *
68559 CATAAATCAGAG
1 CAGAAATCAGAA
*
68571 CAGAAATCATAA
1 CAGAAATCAGAA
*
68583 CAGAATTCAGA
1 CAGAAATCAGA
68594 GTAGAAACCA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.53, C:0.17, G:0.15, T:0.15
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:68574 original size:24 final size:24
Alignment explanation
Indices: 68547--68605 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
68537 ACGGAGATAT
*
68547 CAGAAATCAGAACATAAATCAGAG
1 CAGAAATCAGAACAGAAATCAGAG
* *
68571 CAGAAATCATAACAGAATTCAGAG
1 CAGAAATCAGAACAGAAATCAGAG
* *
68595 TAGAAACCAGA
1 CAGAAATCAGA
68606 TAAAATATTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.14
Consensus pattern (24 bp):
CAGAAATCAGAACAGAAATCAGAG
Found at i:69923 original size:14 final size:14
Alignment explanation
Indices: 69904--69931 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
69894 CGGGTCAGGT
69904 CGGGTTGGGTCAAA
1 CGGGTTGGGTCAAA
69918 CGGGTTGGGTCAAA
1 CGGGTTGGGTCAAA
69932 ATTGGGGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.43, T:0.21
Consensus pattern (14 bp):
CGGGTTGGGTCAAA
Found at i:70875 original size:2 final size:2
Alignment explanation
Indices: 70811--70866 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
70801 AGTGTAAAAA
70811 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
70853 AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT A
70867 CTCATATATC
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72254 original size:14 final size:15
Alignment explanation
Indices: 72221--72260 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
72211 TAATAATTTG
72221 TTTTAATTTAATATAA
1 TTTT-ATTTAATATAA
72237 -TTTATTT-ATATAA
1 TTTTATTTAATATAA
72250 TTTTA-TTAATA
1 TTTTATTTAATA
72261 AATCCATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.36
14 11 0.50
15 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTATTTAATATAA
Done.